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- PDB-4cn3: Crystal Structure of the Human Retinoid X Receptor DNA-Binding Do... -

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Basic information

Entry
Database: PDB / ID: 4cn3
TitleCrystal Structure of the Human Retinoid X Receptor DNA-Binding Domain Bound to the Human Gde1SpA Response Element
Components
  • (RETINOIC ACID RECEPTOR RXR- ...) x 2
  • 5'-D(*CP*TP*AP*GP*TP*TP*CP*AP*AP*AP*GP*TP*TP*CP *AP*CP*A)-3'
  • 5'-D(*TP*GP*TP*GP*AP*AP*CP*TP*TP*TP*GP*AP*AP*CP *TP*AP*G)-3'
KeywordsTRANSCRIPTION/DNA / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


positive regulation of transporter activity / retinoic acid-responsive element binding / NR1H2 & NR1H3 regulate gene expression linked to gluconeogenesis / NR1H2 & NR1H3 regulate gene expression linked to triglyceride lipolysis in adipose / NR1H2 & NR1H3 regulate gene expression to limit cholesterol uptake / positive regulation of thyroid hormone receptor signaling pathway / NR1H2 & NR1H3 regulate gene expression linked to lipogenesis / Carnitine metabolism / ion binding / Regulation of pyruvate dehydrogenase (PDH) complex ...positive regulation of transporter activity / retinoic acid-responsive element binding / NR1H2 & NR1H3 regulate gene expression linked to gluconeogenesis / NR1H2 & NR1H3 regulate gene expression linked to triglyceride lipolysis in adipose / NR1H2 & NR1H3 regulate gene expression to limit cholesterol uptake / positive regulation of thyroid hormone receptor signaling pathway / NR1H2 & NR1H3 regulate gene expression linked to lipogenesis / Carnitine metabolism / ion binding / Regulation of pyruvate dehydrogenase (PDH) complex / retinoic acid binding / positive regulation of vitamin D receptor signaling pathway / nuclear vitamin D receptor binding / Signaling by Retinoic Acid / DNA binding domain binding / nuclear steroid receptor activity / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / LBD domain binding / Synthesis of bile acids and bile salts / positive regulation of cholesterol efflux / retinoic acid receptor signaling pathway / Endogenous sterols / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / positive regulation of bone mineralization / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / response to retinoic acid / Recycling of bile acids and salts / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / peroxisome proliferator activated receptor signaling pathway / RORA activates gene expression / Regulation of lipid metabolism by PPARalpha / hormone-mediated signaling pathway / BMAL1:CLOCK,NPAS2 activates circadian gene expression / Activation of gene expression by SREBF (SREBP) / transcription coregulator binding / nuclear receptor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / peptide binding / Heme signaling / SUMOylation of intracellular receptors / mRNA transcription by RNA polymerase II / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / Cytoprotection by HMOX1 / Transcriptional regulation of white adipocyte differentiation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Nuclear Receptor transcription pathway / Transcriptional regulation of granulopoiesis / RNA polymerase II transcription regulator complex / nuclear receptor activity / sequence-specific double-stranded DNA binding / Circadian Clock / double-stranded DNA binding / transcription regulator complex / sequence-specific DNA binding / cell differentiation / receptor complex / 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 / positive regulation of DNA-templated transcription / enzyme binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / mitochondrion / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytosol
Similarity search - Function
Erythroid Transcription Factor GATA-1, subunit A / Erythroid Transcription Factor GATA-1; Chain A / Nuclear/hormone receptor activator site AF-1 / Nuclear/hormone receptor activator site AF-1 / Retinoid X receptor/HNF4 / 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. ...Erythroid Transcription Factor GATA-1, subunit A / Erythroid Transcription Factor GATA-1; Chain A / Nuclear/hormone receptor activator site AF-1 / Nuclear/hormone receptor activator site AF-1 / Retinoid X receptor/HNF4 / 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) / Retinoic acid receptor RXR-alpha
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsMcEwen, A.G. / Poussin-Courmontagne, P. / Osz, J. / Rochel, N.
CitationJournal: Sci.Rep. / Year: 2015
Title: Structural Basis of Natural Promoter Recognition by the Retinoid X Nuclear Receptor.
Authors: Osz, J. / Mcewen, A.G. / Poussin-Courmontagne, P. / Moutier, E. / Birck, C. / Davidson, I. / Moras, D. / Rochel, N.
History
DepositionJan 21, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 18, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_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
A: RETINOIC ACID RECEPTOR RXR-ALPHA
B: RETINOIC ACID RECEPTOR RXR-ALPHA
C: RETINOIC ACID RECEPTOR RXR-ALPHA
D: RETINOIC ACID RECEPTOR RXR-ALPHA
E: 5'-D(*CP*TP*AP*GP*TP*TP*CP*AP*AP*AP*GP*TP*TP*CP *AP*CP*A)-3'
F: 5'-D(*TP*GP*TP*GP*AP*AP*CP*TP*TP*TP*GP*AP*AP*CP *TP*AP*G)-3'
G: 5'-D(*CP*TP*AP*GP*TP*TP*CP*AP*AP*AP*GP*TP*TP*CP *AP*CP*A)-3'
H: 5'-D(*TP*GP*TP*GP*AP*AP*CP*TP*TP*TP*GP*AP*AP*CP *TP*AP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,40016
Polymers61,8768
Non-polymers5238
Water5,819323
1
B: RETINOIC ACID RECEPTOR RXR-ALPHA
C: RETINOIC ACID RECEPTOR RXR-ALPHA
G: 5'-D(*CP*TP*AP*GP*TP*TP*CP*AP*AP*AP*GP*TP*TP*CP *AP*CP*A)-3'
H: 5'-D(*TP*GP*TP*GP*AP*AP*CP*TP*TP*TP*GP*AP*AP*CP *TP*AP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1998
Polymers30,9384
Non-polymers2624
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4680 Å2
ΔGint-26.3 kcal/mol
Surface area14880 Å2
MethodPISA
2
A: RETINOIC ACID RECEPTOR RXR-ALPHA
D: RETINOIC ACID RECEPTOR RXR-ALPHA
E: 5'-D(*CP*TP*AP*GP*TP*TP*CP*AP*AP*AP*GP*TP*TP*CP *AP*CP*A)-3'
F: 5'-D(*TP*GP*TP*GP*AP*AP*CP*TP*TP*TP*GP*AP*AP*CP *TP*AP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2008
Polymers30,9394
Non-polymers2624
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4920 Å2
ΔGint-23 kcal/mol
Surface area14360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.910, 69.280, 138.860
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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RETINOIC ACID RECEPTOR RXR- ... , 2 types, 4 molecules ABCD

