1M7W

HNF4a ligand binding domain with bound fatty acid

> Summary

Summary for 1M7W

DescriptorHepatocyte nuclear factor 4-alpha
Functional Keywordstranscription factor
Biological sourceRattus rattus (black rat)
Cellular locationNucleus P22449
Total number of polymer chains4
Total molecular weight113283.84
Authors
Dhe-Paganon, S.,Duda, K.,Iwamoto, M.,Chi, Y.I.,Shoelson, S.E. (deposition date: 2002-07-22, release date: 2003-07-01, modification date: 2009-02-24)
Primary citation
Dhe-Paganon, S.,Duda, K.,Iwamoto, M.,Chi, Y.I.,Shoelson, S.E.
Crystal structure of the HNF4 alpha ligand binding domain in complex with endogenous fatty acid ligand
J.Biol.Chem., 277:37973-37976, 2002
PubMed: 12193589
DOI: 10.1074/jbc.C200420200
MImport into Mendeley
Experimental method
X-RAY DIFFRACTION (2.8 Å)
?

Structure validation

ClashscoreRamachandran outliersSidechain outliers305.5%8.4%MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

Molmil generated image of 1m7w
no rotation
Molmil generated image of 1m7w
rotated about x axis by 90°
Molmil generated image of 1m7w
rotated about y axis by 90°

More Biological unit images

Molmil generated image of 1m7w
no rotation
Molmil generated image of 1m7w
rotated about x axis by 90°
Molmil generated image of 1m7w
rotated about y axis by 90°
(*)In the case of coarse surface representation, the asymmetric unit is shown as red ribbon representation.
Coordinate files for Biological unit (1m7w.pdb1.gz [73.88 KB])
Coordinate files for Biological unit (1m7w.pdb2.gz [74.4 KB])
Coordinate files for Biological unit (1m7w.pdb3.gz [288.3 KB])
Coordinate files for Biological unit (1m7w.pdb4.gz [145.26 KB])
Coordinate files for Biological unit (1m7w.pdb5.gz [145.48 KB])
Coordinate files for Biological unit (1m7w.pdb6.gz [145.18 KB])
Coordinate files for Biological unit (1m7w.pdb7.gz [74.06 KB])
Coordinate files for Biological unit (1m7w.pdb8.gz [73.92 KB])

> Structural details

Entity

Chain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
A, B, C, DHepatocyte nuclear factor 4-alphapolymer25028120.64
UniProt (P22449)
Pfam (PF00104)
Rattus rattus (black rat)HNF-4-alpha, Transcription factor HNF-4, Transcription factor 14
LAURIC ACIDnon-polymer200.34
waterwater18.074

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains4
Total molecular weight112482.6
Non-Polymers*Number of molecules4
Total molecular weight801.3
All*Total molecular weight113283.8
*Water molecules are not included.

> Experimental details

Refinement Statistics

Experimental method:X-RAY DIFFRACTION (2.8 Å)

Cell axes102.288102.288227.688
Cell angles90.0090.0090.00
SpacegroupP 41 21 2
Resolution limits20.00 - 2.80
the highest resolution shell value -
R-work0.23700 (0.23200*)
R-free0.28200
RMSD bond length0.008*
RMSD bond angle1.350*

Data Collection Statistics

Resolution limits20.00 - 2.80
the highest resolution shell value -
Number of reflections29727
I/sigma(I)0.5

Crystallization Conditions

crystal IDmethodpHpH rangetemperatureunit
1Vapor diffusion, sitting drop*7.5 (8.0*)R.T.*

Crystallization Reagents

IDcrystal IDsolution IDreagent nameconcentrationdetails
Crystallization Reagents in Literatures*
IDcrystal IDsolutionreagent nameconcentration (unit)details
11dropprotein25 (mg/ml)
21reservoirsodium citrate0.1 (M)pH8.0
31reservoirammonium acetate0.7 (M)
41reservoirMPD16 (%)
51reservoirdithiothreitol10 (mM)
Annotated Information is extracted from Literature Info*

> Functional details

?

