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- PDB-3cjw: Crystal structure of the human COUP-TFII ligand binding domain -

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Basic information

Entry
Database: PDB / ID: 3cjw
TitleCrystal structure of the human COUP-TFII ligand binding domain
ComponentsCOUP transcription factor 2
KeywordsTRANSCRIPTION / COUP-TFII / nuclear receptor / ligand binding domain / orphan receptor / three-layered helical sandwich / DNA-binding / Metal-binding / Nucleus / Receptor / Transcription regulation / Zinc / Zinc-finger
Function / homology
Function and homology information


: / radial pattern formation / anatomical structure development / maternal placenta development / trophoblast giant cell differentiation / positive regulation of systemic arterial blood pressure / placenta blood vessel development / negative regulation of cyclin-dependent protein serine/threonine kinase activity / retinoic acid binding / fertilization ...: / radial pattern formation / anatomical structure development / maternal placenta development / trophoblast giant cell differentiation / positive regulation of systemic arterial blood pressure / placenta blood vessel development / negative regulation of cyclin-dependent protein serine/threonine kinase activity / retinoic acid binding / fertilization / blood vessel morphogenesis / limb development / negative regulation of endothelial cell migration / anterior/posterior pattern specification / negative regulation of endothelial cell proliferation / skeletal muscle tissue development / forebrain development / RNA polymerase II transcription regulatory region sequence-specific DNA binding / neuron migration / Transcriptional regulation of white adipocyte differentiation / nuclear receptor activity / response to estradiol / sequence-specific DNA binding / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / zinc ion binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
Retinoid X Receptor / Retinoid X Receptor / 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 ...Retinoid X Receptor / Retinoid X Receptor / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
COUP transcription factor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.48 Å
AuthorsKruse, S.W. / Reynolds, R. / Vonrhein, C. / Xu, H.E.
CitationJournal: Plos Biol. / Year: 2008
Title: Identification of COUP-TFII Orphan Nuclear Receptor as a Retinoic Acid-Activated Receptor.
Authors: Kruse, S.W. / Suino-Powell, K. / Zhou, X.E. / Kretschman, J.E. / Reynolds, R. / Vonrhein, C. / Xu, Y. / Wang, L. / Tsai, S.Y. / Tsai, M.J. / Xu, H.E.
History
DepositionMar 14, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 6, 2020Group: Database references / Derived calculations / Source and taxonomy
Category: entity_src_gen / pdbx_struct_assembly ...entity_src_gen / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / struct_ref_seq_dif
Item: _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id ..._entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression / _pdbx_struct_assembly_prop.biol_id / _pdbx_struct_assembly_prop.value / _struct_ref_seq_dif.details
Revision 1.3Feb 21, 2024Group: 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

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Assembly

Deposited unit
A: COUP transcription factor 2


Theoretical massNumber of molelcules
Total (without water)27,3121
Polymers27,3121
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: COUP transcription factor 2

A: COUP transcription factor 2


Theoretical massNumber of molelcules
Total (without water)54,6232
Polymers54,6232
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area1850 Å2
ΔGint-8 kcal/mol
Surface area19650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.854, 47.762, 43.128
Angle α, β, γ (deg.)90.000, 100.870, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein COUP transcription factor 2 / COUP-TF2 / COUP-TF II / Nuclear receptor subfamily 2 group F member 2 / Apolipoprotein AI ...COUP-TF2 / COUP-TF II / Nuclear receptor subfamily 2 group F member 2 / Apolipoprotein AI regulatory protein 1 / ARP-1


Mass: 27311.561 Da / Num. of mol.: 1 / Fragment: ligand binding domain, residues 173-412
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NR2F2, ARP1, TFCOUP2 / Plasmid: pET24 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P24468

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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: 1.81 Å3/Da / Density % sol: 32.12 %
Crystal growTemperature: 293 K / Method: hanging drop / pH: 5.6
Details: 1.5M Imidazole, pH 5.6, hanging drop, temperature 293K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 0.7, 1.0, 1.4, 1.8
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.71
211
31.41
41.81
ReflectionResolution: 1.48→50 Å / Num. obs: 32718

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT3.004data extraction
RefinementResolution: 1.48→6 Å
RfactorNum. reflection% reflection
Rfree0.2379 1919 -
Rwork0.1684 --
obs-29483 7.7 %
Displacement parametersBiso mean: 34.493 Å2
Refinement stepCycle: LAST / Resolution: 1.48→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1636 0 0 0 1636

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