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- PDB-1g2y: HNF-1ALPHA DIMERIZATION DOMAIN, WITH SELENOMETHIONINE SUBSTITUED ... -

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Basic information

Entry
Database: PDB / ID: 1g2y
TitleHNF-1ALPHA DIMERIZATION DOMAIN, WITH SELENOMETHIONINE SUBSTITUED AT LEU 12
ComponentsHEPATOCYTE NUCLEAR FACTOR 1-ALPHA
KeywordsTRANSCRIPTION / dimerization domain / four-helix bundle / transcription factor / selenomethionine
Function / homology
Function and homology information


paraxial mesoderm formation / apoptotic nuclear changes / regulation of NADP metabolic process / renal D-glucose absorption / cellular response to rapamycin / regulation of hormone secretion / 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 / cellular response to rapamycin / regulation of hormone secretion / reproductive structure development / bile acid biosynthetic process / cellular response to L-leucine / reverse cholesterol transport / pancreas development / negative regulation of miRNA processing / pronucleus / regulation of Wnt signaling pathway / embryonic limb morphogenesis / heme biosynthetic process / positive regulation of mitochondrial membrane potential / insulin secretion / bile acid and bile salt transport / D-glucose import / positive regulation of ATP biosynthetic process / blastocyst development / photoreceptor outer segment / bone resorption / response to glucose / fatty acid transport / cholesterol metabolic process / placenta development / cellular response to glucose stimulus / liver development / positive regulation of insulin secretion / transcription coactivator binding / fatty acid biosynthetic process / intracellular protein localization / glucose homeostasis / response to oxidative stress / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription regulator complex / transcription by RNA polymerase II / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / transcription cis-regulatory region binding / protein dimerization activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin remodeling / 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 Å
AuthorsRose, R.B. / Endrizzi, J.A. / Cronk, J.D. / Holton, J. / Alber, T.
Citation
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.
#1: 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.
History
DepositionOct 23, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 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 1.4Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)13,8084
Polymers13,8084
Non-polymers00
Water3,171176
1
A: HEPATOCYTE NUCLEAR FACTOR 1-ALPHA
C: HEPATOCYTE NUCLEAR FACTOR 1-ALPHA


Theoretical massNumber of molelcules
Total (without water)6,9042
Polymers6,9042
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1290 Å2
ΔGint-14 kcal/mol
Surface area4540 Å2
MethodPISA
2
B: HEPATOCYTE NUCLEAR FACTOR 1-ALPHA
D: HEPATOCYTE NUCLEAR FACTOR 1-ALPHA


Theoretical massNumber of molelcules
Total (without water)6,9042
Polymers6,9042
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1350 Å2
ΔGint-14 kcal/mol
Surface area4360 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4760 Å2
ΔGint-53 kcal/mol
Surface area6790 Å2
MethodPISA
4
A: HEPATOCYTE NUCLEAR FACTOR 1-ALPHA
C: HEPATOCYTE NUCLEAR FACTOR 1-ALPHA

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


Theoretical massNumber of molelcules
Total (without water)13,8084
Polymers13,8084
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_556x,y,z+11
Buried area3480 Å2
ΔGint-39 kcal/mol
Surface area8060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.270, 47.880, 40.470
Angle α, β, γ (deg.)90.00, 93.60, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThere are two HNF-1alpha dimers in the asymmetric unit: monomers A and C, and monomers B and D.

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Components

#1: Protein/peptide
HEPATOCYTE NUCLEAR FACTOR 1-ALPHA / HNF-1A / LIVER SPECIFIC TRANSCRIPTION FACTOR LF-B1


Mass: 3451.884 Da / Num. of mol.: 4 / Fragment: DIMERIZATION DOMAIN, RESIDUES 1-32 / Mutation: L12(MSE) / Source method: obtained synthetically
Details: This peptide was chemically synthesized. The sequence of this peptide naturally occurs in mouse (Mus musculus), with a point mutation at position 12.
References: UniProt: P22361
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / 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: 2.19 Å3/Da / Density % sol: 43.83 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 4000, Tris-HCl, lithium sulphate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlpeptide1drop
230 %PEG40001reservoir
3100 mMTris-HCl1reservoir
40.2 M1reservoirLiSO4

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.95372, 0.97957, 0.9798, 1.07812
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 28, 1999 / Details: Double crystal
RadiationMonochromator: double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.953721
20.979571
30.97981
41.078121
ReflectionResolution: 1→30.9 Å / Num. all: 55221 / Num. obs: 55221 / % possible obs: 86.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.8 % / Biso Wilson estimate: 7.4 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 16.8
Reflection shellResolution: 1→1.05 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.101 / Mean I/σ(I) obs: 9.2 / Num. unique all: 55221 / % possible all: 73.1
Reflection
*PLUS
Reflection shell
*PLUS
% possible obs: 73.1 %

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Processing

Software
NameVersionClassification
SOLVEphasing
CNSrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD
Starting model: wARP model

Resolution: 1→30.88 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 499172.87 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.198 1657 3 %RANDOM
Rwork0.195 ---
all0.195 55129 --
obs0.195 55129 85.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 98.59 Å2 / ksol: 0.372 e/Å3
Displacement parametersBiso mean: 16 Å2
Baniso -1Baniso -2Baniso -3
1--0.38 Å20 Å2-0.43 Å2
2--0.57 Å20 Å2
3----0.19 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.14 Å0.14 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 1→30.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms863 0 0 176 1039
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.02
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONc_dihedral_angle_d18
X-RAY DIFFRACTIONc_improper_angle_d2.91
X-RAY DIFFRACTIONc_mcbond_it6.391.5
X-RAY DIFFRACTIONc_mcangle_it6.212
X-RAY DIFFRACTIONc_scbond_it11.632
X-RAY DIFFRACTIONc_scangle_it13.492.5
LS refinement shellResolution: 1→1.06 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.375 222 2.9 %
Rwork0.398 7390 -
obs--71 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
σ(F): 0 / Num. reflection Rfree: 5640 / % reflection Rfree: 9 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 16 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg18
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg2.91
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.375 / % reflection Rfree: 2.9 % / Rfactor Rwork: 0.398

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