We apologize for Proteopedia being slow to respond. For the past two years, a new implementation of Proteopedia has been being built. Soon, it will replace this 18-year old system. All existing content will be moved to the new system at a date that will be announced here.

1lfg

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (09:38, 25 December 2024) (edit) (undo)
 
(18 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1lfg.gif|left|200px]]<br /><applet load="1lfg" size="350" color="white" frame="true" align="right" spinBox="true"
 
-
caption="1lfg, resolution 2.2&Aring;" />
 
-
'''MOLECULAR REPLACEMENT SOLUTION OF THE STRUCTURE OF APOLACTOFERRIN, A PROTEIN DISPLAYING LARGE-SCALE CONFORMATIONAL CHANGE'''<br />
 
-
==Overview==
+
==Structure of diferric human lactoferrin==
-
The crystal structure of an orthorhombic form of human apolactoferrin (ApoLf) has been determined from 2.8 A diffractometer data by molecular replacement methods. A variety of search models derived from the diferric lactoferrin structure (Fe2Lf) were used to obtain a consistent solution to the rotation function. An R-factor search gave the correct translational solution and the model was refined by rigid-body least-squares refinement (program CORELS). Only three of the four domains were located correctly by this procedure, however; the fourth was finally placed correctly by rotating it manually onto three strands of electron density which were recognized as part of its central beta-sheet. The final model, refined by restrained least-squares methods to an R factor of 0.214 for data in the resolution range 10.0 to 2.8 A, shows a large domain movement in the N-terminal half of the molecule (a 54 degree rotation of domain N2) and smaller domain movements elsewhere, when compared with Fe2Lf. A feature of the crystal structure is that although the ApoLf and Fe2Lf unit cells appear very similar, their crystal packing and molecular structures are quite different.
+
<StructureSection load='1lfg' size='340' side='right'caption='[[1lfg]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
 +
== Structural highlights ==
 +
<table><tr><td colspan='2'>[[1lfg]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. The January 2016 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Siderocalin'' by David Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2016_1 10.2210/rcsb_pdb/mom_2016_1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LFG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1LFG FirstGlance]. <br>
 +
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.2&#8491;</td></tr>
 +
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CO3:CARBONATE+ION'>CO3</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></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=1lfg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lfg OCA], [https://pdbe.org/1lfg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1lfg RCSB], [https://www.ebi.ac.uk/pdbsum/1lfg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1lfg ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/TRFL_HUMAN TRFL_HUMAN] Transferrins are iron binding transport proteins which can bind two Fe(3+) ions in association with the binding of an anion, usually bicarbonate.<ref>PMID:12535064</ref> <ref>PMID:22320386</ref> Lactotransferrin has antimicrobial activity which depends on the extracellular cation concentration.<ref>PMID:12535064</ref> <ref>PMID:22320386</ref> Lactoferroxins A, B and C have opioid antagonist activity. Lactoferroxin A shows preference for mu-receptors, while lactoferroxin B and C have somewhat higher degrees of preference for kappa-receptors than for mu-receptors.<ref>PMID:12535064</ref> <ref>PMID:22320386</ref> The lactotransferrin transferrin-like domain 1 functions as a serine protease of the peptidase S60 family that cuts arginine rich regions. This function contributes to the antimicrobial activity.<ref>PMID:12535064</ref> <ref>PMID:22320386</ref> Isoform DeltaLf: transcription factor with antiproliferative properties and inducing cell cycle arrest. Binds to DeltaLf response element found in the SKP1, BAX, DCPS, and SELH promoters.<ref>PMID:12535064</ref> <ref>PMID:22320386</ref>
 +
== Evolutionary Conservation ==
 +
[[Image:Consurf_key_small.gif|200px|right]]
 +
Check<jmol>
 +
<jmolCheckbox>
 +
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/lf/1lfg_consurf.spt"</scriptWhenChecked>
 +
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
 +
<text>to colour the structure by Evolutionary Conservation</text>
 +
</jmolCheckbox>
 +
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1lfg ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
The three-dimensional structure of the diferric form of human lactoferrin has been refined at 2.2 A resolution, using synchrotron data combined with a lower resolution (3.2 A) diffractometer data set. Following restrained least-squares refinement and model rebuilding the final model comprises 5330 protein atoms (691 residues), 2Fe(3+) and 2CO(3)(2-) ions, 469 solvent molecules and 98 carbohydrate atoms (eight sugar residues). Root-mean-square deviations from standard geometry are 0.015 A for bond lengths and 0.038 A for angle (1-3) distances, and the final crystallographic R-factor is 0.179 for all 39 113 reflections in the resolution range 8.0-2.2 A. A close structural similarity is seen between the two lobes of the molecule, with differences mainly in loops and turns. The two binding sites are extremely similar, the only apparent differences being a slightly more asymmetric bidentate binding of the carbonate ion to the metal, and a slightly longer Fe-O bond to one of the Tyr ligands, in the N-lobe site relative to the C-lobe site. Distinct differences are seen in the interactions made by two cationic groups, Arg210 and Lys546, behind the iron site, and these may influence the stability of the two metal sites. Analysis of interdomain and interlobe interactions shows that these are few in number which is consistent with the known flexibility of the molecule with respect to domain and lobe movements. Internal water molecules are found in discrete sites and in two large clusters (in the two interdomain clefts) and one tightly bound water molecule is present 3.8 A from the Fe atom in each lobe. The carbohydrate is weakly defined and has been modelled to a limited extent; two sugar residues of the N-lobe glycan and six of the C-lobe glycan. Only one direct protein-carbohydrate contact can be found.
-
==Disease==
+
Structure of human diferric lactoferrin refined at 2.2 A resolution.,Haridas M, Anderson BF, Baker EN Acta Crystallogr D Biol Crystallogr. 1995 Sep 1;51(Pt 5):629-46. PMID:15299793<ref>PMID:15299793</ref>
-
Known disease associated with this structure: Deafness, autosomal dominant 1 OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=602121 602121]]
+
-
==About this Structure==
+
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-
1LFG is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/ ] with <scene name='pdbligand=NAG:'>NAG</scene>, <scene name='pdbligand=FUC:'>FUC</scene>, <scene name='pdbligand=FE:'>FE</scene> and <scene name='pdbligand=CO3:'>CO3</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LFG OCA].
+
</div>
 +
<div class="pdbe-citations 1lfg" style="background-color:#fffaf0;"></div>
-
==Reference==
+
==See Also==
-
Molecular replacement solution of the structure of apolactoferrin, a protein displaying large-scale conformational change., Norris GE, Anderson BF, Baker EN, Acta Crystallogr B. 1991 Dec 1;47 ( Pt 6):998-1004. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=1772635 1772635]
+
*[[Lactoferrin|Lactoferrin]]
-
[[Category: Single protein]]
+
== References ==
-
[[Category: Anderson, B F.]]
+
<references/>
-
[[Category: Baker, E N.]]
+
__TOC__
-
[[Category: Haridas, M.]]
+
</StructureSection>
-
[[Category: CO3]]
+
[[Category: Homo sapiens]]
-
[[Category: FE]]
+
[[Category: Large Structures]]
-
[[Category: FUC]]
+
[[Category: RCSB PDB Molecule of the Month]]
-
[[Category: NAG]]
+
[[Category: Siderocalin]]
-
[[Category: transferrin]]
+
[[Category: Anderson BF]]
-
 
+
[[Category: Baker EN]]
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 13:44:31 2008''
+
[[Category: Haridas M]]

Current revision

Structure of diferric human lactoferrin

PDB ID 1lfg

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1lfg"
Personal tools