OCA at 08:11, 17 October 2018

OCA — Wed, 17 Oct 2018 08:11:01 GMT

←Older revision		Revision as of 08:11, 17 October 2018
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-	'''Unreleased structure'''

-	The entry ~~6hal~~ is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==Human carbonmonoxy hemoglobin SFX dataset==
		+	<StructureSection load='6hal' size='340' side='right' caption='[[6hal]], [[Resolution\|resolution]] 2.20Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6hal]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6HAL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6HAL FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CMO:CARBON+MONOXIDE'>CMO</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></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=6hal FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6hal OCA], [http://pdbe.org/6hal PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6hal RCSB], [http://www.ebi.ac.uk/pdbsum/6hal PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6hal ProSAT]</span></td></tr>
		+	</table>
		+	== Disease ==
		+	[[http://www.uniprot.org/uniprot/HBA_HUMAN HBA_HUMAN]] Defects in HBA1 may be a cause of Heinz body anemias (HEIBAN) [MIM:[http://omim.org/entry/140700 140700]]. This is a form of non-spherocytic hemolytic anemia of Dacie type 1. After splenectomy, which has little benefit, basophilic inclusions called Heinz bodies are demonstrable in the erythrocytes. Before splenectomy, diffuse or punctate basophilia may be evident. Most of these cases are probably instances of hemoglobinopathy. The hemoglobin demonstrates heat lability. Heinz bodies are observed also with the Ivemark syndrome (asplenia with cardiovascular anomalies) and with glutathione peroxidase deficiency.<ref>PMID:2833478</ref> Defects in HBA1 are the cause of alpha-thalassemia (A-THAL) [MIM:[http://omim.org/entry/604131 604131]]. The thalassemias are the most common monogenic diseases and occur mostly in Mediterranean and Southeast Asian populations. The hallmark of alpha-thalassemia is an imbalance in globin-chain production in the adult HbA molecule. The level of alpha chain production can range from none to very nearly normal levels. Deletion of both copies of each of the two alpha-globin genes causes alpha(0)-thalassemia, also known as homozygous alpha thalassemia. Due to the complete absence of alpha chains, the predominant fetal hemoglobin is a tetramer of gamma-chains (Bart hemoglobin) that has essentially no oxygen carrying capacity. This causes oxygen starvation in the fetal tissues leading to prenatal lethality or early neonatal death. The loss of three alpha genes results in high levels of a tetramer of four beta chains (hemoglobin H), causing a severe and life-threatening anemia known as hemoglobin H disease. Untreated, most patients die in childhood or early adolescence. The loss of two alpha genes results in mild alpha-thalassemia, also known as heterozygous alpha-thalassemia. Affected individuals have small red cells and a mild anemia (microcytosis). If three of the four alpha-globin genes are functional, individuals are completely asymptomatic. Some rare forms of alpha-thalassemia are due to point mutations (non-deletional alpha-thalassemia). The thalassemic phenotype is due to unstable globin alpha chains that are rapidly catabolized prior to formation of the alpha-beta heterotetramers. Note=Alpha(0)-thalassemia is associated with non-immune hydrops fetalis, a generalized edema of the fetus with fluid accumulation in the body cavities due to non-immune causes. Non-immune hydrops fetalis is not a diagnosis in itself but a symptom, a feature of many genetic disorders, and the end-stage of a wide variety of disorders. Defects in HBA1 are the cause of hemoglobin H disease (HBH) [MIM:[http://omim.org/entry/613978 613978]]. HBH is a form of alpha-thalassemia due to the loss of three alpha genes. This results in high levels of a tetramer of four beta chains (hemoglobin H), causing a severe and life-threatening anemia. Untreated, most patients die in childhood or early adolescence.<ref>PMID:10569720</ref> [[http://www.uniprot.org/uniprot/HBB_HUMAN HBB_HUMAN]] Defects in HBB may be a cause of Heinz body anemias (HEIBAN) [MIM:[http://omim.org/entry/140700 140700]]. This is a form of non-spherocytic hemolytic anemia of Dacie type 1. After splenectomy, which has little benefit, basophilic inclusions called Heinz bodies are demonstrable in the erythrocytes. Before splenectomy, diffuse or punctate basophilia may be evident. Most of these cases are probably instances of hemoglobinopathy. The hemoglobin demonstrates heat lability. Heinz bodies are observed also with the Ivemark syndrome (asplenia with cardiovascular anomalies) and with glutathione peroxidase deficiency.