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- PDB-2gyp: Diabetes mellitus due to a frustrated Schellman motif in HNF-1a -

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Basic information

Entry
Database: PDB / ID: 2gyp
TitleDiabetes mellitus due to a frustrated Schellman motif in HNF-1a
ComponentsHepatocyte nuclear factor 1-alpha
KeywordsTRANSCRIPTION REGULATOR / energy landscape / gene regulation / protein engineering / protein stability / protein structure
Function / homology
Function and homology information


renal D-glucose absorption / pancreas development / insulin secretion / D-glucose import / Regulation of gene expression in beta cells / positive regulation of transcription initiation by RNA polymerase II / liver development / glucose homeostasis / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor activity, RNA polymerase II-specific ...renal D-glucose absorption / pancreas development / insulin secretion / D-glucose import / Regulation of gene expression in beta cells / positive regulation of transcription initiation by RNA polymerase II / liver development / glucose homeostasis / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription cis-regulatory region binding / protein dimerization activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein heterodimerization activity / regulation of transcription by RNA polymerase II / chromatin / positive regulation of DNA-templated transcription / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA 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 / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsNarayana, N. / Phillips, N.B. / Hua, Q.X. / Jia, W. / Weiss, M.A.
Citation
Journal: J.Mol.Biol. / Year: 2006
Title: Diabetes mellitus due to misfolding of a beta-cell transcription factor: stereospecific frustration of a Schellman motif in HNF-1alpha.
Authors: Narayana, N. / Phillips, N.B. / Hua, Q.X. / Jia, W. / Weiss, M.A.
#1: Journal: J.Mol.Biol. / Year: 2001
Title: The dimerization domain of HNF-1a: structure and plasticity of an intertwined four-helix bundle with application to diabetes mellitus
#2: Journal: Biochemistry / Year: 2000
Title: High-resolution structure of the HNF-1a dimerization domain
#3: Journal: Proc.Natl.Acad.Sci.USA / Year: 2000
Title: Diabetes-associated mutations in a b-cell transcription factor destabilize an anti-parallel "mini-zipper" in a dimerization interface
History
DepositionMay 9, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.name / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.6Nov 6, 2024Group: Structure summary / Category: 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)7,1382
Polymers7,1382
Non-polymers00
Water1,11762
1
A: Hepatocyte nuclear factor 1-alpha

A: Hepatocyte nuclear factor 1-alpha


Theoretical massNumber of molelcules
Total (without water)7,1382
Polymers7,1382
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area1620 Å2
ΔGint-19 kcal/mol
Surface area4960 Å2
MethodPISA, PQS
2
B: Hepatocyte nuclear factor 1-alpha

B: Hepatocyte nuclear factor 1-alpha


Theoretical massNumber of molelcules
Total (without water)7,1382
Polymers7,1382
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area1640 Å2
ΔGint-19 kcal/mol
Surface area5000 Å2
MethodPISA, PQS
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)14,2774
Polymers14,2774
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area4400 Å2
ΔGint-49 kcal/mol
Surface area8810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)29.180, 42.950, 42.370
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein/peptide Hepatocyte nuclear factor 1-alpha / HNF-1A / Liver-specific transcription factor LF-B1 / LFB1 / Transcription factor 1 / TCF-1


Mass: 3569.149 Da / Num. of mol.: 2 / Fragment: Dimerization domain / Mutation: G20(DAL) / Source method: obtained synthetically
Details: The sequence was chemcially synthesized. The source is naturally found in Homo sapiens (human).
References: UniProt: P20823
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 1.86 Å3/Da / Density % sol: 33.86 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 2 mM peptide in 100 mM Bicine buffer. Reservoir solution contained 5 mM Magnesium Formate and 30% PEG400, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.948 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Aug 15, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.948 Å / Relative weight: 1
ReflectionResolution: 1.4→20 Å / Num. all: 10642 / Num. obs: 10079 / % possible obs: 92 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 6 / Redundancy: 10 % / Rsym value: 0.067 / Net I/σ(I): 6

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Processing

Software
NameClassification
TNTrefinement
MOSFLMdata reduction
CNSrefinement
ADSCdata collection
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: coordinates from 1JB6

1jb6


Resolution: 1.4→20 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 3 / σ(I): 6 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.288 550 -RANDOM
Rwork0.228 ---
all0.236 10642 --
obs0.23 10079 92 %-
Refinement stepCycle: LAST / Resolution: 1.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms500 0 0 62 562
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_deg2.22
X-RAY DIFFRACTIONt_bond_d0.01
X-RAY DIFFRACTIONt_dihedral_angle_d16.34

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