Functional Information from GO Data

ChainGOidnamespacecontents
A0005737cellular_componentcytoplasm
A0005634cellular_componentnucleus
A0005667cellular_componenttranscription factor complex
A0003677molecular_functionDNA binding
A0005504molecular_functionfatty acid binding
A0000062molecular_functionfatty-acyl-CoA binding
A0016290molecular_functionpalmitoyl-CoA hydrolase activity
A0042803molecular_functionprotein homodimerization activity
A0070491molecular_functionrepressing transcription factor binding
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
A0008134molecular_functiontranscription factor binding
A0001077molecular_functiontranscriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding
A0008270molecular_functionzinc ion binding
A0006637biological_processacyl-CoA metabolic process
A0007568biological_processaging
A0030154biological_processcell differentiation
A0045216biological_processcell-cell junction organization
A0071456biological_processcellular response to hypoxia
A0007164biological_processestablishment of tissue polarity
A1902569biological_processnegative regulation of activation of JAK2 kinase activity
A0008285biological_processnegative regulation of cell proliferation
A0045930biological_processnegative regulation of mitotic cell cycle
A0033159biological_processnegative regulation of protein import into nucleus, translocation
A0043433biological_processnegative regulation of sequence-specific DNA binding transcription factor activity
A0042524biological_processnegative regulation of tyrosine phosphorylation of Stat5 protein
A0045723biological_processpositive regulation of fatty acid biosynthetic process
A0045722biological_processpositive regulation of gluconeogenesis
A0045944biological_processpositive regulation of transcription from RNA polymerase II promoter
A0045893biological_processpositive regulation of transcription, DNA-templated
A0032534biological_processregulation of microvillus assembly
A0006355biological_processregulation of transcription, DNA-templated
A0051591biological_processresponse to cAMP
A0042493biological_processresponse to drug
A0009749biological_processresponse to glucose
B0005737cellular_componentcytoplasm
B0005634cellular_componentnucleus
B0005667cellular_componenttranscription factor complex
B0003677molecular_functionDNA binding
B0005504molecular_functionfatty acid binding
B0000062molecular_functionfatty-acyl-CoA binding
B0016290molecular_functionpalmitoyl-CoA hydrolase activity
B0042803molecular_functionprotein homodimerization activity
B0070491molecular_functionrepressing transcription factor binding
B0004879molecular_functionRNA polymerase II transcription factor activity, ligand-activated sequence-specific DNA binding
B0043565molecular_functionsequence-specific DNA binding
B0003707molecular_functionsteroid hormone receptor activity
B0003700molecular_functiontranscription factor activity, sequence-specific DNA binding
B0008134molecular_functiontranscription factor binding
B0001077molecular_functiontranscriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding
B0008270molecular_functionzinc ion binding
B0006637biological_processacyl-CoA metabolic process
B0007568biological_processaging
B0030154biological_processcell differentiation
B0045216biological_processcell-cell junction organization
B0071456biological_processcellular response to hypoxia
B0007164biological_processestablishment of tissue polarity
B1902569biological_processnegative regulation of activation of JAK2 kinase activity
B0008285biological_processnegative regulation of cell proliferation
B0045930biological_processnegative regulation of mitotic cell cycle
B0033159biological_processnegative regulation of protein import into nucleus, translocation
B0043433biological_processnegative regulation of sequence-specific DNA binding transcription factor activity
B0042524biological_processnegative regulation of tyrosine phosphorylation of Stat5 protein
B0045723biological_processpositive regulation of fatty acid biosynthetic process
B0045722biological_processpositive regulation of gluconeogenesis
B0045944biological_processpositive regulation of transcription from RNA polymerase II promoter
B0045893biological_processpositive regulation of transcription, DNA-templated
B0032534biological_processregulation of microvillus assembly
B0006355biological_processregulation of transcription, DNA-templated
B0051591biological_processresponse to cAMP
B0042493biological_processresponse to drug
B0009749biological_processresponse to glucose
C0005737cellular_componentcytoplasm
C0005634cellular_componentnucleus
C0005667cellular_componenttranscription factor complex