<ref>PMID:186485</ref> <ref>PMID:6259091</ref> <ref>PMID:2599881</ref> <ref>PMID:8704193</ref> Defects in HBB are the cause of beta-thalassemia (B-THAL) [MIM:[http://omim.org/entry/613985 613985]]. A form of thalassemia. Thalassemias are common monogenic diseases occurring mostly in Mediterranean and Southeast Asian populations. The hallmark of beta-thalassemia is an imbalance in globin-chain production in the adult HbA molecule. Absence of beta chain causes beta(0)-thalassemia, while reduced amounts of detectable beta globin causes beta(+)-thalassemia. In the severe forms of beta-thalassemia, the excess alpha globin chains accumulate in the developing erythroid precursors in the marrow. Their deposition leads to a vast increase in erythroid apoptosis that in turn causes ineffective erythropoiesis and severe microcytic hypochromic anemia. Clinically, beta-thalassemia is divided into thalassemia major which is transfusion dependent, thalassemia intermedia (of intermediate severity), and thalassemia minor that is asymptomatic.<ref>PMID:1971109</ref> Defects in HBB are the cause of sickle cell anemia (SKCA) [MIM:[http://omim.org/entry/603903 603903]]; also known as sickle cell disease. Sickle cell anemia is characterized by abnormally shaped red cells resulting in chronic anemia and periodic episodes of pain, serious infections and damage to vital organs. Normal red blood cells are round and flexible and flow easily through blood vessels, but in sickle cell anemia, the abnormal hemoglobin (called Hb S) causes red blood cells to become stiff. They are C-shaped and resembles a sickle. These stiffer red blood cells can led to microvascular occlusion thus cutting off the blood supply to nearby tissues. Defects in HBB are the cause of beta-thalassemia dominant inclusion body type (B-THALIB) [MIM:[http://omim.org/entry/603902 603902]]. An autosomal dominant form of beta thalassemia characterized by moderate anemia, lifelong jaundice, cholelithiasis and splenomegaly, marked morphologic changes in the red cells, erythroid hyperplasia of the bone marrow with increased numbers of multinucleate red cell precursors, and the presence of large inclusion bodies in the normoblasts, both in the marrow and in the peripheral blood after splenectomy.<ref>PMID:1971109</ref>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/HBA_HUMAN HBA_HUMAN]] Involved in oxygen transport from the lung to the various peripheral tissues. [[http://www.uniprot.org/uniprot/HBB_HUMAN HBB_HUMAN]] Involved in oxygen transport from the lung to the various peripheral tissues.<ref>PMID:16904236</ref> LVV-hemorphin-7 potentiates the activity of bradykinin, causing a decrease in blood pressure.<ref>PMID:16904236</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Crystallography chips are fixed-target supports consisting of a film (for example Kapton) or wafer (for example silicon) that is processed using semiconductor-microfabrication techniques to yield an array of wells or through-holes in which single microcrystals can be lodged for raster-scan probing. Although relatively expensive to fabricate, chips offer an efficient means of high-throughput sample presentation for serial diffraction data collection at synchrotron or X-ray free-electron laser (XFEL) sources. Truly efficient loading of a chip (one microcrystal per well and no wastage during loading) is nonetheless challenging. The wells or holes must match the microcrystal size of interest, requiring that a large stock of chips be maintained. Raster scanning requires special mechanical drives to step the chip rapidly and with micrometre precision from well to well. Here, a `chip-less' adaptation is described that essentially eliminates the challenges of loading and precision scanning, albeit with increased, yet still relatively frugal, sample usage. The device consists simply of two sheets of Mylar with the crystal solution sandwiched between them. This sheet-on-sheet (SOS) sandwich structure has been employed for serial femtosecond crystallography data collection with micrometre-sized crystals at an XFEL. The approach is also well suited to time-resolved pump-probe experiments, in particular for long time delays. The SOS sandwich enables measurements under XFEL beam conditions that would damage conventional chips, as documented here. The SOS sheets hermetically seal the sample, avoiding desiccation of the sample provided that the X-ray beam does not puncture the sheets. This is the case with a synchrotron beam but not with an XFEL beam. In the latter case, desiccation, setting radially outwards from each punched hole, sets lower limits on the speed and line spacing of the raster scan. It is shown that these constraints are easily accommodated.

