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- PDB-2gpp: Estrogen Related Receptor-gamma ligand binding domain complexed w... -

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Basic information

Entry
Database: PDB / ID: 2gpp
TitleEstrogen Related Receptor-gamma ligand binding domain complexed with a RIP140 peptide and synthetic ligand GSK4716
Components
  • Estrogen-related receptor gamma
  • Nuclear receptor-interacting protein 1
KeywordsTRANSCRIPTION / Estrogen related receptor / ERR / ERRg / ESRRG / Nuclear Receptor / Steroid Receptor / RIP140
Function / homology
Function and homology information


ovarian follicle rupture / AF-2 domain binding / NR1H2 & NR1H3 regulate gene expression linked to gluconeogenesis / nuclear glucocorticoid receptor binding / NR1H2 & NR1H3 regulate gene expression linked to lipogenesis / lipid storage / histone deacetylase complex / nuclear steroid receptor activity / estrogen response element binding / nuclear retinoid X receptor binding ...ovarian follicle rupture / AF-2 domain binding / NR1H2 & NR1H3 regulate gene expression linked to gluconeogenesis / nuclear glucocorticoid receptor binding / NR1H2 & NR1H3 regulate gene expression linked to lipogenesis / lipid storage / histone deacetylase complex / nuclear steroid receptor activity / estrogen response element binding / nuclear retinoid X receptor binding / retinoic acid receptor signaling pathway / steroid binding / SUMOylation of transcription cofactors / nuclear estrogen receptor binding / nuclear receptor binding / circadian regulation of gene expression / cellular response to estradiol stimulus / Heme signaling / circadian rhythm / Nuclear Receptor transcription pathway / histone deacetylase binding / fibrillar center / nuclear receptor activity / sequence-specific double-stranded DNA binding / : / transcription corepressor activity / positive regulation of cold-induced thermogenesis / DNA-binding transcription activator activity, RNA polymerase II-specific / Estrogen-dependent gene expression / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription coactivator activity / nuclear speck / RNA polymerase II cis-regulatory region sequence-specific DNA binding / signaling receptor binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / chromatin / nucleolus / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytosol
Similarity search - Function
Nuclear receptor-interacting protein 1 / Nuclear receptor-interacting protein 1, repression domain 1 / Nuclear receptor-interacting protein 1, repression domain 2 / Nuclear receptor-interacting protein 1, repression domain 3 / Nuclear receptor-interacting protein 1, repression domain 4 / Nuclear receptor-interacting protein 1 repression 1 / Nuclear receptor-interacting protein 1 repression 2 / Nuclear receptor-interacting protein 1 repression 3 / Nuclear receptor-interacting protein 1 repression 4 / Oestrogen-related receptor ...Nuclear receptor-interacting protein 1 / Nuclear receptor-interacting protein 1, repression domain 1 / Nuclear receptor-interacting protein 1, repression domain 2 / Nuclear receptor-interacting protein 1, repression domain 3 / Nuclear receptor-interacting protein 1, repression domain 4 / Nuclear receptor-interacting protein 1 repression 1 / Nuclear receptor-interacting protein 1 repression 2 / Nuclear receptor-interacting protein 1 repression 3 / Nuclear receptor-interacting protein 1 repression 4 / Oestrogen-related receptor / Retinoic acid receptor / Estrogen receptor/oestrogen-related receptor / : / Retinoid X Receptor / Retinoid X Receptor / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Double treble clef zinc finger, C4 type / 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
4-HYDROXY-N'-(4-ISOPROPYLBENZYL)BENZOHYDRAZIDE / Nuclear receptor-interacting protein 1 / Estrogen-related receptor gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsWang, L. / Zuercher, W.J. / Consler, T.G. / Lambert, M.H. / Miller, A.B. / Osband-miller, L.A. / McKee, D.D. / Willson, T.M. / Nolte, R.T.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: X-ray crystal structures of the estrogen-related receptor-gamma ligand binding domain in three functional states reveal the molecular basis of small molecule regulation.
Authors: Wang, L. / Zuercher, W.J. / Consler, T.G. / Lambert, M.H. / Miller, A.B. / Orband-Miller, L.A. / McKee, D.D. / Willson, T.M. / Nolte, R.T.
History
DepositionApr 18, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2006Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_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: Estrogen-related receptor gamma
B: Estrogen-related receptor gamma
C: Nuclear receptor-interacting protein 1
D: Nuclear receptor-interacting protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,1205
Polymers57,8354
Non-polymers2841
Water45025
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)203.81, 203.81, 53.46
Angle α, β, γ (deg.)90, 90, 120
Int Tables number146
Space group name H-MH3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D

NCS domain segments:

Component-ID: 1 / Refine code: 5

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROLYSLYSAA233 - 4575 - 229
21PROPROALAALABB233 - 4565 - 228
12SERSERTHRTHRCC378 - 38813 - 23
22SERSERPROPRODD378 - 39013 - 25

NCS ensembles :
ID
1
2

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Components

#1: Protein Estrogen-related receptor gamma / Estrogen receptor-related protein 3 / ERR gamma-2


Mass: 26084.373 Da / Num. of mol.: 2 / Fragment: Residues (229-458)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ESRRG / Plasmid: pRSET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P62508
#2: Protein/peptide Nuclear receptor-interacting protein 1 / Nuclear factor RIP140 / Receptor-interacting protein 140


Mass: 2833.291 Da / Num. of mol.: 2 / Fragment: Residues (366-390) / Source method: obtained synthetically
Details: Chemically synthesized. Occurs naturally in Humans.
References: UniProt: P48552
#3: Chemical ChemComp-1BA / 4-HYDROXY-N'-(4-ISOPROPYLBENZYL)BENZOHYDRAZIDE


Mass: 284.353 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H20N2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 3.69 Å3/Da / Density % sol: 66.7 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 9% PEG 20K 0.1M MES buffer, pH 7.5, vapor diffusion, hanging drop, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 25371 / Num. obs: 25066 / % possible obs: 98.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 9.5 % / Rmerge(I) obs: 0.064 / Χ2: 1.029
Reflection shell
Resolution (Å)% possible obs (%)Redundancy (%)Rmerge(I) obsNum. measured obsΧ2
2.6-2.6484.93.20.40310760.858
2.64-2.6993.53.80.43111750.869
2.69-2.7498.64.60.34512480.876
2.74-2.899.75.40.36712950.911
2.8-2.861006.30.39712340.892
2.86-2.931007.50.36212760.904
2.93-31008.90.35812700.908
3-3.0810010.10.32712580.947
3.08-3.1710011.10.28512820.979
3.17-3.2810011.40.2112571.044
3.28-3.3910011.50.1612811.137
3.39-3.5310011.60.12112621.121
3.53-3.6910011.70.09212831.171
3.69-3.8810011.70.07512551.103
3.88-4.1310011.70.06112831.152
4.13-4.4510011.70.05212561.142
4.45-4.8910011.70.04712871.153
4.89-5.610011.70.04612600.957
5.6-7.0510011.60.04612590.986
7.05-5099.310.70.03712690.856

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
AMoREphasing
REFMAC5.2.0005refinement
PDB_EXTRACT1.7data extraction
ADSCdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GP7

2gp7


Resolution: 2.6→45.74 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.913 / SU B: 9.449 / SU ML: 0.198 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.397 / ESU R Free: 0.269 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.257 764 3 %RANDOM
Rwork0.232 ---
all0.233 25372 --
obs0.233 25065 98.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 44.602 Å2
Baniso -1Baniso -2Baniso -3
1--0.86 Å2-0.43 Å20 Å2
2---0.86 Å20 Å2
3---1.29 Å2
Refinement stepCycle: LAST / Resolution: 2.6→45.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3760 0 21 25 3806
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0223849
X-RAY DIFFRACTIONr_bond_other_d0.0010.023619
X-RAY DIFFRACTIONr_angle_refined_deg1.2151.9985210
X-RAY DIFFRACTIONr_angle_other_deg0.73338455
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5765473
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.50325.849159
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.57915730
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.941510
X-RAY DIFFRACTIONr_chiral_restr0.060.2614
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024176
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02679
X-RAY DIFFRACTIONr_nbd_refined0.230.2945
X-RAY DIFFRACTIONr_nbd_other0.1670.23558
X-RAY DIFFRACTIONr_nbtor_refined0.1880.21914
X-RAY DIFFRACTIONr_nbtor_other0.0880.22198
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.2108
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1780.26
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1980.228
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0020.21
X-RAY DIFFRACTIONr_mcbond_it0.6091.52570
X-RAY DIFFRACTIONr_mcbond_other0.1461.5953
X-RAY DIFFRACTIONr_mcangle_it0.93923843
X-RAY DIFFRACTIONr_scbond_it1.22231602
X-RAY DIFFRACTIONr_scangle_it1.9114.51367
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberRmsTypeWeight
1A13160.43MEDIUM POSITIONAL0.5
1A21230.79LOOSE POSITIONAL5
1A13161.2MEDIUM THERMAL2
1A21231.72LOOSE THERMAL10
2C650.54MEDIUM POSITIONAL0.5
2C1081.03LOOSE POSITIONAL5
2C650.89MEDIUM THERMAL2
2C1081.46LOOSE THERMAL10
LS refinement shellResolution: 2.6→2.67 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 37 -
Rwork0.327 1590 -
all-1627 -
obs--86.96 %

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