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- PDB-5l0m: hLRH-1 DNA Binding Domain - 12bp Oct4 promoter complex -

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Basic information

Entry
Database: PDB / ID: 5l0m
TitlehLRH-1 DNA Binding Domain - 12bp Oct4 promoter complex
Components
  • DNA (5'-D(*CP*TP*AP*GP*CP*CP*TP*TP*GP*AP*CP*C)-3')
  • DNA (5'-D(*GP*GP*TP*CP*AP*AP*GP*GP*CP*TP*AP*G)-3')
  • Nuclear receptor subfamily 5 group A member 2
KeywordsTranscription/dna / LRH-1 / Nuclear Receptor / OCT4 / DBD / Transcription-dna complex
Function / homology
Function and homology information


Regulation of gene expression in early pancreatic precursor cells / pancreas morphogenesis / calcineurin-mediated signaling / acinar cell differentiation / tissue development / bile acid metabolic process / embryo development ending in birth or egg hatching / homeostatic process / positive regulation of viral genome replication / hormone-mediated signaling pathway ...Regulation of gene expression in early pancreatic precursor cells / pancreas morphogenesis / calcineurin-mediated signaling / acinar cell differentiation / tissue development / bile acid metabolic process / embryo development ending in birth or egg hatching / homeostatic process / positive regulation of viral genome replication / hormone-mediated signaling pathway / cholesterol homeostasis / cellular response to leukemia inhibitory factor / transcription coregulator binding / SUMOylation of intracellular receptors / phospholipid binding / Nuclear Receptor transcription pathway / RNA polymerase II transcription regulator complex / nuclear receptor activity / sequence-specific double-stranded DNA binding / regulation of cell population proliferation / DNA-binding transcription activator activity, RNA polymerase II-specific / Estrogen-dependent gene expression / sequence-specific DNA binding / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin binding / regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Nuclear hormone receptor family 5 / 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 family 5 / 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 5 group A member 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.197 Å
AuthorsTuntland, M.L. / Ortlund, E.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)4R01DK095750-05 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 27, 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 / _pdbx_audit_support.grant_number
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 4, 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
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: Nuclear receptor subfamily 5 group A member 2
C: DNA (5'-D(*CP*TP*AP*GP*CP*CP*TP*TP*GP*AP*CP*C)-3')
B: DNA (5'-D(*GP*GP*TP*CP*AP*AP*GP*GP*CP*TP*AP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7016
Polymers20,4783
Non-polymers2233
Water90150
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3940 Å2
ΔGint-12 kcal/mol
Surface area8770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.931, 40.931, 105.055
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Nuclear receptor subfamily 5 group A member 2 / Alpha-1-fetoprotein transcription factor / B1-binding factor / hB1F / CYP7A promoter-binding factor ...Alpha-1-fetoprotein transcription factor / B1-binding factor / hB1F / CYP7A promoter-binding factor / Hepatocytic transcription factor / Liver receptor homolog 1 / LRH-1


Mass: 13152.337 Da / Num. of mol.: 1 / Fragment: unp residues 79-187
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NR5A2, B1F, CPF, FTF / Plasmid: pMALCH10T / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 pLysS / References: UniProt: O00482

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DNA chain , 2 types, 2 molecules CB

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


Mass: 3598.355 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse)
#3: DNA chain DNA (5'-D(*GP*GP*TP*CP*AP*AP*GP*GP*CP*TP*AP*G)-3')


Mass: 3727.441 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse)

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Non-polymers , 3 types, 53 molecules

#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / 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: 2.15 Å3/Da / Density % sol: 42.76 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.2 M calcium acetate and 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Nov 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 8862 / % possible obs: 99.8 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 24.3

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2A66

2a66


Resolution: 2.197→28.943 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 22.42
RfactorNum. reflection% reflection
Rfree0.197 869 9.89 %
Rwork0.1535 --
obs0.158 8789 99.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.197→28.943 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms778 486 8 50 1322
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0161339
X-RAY DIFFRACTIONf_angle_d1.6511891
X-RAY DIFFRACTIONf_dihedral_angle_d26.204552
X-RAY DIFFRACTIONf_chiral_restr0.069199
X-RAY DIFFRACTIONf_plane_restr0.009162
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1966-2.33420.25471450.20421296X-RAY DIFFRACTION98
2.3342-2.51430.21891460.18861327X-RAY DIFFRACTION100
2.5143-2.76720.25741390.18021333X-RAY DIFFRACTION100
2.7672-3.16720.22481420.17631326X-RAY DIFFRACTION100
3.1672-3.98860.19861450.14281301X-RAY DIFFRACTION99
3.9886-28.94510.16961520.13841337X-RAY DIFFRACTION100

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