-	~~Authors~~: Doak, B., Gorel, A., Foucar, L., Barends, ~~T.R.M., Gruenbein, M.L.~~, Hilpert, M., Kloos, M~~., Nass Kovacs, G.~~, Roome~~, C.M.~~, Shoeman~~, R.L.~~, Stricker, M., Tono, K., You, D., Ueda, K., Sherrell, D.A., ~~Owen, R~~.L.~~, Schlichting, I~~.	+	Crystallography on a chip - without the chip: sheet-on-sheet sandwich.,Doak RB, Nass Kovacs G, Gorel A, Foucar L, Barends TRM, Grunbein ML, Hilpert M, Kloos M, Roome CM, Shoeman RL, Stricker M, Tono K, You D, Ueda K, Sherrell DA, Owen RL, Schlichting I Acta Crystallogr D Struct Biol. 2018 Oct 1;74(Pt 10):1000-1007. doi:, 10.1107/S2059798318011634. Epub 2018 Oct 2. PMID:30289410<ref>PMID:30289410</ref>

-	~~Description~~: ~~Human carbonmonoxy hemoglobin SFX dataset~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
-	[[Category: ~~Stricker~~, M]]	+	<div class="pdbe-citations 6hal" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Shoeman~~, ~~R.L~~]]	+	== References ==
-	[[Category: ~~Hilpert~~, M]]	+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Homo sapiens]]
		+	[[Category: Barends, T R.M]]
		+	[[Category: Doak, B]]
		+	[[Category: Foucar, L]]
	[[Category: Gorel, A]]		[[Category: Gorel, A]]
-	[[Category: ~~Sherrell~~, ~~D.A~~]]	+	[[Category: Gruenbein, M L]]
-	[[Category: ~~Nass Kovacs~~, ~~G]]~~	+	[[Category: Hilpert, M]]
-	~~[[Category: Tono, K~~]]	+
	[[Category: Kloos, M]]		[[Category: Kloos, M]]
-	[[Category: ~~Foucar~~, L]]	+	[[Category: Kovacs, G Nass]]
-	[[Category: Owen, R.L]]	+	[[Category: Owen, R L]]
		+	[[Category: Roome, C M]]
	[[Category: Schlichting, I]]		[[Category: Schlichting, I]]
-	[[Category: ~~You~~, D]]	+	[[Category: Sherrell, D A]]
-	[[Category: ~~Barends~~, T.R.M]]	+	[[Category: Shoeman, R L]]
-	[[Category: ~~Roome~~, C.M]]	+	[[Category: Stricker, M]]
-	[[Category: ~~Gruenbein~~, ~~M.L~~]]	+	[[Category: Tono, K]]
	[[Category: Ueda, K]]		[[Category: Ueda, K]]
-	[[Category: ~~Doak~~, B]]	+	[[Category: You, D]]
		+	[[Category: Human carbonmonoxy hemoglobin]]
		+	[[Category: Oxygen transport]]
		+	[[Category: R-state]]
		+	[[Category: Sfx]]

OCA at 04:53, 22 August 2018

OCA — Wed, 22 Aug 2018 04:53:21 GMT

←Older revision		Revision as of 04:53, 22 August 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6hal is ON HOLD	+	The entry 6hal is ON HOLD until Paper Publication

