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- PDB-1jb6: Crystal Structure of Dimerization Domain (1-33) of HNF-1alpha -

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Basic information

Entry
Database: PDB / ID: 1jb6
TitleCrystal Structure of Dimerization Domain (1-33) of HNF-1alpha
ComponentsHEPATOCYTE NUCLEAR FACTOR 1-ALPHA
KeywordsTRANSCRIPTION / Four-helix bundle / non-canonical turn
Function / homology
Function and homology information


paraxial mesoderm formation / apoptotic nuclear changes / regulation of NADP metabolic process / renal D-glucose absorption / regulation of hormone secretion / cellular response to rapamycin / reproductive structure development / bile acid biosynthetic process / cellular response to L-leucine / reverse cholesterol transport ...paraxial mesoderm formation / apoptotic nuclear changes / regulation of NADP metabolic process / renal D-glucose absorption / regulation of hormone secretion / cellular response to rapamycin / reproductive structure development / bile acid biosynthetic process / cellular response to L-leucine / reverse cholesterol transport / pronucleus / pancreas development / regulation of Wnt signaling pathway / negative regulation of miRNA processing / embryonic limb morphogenesis / positive regulation of mitochondrial membrane potential / insulin secretion / heme biosynthetic process / bile acid and bile salt transport / positive regulation of ATP biosynthetic process / D-glucose import / blastocyst development / photoreceptor outer segment / bone resorption / fatty acid transport / response to glucose / cholesterol metabolic process / liver development / placenta development / cellular response to glucose stimulus / transcription coactivator binding / positive regulation of insulin secretion / fatty acid biosynthetic process / protein localization / glucose homeostasis / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription regulator complex / response to oxidative stress / transcription by RNA polymerase II / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / transcription cis-regulatory region binding / protein dimerization activity / chromatin remodeling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / chromatin binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / chromatin / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Hepatocyte nuclear factor 1, alpha isoform C-terminal / Hepatocyte nuclear factor 1 (HNF-1), alpha isoform C terminus / Hepatocyte nuclear factor 1, beta isoform, C-terminal / Hepatocyte nuclear factor 1, N-terminal domain superfamily / Hepatocyte nuclear factor 1 / Hepatocyte nuclear factor 1 (HNF-1), beta isoform C terminus / Hepatocyte nuclear factor 1, N-terminal / HNF-1, dimerization domain / HNF-1, POU-specific (POUs) atypical domain / Hepatocyte nuclear factor 1 (HNF-1), N terminus ...Hepatocyte nuclear factor 1, alpha isoform C-terminal / Hepatocyte nuclear factor 1 (HNF-1), alpha isoform C terminus / Hepatocyte nuclear factor 1, beta isoform, C-terminal / Hepatocyte nuclear factor 1, N-terminal domain superfamily / Hepatocyte nuclear factor 1 / Hepatocyte nuclear factor 1 (HNF-1), beta isoform C terminus / Hepatocyte nuclear factor 1, N-terminal / HNF-1, dimerization domain / HNF-1, POU-specific (POUs) atypical domain / Hepatocyte nuclear factor 1 (HNF-1), N terminus / POU-specific (POUs) atypical domain profile. / HNF-1 dimerization (HNF-p1) domain profile. / 'Homeobox' domain signature. / 'Homeobox' domain profile. / Homeodomain / Homeobox domain / Lambda repressor-like, DNA-binding domain superfamily / Homeobox-like domain superfamily
Similarity search - Domain/homology
Hepatocyte nuclear factor 1-alpha
Similarity search - Component
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
AuthorsNarayana, N. / Hua, Q.-X. / Weiss, M.A.
Citation
Journal: J.Mol.Biol. / Year: 2001
Title: The dimerization domain of HNF-1alpha: structure and plasticity of an intertwined four-helix bundle with application to diabetes mellitus.
Authors: Narayana, N. / Hua, Q. / Weiss, M.A.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2000
Title: Diabetes-Associated Mutations in a beta-Cell Transcription factor Destabilize an Antiparallel "Mini-Zipper" in a Dimerization Interface
Authors: Hua, Q.X. / Zhao, M. / Narayana, N. / Nakagawa, S.H. / Jia, W. / Weiss, M.A.
#2: Journal: Nat.Struct.Biol. / Year: 2000
Title: Structural Basis of Dimerization, Coactivator Recognition and MODY3 Mutations in HNF-1alpha
Authors: Rose, R.B. / Bayle, J.H. / Endrizzi, J.A. / Cronk, J.D. / Crabtree, G.R. / Alber, T.
#3: Journal: Biochemistry / Year: 2000
Title: High-Resolution Structure of the HNF-1alpha Dimerization Domain
Authors: Rose, R.B. / Endrizzi, J.A. / Cronk, J.D. / Holton, J. / Alber, T.
#4: Journal: BIO*ESSAYS / Year: 1992
Title: HNF1, A Homeoprotein Member of the Hepatic Transcription Regulatory Network
Authors: Tronche, F. / Yaniv, M.
#5: Journal: DIABETES METAB. / Year: 1997
Title: Maturity-onset Diabetes of the Young (MODY), MODY Genes and Non-Insulin-Dependent Diabetes mellitus
Authors: Velho, G. / Froguel, P.
History
DepositionJun 1, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 11, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.5Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HEPATOCYTE NUCLEAR FACTOR 1-ALPHA
B: HEPATOCYTE NUCLEAR FACTOR 1-ALPHA


