5dvk - Revision history

OCA at 22:01, 28 June 2023

OCA — Wed, 28 Jun 2023 22:01:35 GMT

←Older revision		Revision as of 22:01, 28 June 2023
Line 3:		Line 3:
	<StructureSection load='5dvk' size='340' side='right'caption='[[5dvk]], [[Resolution\|resolution]] 2.60Å' scene=''>		<StructureSection load='5dvk' size='340' side='right'caption='[[5dvk]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5dvk]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DVK OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5DVK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5dvk]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DVK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5DVK FirstGlance]. <br>
-	</td></tr><tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat">[[5di8\|5di8]], [[5dj0\|5dj0]], [[5dj2\|5dj2]], [[5dj6\|5dj6]], [[5dj8\|5dj8]], [[5dja\|5dja]], [[5djc\|5djc]], [[5djd\|5djd]], [[5djx\|5djx]], [[5djy\|5djy]], [[5djz\|5djz]], [[5dk0\|5dk0]], [[5dk2\|5dk2]], [[5dvl\|5dvl]], [[5dvm\|5dvm]], [[5dvn\|5dvn]], [[5dvo\|5dvo]]</td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.6Å</td></tr>
-	~~<tr~~ id~~='gene'><td class~~="~~sblockLbl~~">~~<b>~~[[~~Gene~~\|~~Gene:~~]]~~</b></td><td class="sblockDat">IGHG1 ([http://www~~.~~ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info~~&~~srchmode=5&id=9606 HUMAN])~~</td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5dvk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dvk OCA], [https://pdbe.org/5dvk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5dvk RCSB], [https://www.ebi.ac.uk/pdbsum/5dvk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5dvk ProSAT]</span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=5dvk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dvk OCA], [~~http~~://pdbe.org/5dvk PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5dvk RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5dvk PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5dvk ProSAT]</span></td></tr>	+
	</table>		</table>
	== Disease ==		== Disease ==
-	[~~[http~~://www.uniprot.org/uniprot/IGHG1_HUMAN IGHG1_HUMAN]] Defects in IGHG1 are a cause of multiple myeloma (MM) [MIM:[~~http~~://omim.org/entry/254500 254500]]. MM is a malignant tumor of plasma cells usually arising in the bone marrow and characterized by diffuse involvement of the skeletal system, hyperglobulinemia, Bence-Jones proteinuria and anemia. Complications of multiple myeloma are bone pain, hypercalcemia, renal failure and spinal cord compression. The aberrant antibodies that are produced lead to impaired humoral immunity and patients have a high prevalence of infection. Amyloidosis may develop in some patients. Multiple myeloma is part of a spectrum of diseases ranging from monoclonal gammopathy of unknown significance (MGUS) to plasma cell leukemia. Note=A chromosomal aberration involving IGHG1 is found in multiple myeloma. Translocation t(11;14)(q13;q32) with the IgH locus. Translocation t(11;14)(q13;q32) with CCND1; translocation t(4;14)(p16.3;q32.3) with FGFR3; translocation t(6;14)(p25;q32) with IRF4.	+	[https://www.uniprot.org/uniprot/IGHG1_HUMAN IGHG1_HUMAN] Defects in IGHG1 are a cause of multiple myeloma (MM) [MIM:[https://omim.org/entry/254500 254500]. MM is a malignant tumor of plasma cells usually arising in the bone marrow and characterized by diffuse involvement of the skeletal system, hyperglobulinemia, Bence-Jones proteinuria and anemia. Complications of multiple myeloma are bone pain, hypercalcemia, renal failure and spinal cord compression. The aberrant antibodies that are produced lead to impaired humoral immunity and patients have a high prevalence of infection. Amyloidosis may develop in some patients. Multiple myeloma is part of a spectrum of diseases ranging from monoclonal gammopathy of unknown significance (MGUS) to plasma cell leukemia. Note=A chromosomal aberration involving IGHG1 is found in multiple myeloma. Translocation t(11;14)(q13;q32) with the IgH locus. Translocation t(11;14)(q13;q32) with CCND1; translocation t(4;14)(p16.3;q32.3) with FGFR3; translocation t(6;14)(p25;q32) with IRF4.
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/IGHG1_HUMAN IGHG1_HUMAN]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 23:		Line 24:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Aldaz, H]]	+	[[Category: Synthetic construct]]
-	[[Category: Atwell, S]]	+	[[Category: Aldaz H]]
-	[[Category: Chamberlain~~, A K~~]]	+	[[Category: Atwell S]]
-	[[Category: Demarest~~, S J~~]]	+	[[Category: Chamberlain AK]]
-	[[Category: Dhanani~~, S H~~]]	+	[[Category: Demarest SJ]]
-	[[Category: Fitchett~~, J R~~]]	+	[[Category: Dhanani SH]]
-	[[Category: Froning~~, K J~~]]	+	[[Category: Fitchett JR]]
-	[[Category: Gutierrez, B]]	+	[[Category: Froning KJ]]
-	[[Category: Hendle, J]]	+	[[Category: Gutierrez B]]
-	[[Category: Huang, F]]	+	[[Category: Hendle J]]
-	[[Category: Kuhlman, B]]	+	[[Category: Huang F]]
-	[[Category: Leaver-Fay, A]]	+	[[Category: Kuhlman B]]
-	[[Category: Lu, F]]	+	[[Category: Leaver-Fay A]]
-	[[Category: Pustilnik, A]]	+	[[Category: Lu F]]
-	[[Category: Yuan, R]]	+	[[Category: Pustilnik A]]
-	~~[[Category: Fc]]~~	+	[[Category: Yuan R]]
-	~~[[Category: Head-to-tail homodimer]]~~	+
-	~~[[Category: Immune system]]~~	+
-	~~[[Category: Immunoglobulin~~]]	+