	Authors: Doak, B., Gorel, A., Foucar, L., Barends, T.R.M., Gruenbein, M.L., Hilpert, M., Kloos, M., Nass Kovacs, G., Roome, C.M., Shoeman, R.L., Stricker, M., Tono, K., You, D., Ueda, K., Sherrell, D.A., Owen, R.L., Schlichting, I.		Authors: Doak, B., Gorel, A., Foucar, L., Barends, T.R.M., Gruenbein, M.L., Hilpert, M., Kloos, M., Nass Kovacs, G., Roome, C.M., Shoeman, R.L., Stricker, M., Tono, K., You, D., Ueda, K., Sherrell, D.A., Owen, R.L., Schlichting, I.
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	[[Category: Sherrell, D.A]]		[[Category: Sherrell, D.A]]
	[[Category: Nass Kovacs, G]]		[[Category: Nass Kovacs, G]]
-	[[Category: Foucar, L]]
-	[[Category: Kloos, M]]
	[[Category: Tono, K]]		[[Category: Tono, K]]
		+	[[Category: Kloos, M]]
		+	[[Category: Foucar, L]]
	[[Category: Owen, R.L]]		[[Category: Owen, R.L]]
-	[[Category: Barends, T.R.M]]
-	[[Category: You, D]]
	[[Category: Schlichting, I]]		[[Category: Schlichting, I]]
-	[[Category: ~~Gruenbein~~, M.L]]	+	[[Category: You, D]]
		+	[[Category: Barends, T.R.M]]
	[[Category: Roome, C.M]]		[[Category: Roome, C.M]]
		+	[[Category: Gruenbein, M.L]]
	[[Category: Ueda, K]]		[[Category: Ueda, K]]
	[[Category: Doak, B]]		[[Category: Doak, B]]

OCA: Protected "6hal" [edit=sysop:move=sysop]

OCA — Wed, 15 Aug 2018 15:03:09 GMT

Protected "6hal" [edit=sysop:move=sysop]

←Older revision

Revision as of 15:03, 15 August 2018

OCA: New page: '''Unreleased structure''' The entry 6hal is ON HOLD Authors: Doak, B., Gorel, A., Foucar, L., Barends, T.R.M., Gruenbein, M.L., Hilpert, M., Kloos, M., Nass Kovacs, G., Roome, C.M., Sh...

OCA — Wed, 15 Aug 2018 15:03:07 GMT

New page: '''Unreleased structure''' The entry 6hal is ON HOLD Authors: Doak, B., Gorel, A., Foucar, L., Barends, T.R.M., Gruenbein, M.L., Hilpert, M., Kloos, M., Nass Kovacs, G., Roome, C.M., Sh...

New page

'''Unreleased structure'''

The entry 6hal is ON HOLD

Authors: Doak, B., Gorel, A., Foucar, L., Barends, T.R.M., Gruenbein, M.L., Hilpert, M., Kloos, M., Nass Kovacs, G., Roome, C.M., Shoeman, R.L., Stricker, M., Tono, K., You, D., Ueda, K., Sherrell, D.A., Owen, R.L., Schlichting, I.

Description: Human carbonmonoxy hemoglobin SFX dataset
[[Category: Unreleased Structures]]
[[Category: Stricker, M]]
[[Category: Shoeman, R.L]]
[[Category: Hilpert, M]]
[[Category: Gorel, A]]
[[Category: Sherrell, D.A]]
[[Category: Nass Kovacs, G]]
[[Category: Foucar, L]]
[[Category: Kloos, M]]
[[Category: Tono, K]]
[[Category: Owen, R.L]]
[[Category: Barends, T.R.M]]
[[Category: You, D]]
[[Category: Schlichting, I]]
[[Category: Gruenbein, M.L]]
[[Category: Roome, C.M]]
[[Category: Ueda, K]]
[[Category: Doak, B]]

6hal - Revision history

OCA at 08:11, 17 October 2018

OCA at 04:53, 22 August 2018

OCA: Protected "6hal" [edit=sysop:move=sysop]

OCA: New page: '''Unreleased structure''' The entry 6hal is ON HOLD Authors: Doak, B., Gorel, A., Foucar, L., Barends, T.R.M., Gruenbein, M.L., Hilpert, M., Kloos, M., Nass Kovacs, G., Roome, C.M., Sh...