2fol: Difference between revisions

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New page: left|200px<br /> <applet load="2fol" size="450" color="white" frame="true" align="right" spinBox="true" caption="2fol, resolution 2.631Å" /> '''Crystal structure ...
 
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[[Image:2fol.gif|left|200px]]<br />
<applet load="2fol" size="450" color="white" frame="true" align="right" spinBox="true"
caption="2fol, resolution 2.631&Aring;" />
'''Crystal structure of human RAB1A in complex with GDP'''<br />


==Overview==
==Crystal structure of human RAB1A in complex with GDP==
Rapid protein-structure determination relies greatly on software that can, automatically build a protein model into an experimental electron-density, map. In favorable circumstances, various software systems are capable of, building over 90% of the final model. However, completeness falls off, rapidly with the resolution of the diffraction data. Manual completion of, these partial models is usually feasible, but is time-consuming and prone, to subjective interpretation. Except for the N- and C-termini of the, chain, the end points of each missing fragment are known from the initial, model. Hence, fitting fragments reduces to an inverse-kinematics problem., A method has been developed that combines fast inverse-kinematics, algorithms with a real-space torsion-angle refinement procedure in a, two-stage approach to fit missing main-chain fragments into the electron, density between two anchor points. The first stage samples a large number, of closing conformations, guided by the electron density. These candidates, are ranked according to density fit. In a subsequent refinement stage, optimization steps are projected onto a carefully chosen subspace of, conformation space to preserve rigid geometry and closure. Experimental, results show that fitted fragments are in excellent agreement with the, final refined structure for lengths of up to 12-15 residues in areas of, weak or ambiguous electron density, even at medium to low resolution.
<StructureSection load='2fol' size='340' side='right'caption='[[2fol]], [[Resolution|resolution]] 2.63&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[2fol]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FOL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2FOL 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]] 2.631&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=UNX:UNKNOWN+ATOM+OR+ION'>UNX</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=2fol FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fol OCA], [https://pdbe.org/2fol PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2fol RCSB], [https://www.ebi.ac.uk/pdbsum/2fol PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2fol ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/RAB1A_HUMAN RAB1A_HUMAN] Probably required for transit of protein from the ER through Golgi compartment. Binds GTP and GDP and possesses intrinsic GTPase activity.
== 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/fo/2fol_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=2fol ConSurf].
<div style="clear:both"></div>


==About this Structure==
==See Also==
2FOL is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] with MG, GDP and UNX as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2FOL OCA].
*[[Ras-related protein Rab 3D structures|Ras-related protein Rab 3D structures]]
 
__TOC__
==Reference==
</StructureSection>
Real-space protein-model completion: an inverse-kinematics approach., van den Bedem H, Lotan I, Latombe JC, Deacon AM, Acta Crystallogr D Biol Crystallogr. 2005 Jan;61(Pt 1):2-13. Epub 2004 Dec, 17. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15608370 15608370]
[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
[[Category: Single protein]]
[[Category: Large Structures]]
[[Category: Arrowsmith, C.]]
[[Category: Arrowsmith C]]
[[Category: Bochkarev, A.]]
[[Category: Bochkarev A]]
[[Category: Edwards, A.]]
[[Category: Edwards A]]
[[Category: Park, H.]]
[[Category: Park H]]
[[Category: SGC, Structural.Genomics.Consortium.]]
[[Category: Shen L]]
[[Category: Shen, L.]]
[[Category: Shen Y]]
[[Category: Shen, Y.]]
[[Category: Sundstrom M]]
[[Category: Sundstrom, M.]]
[[Category: Tempel W]]
[[Category: Tempel, W.]]
[[Category: Wang J]]
[[Category: Wang, J.]]
[[Category: Weigelt J]]
[[Category: Weigelt, J.]]
[[Category: GDP]]
[[Category: MG]]
[[Category: UNX]]
[[Category: g-protein]]
[[Category: gtp analogue]]
[[Category: rab]]
[[Category: sgc]]
[[Category: struct ural genomics consortium]]
[[Category: structural genomics]]
[[Category: structural genomics consortium]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Mon Nov 12 22:08:27 2007''

Latest revision as of 12:30, 30 August 2023

Crystal structure of human RAB1A in complex with GDPCrystal structure of human RAB1A in complex with GDP

Structural highlights

2fol is a 1 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.631Å
Ligands:, ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RAB1A_HUMAN Probably required for transit of protein from the ER through Golgi compartment. Binds GTP and GDP and possesses intrinsic GTPase activity.

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

2fol, resolution 2.63Å

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