C0003677molecular_functionDNA binding
C0005504molecular_functionfatty acid binding
C0000062molecular_functionfatty-acyl-CoA binding
C0016290molecular_functionpalmitoyl-CoA hydrolase activity
C0042803molecular_functionprotein homodimerization activity
C0070491molecular_functionrepressing transcription factor binding
C0004879molecular_functionRNA polymerase II transcription factor activity, ligand-activated sequence-specific DNA binding
C0043565molecular_functionsequence-specific DNA binding
C0003707molecular_functionsteroid hormone receptor activity
C0003700molecular_functiontranscription factor activity, sequence-specific DNA binding
C0008134molecular_functiontranscription factor binding
C0001077molecular_functiontranscriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding
C0008270molecular_functionzinc ion binding
C0006637biological_processacyl-CoA metabolic process
C0007568biological_processaging
C0030154biological_processcell differentiation
C0045216biological_processcell-cell junction organization
C0071456biological_processcellular response to hypoxia
C0007164biological_processestablishment of tissue polarity
C1902569biological_processnegative regulation of activation of JAK2 kinase activity
C0008285biological_processnegative regulation of cell proliferation
C0045930biological_processnegative regulation of mitotic cell cycle
C0033159biological_processnegative regulation of protein import into nucleus, translocation
C0043433biological_processnegative regulation of sequence-specific DNA binding transcription factor activity
C0042524biological_processnegative regulation of tyrosine phosphorylation of Stat5 protein
C0045723biological_processpositive regulation of fatty acid biosynthetic process
C0045722biological_processpositive regulation of gluconeogenesis
C0045944biological_processpositive regulation of transcription from RNA polymerase II promoter
C0045893biological_processpositive regulation of transcription, DNA-templated
C0032534biological_processregulation of microvillus assembly
C0006355biological_processregulation of transcription, DNA-templated
C0051591biological_processresponse to cAMP
C0042493biological_processresponse to drug
C0009749biological_processresponse to glucose
D0005737cellular_componentcytoplasm
D0005634cellular_componentnucleus
D0005667cellular_componenttranscription factor complex
D0003677molecular_functionDNA binding
D0005504molecular_functionfatty acid binding
D0000062molecular_functionfatty-acyl-CoA binding
D0016290molecular_functionpalmitoyl-CoA hydrolase activity
D0042803molecular_functionprotein homodimerization activity
D0070491molecular_functionrepressing transcription factor binding
D0004879molecular_functionRNA polymerase II transcription factor activity, ligand-activated sequence-specific DNA binding
D0043565molecular_functionsequence-specific DNA binding
D0003707molecular_functionsteroid hormone receptor activity
D0003700molecular_functiontranscription factor activity, sequence-specific DNA binding
D0008134molecular_functiontranscription factor binding
D0001077molecular_functiontranscriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding
D0008270molecular_functionzinc ion binding
D0006637biological_processacyl-CoA metabolic process
D0007568biological_processaging
D0030154biological_processcell differentiation
D0045216biological_processcell-cell junction organization
D0071456biological_processcellular response to hypoxia
D0007164biological_processestablishment of tissue polarity
D1902569biological_processnegative regulation of activation of JAK2 kinase activity
D0008285biological_processnegative regulation of cell proliferation
D0045930biological_processnegative regulation of mitotic cell cycle
D0033159biological_processnegative regulation of protein import into nucleus, translocation
D0043433biological_processnegative regulation of sequence-specific DNA binding transcription factor activity
D0042524biological_processnegative regulation of tyrosine phosphorylation of Stat5 protein
D0045723biological_processpositive regulation of fatty acid biosynthetic process
D0045722biological_processpositive regulation of gluconeogenesis
D0045944biological_processpositive regulation of transcription from RNA polymerase II promoter
D0045893biological_processpositive regulation of transcription, DNA-templated
D0032534biological_processregulation of microvillus assembly
D0006355biological_processregulation of transcription, DNA-templated
D0051591biological_processresponse to cAMP
D0042493biological_processresponse to drug
D0009749biological_processresponse to glucose
?

