1LV2

Hepatocyte Nuclear Factor 4 is a Transcription Factor that Constitutively Binds Fatty Acids

> Summary

Summary for 1LV2

DescriptorHepatocyte nuclear factor 4-gamma
Functional Keywordsdiabetes, fatty acids, hnf4, mody, nuclear receptor, transcription factor, transcription
Biological sourceHomo sapiens (human)
Cellular locationNucleus (By similarity) Q14541
Total number of polymer chains1
Total molecular weight26111.52
Authors
Wisely, B.,Miller, A.B.,Davis, R.G.,Spitzer, T.,Shearer, B.,Moore, J.T.,Johnson, R.,Sefler, A.,Willson, T.M.,Williams, S.P. (deposition date: 2002-05-24, release date: 2002-12-18, modification date: 2011-11-16)
Primary citation
Wisely, G.B.,Miller, A.B.,Davis, R.G.,Jr Thornquest, A.D.,Johnson, R.,Spitzer, T.,Sefler, A.,Shearer, B.,Moore, J.T.,Willson, T.M.,Williams, S.P.
Hepatocyte Nuclear Factor 4 Is a Transcription Factor that Constitutively Binds Fatty Acids.
Structure, 10:1225-1234, 2002
PubMed: 12220494
DOI: 10.1016/S0969-2126(02)00829-8
MImport into Mendeley
Experimental method
X-RAY DIFFRACTION (2.7 Å)
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Structure validation

ClashscoreRamachandran outliersSidechain outliers272.3%9.3%MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

Molmil generated image of 1lv2
no rotation
Molmil generated image of 1lv2
rotated about x axis by 90°
Molmil generated image of 1lv2
rotated about y axis by 90°

> Structural details

Entity

Chain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
AHepatocyte nuclear factor 4-gammapolymer22925855.11
UniProt (Q14541)
Pfam (PF00104)
Homo sapiens (human)@PDBjHNF-4-gamma
PALMITIC ACIDnon-polymer256.41
waterwater18.014

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains1
Total molecular weight25855.1
Non-Polymers*Number of molecules1
Total molecular weight256.4
All*Total molecular weight26111.5
*Water molecules are not included.

> Experimental details

Refinement Statistics

Cell axes152.708152.70893.421
Cell angles90.0090.0090.00
SpacegroupI 41 2 2
Resolution limits19.92 - 2.70
the highest resolution shell value2.870 - 2.700
R-factor0.247
R-work0.24500 (0.24800*)
the highest resolution shell value0.365
R-free0.26400 (0.26800*)
the highest resolution shell value0.414
RMSD bond length0.010 (0.009*)
RMSD bond angle1.600 (1.675*)

Data Collection Statistics

Resolution limits22.40 (50.00*) - 2.70
the highest resolution shell value -
Number of reflections15108 (18866*)
Number of measurements1308098*
Rmerge_l_obs0.048
the highest resolution shell value0.400 (0.320*)
Completeness97.9 (98.4*)
the highest resolution shell value93.7*
Redundancy15.8
the highest resolution shell value15.4
I/sigma(I)1

Crystallization Conditions

crystal IDmethodpHpH rangetemperatureunit
1VAPOR DIFFUSION, HANGING DROP (Vapor diffusion*)5.5 (8.0*)21unknown*

Crystallization Reagents

IDcrystal IDsolution IDreagent nameconcentrationdetails
Crystallization Reagents in Literatures*
IDcrystal IDsolutionreagent nameconcentration (unit)details
11dropprotein30 (mg/ml)
21dropTris10 (mM)pH8.0
31dropEDTA0.1 (mM)
41drop150 (mM)
51dropdithiothreitol10 (mM)
61droppropane-diol5 (%)
71reservoirammonium dihydrogen phosphate/diammonium hydrogen phosphate0.75 (M)pH5.0
81reservoirdithiothreitol10 (mM)
Annotated Information is extracted from Literature Info*

> Functional details

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Functional Information from GO Data

ChainGOidnamespacecontents
A0005654cellular_componentnucleoplasm
A0004879molecular_functionRNA polymerase II transcription factor activity, ligand-activated sequence-specific DNA binding
A0043565molecular_functionsequence-specific DNA binding
A0003707molecular_functionsteroid hormone receptor activity
A0003700molecular_functiontranscription factor activity, sequence-specific DNA binding
A0008270molecular_functionzinc ion binding
A0031018biological_processendocrine pancreas development
A0010467biological_processgene expression
A0045893biological_processpositive regulation of transcription, DNA-templated
A0006357biological_processregulation of transcription from RNA polymerase II promoter
A0006367biological_processtranscription initiation from RNA polymerase II promoter
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Functional Information from PDB Data

site_idNumber of ResiduesDetails
AC18BINDING SITE FOR RESIDUE PLM A 328
ChainResidue
AILE37
ASER43
AARG88
ALEU98
AGLY99
AILE113
AILE207
AVAL210

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Functional Information from PDB atom coordinates for the "HETATM" binding sites

site_idNumber of ResiduesDetails
PLM_1lv2_A_32825PALMITIC ACID binding site
ChainResidueligand
AILE135PLM: PALMITIC ACID
AVAL138PLM: PALMITIC ACID
ASER141-MET142PLM: PALMITIC ACID
AGLN145PLM: PALMITIC ACID
ALEU179-LEU180PLM: PALMITIC ACID
AGLY182-ALA183PLM: PALMITIC ACID
AARG186PLM: PALMITIC ACID
ALEU194-GLY197PLM: PALMITIC ACID
AILE202PLM: PALMITIC ACID
AGLU210-ILE211PLM: PALMITIC ACID
AVAL214-ALA215PLM: PALMITIC ACID
AVAL218PLM: PALMITIC ACID
AMET301PLM: PALMITIC ACID
AGLN304-ILE305PLM: PALMITIC ACID
AVAL308PLM: PALMITIC ACID
AVAL314PLM: PALMITIC ACID

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Functional Information from PROSITE/UniProt

site_idNumber of ResiduesDetails
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Functional Information from SwissProt/UniProt

site_idNumber of ResiduesDetails
SWS_FT_FI11Nuclear receptor.
ChainResidueDetails
ANA*

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Catalytic Information from CSA

site_idNumber of ResiduesDetails
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Catalytic Information from CATRES

site_idNumber of ResiduesDetails

> Sequence Neighbor

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