#1: Protein RETINOIC ACID RECEPTOR RXR-ALPHA / NUCLEAR RECEPTOR SUBFAMILY 2 GROUP B MEMBER 1 / RETINOID X RECEPTOR ALPHA


Mass: 10262.926 Da / Num. of mol.: 3 / Fragment: DNA-BINDING DOMAIN, RESIDUES 130-212
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PHXGW / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P19793
#2: Protein RETINOIC ACID RECEPTOR RXR-ALPHA / NUCLEAR RECEPTOR SUBFAMILY 2 GROUP B MEMBER 1 / RETINOID X RECEPTOR ALPHA


Mass: 10263.910 Da / Num. of mol.: 1 / Fragment: DNA-BINDING DOMAIN, RESIDUES 130-212
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PHXGW / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P19793

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DNA chain , 2 types, 4 molecules EGFH

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


Mass: 5170.386 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human)
#4: DNA chain 5'-D(*TP*GP*TP*GP*AP*AP*CP*TP*TP*TP*GP*AP*AP*CP *TP*AP*G)-3'


Mass: 5241.420 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human)

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Non-polymers , 2 types, 331 molecules

#5: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 323 / 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: 2.04 Å3/Da / Density % sol: 46.1 % / Description: NONE
Crystal growpH: 6.11 / Details: 20% PEG 3350, 0.2M NH4CL, pH 6.11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 19, 2010 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 2.3→69.6 Å / Num. obs: 23573 / % possible obs: 95.1 % / Observed criterion σ(I): -3 / Redundancy: 6 % / Biso Wilson estimate: 41.34 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 9.7
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 3.5 / % possible all: 86.8

