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- PDB-1f93: CRYSTAL STRUCTURE OF A COMPLEX BETWEEN THE DIMERIZATION DOMAIN OF... -

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Basic information

Entry
Database: PDB / ID: 1f93
TitleCRYSTAL STRUCTURE OF A COMPLEX BETWEEN THE DIMERIZATION DOMAIN OF HNF-1 ALPHA AND THE COACTIVATOR DCOH
Components
  • DIMERIZATION COFACTOR OF HEPATOCYTE NUCLEAR FACTOR 1-ALPHA
  • HEPATOCYTE NUCLEAR FACTOR 1-ALPHA
KeywordsTRANSCRIPTION / four-helix bundle / transcriptional activator-coactivator complex / dimerization domain
Function / homology
Function and homology information


paraxial mesoderm formation / Phenylalanine metabolism / regulation of protein binding / 4a-hydroxytetrahydrobiopterin dehydratase / 4-alpha-hydroxytetrahydrobiopterin dehydratase activity / L-phenylalanine metabolic process / apoptotic nuclear changes / regulation of NADP metabolic process / renal D-glucose absorption / phenylalanine 4-monooxygenase activity ...paraxial mesoderm formation / Phenylalanine metabolism / regulation of protein binding / 4a-hydroxytetrahydrobiopterin dehydratase / 4-alpha-hydroxytetrahydrobiopterin dehydratase activity / L-phenylalanine metabolic process / apoptotic nuclear changes / regulation of NADP metabolic process / renal D-glucose absorption / phenylalanine 4-monooxygenase activity / cellular response to rapamycin / regulation of hormone secretion / reproductive structure development / bile acid biosynthetic process / tetrahydrobiopterin 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 / transcription coactivator activity / 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 / Transcriptional coactivator/pterin dehydratase / Pterin 4 alpha carbinolamine dehydratase / Hepatocyte nuclear factor 1, beta isoform, C-terminal / Hepatocyte nuclear factor 1, N-terminal domain superfamily / Pterin 4 alpha carbinolamine dehydratase superfamily / Hepatocyte nuclear factor 1 / Pterin 4 alpha carbinolamine dehydratase / Hepatocyte nuclear factor 1 (HNF-1), beta isoform C terminus ...Hepatocyte nuclear factor 1, alpha isoform C-terminal / Hepatocyte nuclear factor 1 (HNF-1), alpha isoform C terminus / Transcriptional coactivator/pterin dehydratase / Pterin 4 alpha carbinolamine dehydratase / Hepatocyte nuclear factor 1, beta isoform, C-terminal / Hepatocyte nuclear factor 1, N-terminal domain superfamily / Pterin 4 alpha carbinolamine dehydratase superfamily / Hepatocyte nuclear factor 1 / Pterin 4 alpha carbinolamine dehydratase / 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 / Gyrase A; domain 2 / Homeobox-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Hepatocyte nuclear factor 1-alpha / Pterin-4-alpha-carbinolamine dehydratase
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.6 Å
AuthorsRose, R.B. / Bayle, J.H. / Endrizzi, J.A. / Cronk, J.D. / Crabtree, G.R. / Alber, T.
Citation
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.
#1: Journal: Science / Year: 1995
Title: Crystal structure of DCoH, a bifunctional, protein-binding transcriptional coactivator
Authors: Endrizzi, J.A. / Cronk, J.D. / Weidong, W. / Crabtree, G.R. / Alber, T.
#2: Journal: Protein Sci. / Year: 1996
Title: High-resolution structures of the bifunctional enzyme and transcriptional coactivator DCoH and its complex with a product analogue
Authors: Cronk, J.D. / Endrizzi, J.A. / Alber, T.
History
DepositionJul 6, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 20, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_sheet
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 / _struct_sheet.number_strands

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DIMERIZATION COFACTOR OF HEPATOCYTE NUCLEAR FACTOR 1-ALPHA
B: DIMERIZATION COFACTOR OF HEPATOCYTE NUCLEAR FACTOR 1-ALPHA
C: DIMERIZATION COFACTOR OF HEPATOCYTE NUCLEAR FACTOR 1-ALPHA
D: DIMERIZATION COFACTOR OF HEPATOCYTE NUCLEAR FACTOR 1-ALPHA
E: HEPATOCYTE NUCLEAR FACTOR 1-ALPHA
F: HEPATOCYTE NUCLEAR FACTOR 1-ALPHA
G: HEPATOCYTE NUCLEAR FACTOR 1-ALPHA
H: HEPATOCYTE NUCLEAR FACTOR 1-ALPHA


