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- PDB-1vtn: CO-CRYSTAL STRUCTURE OF THE HNF-3/FORK HEAD DNA-RECOGNITION MOTIF... -

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Basic information

Entry
Database: PDB / ID: 1vtn
TitleCO-CRYSTAL STRUCTURE OF THE HNF-3/FORK HEAD DNA-RECOGNITION MOTIF RESEMBLES HISTONE H5
Components
  • DNA (5'-D(*GP*AP*CP*TP*AP*AP*GP*TP*CP*AP*AP*CP*C)-3')
  • DNA (5'-D(*GP*GP*TP*TP*GP*AP*CP*TP*TP*AP*GP*TP*C)-3')
  • HNF-3/FORK HEAD DNA-RECOGNITION MOTIF
KeywordsTRANSCRIPTION/DNA / PROTEIN-DNA COMPLEX / DOUBLE HELIX / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


hematopoietic stem cell homeostasis / multicellular organism development / intracellular glucose homeostasis / Regulation of gene expression in beta cells / transcription factor binding / anatomical structure morphogenesis / cellular response to starvation / sequence-specific double-stranded DNA binding / actin cytoskeleton / chromatin organization ...hematopoietic stem cell homeostasis / multicellular organism development / intracellular glucose homeostasis / Regulation of gene expression in beta cells / transcription factor binding / anatomical structure morphogenesis / cellular response to starvation / sequence-specific double-stranded DNA binding / actin cytoskeleton / chromatin organization / spermatogenesis / cell differentiation / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein domain specific binding / chromatin / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus
Similarity search - Function
Fork-head N-terminal / Forkhead N-terminal region / Fork head domain conserved site1 / Fork head domain signature 1. / Fork head domain / Forkhead domain / Fork head domain profile. / FORKHEAD / Fork head domain conserved site 2 / Fork head domain signature 2. ...Fork-head N-terminal / Forkhead N-terminal region / Fork head domain conserved site1 / Fork head domain signature 1. / Fork head domain / Forkhead domain / Fork head domain profile. / FORKHEAD / Fork head domain conserved site 2 / Fork head domain signature 2. / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Hepatocyte nuclear factor 3-gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsClark, K.L. / Halay, E.D. / Lai, E. / Burley, S.K.
CitationJournal: Nature / Year: 1993
Title: Co-Crystal Structure of the HNF-3/Fork Head DNA-Recognition Motif Resembles Histone H5
Authors: Clark, K.L. / Halay, E.D. / Lai, E. / Burley, S.K.
History
DepositionJan 6, 1995Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 13, 2011Provider: repository / Type: Initial release
Revision 1.1Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA (5'-D(*GP*AP*CP*TP*AP*AP*GP*TP*CP*AP*AP*CP*C)-3')
B: DNA (5'-D(*GP*GP*TP*TP*GP*AP*CP*TP*TP*AP*GP*TP*C)-3')
C: HNF-3/FORK HEAD DNA-RECOGNITION MOTIF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0184
Polymers19,9943
Non-polymers241
Water905
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3470 Å2
ΔGint-33 kcal/mol
Surface area9210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.600, 74.600, 85.050
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: DNA chain DNA (5'-D(*GP*AP*CP*TP*AP*AP*GP*TP*CP*AP*AP*CP*C)-3')


Mass: 3944.601 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*GP*GP*TP*TP*GP*AP*CP*TP*TP*AP*GP*TP*C)-3')


Mass: 3997.607 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein HNF-3/FORK HEAD DNA-RECOGNITION MOTIF


Mass: 12051.863 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P55318
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

Crystal growMethod: vapor diffusion / pH: 5.5 / Details: pH 5.50, VAPOR DIFFUSION
Components of the solutions
IDConc.NameCrystal-IDDetailsSol-IDVolume (Å3)
12 WATER1311
25 DTT1614
38 KCL1917
411 NH4 ACETATE112110
514 MGCL2115113
617 K ACETATE118116
720 WATER121219
823 DTT124222
926 KCL127225
1029 MGCL2130228
1132 K ACETATE133231

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Data collection

DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 2.5 Å / Num. all: 100640 / Num. obs: 18352

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Processing

SoftwareName: X-PLOR / Classification: refinement
RefinementResolution: 2.5→6 Å /
RfactorNum. reflection
Rwork0.211 -
obs0.211 18352
Refinement stepCycle: LAST / Resolution: 2.5→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms848 527 1 5 1381

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