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- PDB-8ifo: Crystal structure of estrogen related receptor-gamma DNA binding ... -

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Basic information

Entry
Database: PDB / ID: 8ifo
TitleCrystal structure of estrogen related receptor-gamma DNA binding domain complexed with Pla2g12b promoter
Components
  • DNA (5'-D(*GP*AP*GP*GP*AP*CP*AP*AP*AP*GP*GP*TP*GP*AP*AP*AP*C)-3')
  • DNA (5'-D(*GP*TP*TP*TP*CP*AP*CP*CP*TP*TP*TP*GP*TP*CP*CP*TP*C)-3')
  • Estrogen-related receptor gamma
KeywordsTRANSCRIPTION / nuclear receptor / ERR3 / PLA2G12B / DR1
Function / homology
Function and homology information


AF-2 domain binding / nuclear steroid receptor activity / retinoic acid receptor signaling pathway / estrogen response element binding / intracellular steroid hormone receptor signaling pathway / steroid binding / Nuclear Receptor transcription pathway / nuclear receptor activity / sequence-specific double-stranded DNA binding / positive regulation of cold-induced thermogenesis ...AF-2 domain binding / nuclear steroid receptor activity / retinoic acid receptor signaling pathway / estrogen response element binding / intracellular steroid hormone receptor signaling pathway / steroid binding / Nuclear Receptor transcription pathway / nuclear receptor activity / sequence-specific double-stranded DNA binding / positive regulation of cold-induced thermogenesis / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor activity, RNA polymerase II-specific / chromatin / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / identical protein binding
Similarity search - Function
Oestrogen-related receptor / Retinoic acid receptor / Estrogen receptor/oestrogen-related 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 ...Oestrogen-related receptor / Retinoic acid receptor / Estrogen receptor/oestrogen-related 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
Similarity search - Domain/homology
MALONATE ION / DNA / DNA (> 10) / Estrogen-related receptor gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsXu, T. / Zhen, X. / Liu, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2023
Title: ERR gamma-DBD undergoes dimerization and conformational rearrangement upon binding to the downstream site of the DR1 element.
Authors: Zhen, X. / Gan, Q. / Qu, L. / Dong, Y. / Pan, C. / Liu, J. / Wang, N. / Xu, T.
History
DepositionFeb 19, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 29, 2023Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / citation / Item: _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Estrogen-related receptor gamma
B: Estrogen-related receptor gamma
C: DNA (5'-D(*GP*AP*GP*GP*AP*CP*AP*AP*AP*GP*GP*TP*GP*AP*AP*AP*C)-3')
D: DNA (5'-D(*GP*TP*TP*TP*CP*AP*CP*CP*TP*TP*TP*GP*TP*CP*CP*TP*C)-3')
F: Estrogen-related receptor gamma
G: DNA (5'-D(*GP*AP*GP*GP*AP*CP*AP*AP*AP*GP*GP*TP*GP*AP*AP*AP*C)-3')
H: DNA (5'-D(*GP*TP*TP*TP*CP*AP*CP*CP*TP*TP*TP*GP*TP*CP*CP*TP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,13817
Polymers57,3747
Non-polymers76410
Water1,56787
1
A: Estrogen-related receptor gamma
B: Estrogen-related receptor gamma
C: DNA (5'-D(*GP*AP*GP*GP*AP*CP*AP*AP*AP*GP*GP*TP*GP*AP*AP*AP*C)-3')
D: DNA (5'-D(*GP*TP*TP*TP*CP*AP*CP*CP*TP*TP*TP*GP*TP*CP*CP*TP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,31011
Polymers34,7784
Non-polymers5317
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5780 Å2
ΔGint-25 kcal/mol
Surface area13490 Å2
MethodPISA
2
F: Estrogen-related receptor gamma
G: DNA (5'-D(*GP*AP*GP*GP*AP*CP*AP*AP*AP*GP*GP*TP*GP*AP*AP*AP*C)-3')
H: DNA (5'-D(*GP*TP*TP*TP*CP*AP*CP*CP*TP*TP*TP*GP*TP*CP*CP*TP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8296
Polymers22,5963
Non-polymers2333
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3690 Å2
ΔGint-42 kcal/mol
Surface area9850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.403, 74.434, 111.020
Angle α, β, γ (deg.)90.00, 104.98, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
44
55
/ NCS ensembles :
ID
1
2
3
4
5

