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- PDB-5krb: GCNF DNA Binding Domain - Oct4 DR0 Complex -

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Basic information

Entry
Database: PDB / ID: 5krb
TitleGCNF DNA Binding Domain - Oct4 DR0 Complex
Components
  • DNA (5'-D(*AP*GP*AP*GP*GP*TP*CP*AP*AP*GP*GP*CP*TP*AP*GP*A)-3')
  • DNA (5'-D(*TP*CP*TP*AP*GP*CP*CP*TP*TP*GP*AP*CP*CP*TP*CP*T)-3')
  • Nuclear receptor subfamily 6 group A member 1
Keywordstranscription/dna / Nuclear Receptor / Transcription Factor / DNA Binding / Development / Protein-DNA complex / transcription-dna complex
Function / homology
Function and homology information


Nuclear Receptor transcription pathway / multicellular organism development / gamete generation / nuclear receptor activity / sequence-specific double-stranded DNA binding / spermatogenesis / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription regulator complex / sequence-specific DNA binding / cell differentiation ...Nuclear Receptor transcription pathway / multicellular organism development / gamete generation / nuclear receptor activity / sequence-specific double-stranded DNA binding / spermatogenesis / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription regulator complex / sequence-specific DNA binding / cell differentiation / RNA polymerase II cis-regulatory region sequence-specific DNA binding / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleus
Similarity search - Function
Erythroid Transcription Factor GATA-1, subunit A / Erythroid Transcription Factor GATA-1; Chain A / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Zinc finger, C4 type (two domains) / Nuclear hormone receptors DNA-binding domain profile. / c4 zinc finger in nuclear hormone receptors / Nuclear hormone receptor, ligand-binding domain / Nuclear hormone receptor-like domain superfamily ...Erythroid Transcription Factor GATA-1, subunit A / Erythroid Transcription Factor GATA-1; Chain A / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Zinc finger, C4 type (two domains) / Nuclear hormone receptors DNA-binding domain profile. / c4 zinc finger in nuclear hormone receptors / Nuclear hormone receptor, ligand-binding domain / Nuclear hormone receptor-like domain superfamily / Ligand-binding domain of nuclear hormone receptor / Nuclear receptor (NR) ligand-binding (LBD) domain profile. / Ligand binding domain of hormone receptors / Zinc finger, NHR/GATA-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Nuclear receptor subfamily 6 group A member 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.101 Å
AuthorsWeikum, E.R. / Ortlund, E.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)1R01DK095750-01 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1F31GM113397-01A1 United States
CitationJournal: J. Mol. Biol. / Year: 2016
Title: A Structural Investigation into Oct4 Regulation by Orphan Nuclear Receptors, Germ Cell Nuclear Factor (GCNF), and Liver Receptor Homolog-1 (LRH-1).
Authors: Weikum, E.R. / Tuntland, M.L. / Murphy, M.N. / Ortlund, E.A.
History
DepositionJul 7, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 4, 2017Group: Database references
Revision 1.2Apr 5, 2017Group: Database references
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.6Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA (5'-D(*AP*GP*AP*GP*GP*TP*CP*AP*AP*GP*GP*CP*TP*AP*GP*A)-3')
B: Nuclear receptor subfamily 6 group A member 1
E: DNA (5'-D(*TP*CP*TP*AP*GP*CP*CP*TP*TP*GP*AP*CP*CP*TP*CP*T)-3')
G: Nuclear receptor subfamily 6 group A member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5538
Polymers29,2924
Non-polymers2624
Water77543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5320 Å2
ΔGint-30 kcal/mol
Surface area13200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.649, 69.469, 84.536
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 4996.268 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse)
#2: Protein Nuclear receptor subfamily 6 group A member 1 / Germ cell nuclear factor / mGCNF / Retinoid receptor-related testis-specific receptor / RTR


Mass: 9747.570 Da / Num. of mol.: 2 / Mutation: C104S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Nr6a1, Gcnf / Plasmid: LIC MBP / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / Variant (production host): pLysS / References: UniProt: Q64249
#3: DNA chain DNA (5'-D(*TP*CP*TP*AP*GP*CP*CP*TP*TP*GP*AP*CP*CP*TP*CP*T)-3')


Mass: 4800.115 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse)
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / Source method: isolated from a natural source / Formula: H2O

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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: 2.75 Å3/Da / Density % sol: 55.21 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.1M Tris pH 8.5, 20% PEG 3350, 3% glycerol

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jan 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 18322 / % possible obs: 96.2 % / Redundancy: 5.2 % / Biso Wilson estimate: 46.64 Å2 / Rmerge(I) obs: 0.152 / Rpim(I) all: 0.069 / Rrim(I) all: 0.167 / Χ2: 1.695 / Net I/av σ(I): 17.342 / Net I/σ(I): 8.9 / Num. measured all: 95317
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.1-2.183.50.65614860.690.3710.7580.90980.2
2.18-2.263.80.56616410.7980.3060.6461.03687.9
2.26-2.3740.46617850.8450.2510.5321.1695.4
2.37-2.494.30.40418660.9040.210.4571.34699.1
2.49-2.654.70.37618720.9290.1860.4211.49599.9
2.65-2.855.60.40318940.9370.1840.4441.54299.8
2.85-3.146.40.30518960.9750.1310.3321.77299.7
3.14-3.596.40.15319030.9910.070.1692.06799.8
3.59-4.526.40.1319390.9820.0570.1432.17699.8
4.52-506.20.12720400.9780.0570.142.07399.4

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data scaling
PDB_EXTRACT3.2data extraction
PHASERphasing
Cootmodel building
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Previous low resolution structure

Resolution: 2.101→37.944 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 33.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2683 910 4.99 %
Rwork0.2156 17318 -
obs0.2183 18228 95.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 163.51 Å2 / Biso mean: 61.9231 Å2 / Biso min: 36.75 Å2
Refinement stepCycle: final / Resolution: 2.101→37.944 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1244 650 4 43 1941
Biso mean--51.78 54.58 -
Num. residues----188
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031983
X-RAY DIFFRACTIONf_angle_d0.5652775
X-RAY DIFFRACTIONf_chiral_restr0.036295
X-RAY DIFFRACTIONf_plane_restr0.002246
X-RAY DIFFRACTIONf_dihedral_angle_d18.8411107
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1005-2.21120.341080.31172037214581
2.2112-2.34980.32481230.29142365248893
2.3498-2.53120.30651330.27672524265799
2.5312-2.78580.32431350.266225552690100
2.7858-3.18870.34531350.281625562691100
3.1887-4.01680.29441340.20632574270898
4.0168-37.94970.20961420.16872707284999

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