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- PDB-2a66: Human Liver Receptor Homologue DNA-Binding Domain (hLRH-1 DBD) in... -

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Basic information

Entry
Database: PDB / ID: 2a66
TitleHuman Liver Receptor Homologue DNA-Binding Domain (hLRH-1 DBD) in Complex with dsDNA from the hCYP7A1 Promoter
Components
  • 5'-D(*CP*TP*GP*GP*CP*CP*TP*TP*GP*AP*AP*C)-3'
  • 5'-D(*GP*TP*TP*CP*AP*AP*GP*GP*CP*CP*AP*G)-3'
  • Orphan nuclear receptor NR5A2
KeywordsTRANSCRIPTION/DNA / nuclear receptor / protein-DNA complex / zinc finger / DNA-binding domain / transcription factor / Ftz-F1 / C-terminal extension / 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 / cellular response to leukemia inhibitory factor / transcription coregulator binding / cholesterol homeostasis / 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 / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / 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
ACETATE ION / DNA / DNA (> 10) / Nuclear receptor subfamily 5 group A member 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsSolomon, I.H. / Hager, J.M. / Safi, R. / McDonnell, D.P. / Redinbo, M.R. / Ortlund, E.A.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Crystal Structure of the Human LRH-1 DBD-DNA Complex Reveals Ftz-F1 Domain Positioning is Required for Receptor Activity.
Authors: Solomon, I.H. / Hager, J.M. / Safi, R. / McDonnell, D.P. / Redinbo, M.R. / Ortlund, E.A.
History
DepositionJul 1, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: 5'-D(*GP*TP*TP*CP*AP*AP*GP*GP*CP*CP*AP*G)-3'
C: 5'-D(*CP*TP*GP*GP*CP*CP*TP*TP*GP*AP*AP*C)-3'
A: Orphan nuclear receptor NR5A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7256
Polymers20,5353
Non-polymers1903
Water1,54986
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.770, 40.770, 104.850
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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DNA chain , 2 types, 2 molecules BC

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


Mass: 3687.417 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: synthesized oligonucleotide based on CYP7A1 gene promoter
Source: (natural) Homo sapiens (human)
#2: DNA chain 5'-D(*CP*TP*GP*GP*CP*CP*TP*TP*GP*AP*AP*C)-3'


Mass: 3638.379 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: synthesized oligonucleotide based on CYP7A1 gene promoter
Source: (natural) Homo sapiens (human)

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Protein , 1 types, 1 molecules A

#3: Protein Orphan nuclear receptor NR5A2 / Alpha-1-fetoprotein transcription factor / Hepatocytic transcription factor / B1-binding factor / ...Alpha-1-fetoprotein transcription factor / Hepatocytic transcription factor / B1-binding factor / hB1F / CYP7A1 promoter binding factor


Mass: 13209.390 Da / Num. of mol.: 1 / Fragment: residues 79-187, NR C4-type
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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Non-polymers , 3 types, 89 molecules

#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / 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: 3.3 Å3/Da / Density % sol: 62.78 %
Crystal growTemperature: 295 K / pH: 6
Details: magnesium acetate, ammonium acetate, sodium cacodylate, PEG 8000, glycerol, sodium azide, hexaamine cobalt (III) trichloride, pH 6.0, hanging drop, temperature 295K, pH 6.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 22, 2005 / Details: MIRRORS
RadiationMonochromator: DCM / Protocol: 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: 8687 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 5.5 % / Biso Wilson estimate: 23.1 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 27.6
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.441 / Mean I/σ(I) obs: 3.2 / % possible all: 100

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Phasing

Phasing MRRfactor: 0.461 / Cor.coef. Fo:Fc: 0.491
Highest resolutionLowest resolution
Rotation3 Å22.24 Å
Translation3 Å22.24 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
CNSrefinement
PDB_EXTRACT1.7data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY: 1CIT

1cit


Resolution: 2.2→22.24 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 275996.63 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.226 648 7.7 %RANDOM
Rwork0.196 ---
obs0.196 8437 96.9 %-
all-8687 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 56.0581 Å2 / ksol: 0.3609 e/Å3
Displacement parametersBiso mean: 34.85 Å2
Baniso -1Baniso -2Baniso -3
1--0.668 Å20 Å20 Å2
2---0.668 Å20 Å2
3---1.337 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 2.2→22.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms750 486 6 86 1328
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d19.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.11
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.41.5
X-RAY DIFFRACTIONc_mcangle_it2.252
X-RAY DIFFRACTIONc_scbond_it2.032
X-RAY DIFFRACTIONc_scangle_it3.032.5
LS refinement shellResolution: 2.2→2.26 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.209 98 7.6 %
Rwork0.224 577 -
obs--92.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:PROTEIN_REP.PARAMCNS_TOPPAR:PROTEIN.TOP
X-RAY DIFFRACTION2CNS_TOPPAR:DNA-RNA_REP.PARAMCNS_TOPPAR:DNA-RNA.TOP
X-RAY DIFFRACTION3CNS_TOPPAR:WATER_REP.PARAMCNS_TOPPAR:WATER.TOP
X-RAY DIFFRACTION4CNS_TOPPAR:ION.PARAMCNS_TOPPAR:ION.TOP
X-RAY DIFFRACTION5ACT.PARACT.TOP

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