Theoretical massNumber of molelcules
Total (without water)62,1818
Polymers62,1818
Non-polymers00
Water1,11762
1
A: DIMERIZATION COFACTOR OF HEPATOCYTE NUCLEAR FACTOR 1-ALPHA
B: DIMERIZATION COFACTOR OF HEPATOCYTE NUCLEAR FACTOR 1-ALPHA
E: HEPATOCYTE NUCLEAR FACTOR 1-ALPHA
F: HEPATOCYTE NUCLEAR FACTOR 1-ALPHA


Theoretical massNumber of molelcules
Total (without water)31,0904
Polymers31,0904
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4950 Å2
ΔGint-36 kcal/mol
Surface area12840 Å2
MethodPISA
2
C: DIMERIZATION COFACTOR OF HEPATOCYTE NUCLEAR FACTOR 1-ALPHA
D: DIMERIZATION COFACTOR OF HEPATOCYTE NUCLEAR FACTOR 1-ALPHA
G: HEPATOCYTE NUCLEAR FACTOR 1-ALPHA
H: HEPATOCYTE NUCLEAR FACTOR 1-ALPHA


Theoretical massNumber of molelcules
Total (without water)31,0904
Polymers31,0904
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4840 Å2
ΔGint-37 kcal/mol
Surface area12240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.480, 82.750, 70.640
Angle α, β, γ (deg.)90.00, 97.83, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a heterotetramer consisting of a DCoH dimer and an HNF-1 alpha dimerization domain dimer. There are two heterotetramers in the asymmetric unit.

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Components

#1: Protein
DIMERIZATION COFACTOR OF HEPATOCYTE NUCLEAR FACTOR 1-ALPHA / PTERIN-4-ALPHA-CARBINOLAMINE DEHYDRATASE / PHS / DCOH


Mass: 12158.288 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Organ: LIVER / Plasmid: PGEX GST FUSION PLASMID (PHARMACIA) / Production host: Escherichia coli (E. coli) / References: UniProt: P61459
#2: Protein/peptide
HEPATOCYTE NUCLEAR FACTOR 1-ALPHA


Mass: 3386.951 Da / Num. of mol.: 4 / Fragment: DIMERIZATION DOMAIN (RESIDUES 1-32) / Source method: obtained synthetically
Details: THIS PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THIS PEPTIDE NATURALLY OCCURS IN MOUSE (MUS MUSCULUS)
References: UniProt: P22361
#3: 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: 2.3 Å3/Da / Density % sol: 46.61 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5
Details: PEG 8000, potassium succinate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion / Details: used microseeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
213 %(w/v)PEG80001drop
3100 mMpotassium succinate1drop
415 %(v/v)PEG4001reservoir
514 %(w/v)PEG80001reservoir
6100 mMpotassium succinate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL1-5 / Wavelength: 1.0688
DetectorType: ADSC QUANTUM / Detector: CCD / Date: Jan 1, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0688 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. all: 59400 / Num. obs: 16500 / % possible obs: 95 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Biso Wilson estimate: 43.3 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 22
Reflection shellResolution: 2.6→2.67 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.3 / Num. unique all: 1800 / % possible all: 95
Reflection
*PLUS
% possible obs: 95 % / Num. measured all: 59400 / Rmerge(I) obs: 0.057
Reflection shell
*PLUS
% possible obs: 95 % / Rmerge(I) obs: 0.243 / Mean I/σ(I) obs: 2.6

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Processing

Software
NameVersionClassification
SHARPphasing
CNS0.4refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementResolution: 2.6→20.1 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 912032.47 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh and Huber / Details: used non-crystallographic symmetry
RfactorNum. reflection% reflectionSelection details
Rfree0.299 1296 7.8 %RANDOM
Rwork0.257 ---
all0.26 59400 --
obs0.257 16569 95.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 55.35 Å2 / ksol: 0.36 e/Å3
Displacement parametersBiso mean: 58.7 Å2
Baniso -1Baniso -2Baniso -3
1--4.32 Å20 Å2-2.73 Å2
2---2.19 Å20 Å2
3---6.51 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.45 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.6→20.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4044 0 0 62 4106
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d20.2
X-RAY DIFFRACTIONc_improper_angle_d0.6
X-RAY DIFFRACTIONc_mcbond_it3.461.5
X-RAY DIFFRACTIONc_mcangle_it5.092
X-RAY DIFFRACTIONc_scbond_it5.222
X-RAY DIFFRACTIONc_scangle_it6.942.5
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.371 230 8 %
Rwork0.31 2629 -
obs--99.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 0.4 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 7.8 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 58.7 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.0062
X-RAY DIFFRACTIONc_angle_deg1.103
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg20.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.6
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: 0.371 / % reflection Rfree: 8 % / Rfactor Rwork: 0.31

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