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- PDB-4cn5: Crystal Structure of the Human Retinoid X Receptor DNA-Binding Do... -

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Basic information

Entry
Database: PDB / ID: 4cn5
TitleCrystal Structure of the Human Retinoid X Receptor DNA-Binding Domain Bound to the Human Nr1d1 Response Element
Components
  • 5'-D(*AP*TP*TP*GP*AP*AP*CP*TP*CP*TP*GP*AP*CP*CP *CP*CP*AP)-3'
  • 5'-D(*TP*GP*GP*GP*GP*TP*CP*AP*GP*AP*GP*TP*TP*CP *AP*AP*TP)-3'
  • RETINOIC ACID RECEPTOR RXR-ALPHA
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 mediated signaling pathway / NR1H2 & NR1H3 regulate gene expression linked to lipogenesis / Carnitine metabolism / anatomical structure development / ion binding ...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 mediated signaling pathway / NR1H2 & NR1H3 regulate gene expression linked to lipogenesis / Carnitine metabolism / anatomical structure development / 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 / positive regulation of cholesterol efflux / Synthesis of bile acids and bile salts / 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 / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / response to retinoic acid / Recycling of bile acids and salts / 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 / SUMOylation of intracellular receptors / Heme signaling / mRNA transcription by RNA polymerase II / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / Cytoprotection by HMOX1 / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / Transcriptional regulation of granulopoiesis / RNA polymerase II transcription regulator complex / nuclear receptor activity / Circadian Clock / sequence-specific double-stranded DNA binding / 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 / negative regulation of transcription by RNA polymerase II / enzyme binding / 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 / Nuclear/hormone receptor activator site AF-1 / Nuclear/hormone receptor activator site AF-1 / Erythroid Transcription Factor GATA-1; Chain A / 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 / Nuclear/hormone receptor activator site AF-1 / Nuclear/hormone receptor activator site AF-1 / Erythroid Transcription Factor GATA-1; Chain A / 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
: / NITRATE ION / DNA / DNA (> 10) / Retinoic acid receptor RXR-alpha
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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: 5'-D(*TP*GP*GP*GP*GP*TP*CP*AP*GP*AP*GP*TP*TP*CP *AP*AP*TP)-3'
D: 5'-D(*AP*TP*TP*GP*AP*AP*CP*TP*CP*TP*GP*AP*CP*CP *CP*CP*AP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,59718
Polymers30,9404
Non-polymers65714
Water5,675315
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7800 Å2
ΔGint-87.1 kcal/mol
Surface area12790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.286, 44.327, 63.915
Angle α, β, γ (deg.)90.00, 98.95, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 2 molecules AB

#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.: 2 / Fragment: DNA-BINDING DOMAIN, RESIDUES 126-212
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, 2 molecules CD

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


Mass: 5282.432 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human)
#3: DNA chain 5'-D(*AP*TP*TP*GP*AP*AP*CP*TP*CP*TP*GP*AP*CP*CP *CP*CP*AP)-3'


Mass: 5131.350 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human)

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Non-polymers , 5 types, 329 molecules

#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#5: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#6: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#7: Chemical ChemComp-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 315 / 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: 2.33 Å3/Da / Density % sol: 52.9 % / Description: NONE
Crystal growpH: 6.6 / Details: 20% PEG 3350, 0.2M KNO3, pH 6.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 1.2833
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 8, 2013 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2833 Å / Relative weight: 1
ReflectionResolution: 2→43 Å / Num. obs: 19176 / % possible obs: 98.3 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 24.12 Å2 / Rmerge(I) obs: 0.03 / Net I/σ(I): 27.2
Reflection shellResolution: 2→2.05 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.12 / Mean I/σ(I) obs: 9.4 / % possible all: 98.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DSZ

1dsz


Resolution: 2→43.093 Å / SU ML: 0.22 / σ(F): 1.91 / Phase error: 24.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.227 1881 5.2 %
Rwork0.1673 --
obs0.1705 19153 95.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.23 Å2
Refinement stepCycle: LAST / Resolution: 2→43.093 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1275 691 17 315 2298
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062068
X-RAY DIFFRACTIONf_angle_d1.1842899
X-RAY DIFFRACTIONf_dihedral_angle_d21.202848
X-RAY DIFFRACTIONf_chiral_restr0.063303
X-RAY DIFFRACTIONf_plane_restr0.004254
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.05410.2971130.20562682X-RAY DIFFRACTION97
2.0541-2.11450.26561620.19422700X-RAY DIFFRACTION99
2.1145-2.18280.23641370.19772726X-RAY DIFFRACTION99
2.1828-2.26080.41361610.31132182X-RAY DIFFRACTION81
2.2608-2.35130.241570.20972592X-RAY DIFFRACTION93
2.3513-2.45830.22081500.1692739X-RAY DIFFRACTION99
2.4583-2.58790.20911270.16832733X-RAY DIFFRACTION99
2.5879-2.750.26681200.17742751X-RAY DIFFRACTION99
2.75-2.96230.27861490.18422737X-RAY DIFFRACTION99
2.9623-3.26030.25251180.17122726X-RAY DIFFRACTION98
3.2603-3.73180.18021550.13752548X-RAY DIFFRACTION92
3.7318-4.70080.20861580.13072542X-RAY DIFFRACTION93
4.7008-43.10250.1651740.13892491X-RAY DIFFRACTION92
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)
13.8760.43041.19544.77680.69224.3401-0.20720.08590.18520.05940.09280.0048-0.23530.24430.05470.2008-0.0305-0.06570.08980.0040.1703-25.6533-4.763526.4335
23.731-0.32811.45823.61430.34824.04490.41050.1044-0.9020.09950.23360.34260.9579-0.1702-0.15180.3708-0.0574-0.15660.19750.04650.4098-38.7137-29.502110.0335
32.03931.54061.21751.43441.382.7333-0.31920.3414-0.096-0.10850.2876-0.2239-0.26840.54390.03020.1736-0.0133-0.0240.2491-0.00660.2263-26.1252-13.260312.5427
42.04590.09830.18732.48230.43414.5425-0.23960.3051-0.2149-0.05630.4091-0.2177-0.29020.68180.14170.06380.0155-0.0120.1805-0.03870.1714-25.9815-15.622212.7459
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C
4X-RAY DIFFRACTION4CHAIN D

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