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- PDB-3lbd: LIGAND-BINDING DOMAIN OF THE HUMAN RETINOIC ACID RECEPTOR GAMMA B... -

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Basic information

Entry
Database: PDB / ID: 3lbd
TitleLIGAND-BINDING DOMAIN OF THE HUMAN RETINOIC ACID RECEPTOR GAMMA BOUND TO 9-CIS RETINOIC ACID
ComponentsRETINOIC ACID RECEPTOR GAMMA
KeywordsNUCLEAR RECEPTOR / RETINOIC ACID RECEPTOR / ALL-TRANS RETINOIC ACID / LIGAND-BINDING DOMAIN / COMPLEX / HOLO FORM / TRANSCRIPTION REGULATION / LIGAND-DEPENDENT / ACTIVE CONFORMATION / Structural Proteomics in Europe / SPINE / Structural Genomics
Function / homology
Function and homology information


regulation of myeloid cell differentiation / Harderian gland development / trachea cartilage development / growth plate cartilage chondrocyte growth / embryonic eye morphogenesis / embryonic camera-type eye development / glandular epithelial cell development / prostate gland epithelium morphogenesis / positive regulation of programmed cell death / negative regulation of chondrocyte differentiation ...regulation of myeloid cell differentiation / Harderian gland development / trachea cartilage development / growth plate cartilage chondrocyte growth / embryonic eye morphogenesis / embryonic camera-type eye development / glandular epithelial cell development / prostate gland epithelium morphogenesis / positive regulation of programmed cell death / negative regulation of chondrocyte differentiation / embryonic hindlimb morphogenesis / anterior/posterior pattern specification / regulation of myelination / Signaling by Retinoic Acid / regulation of cell size / face development / canonical Wnt signaling pathway / nuclear retinoid X receptor binding / response to retinoic acid / retinoic acid receptor signaling pathway / negative regulation of stem cell proliferation / cellular response to retinoic acid / cellular response to leukemia inhibitory factor / stem cell proliferation / neural tube closure / multicellular organism growth / Nuclear Receptor transcription pathway / Activation of anterior HOX genes in hindbrain development during early embryogenesis / nuclear receptor activity / sequence-specific double-stranded DNA binding / transcription regulator complex / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / positive regulation of apoptotic process / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of cell population proliferation / apoptotic process / positive regulation of cell population proliferation / chromatin binding / positive regulation of gene expression / chromatin / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / nucleus / membrane / cytoplasm
Similarity search - Function
: / : / Retinoic acid receptor / Retinoid X Receptor / Retinoid X Receptor / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Double treble clef zinc finger, C4 type / Nuclear hormone receptors DNA-binding domain profile. ...: / : / Retinoic acid receptor / Retinoid X Receptor / Retinoid X Receptor / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Double treble clef zinc finger, C4 type / 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
(9cis)-retinoic acid / Retinoic acid receptor gamma / Retinoic acid receptor gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement / Resolution: 2.4 Å
AuthorsKlaholz, B.P. / Renaud, J.-P. / Mitschler, A. / Moras, D. / Structural Proteomics in Europe (SPINE)
Citation
Journal: Nat.Struct.Biol. / Year: 1998
Title: Conformational adaptation of agonists to the human nuclear receptor RAR gamma.
Authors: Klaholz, B.P. / Renaud, J.P. / Mitschler, A. / Zusi, C. / Chambon, P. / Gronemeyer, H. / Moras, D.
#1: Journal: Nature / Year: 1995
Title: Crystal Structure of the Rar-Gamma Ligand-Binding Domain Bound to All-Trans Retinoic Acid
Authors: Renaud, J.P. / Rochel, N. / Ruff, M. / Vivat, V. / Chambon, P. / Gronemeyer, H. / Moras, D.
History
DepositionFeb 4, 1998Processing site: BNL
Revision 1.0Mar 2, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2016Group: Non-polymer description
Revision 1.4Aug 9, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RETINOIC ACID RECEPTOR GAMMA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4932
Polymers30,1931
Non-polymers3001
Water2,846158
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.666, 60.666, 155.134
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein RETINOIC ACID RECEPTOR GAMMA / E DOMAIN


Mass: 30193.055 Da / Num. of mol.: 1 / Fragment: LBD, LIGAND-BINDING DOMAIN, RESIDUES 178 - 423
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: BL21 / Cellular location: CYTOPLASM / Gene: HRARGAMMA / Plasmid: PET-15B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P22932, UniProt: P13631*PLUS
#2: Chemical ChemComp-9CR / (9cis)-retinoic acid


Mass: 300.435 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H28O2 / Comment: anticancer, antineoplastic*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / 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: 2.36 Å3/Da / Density % sol: 33 %
Crystal growpH: 7 / Details: pH 7.0
Crystal grow
*PLUS
Temperature: 17 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
14.0 mg/mlprotein1drop
20.4 mM9-cis retinoic acid1drop
310 mMTris-HCl1drop
415 mMdithiothreitol1drop
5500 mM1dropNaCl
60.15 mMn-dodecyl-beta-D-maltoside1drop
72 mMCHAPS1drop
84 %glycerol1drop
92 %ethanol1drop
100.1 MPIPES1reservoir
110.9-1.1 M1reservoirNaOAc

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Data collection

DiffractionMean temperature: 123 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.975
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 1, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.975 Å / Relative weight: 1
ReflectionResolution: 2.4→15 Å / Num. obs: 11390 / % possible obs: 98.45 % / Redundancy: 4.45 % / Rsym value: 0.074 / Net I/σ(I): 25.43
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 7.29 / Rsym value: 0.3 / % possible all: 97.8
Reflection
*PLUS
Rmerge(I) obs: 0.074
Reflection shell
*PLUS
% possible obs: 97.8 % / Rmerge(I) obs: 0.3

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Processing

Software
NameVersionClassification
X-PLOR3.851model building
X-PLOR3.851refinement
MARXDSdata reduction
MARSCALEdata scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: molecular replacement
Starting model: 2LBD

2lbd


Resolution: 2.4→5 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 3
RfactorNum. reflection% reflectionSelection details
Rfree0.267 1 5 %RANDOM (FREERFLAG, CCP4)
Rwork0.172 ---
obs0.172 9576 84 %-
Displacement parametersBiso mean: 36.2 Å2
Refinement stepCycle: LAST / Resolution: 2.4→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1862 0 22 158 2042
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.504
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d21
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.48
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.PEP
X-RAY DIFFRACTION39CRA.PARTOPH19.SOL
X-RAY DIFFRACTION49CRA.TOP
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg21
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.48

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