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- PDB-4cn7: Crystal Structure of the Human Retinoid X Receptor DNA-Binding Do... -

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Basic information

Entry
Database: PDB / ID: 4cn7
TitleCrystal Structure of the Human Retinoid X Receptor DNA-Binding Domain Bound to an idealized DR1 Response Element
Components
  • 5'-D(*CP*TP*AP*GP*GP*TP*CP*AP*AP*AP*GP*GP*TP*CP *AP*GP)-3'
  • 5'-D(*CP*TP*GP*AP*CP*CP*TP*TP*TP*GP*AP*CP*CP*TP *AP*GP)-3'
  • RETINOIC ACID RECEPTOR RXR-ALPHA
KeywordsTRANSCRIPTION/DNA / TRANSCRIPTION-DNA COMPLEX / TRANSCRIPTION
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: 2.34 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: 5'-D(*CP*TP*AP*GP*GP*TP*CP*AP*AP*AP*GP*GP*TP*CP *AP*GP)-3'
D: 5'-D(*CP*TP*GP*AP*CP*CP*TP*TP*TP*GP*AP*CP*CP*TP *AP*GP)-3'
E: RETINOIC ACID RECEPTOR RXR-ALPHA
F: RETINOIC ACID RECEPTOR RXR-ALPHA
G: 5'-D(*CP*TP*AP*GP*GP*TP*CP*AP*AP*AP*GP*GP*TP*CP *AP*GP)-3'
H: 5'-D(*CP*TP*GP*AP*CP*CP*TP*TP*TP*GP*AP*CP*CP*TP *AP*GP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,27419
Polymers60,6448
Non-polymers63011
Water2,720151
1
E: RETINOIC ACID RECEPTOR RXR-ALPHA
F: RETINOIC ACID RECEPTOR RXR-ALPHA
G: 5'-D(*CP*TP*AP*GP*GP*TP*CP*AP*AP*AP*GP*GP*TP*CP *AP*GP)-3'
H: 5'-D(*CP*TP*GP*AP*CP*CP*TP*TP*TP*GP*AP*CP*CP*TP *AP*GP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5848
Polymers30,3224
Non-polymers2624
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5120 Å2
ΔGint-22.9 kcal/mol
Surface area13180 Å2
MethodPISA
2
A: RETINOIC ACID RECEPTOR RXR-ALPHA
B: RETINOIC ACID RECEPTOR RXR-ALPHA
C: 5'-D(*CP*TP*AP*GP*GP*TP*CP*AP*AP*AP*GP*GP*TP*CP *AP*GP)-3'
D: 5'-D(*CP*TP*GP*AP*CP*CP*TP*TP*TP*GP*AP*CP*CP*TP *AP*GP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,69011
Polymers30,3224
Non-polymers3687
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5470 Å2
ΔGint-57.1 kcal/mol
Surface area13400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.630, 65.350, 209.120
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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Protein , 1 types, 4 molecules ABEF

#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.: 4 / 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 CGDH

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


Mass: 4947.229 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human)
#3: DNA chain 5'-D(*CP*TP*GP*AP*CP*CP*TP*TP*TP*GP*AP*CP*CP*TP *AP*GP)-3'


Mass: 4849.153 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human)

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Non-polymers , 3 types, 162 molecules

#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / 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: 7
Details: 20% PEG 3350, 0.1M NH4CL, 0.1M MGCL2, 0.1M MOPS PH 7

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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: Nov 8, 2013 / 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: 2.34→40.8 Å / Num. obs: 22310 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Redundancy: 4.4 % / Biso Wilson estimate: 65.22 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 11.3
Reflection shellResolution: 2.34→2.42 Å / Redundancy: 3.9 % / Rmerge(I) obs: 1.02 / Mean I/σ(I) obs: 1.1 / % possible all: 86.7

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Processing

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

1dsz


Resolution: 2.34→40.82 Å / Cor.coef. Fo:Fc: 0.9386 / Cor.coef. Fo:Fc free: 0.926 / SU R Cruickshank DPI: 0.311 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.369 / SU Rfree Blow DPI: 0.212 / SU Rfree Cruickshank DPI: 0.204
RfactorNum. reflection% reflectionSelection details
Rfree0.2093 1113 5 %RANDOM
Rwork0.1731 ---
obs0.175 22248 98.1 %-
Displacement parametersBiso mean: 66.96 Å2
Baniso -1Baniso -2Baniso -3
1--17.8228 Å20 Å20 Å2
2---2.8691 Å20 Å2
3---20.6918 Å2
Refine analyzeLuzzati coordinate error obs: 0.445 Å
Refinement stepCycle: LAST / Resolution: 2.34→40.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2463 1300 11 151 3925
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013953HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.265559HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1684SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes55HARMONIC2
X-RAY DIFFRACTIONt_gen_planes439HARMONIC5
X-RAY DIFFRACTIONt_it3953HARMONIC20
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.67
X-RAY DIFFRACTIONt_other_torsion19.13
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion509SEMIHARMONIC5
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_contact3918SEMIHARMONIC4
LS refinement shellResolution: 2.34→2.45 Å / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.3236 126 4.99 %
Rwork0.2552 2397 -
all0.2585 2523 -
obs--98.1 %
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)
12.42620.48360.86095.43970.44298.0432-0.1715-0.139-0.12170.24230.14980.40650.28890.0090.02170.2146-0.0086-0.0645-0.304-0.0059-0.19020.1029-6.5646-3.5694
23.09821.47040.21355.89520.29725.34670.1414-0.03230.05120.1644-0.02760.0468-0.54420.1349-0.11380.2006-0.0420.0056-0.23390.0245-0.233712.619716.476316.4697
34.5038-0.7758-0.94688.31550.18898.31540.108-0.21650.4757-0.21010.099-0.2003-0.5442-0.5426-0.2070.15190.12330.043-0.233-0.0041-0.291811.779717.605463.2835
44.5210.69311.21873.45880.04447.59850.1219-0.1944-0.1809-0.07050.01680.3234-0.0738-0.5442-0.1387-0.03050.00770.0102-0.08970.048-0.16761.04333.090635.5661
51.56281.00181.89951.57892.20027.55410.06340.2493-0.2073-0.16760.30730.04010.13180.5442-0.37060.23210.0618-0.0475-0.1795-0.0537-0.224115.02010.75712.6435
61.453-0.36472.84641.86391.25948.31540.16680.0031-0.02150.43110.09760.06160.46350.1903-0.26440.20280.0783-0.0115-0.06320.0764-0.28113.30054.592653.1785
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|127 - A|302 }
2X-RAY DIFFRACTION2{ B|132 - B|302 }
3X-RAY DIFFRACTION3{ E|131 - E|302 }
4X-RAY DIFFRACTION4{ F|131 - F|302 }
5X-RAY DIFFRACTION5{ C|1 - C|16 D|1 - D|16 }
6X-RAY DIFFRACTION6{ G|1 - G|16 H|1 - H|16 }

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