1JB6

Crystal Structure of Dimerization Domain (1-33) of HNF-1alpha

> Summary

Summary for 1JB6

Related1g39 1g2y 1g2z 1f93
DescriptorHEPATOCYTE NUCLEAR FACTOR 1-ALPHA
Functional Keywordsfour-helix bundle, non-canonical turn, transcription
Cellular locationNucleus P22361
Total number of polymer chains2
Total molecular weight7240.18
Authors
Narayana, N.,Hua, Q.-X.,Weiss, M.A. (deposition date: 2001-06-01, release date: 2001-07-11, modification date: 2011-07-13)
Primary citation
Narayana, N.,Hua, Q.,Weiss, M.A.
The dimerization domain of HNF-1alpha: structure and plasticity of an intertwined four-helix bundle with application to diabetes mellitus.
J.Mol.Biol., 310:635-658, 2001
PubMed: 11439029
DOI: 10.1006/jmbi.2001.4780
MImport into Mendeley
Experimental method
X-RAY DIFFRACTION (1.7 Å)
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Structure validation

RfreeClashscoreRamachandran outliersSidechain outliersRSRZ outliers0.260704.1%8.6%MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

Molmil generated image of 1jb6
no rotation
Molmil generated image of 1jb6
rotated about x axis by 90°
Molmil generated image of 1jb6
rotated about y axis by 90°

> Structural details

Entity

Chain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
A, BHEPATOCYTE NUCLEAR FACTOR 1-ALPHApolymer333620.12
UniProt (P22361)
Pfam (PF04814)
HNF-1A
waterwater18.055

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains2
Total molecular weight7240.2
Non-Polymers*Number of molecules0
Total molecular weight0.0
All*Total molecular weight7240.2
*Water molecules are not included.

> Experimental details

Refinement Statistics

Experimental method:X-RAY DIFFRACTION (1.7 Å)

Cell axes28.42042.19042.430
Cell angles90.0090.0090.00
SpacegroupP 21 21 2
Resolution limits40.00 - 1.70
the highest resolution shell value1.780 - 1.700
R-factor0.231*
R-work0.23100
the highest resolution shell value0.220
R-free0.24500
the highest resolution shell value0.262
RMSD bond length0.004
RMSD bond angle0.800

Data Collection Statistics

Resolution limits40.00 - 1.70
the highest resolution shell value -
Number of reflections5245
Completeness88.0
Redundancy6
the highest resolution shell value5

Crystallization Conditions

crystal IDmethodpHpH rangetemperatureunit
1VAPOR DIFFUSION, HANGING DROP7.5 (7.0*)277 (4*)*

Crystallization Reagents

IDcrystal IDsolution IDreagent nameconcentrationdetails
Crystallization Reagents in Literatures*
IDcrystal IDsolutionreagent nameconcentration (unit)details
11droppeptide3 (mM)
21dropTris-HCl50 (mM)
31dropdithiothreitol2 (mM)
41reservoirMPD20 (%(v/v))
51reservoirTris-HCl50 (mM)
61reservoirdithiothreitol1 (mM)
Annotated Information is extracted from Literature Info*

> Functional details

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Functional Information from GO Data