Functional Information from PDB Data

site_idNumber of ResiduesDetails
AC16BINDING SITE FOR RESIDUE DAO A 700
ChainResidue
ASER49
AGLN53
AARG94
ALEU104
AGLY105
AMET120

AC29BINDING SITE FOR RESIDUE DAO B 701
ChainResidue
BHOH
BSER49
BMET50
BGLN53
BARG94
BLEU104
BGLY105
BLEU117
BMET120

AC311BINDING SITE FOR RESIDUE DAO C 702
ChainResidue
CHOH
CVAL46
CSER49
CGLN53
CALA91
CARG94
CLEU104
CGLY105
CMET120
CILE127
CILE214

AC47BINDING SITE FOR RESIDUE DAO D 703
ChainResidue
DSER49
DGLN53
DARG94
DLEU104
DGLY105
DMET120
DSER124

?

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

site_idNumber of ResiduesDetails
DAO_1m7w_A_70021LAURIC ACID binding site
ChainResidueligand
AVAL178DAO: LAURIC ACID
ASER181-MET182DAO: LAURIC ACID
AGLN185DAO: LAURIC ACID
ALEU219-LEU220DAO: LAURIC ACID
AALA223DAO: LAURIC ACID
AARG226DAO: LAURIC ACID
ALEU234-GLY237DAO: LAURIC ACID
AVAL242DAO: LAURIC ACID
AMET252DAO: LAURIC ACID
AVAL255-SER256DAO: LAURIC ACID
AILE259DAO: LAURIC ACID
AMET342DAO: LAURIC ACID
AGLN345-ILE346DAO: LAURIC ACID
AILE349DAO: LAURIC ACID

DAO_1m7w_B_70120LAURIC ACID binding site
ChainResidueligand
BVAL178DAO: LAURIC ACID
BSER181-MET182DAO: LAURIC ACID
BGLN185DAO: LAURIC ACID
BLEU219-LEU220DAO: LAURIC ACID
BALA223DAO: LAURIC ACID
BARG226DAO: LAURIC ACID
BLEU234-ASN238DAO: LAURIC ACID
BVAL242DAO: LAURIC ACID
BLEU249DAO: LAURIC ACID
BMET252-SER253DAO: LAURIC ACID
BVAL255-SER256DAO: LAURIC ACID
BILE259DAO: LAURIC ACID

DAO_1m7w_C_70221LAURIC ACID binding site
ChainResidueligand
CILE175DAO: LAURIC ACID
CVAL178-CYS179DAO: LAURIC ACID
CSER181-MET182DAO: LAURIC ACID
CGLN185DAO: LAURIC ACID
CLEU219-LEU220DAO: LAURIC ACID
CALA223DAO: LAURIC ACID
CARG226DAO: LAURIC ACID
CLEU234-GLY237DAO: LAURIC ACID
CVAL242DAO: LAURIC ACID
CLEU249DAO: LAURIC ACID
CMET252DAO: LAURIC ACID
CVAL255DAO: LAURIC ACID
CILE259DAO: LAURIC ACID
CMET342DAO: LAURIC ACID
CILE346DAO: LAURIC ACID

DAO_1m7w_D_70321LAURIC ACID binding site
ChainResidueligand
DVAL178DAO: LAURIC ACID
DSER181-MET182DAO: LAURIC ACID
DGLN185DAO: LAURIC ACID
DLEU219-LEU220DAO: LAURIC ACID
DALA223DAO: LAURIC ACID
DARG226DAO: LAURIC ACID
DLEU234-GLY237DAO: LAURIC ACID
DVAL242DAO: LAURIC ACID
DLEU249DAO: LAURIC ACID
DMET252DAO: LAURIC ACID
DVAL255-SER256DAO: LAURIC ACID
DILE259DAO: LAURIC ACID
DMET342DAO: LAURIC ACID
DGLN345-ILE346DAO: LAURIC ACID

?