OCA at 08:08, 15 April 2020

OCA — Wed, 15 Apr 2020 08:08:50 GMT

←Older revision		Revision as of 08:08, 15 April 2020
Line 1:		Line 1:

	==Fc Design 7.7 B chain homodimer T366V/K409I==		==Fc Design 7.7 B chain homodimer T366V/K409I==
-	<StructureSection load='5dvk' size='340' side='right' caption='[[5dvk]], [[Resolution\|resolution]] 2.60Å' scene=''>	+	<StructureSection load='5dvk' size='340' side='right'caption='[[5dvk]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5dvk]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DVK OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5DVK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5dvk]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DVK OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5DVK FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5di8\|5di8]], [[5dj0\|5dj0]], [[5dj2\|5dj2]], [[5dj6\|5dj6]], [[5dj8\|5dj8]], [[5dja\|5dja]], [[5djc\|5djc]], [[5djd\|5djd]], [[5djx\|5djx]], [[5djy\|5djy]], [[5djz\|5djz]], [[5dk0\|5dk0]], [[5dk2\|5dk2]], [[5dvl\|5dvl]], [[5dvm\|5dvm]], [[5dvn\|5dvn]], [[5dvo\|5dvo]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5di8\|5di8]], [[5dj0\|5dj0]], [[5dj2\|5dj2]], [[5dj6\|5dj6]], [[5dj8\|5dj8]], [[5dja\|5dja]], [[5djc\|5djc]], [[5djd\|5djd]], [[5djx\|5djx]], [[5djy\|5djy]], [[5djz\|5djz]], [[5dk0\|5dk0]], [[5dk2\|5dk2]], [[5dvl\|5dvl]], [[5dvm\|5dvm]], [[5dvn\|5dvn]], [[5dvo\|5dvo]]</td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5dvk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dvk OCA], [http://pdbe.org/5dvk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5dvk RCSB], [http://www.ebi.ac.uk/pdbsum/5dvk PDBsum]</span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">IGHG1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
		+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5dvk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dvk OCA], [http://pdbe.org/5dvk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5dvk RCSB], [http://www.ebi.ac.uk/pdbsum/5dvk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5dvk ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
Line 22:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Aldaz, H]]		[[Category: Aldaz, H]]
	[[Category: Atwell, S]]		[[Category: Atwell, S]]