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Components

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Protein , 1 types, 3 molecules ABF

#1: Protein Estrogen-related receptor gamma / / ERR gamma-2 / Estrogen receptor-related protein 3 / Nuclear receptor subfamily 3 group B member 3


Mass: 12182.291 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ESRRG, ERR3, ERRG2, KIAA0832, NR3B3 / Production host: Escherichia coli (E. coli) / References: UniProt: P62508

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DNA chain , 2 types, 4 molecules CGDH

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


Mass: 5318.488 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse)
#3: DNA chain DNA (5'-D(*GP*TP*TP*TP*CP*AP*CP*CP*TP*TP*TP*GP*TP*CP*CP*TP*C)-3')


Mass: 5095.293 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse)

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Non-polymers , 3 types, 97 molecules

#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-MLI / MALONATE ION / Malonic acid


Mass: 102.046 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H2O4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 87 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.69 Å3/Da / Density % sol: 54.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 0.1 M Sodium malonate pH 6.0, 12% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 9, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.2→53.62 Å / Num. obs: 30806 / % possible obs: 99.2 % / Redundancy: 6.5 % / CC1/2: 0.994 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.036 / Rrim(I) all: 0.091 / Χ2: 0.93 / Net I/σ(I): 9.8 / Num. measured all: 199080
Reflection shellResolution: 2.2→2.27 Å / % possible obs: 98.6 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.509 / Num. measured all: 16364 / Num. unique obs: 2668 / CC1/2: 0.962 / Rpim(I) all: 0.223 / Rrim(I) all: 0.557 / Χ2: 1.04 / Net I/σ(I) obs: 2.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→44.29 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.881 / SU B: 10.501 / SU ML: 0.192 / Cross valid method: THROUGHOUT / ESU R: 0.222 / ESU R Free: 0.196 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26001 1440 4.7 %RANDOM
Rwork0.21859 ---
obs0.22041 29353 98.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 57.604 Å2
Baniso -1Baniso -2Baniso -3
1-8.96 Å2-0 Å21.2 Å2
2---1.07 Å20 Å2
3----7.46 Å2
Refinement stepCycle: 1 / Resolution: 2.2→44.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1813 1382 28 87 3310
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0123402
X-RAY DIFFRACTIONr_bond_other_d0.0010.0182576
X-RAY DIFFRACTIONr_angle_refined_deg1.6511.424842
X-RAY DIFFRACTIONr_angle_other_deg1.4432.0186005
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8265230
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.66218.64696
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.56515368
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1281522
X-RAY DIFFRACTIONr_chiral_restr0.0770.2440
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022860
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02760
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9911.948929
X-RAY DIFFRACTIONr_mcbond_other0.9881.948928
X-RAY DIFFRACTIONr_mcangle_it1.6332.9161156
X-RAY DIFFRACTIONr_mcangle_other1.6332.9171157
X-RAY DIFFRACTIONr_scbond_it3.1734.1192473
X-RAY DIFFRACTIONr_scbond_other3.1744.1182472
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.2856.2313686
X-RAY DIFFRACTIONr_long_range_B_refined6.47835.8834107
X-RAY DIFFRACTIONr_long_range_B_other6.47535.7954098
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A21380.11
12B21380.11
21A21020.12
22F21020.12
31B21930.09
32F21930.09
41C16050.06
42G16050.06
51D14240.04
52H14240.04
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.408 113 -
Rwork0.395 2156 -
obs--98.31 %
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)
18.01721.2178-2.15576.9245-3.28412.6299-0.32020.1148-0.5114-0.26970.24360.05581.8715-0.78120.07660.6177-0.15860.01940.3983-0.01730.5875.4757-25.837719.7254
24.80140.298-2.28234.66950.04237.01150.175-0.10310.02960.1308-0.06640.2907-0.0647-0.208-0.10860.04860.0554-0.03880.36190.03650.5277-0.8731-5.382144.9455
33.5792-0.43640.86365.8942-1.03339.60510.11910.25470.00230.0736-0.19060.28630.1511-0.21310.07150.0146-0.0426-0.01050.3323-0.03360.5084-28.1612-25.51934.6357
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A125 - 200
2X-RAY DIFFRACTION2B124 - 203
3X-RAY DIFFRACTION3F124 - 200

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