ChainGOidnamespacecontents
A0005737cellular_componentcytoplasm
A0005654cellular_componentnucleoplasm
A0005634cellular_componentnucleus
A0001750cellular_componentphotoreceptor outer segment
A0045120cellular_componentpronucleus
A0043234cellular_componentprotein complex
A0005667cellular_componenttranscription factor complex
A0003677molecular_functionDNA binding
A0046983molecular_functionprotein dimerization activity
A0046982molecular_functionprotein heterodimerization activity
A0042803molecular_functionprotein homodimerization activity
A0000978molecular_functionRNA polymerase II core promoter proximal region sequence-specific DNA binding
A0003700molecular_functiontranscription factor activity, sequence-specific DNA binding
A0044212molecular_functiontranscription regulatory region DNA binding
A0001077molecular_functiontranscriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding
A0001228molecular_functiontranscriptional activator activity, RNA polymerase II transcription regulatory region sequence-specific binding
A0015721biological_processbile acid and bile salt transport
A0006699biological_processbile acid biosynthetic process
A0001824biological_processblastocyst development
A0045453biological_processbone resorption
A0008203biological_processcholesterol metabolic process
A0006338biological_processchromatin remodeling
A0030326biological_processembryonic limb morphogenesis
A0031018biological_processendocrine pancreas development
A0006633biological_processfatty acid biosynthetic process
A0015908biological_processfatty acid transport
A0042593biological_processglucose homeostasis
A0046323biological_processglucose import
A0006783biological_processheme biosynthetic process
A0016573biological_processhistone acetylation
A0030073biological_processinsulin secretion
A0001889biological_processliver development
A0000122biological_processnegative regulation of transcription from RNA polymerase II promoter
A0048341biological_processparaxial mesoderm formation
A0001890biological_processplacenta development
A0045944biological_processpositive regulation of transcription from RNA polymerase II promoter
A0060261biological_processpositive regulation of transcription initiation from RNA polymerase II promoter
A0045893biological_processpositive regulation of transcription, DNA-templated
A0008104biological_processprotein localization
A0046883biological_processregulation of hormone secretion
A0050796biological_processregulation of insulin secretion
A0006357biological_processregulation of transcription from RNA polymerase II promoter
A0006355biological_processregulation of transcription, DNA-templated
A0030111biological_processregulation of Wnt signaling pathway
A0035623biological_processrenal glucose absorption
A0048608biological_processreproductive structure development
A0009749biological_processresponse to glucose
A0006979biological_processresponse to oxidative stress
A0043691biological_processreverse cholesterol transport
A0060395biological_processSMAD protein signal transduction
B0005737cellular_componentcytoplasm
B0005654cellular_componentnucleoplasm
B0005634cellular_componentnucleus
B0001750cellular_componentphotoreceptor outer segment
B0045120cellular_componentpronucleus
B0043234cellular_componentprotein complex
B0005667cellular_componenttranscription factor complex
B0003677molecular_functionDNA binding
B0046983molecular_functionprotein dimerization activity
B0046982molecular_functionprotein heterodimerization activity
B0042803molecular_functionprotein homodimerization activity
B0000978molecular_functionRNA polymerase II core promoter proximal region sequence-specific DNA binding
B0003700molecular_functiontranscription factor activity, sequence-specific DNA binding
B0044212molecular_functiontranscription regulatory region DNA binding
B0001077molecular_functiontranscriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding
B0001228molecular_functiontranscriptional activator activity, RNA polymerase II transcription regulatory region sequence-specific binding
B0015721biological_processbile acid and bile salt transport
B0006699biological_processbile acid biosynthetic process
B0001824biological_processblastocyst development
B0045453biological_processbone resorption
B0008203biological_processcholesterol metabolic process
B0006338biological_processchromatin remodeling
B0030326biological_processembryonic limb morphogenesis
B0031018biological_processendocrine pancreas development
B0006633biological_processfatty acid biosynthetic process
B0015908biological_processfatty acid transport
B0042593biological_processglucose homeostasis
B0046323biological_processglucose import
B0006783biological_processheme biosynthetic process
B0016573biological_processhistone acetylation
B0030073biological_processinsulin secretion
B0001889biological_processliver development
B0000122biological_processnegative regulation of transcription from RNA polymerase II promoter
B0048341biological_processparaxial mesoderm formation
B0001890biological_processplacenta development
B0045944biological_processpositive regulation of transcription from RNA polymerase II promoter
B0060261biological_processpositive regulation of transcription initiation from RNA polymerase II promoter
B0045893biological_processpositive regulation of transcription, DNA-templated
B0008104biological_processprotein localization
B0046883biological_processregulation of hormone secretion
B0050796biological_processregulation of insulin secretion
B0006357biological_processregulation of transcription from RNA polymerase II promoter
B0006355biological_processregulation of transcription, DNA-templated
B0030111biological_processregulation of Wnt signaling pathway
B0035623biological_processrenal glucose absorption
B0048608biological_processreproductive structure development
B0009749biological_processresponse to glucose
B0006979biological_processresponse to oxidative stress
B0043691biological_processreverse cholesterol transport
B0060395biological_processSMAD protein signal transduction
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Functional Information from PDB Data

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

site_idNumber of ResiduesDetails
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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_FI11Homeobox; HNF1-type.
ChainResidueDetails
ANA*

SWS_FT_FI21Homeobox; HNF1-type.
ChainResidueDetails
BNA*

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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

> Downloads

Resources

File formatFile name (file size)
PDBallpdb1jb6.ent.gz (15.92 KB)
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all (no-compress)pdb1jb6.ent (75.86 KB)
header onlypdb1jb6.ent.gz (5.57 KB)
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PDBx/mmCIF1jb6.cif.gz (20.48 KB)
PDBMLall1jb6.xml.gz (29.26 KB)
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no-atom1jb6-noatom.xml.gz (10.36 KB)
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ext-atom1jb6-extatom.xml.gz (12.44 KB)
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PDBMLplusall1jb6-plus.xml.gz (32.38 KB)
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no-atom1jb6-plus-noatom.xml.gz (13.48 KB)
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add only1jb6-add.xml.gz (3.12 KB)
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RDF1jb6.rdf.gz (17.99 KB)
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Structure factorsr1jb6sf.ent.gz (89.86 KB)
Biological unit (PDB format)1jb6.pdb1.gz (9.47 KB) (A)
*author and software defined assembly, 2 molecule(s) (dimeric)
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1jb6.pdb2.gz (8.06 KB) (B)
*author and software defined assembly, 2 molecule(s) (dimeric)
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1jb6.pdb3.gz (22.28 KB) (A,B)
*software defined assembly, 4 molecule(s) (tetrameric)
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1jb6.pdb4.gz (42.78 KB) (A,B)
*software defined assembly, 8 molecule(s) (octameric)
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Validation reportsPDF1jb6​_validation.pdf.gz (259.53 KB)
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PDF-full1jb6​_full​_validation.pdf.gz (259.69 KB)
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XML1jb6​_validation.xml.gz (5.83 KB)
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PNG1jb6​_multipercentile​_validation.png.gz (153.7 KB)
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SVG1jb6​_multipercentile​_validation.svg.gz (924 B)
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Sequence (fasta)1jb6​_seq.txt
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