OCA at 16:25, 10 May 2016

OCA — Tue, 10 May 2016 16:25:32 GMT

←Older revision		Revision as of 16:25, 10 May 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5dvk is ~~ON HOLD until Paper~~ Publication	+	==Fc Design 7.7 B chain homodimer T366V/K409I==
		+	<StructureSection load='5dvk' size='340' side='right' caption='[[5dvk]], [[Resolution\|resolution]] 2.60Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5dvk]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DVK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5DVK FirstGlance]. <br>
		+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5di8\|5di8]], [[5dj0\|5dj0]], [[5dj2\|5dj2]], [[5dj6\|5dj6]], [[5dj8\|5dj8]], [[5dja\|5dja]], [[5djc\|5djc]], [[5djd\|5djd]], [[5djx\|5djx]], [[5djy\|5djy]], [[5djz\|5djz]], [[5dk0\|5dk0]], [[5dk2\|5dk2]], [[5dvl\|5dvl]], [[5dvm\|5dvm]], [[5dvn\|5dvn]], [[5dvo\|5dvo]]</td></tr>
		+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5dvk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dvk OCA], [http://pdbe.org/5dvk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5dvk RCSB], [http://www.ebi.ac.uk/pdbsum/5dvk PDBsum]</span></td></tr>
		+	</table>
		+	== Disease ==
		+	[[http://www.uniprot.org/uniprot/IGHG1_HUMAN IGHG1_HUMAN]] Defects in IGHG1 are a cause of multiple myeloma (MM) [MIM:[http://omim.org/entry/254500 254500]]. MM is a malignant tumor of plasma cells usually arising in the bone marrow and characterized by diffuse involvement of the skeletal system, hyperglobulinemia, Bence-Jones proteinuria and anemia. Complications of multiple myeloma are bone pain, hypercalcemia, renal failure and spinal cord compression. The aberrant antibodies that are produced lead to impaired humoral immunity and patients have a high prevalence of infection. Amyloidosis may develop in some patients. Multiple myeloma is part of a spectrum of diseases ranging from monoclonal gammopathy of unknown significance (MGUS) to plasma cell leukemia. Note=A chromosomal aberration involving IGHG1 is found in multiple myeloma. Translocation t(11;14)(q13;q32) with the IgH locus. Translocation t(11;14)(q13;q32) with CCND1; translocation t(4;14)(p16.3;q32.3) with FGFR3; translocation t(6;14)(p25;q32) with IRF4.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	A challenge in the structure-based design of specificity is modeling the negative states, i.e., the complexes that you do not want to form. This is a difficult problem because mutations predicted to destabilize the negative state might be accommodated by small conformational rearrangements. To overcome this challenge, we employ an iterative strategy that cycles between sequence design and protein docking in order to build up an ensemble of alternative negative state conformations for use in specificity prediction. We have applied our technique to the design of heterodimeric CH3 interfaces in the Fc region of antibodies. Combining computationally and rationally designed mutations produced unique designs with heterodimer purities greater than 90%. Asymmetric Fc crystallization was able to resolve the interface mutations; the heterodimer structures confirmed that the interfaces formed as designed. With these CH3 mutations, and those made at the heavy-/light-chain interface, we demonstrate one-step synthesis of four fully IgG-bispecific antibodies.

-	~~Authors: Atwell, S~~., Leaver-Fay, A., Froning, ~~K.J.~~, Aldaz, H., Pustilnik, A., Lu, F., Huang, F., Yuan, R~~., Dhanani~~, S~~.H.~~, Chamberlain~~, A.K.~~, Fitchett, ~~J.R., Gutierrez~~, B.~~, Hendle, J~~.~~, Demarest, S~~.J., ~~Kuhlman, B~~.	+	Computationally Designed Bispecific Antibodies using Negative State Repertoires.,Leaver-Fay A, Froning KJ, Atwell S, Aldaz H, Pustilnik A, Lu F, Huang F, Yuan R, Hassanali S, Chamberlain AK, Fitchett JR, Demarest SJ, Kuhlman B Structure. 2016 Apr 5;24(4):641-51. doi: 10.1016/j.str.2016.02.013. Epub 2016 Mar, 17. PMID:26996964<ref>PMID:26996964</ref>

-	~~Description: Fc Design 7~~.~~7 B chain homodimer T366V~~/~~K409I~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category~~: ~~Unreleased Structures]]~~	+	</div>
-	~~[[Category: Leaver-Fay, A]]~~	+	<div class="pdbe-citations 5dvk" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Aldaz, H]]		[[Category: Aldaz, H]]
-	[[Category: Gutierrez, B]]
-	[[Category: Fitchett, J.R]]
-	[[Category: Dhanani, S.H]]
-	[[Category: Kuhlman, B]]
-	[[Category: Froning, K.J]]
-	[[Category: Demarest, S.J]]
	[[Category: Atwell, S]]		[[Category: Atwell, S]]
		+	[[Category: Chamberlain, A K]]
		+	[[Category: Demarest, S J]]
		+	[[Category: Dhanani, S H]]
		+	[[Category: Fitchett, J R]]
		+	[[Category: Froning, K J]]
		+	[[Category: Gutierrez, B]]
	[[Category: Hendle, J]]		[[Category: Hendle, J]]
-	[[Category: Yuan, R]]
-	[[Category: Lu, F]]
	[[Category: Huang, F]]		[[Category: Huang, F]]
-	[[Category: ~~Chamberlain~~, A.K]]	+	[[Category: Kuhlman, B]]
		+	[[Category: Leaver-Fay, A]]
		+	[[Category: Lu, F]]
	[[Category: Pustilnik, A]]		[[Category: Pustilnik, A]]
		+	[[Category: Yuan, R]]
		+	[[Category: Fc]]
		+	[[Category: Head-to-tail homodimer]]
		+	[[Category: Immune system]]
		+	[[Category: Immunoglobulin]]