Theoretical massNumber of molelcules
Total (without water)7,2402
Polymers7,2402
Non-polymers00
Water99155
1
A: HEPATOCYTE NUCLEAR FACTOR 1-ALPHA

A: HEPATOCYTE NUCLEAR FACTOR 1-ALPHA


Theoretical massNumber of molelcules
Total (without water)7,2402
Polymers7,2402
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area1580 Å2
ΔGint-18 kcal/mol
Surface area5090 Å2
MethodPISA
2
B: HEPATOCYTE NUCLEAR FACTOR 1-ALPHA

B: HEPATOCYTE NUCLEAR FACTOR 1-ALPHA


Theoretical massNumber of molelcules
Total (without water)7,2402
Polymers7,2402
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area1280 Å2
ΔGint-15 kcal/mol
Surface area4210 Å2
MethodPISA
3
A: HEPATOCYTE NUCLEAR FACTOR 1-ALPHA
B: HEPATOCYTE NUCLEAR FACTOR 1-ALPHA

A: HEPATOCYTE NUCLEAR FACTOR 1-ALPHA
B: HEPATOCYTE NUCLEAR FACTOR 1-ALPHA


Theoretical massNumber of molelcules
Total (without water)14,4804
Polymers14,4804
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area4050 Å2
ΔGint-44 kcal/mol
Surface area8110 Å2
MethodPISA
4
A: HEPATOCYTE NUCLEAR FACTOR 1-ALPHA
B: HEPATOCYTE NUCLEAR FACTOR 1-ALPHA

A: HEPATOCYTE NUCLEAR FACTOR 1-ALPHA
B: HEPATOCYTE NUCLEAR FACTOR 1-ALPHA

A: HEPATOCYTE NUCLEAR FACTOR 1-ALPHA
B: HEPATOCYTE NUCLEAR FACTOR 1-ALPHA

A: HEPATOCYTE NUCLEAR FACTOR 1-ALPHA
B: HEPATOCYTE NUCLEAR FACTOR 1-ALPHA


Theoretical massNumber of molelcules
Total (without water)28,9608
Polymers28,9608
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation2_554-x,-y,z-11
MethodPQS
Unit cell
Length a, b, c (Å)28.42, 42.19, 42.43
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number18
Space group name H-MP21212
DetailsThere are two independent molecules in the asymmetric unit. For each molecule, a crystallographic 2-fold axis generates the biological dimer.

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Components

#1: Protein/peptide HEPATOCYTE NUCLEAR FACTOR 1-ALPHA / HNF-1A


Mass: 3620.056 Da / Num. of mol.: 2 / Fragment: Dimerization domain (residues 1-32) / Source method: obtained synthetically
Details: This peptide was chemically synthesized. The sequence of this peptide occurs naturally in Mus musculus (mouse) as well as in Homo sapiens (humans).
References: UniProt: P22361
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.6 Å3/Da / Density % sol: 23 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: MPD, Tris-HCl, DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
13 mMpeptide1drop
250 mMTris-HCl1drop
32 mMdithiothreitol1drop
420 %(v/v)MPD1reservoir
550 mMTris-HCl1reservoir
61 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794, 0.9800, 1.0030
DetectorType: SBC-2 / Detector: CCD / Date: Mar 24, 2000 / Details: mirrors
RadiationMonochromator: Double Crystal Silicon / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97941
20.981
31.0031
ReflectionResolution: 1.7→40 Å / Num. all: 5922 / Num. obs: 5245 / % possible obs: 88 % / Observed criterion σ(F): 3 / Redundancy: 6 % / Rsym value: 0.037
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 5 % / Num. unique all: 584 / Rsym value: 0.024

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Processing

Software
NameVersionClassification
CNSrefinement
d*TREK(D*TREK)data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 1.7→40 Å / σ(F): 3
RfactorNum. reflection% reflectionSelection details
Rfree0.245 296 -Random
Rwork0.231 ---
all-5922 --
obs-5245 88 %-
Refinement stepCycle: LAST / Resolution: 1.7→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms457 0 0 55 512
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_angle_deg0.8
LS refinement shellResolution: 1.7→1.78 Å
RfactorNum. reflection% reflection
Rfree0.262 28 -
Rwork0.22 --
obs-447 77 %
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Lowest resolution: 40 Å / σ(F): 3 / % reflection Rfree: 5 % / Rfactor obs: 0.231
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor Rfree: 0.262 / Rfactor Rwork: 0.22

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