Functional Information from PROSITE/UniProt

site_idNumber of ResiduesDetails
?

Functional Information from SwissProt/UniProt

site_idNumber of ResiduesDetails
SWS_FT_FI11Nuclear receptor.
ChainResidueDetails
ANA*

SWS_FT_FI21Nuclear receptor.
ChainResidueDetails
BNA*

SWS_FT_FI31Nuclear receptor.
ChainResidueDetails
CNA*

SWS_FT_FI41Nuclear receptor.
ChainResidueDetails
DNA*

?

Catalytic Information from CSA

site_idNumber of ResiduesDetails
?

Catalytic Information from CATRES

site_idNumber of ResiduesDetails

> Sequence Neighbor

> Downloads

Resources

File formatFile name (file size)
PDBallpdb1m7w.ent.gz (151.27 KB)
Display
all (no-compress)pdb1m7w.ent (633.92 KB)
header onlypdb1m7w.ent.gz (8.04 KB)
Display
PDBx/mmCIF1m7w.cif.gz (182.6 KB)
PDBMLall1m7w.xml.gz (284.03 KB)
Display
no-atom1m7w-noatom.xml.gz (34.68 KB)
Display
ext-atom1m7w-extatom.xml.gz (168.91 KB)
Display
PDBMLplusall1m7w-plus.xml.gz (288.75 KB)
Display
no-atom1m7w-plus-noatom.xml.gz (39.41 KB)
Display
add only1m7w-add.xml.gz (4.72 KB)
Display
RDF1m7w.rdf.gz (68.08 KB)
Display
Biological unit (PDB format)1m7w.pdb1.gz (73.88 KB) (A,B)
*author defined assembly, 2 molecule(s) (dimeric)
Display
1m7w.pdb2.gz (74.4 KB) (C,D)
*author and software defined assembly, 2 molecule(s) (dimeric)
Display
1m7w.pdb3.gz (288.3 KB) (A,B,C,D)
*software defined assembly, 8 molecule(s) (octameric)
Display
1m7w.pdb4.gz (145.26 KB) (A,B,C,D)
*software defined assembly, 4 molecule(s) (tetrameric)
Display
1m7w.pdb5.gz (145.48 KB) (A,B)
*software defined assembly, 4 molecule(s) (tetrameric)
Display
1m7w.pdb6.gz (145.18 KB) (B,C)
*software defined assembly, 4 molecule(s) (tetrameric)
Display
1m7w.pdb7.gz (74.06 KB) (B)
*software defined assembly, 2 molecule(s) (dimeric)
Display
1m7w.pdb8.gz (73.92 KB) (B,C)
*software defined assembly, 2 molecule(s) (dimeric)
Display
Validation reportsPDF1m7w​_validation.pdf.gz (249.2 KB)
Display
PDF-full1m7w​_full​_validation.pdf.gz (291.75 KB)
Display
XML1m7w​_validation.xml.gz (25.83 KB)
Display
PNG1m7w​_multipercentile​_validation.png.gz (118.4 KB)
Display
SVG1m7w​_multipercentile​_validation.svg.gz (810 B)
Display
Sequence (fasta)1m7w​_seq.txt
Display

PDBj@FacebookPDBj@TwitterwwPDBwwPDB FoundationEM DataBank

Copyright © 2013-2016 Protein Data Bank Japan