OCA at 11:27, 16 December 2015

OCA — Wed, 16 Dec 2015 11:27:23 GMT

←Older revision		Revision as of 11:27, 16 December 2015
Line 7:		Line 7:
	Description: Fc Design 7.7 B chain homodimer T366V/K409I		Description: Fc Design 7.7 B chain homodimer T366V/K409I
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
		+	[[Category: Leaver-Fay, A]]
		+	[[Category: Aldaz, H]]
		+	[[Category: Gutierrez, B]]
	[[Category: Fitchett, J.R]]		[[Category: Fitchett, J.R]]
	[[Category: Dhanani, S.H]]		[[Category: Dhanani, S.H]]
Line 12:		Line 15:
	[[Category: Froning, K.J]]		[[Category: Froning, K.J]]
	[[Category: Demarest, S.J]]		[[Category: Demarest, S.J]]
-	[[Category: Yuan, R]]
-	[[Category: Leaver-Fay, A]]
-	[[Category: Aldaz, H]]
-	[[Category: Gutierrez, B]]
	[[Category: Atwell, S]]		[[Category: Atwell, S]]
	[[Category: Hendle, J]]		[[Category: Hendle, J]]
		+	[[Category: Yuan, R]]
	[[Category: Lu, F]]		[[Category: Lu, F]]
	[[Category: Huang, F]]		[[Category: Huang, F]]
	[[Category: Chamberlain, A.K]]		[[Category: Chamberlain, A.K]]
	[[Category: Pustilnik, A]]		[[Category: Pustilnik, A]]

OCA at 02:12, 1 December 2015

OCA — Tue, 01 Dec 2015 02:12:52 GMT

←Older revision		Revision as of 02:12, 1 December 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5dvk is ON HOLD	+	The entry 5dvk is ON HOLD until Paper Publication

	Authors: Atwell, S., Leaver-Fay, A., Froning, K.J., Aldaz, H., Pustilnik, A., Lu, F., Huang, F., Yuan, R., Dhanani, S.H., Chamberlain, A.K., Fitchett, J.R., Gutierrez, B., Hendle, J., Demarest, S.J., Kuhlman, B.		Authors: Atwell, S., Leaver-Fay, A., Froning, K.J., Aldaz, H., Pustilnik, A., Lu, F., Huang, F., Yuan, R., Dhanani, S.H., Chamberlain, A.K., Fitchett, J.R., Gutierrez, B., Hendle, J., Demarest, S.J., Kuhlman, B.

OCA: Protected "5dvk" [edit=sysop:move=sysop]

OCA — Wed, 30 Sep 2015 13:35:34 GMT

Protected "5dvk" [edit=sysop:move=sysop]

←Older revision

Revision as of 13:35, 30 September 2015

OCA: New page: '''Unreleased structure''' The entry 5dvk is ON HOLD Authors: Atwell, S., Leaver-Fay, A., Froning, K.J., Aldaz, H., Pustilnik, A., Lu, F., Huang, F., Yuan, R., Dhanani, S.H., Chamberlai...

OCA — Wed, 30 Sep 2015 13:35:32 GMT

New page: '''Unreleased structure''' The entry 5dvk is ON HOLD Authors: Atwell, S., Leaver-Fay, A., Froning, K.J., Aldaz, H., Pustilnik, A., Lu, F., Huang, F., Yuan, R., Dhanani, S.H., Chamberlai...

New page

'''Unreleased structure'''

The entry 5dvk is ON HOLD

Authors: Atwell, S., Leaver-Fay, A., Froning, K.J., Aldaz, H., Pustilnik, A., Lu, F., Huang, F., Yuan, R., Dhanani, S.H., Chamberlain, A.K., Fitchett, J.R., Gutierrez, B., Hendle, J., Demarest, S.J., Kuhlman, B.

Description: Fc Design 7.7 B chain homodimer T366V/K409I
[[Category: Unreleased Structures]]
[[Category: Fitchett, J.R]]
[[Category: Dhanani, S.H]]
[[Category: Kuhlman, B]]
[[Category: Froning, K.J]]
[[Category: Demarest, S.J]]
[[Category: Yuan, R]]
[[Category: Leaver-Fay, A]]
[[Category: Aldaz, H]]
[[Category: Gutierrez, B]]
[[Category: Atwell, S]]
[[Category: Hendle, J]]
[[Category: Lu, F]]
[[Category: Huang, F]]
[[Category: Chamberlain, A.K]]
[[Category: Pustilnik, A]]