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DSZ

1dsz


Resolution: 2.35→24.57 Å / Cor.coef. Fo:Fc: 0.9114 / Cor.coef. Fo:Fc free: 0.8842 / SU R Cruickshank DPI: 0.507 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 1.052 / SU Rfree Blow DPI: 0.289 / SU Rfree Cruickshank DPI: 0.273
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=ZN. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=4303. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=0. ...Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=ZN. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=4303. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=0. NUMBER TREATED BY BAD NON-BONDED CONTACTS=8.
RfactorNum. reflection% reflectionSelection details
Rfree0.2493 1040 5.12 %RANDOM
Rwork0.1794 ---
obs0.1831 20297 92.43 %-
Displacement parametersBiso mean: 28.15 Å2
Baniso -1Baniso -2Baniso -3
1-7.207 Å20 Å20 Å2
2---0.277 Å20 Å2
3----6.93 Å2
Refine analyzeLuzzati coordinate error obs: 0.268 Å
Refinement stepCycle: LAST / Resolution: 2.35→24.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2574 1382 8 323 4287
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014183HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.235872HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1841SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes60HARMONIC2
X-RAY DIFFRACTIONt_gen_planes465HARMONIC5
X-RAY DIFFRACTIONt_it4183HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.92
X-RAY DIFFRACTIONt_other_torsion18.97
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion524SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4462SEMIHARMONIC4
LS refinement shellResolution: 2.35→2.48 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.2808 150 5.24 %
Rwork0.187 2712 -
all0.1919 2862 -
obs--92.43 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.51930.0234-0.991.38580.910.7389-0.0154-0.1041-0.09350.23310.0014-0.0130.0090.04370.01390.0552-0.0129-0.0044-0.03640.031-0.11789.9786-17.6371-20.6278
23.8460.75510.34153.7001-1.12212.63260.0084-0.03220.0956-0.05580.06780.0942-0.294-0.0397-0.0763-0.03010.03550.0303-0.04690.0314-0.1139-10.8942-28.014-6.0482
31.3243-0.08580.06381.1001-0.40311.2847-0.04810.01590.0316-0.0998-0.0167-0.11480.09360.02420.06470.04210.00690.0187-0.02890.0182-0.119312.4488-49.2256-16.022
41.9970.7919-0.21243.081-0.08141.78870.0581-0.0280.02590.1282-0.0607-0.1087-0.1520.06380.00260.0280.00950.0024-0.0382-0.0161-0.138434.02884.0999-21.4018
55.68760.88390.25990.55390.06930-0.04640.25980.0218-0.01470.0522-0.0871-0.00560.0783-0.0058-0.03810.038-0.03350.0188-0.0054-0.064118.9242-8.0455-30.7542
65.41641.29960.56580.39750.53980-0.03010.16460.19530.00910.05420.0361-0.13060.0924-0.0241-0.06420.01780.0340.08910.0385-0.090118.943-4.9479-29.7158
78.2991-0.393-0.665700.13450-0.0253-0.1680.02740.0251-0.0029-0.00350.01150.01270.0282-0.0328-0.0308-0.00740.05620.0704-0.0925-1.9307-41.6787-2.8921
83.0056-0.8987-1.24800.18450.9148-0.03270.0285-0.2278-0.0580.03810.0016-0.01960.0784-0.0053-0.0966-0.0374-0.00150.05040.0388-0.0246-2.0029-43.9129-5.2194
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESIDUES 131 - 302
2X-RAY DIFFRACTION2CHAIN B AND RESIDUES 133 - 302
3X-RAY DIFFRACTION3CHAIN C AND RESIDUES 126 - 302
4X-RAY DIFFRACTION4CHAIN D AND RESIDUES 132 - 302
5X-RAY DIFFRACTION5CHAIN E AND RESIDUES 1 - 17
6X-RAY DIFFRACTION6CHAIN F AND RESIDUES 1 - 17
7X-RAY DIFFRACTION7CHAIN G AND RESIDUES 1 - 17
8X-RAY DIFFRACTION8CHAIN H AND RESIDUES 1 - 17

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