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- PDB-2lbd: LIGAND-BINDING DOMAIN OF THE HUMAN RETINOIC ACID RECEPTOR GAMMA B... -

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Basic information

Entry
Database: PDB / ID: 2lbd
TitleLIGAND-BINDING DOMAIN OF THE HUMAN RETINOIC ACID RECEPTOR GAMMA BOUND TO ALL-TRANS 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


Harderian gland development / regulation of myeloid cell differentiation / trachea cartilage development / growth plate cartilage chondrocyte growth / embryonic eye morphogenesis / embryonic camera-type eye development / glandular epithelial cell development / prostate gland epithelium morphogenesis / negative regulation of chondrocyte differentiation / embryonic hindlimb morphogenesis ...Harderian gland development / regulation of myeloid cell differentiation / trachea cartilage development / growth plate cartilage chondrocyte growth / embryonic eye morphogenesis / embryonic camera-type eye development / glandular epithelial cell development / prostate gland epithelium morphogenesis / negative regulation of chondrocyte differentiation / embryonic hindlimb morphogenesis / positive regulation of programmed cell death / anterior/posterior pattern specification / regulation of myelination / Signaling by Retinoic Acid / regulation of cell size / face development / canonical Wnt signaling pathway / retinoic acid receptor signaling pathway / nuclear retinoid X receptor binding / response to retinoic acid / negative regulation of stem cell proliferation / cellular response to retinoic acid / cellular response to leukemia inhibitory factor / hormone-mediated signaling pathway / stem cell proliferation / neural tube closure / multicellular organism growth / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Nuclear Receptor transcription pathway / 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 / chromatin binding / positive regulation of cell population proliferation / chromatin / positive regulation of gene expression / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / membrane / nucleus / 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 / Zinc finger, C4 type (two domains) / 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 / 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
RETINOIC ACID / Retinoic acid receptor gamma / Retinoic acid receptor gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIR / Resolution: 2.06 Å
AuthorsRenaud, J.-P. / Rochel, N. / Ruff, M. / Moras, D. / Structural Proteomics in Europe (SPINE)
Citation
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.
#1: Journal: Nature / Year: 1995
Title: Crystal Structure of the Ligand-Binding Domain of the Human Nuclear Receptor Rxr-Alpha
Authors: Bourguet, W. / Ruff, M. / Chambon, P. / Gronemeyer, H. / Moras, D.
History
DepositionAug 19, 1997Processing site: BNL
Revision 1.0Nov 12, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 21, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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

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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
Water2,144119
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.600, 60.600, 155.300
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)
Description: CDNA CLONING\: KRUST ET AL., PROC.NATL.ACAD.SCI.USA,86,5310-5314,1989
Cell line: BL21 / Cellular location: NUCLEUSCell nucleus / Gene: HUMAN RAR GAMMA A CDNA (NUCLEOTIDES 946 - 1683) / Plasmid: PET-15B / Species (production host): Escherichia coli / Cellular location (production host): CYTOPLASM / Gene (production host): HRARGAMMA / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P22932, UniProt: P13631*PLUS
#2: Chemical ChemComp-REA / RETINOIC ACID / Retinoic acid


Mass: 300.435 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H28O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 119 / 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: 3

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Sample preparation

CrystalDensity Matthews: 2.36 Å3/Da / Density % sol: 33 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7
Details: VAPOR DIFFUSION METHOD, HANGING DROP TECHNIQUE 5UL PROTEIN SOLUTION + 5UL RESERVOIR AGAINST 500UL RESERVOIR, pH 7.0, vapor diffusion - hanging drop
Crystal grow
*PLUS
Temperature: 15 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.75 Msodium acetate1drop
250 mMPIPES1drop
3250 mM1dropNaCl
45 mMTris-HCl1drop
55 mMdithiothreitol1drop
61 mMCHAPS1drop
70.08 mMn-dodecyl-beta-D-maltoside1drop
82 %glycerol1drop
91.5 Msodium acetate1reservoir
10100 mMPIPES1reservoir

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Data collection

DiffractionMean temperature: 268 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.901
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 1, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.901 Å / Relative weight: 1
ReflectionResolution: 2.06→7.99 Å / Num. obs: 17193 / % possible obs: 94.08 % / Observed criterion σ(I): 0 / Redundancy: 3.77 % / Rmerge(I) obs: 0.0974 / Net I/σ(I): 22.8
Reflection shellResolution: 2.06→2.1 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.3323 / Mean I/σ(I) obs: 3.64 / % possible all: 57.5

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
MARXDSdata reduction
MARSCALEdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: SIR / Resolution: 2.06→8 Å / Cross valid method: THROUGHOUT / σ(F): 3
RfactorNum. reflection% reflectionSelection details
Rfree0.313 1 10 %RANDOM (FREERFLAG, CCP4)
Rwork0.21 ---
obs0.21 15632 86 %-
Displacement parametersBiso mean: 21.2 Å2
Refinement stepCycle: LAST / Resolution: 2.06→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1870 0 22 119 2011
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
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_deg1.67
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d21.6
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.57
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 DIFFRACTION3ATRA.PARTOPH19.SOL
X-RAY DIFFRACTION4ATRA.TOP
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.21 / Rfactor Rwork: 0.21
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg21.6
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.57

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