[English] 日本語
Yorodumi
- PDB-5x8x: Crystal Structure of the mutant Human ROR gamma Ligand Binding Do... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5x8x
TitleCrystal Structure of the mutant Human ROR gamma Ligand Binding Domain With Compound A.
Components
  • Nuclear receptor ROR-gamma
  • Nuclear receptor corepressor 2
KeywordsTRANSFERASE/INHIBITOR / Inhibitor / Ternary Complex / Nuclear Receptor / TRANSFERASE-INHIBITOR complex
Function / homology
Function and homology information


Loss of MECP2 binding ability to the NCoR/SMRT complex / nuclear glucocorticoid receptor binding / negative regulation of androgen receptor signaling pathway / regulation of ketone metabolic process / cellular response to sterol / T-helper 17 cell differentiation / regulation of steroid metabolic process / ligand-modulated transcription factor activity / Peyer's patch development / T-helper cell differentiation ...Loss of MECP2 binding ability to the NCoR/SMRT complex / nuclear glucocorticoid receptor binding / negative regulation of androgen receptor signaling pathway / regulation of ketone metabolic process / cellular response to sterol / T-helper 17 cell differentiation / regulation of steroid metabolic process / ligand-modulated transcription factor activity / Peyer's patch development / T-helper cell differentiation / positive regulation of circadian rhythm / RUNX3 Regulates Immune Response and Cell Migration / oxysterol binding / negative regulation of thymocyte apoptotic process / Notch binding / regulation of fat cell differentiation / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / Notch-HLH transcription pathway / regulation of glucose metabolic process / Regulation of MECP2 expression and activity / adipose tissue development / lymph node development / nuclear retinoid X receptor binding / estrous cycle / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / lactation / Regulation of lipid metabolism by PPARalpha / transcription repressor complex / xenobiotic metabolic process / cerebellum development / negative regulation of miRNA transcription / SUMOylation of transcription cofactors / enzyme activator activity / HDACs deacetylate histones / Downregulation of SMAD2/3:SMAD4 transcriptional activity / circadian regulation of gene expression / PPARA activates gene expression / Cytoprotection by HMOX1 / Nuclear Receptor transcription pathway / Transcriptional regulation of white adipocyte differentiation / NOTCH1 Intracellular Domain Regulates Transcription / DNA-binding transcription repressor activity, RNA polymerase II-specific / histone deacetylase binding / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / nuclear matrix / nuclear receptor activity / HCMV Early Events / transcription corepressor activity / sequence-specific double-stranded DNA binding / response to estradiol / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Interleukin-4 and Interleukin-13 signaling / DNA-binding transcription factor activity, RNA polymerase II-specific / nuclear body / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / chromatin binding / regulation of transcription by RNA polymerase II / protein-containing complex binding / chromatin / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / nucleus / membrane
Similarity search - Function
N-CoR, GPS2-interacting domain / : / G-protein pathway suppressor 2-interacting domain / Nuclear receptor ROR / Retinoid-related orphan receptors, DNA-binding domain / SANT domain profile. / Myb domain / SANT domain / Myb-like DNA-binding domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains ...N-CoR, GPS2-interacting domain / : / G-protein pathway suppressor 2-interacting domain / Nuclear receptor ROR / Retinoid-related orphan receptors, DNA-binding domain / SANT domain profile. / Myb domain / SANT domain / Myb-like DNA-binding domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / Retinoid X Receptor / Retinoid X Receptor / Nuclear hormone receptor / Homeobox-like domain superfamily / 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
Chem-82O / RAR related orphan receptor C / Nuclear receptor ROR-gamma / Nuclear receptor corepressor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsNoguchi, M. / Nomura, A. / Murase, K. / Doi, S. / Yamaguchi, K. / Adachi, T.
CitationJournal: Genes Cells / Year: 2017
Title: Ternary complex of human ROR gamma ligand-binding domain, inverse agonist and SMRT peptide shows a unique mechanism of corepressor recruitment
Authors: Noguchi, M. / Nomura, A. / Murase, K. / Doi, S. / Yamaguchi, K. / Hirata, K. / Shiozaki, M. / Hirashima, S. / Kotoku, M. / Yamaguchi, T. / Katsuda, Y. / Steensma, R. / Li, X. / Tao, H. / ...Authors: Noguchi, M. / Nomura, A. / Murase, K. / Doi, S. / Yamaguchi, K. / Hirata, K. / Shiozaki, M. / Hirashima, S. / Kotoku, M. / Yamaguchi, T. / Katsuda, Y. / Steensma, R. / Li, X. / Tao, H. / Tse, B. / Fenn, M. / Babine, R. / Bradley, E. / Crowe, P. / Thacher, S. / Adachi, T. / Kamada, M.
History
DepositionMar 3, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 7, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 28, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_volume ..._citation.country / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jun 17, 2020Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity.pdbx_fragment ..._entity.pdbx_description / _entity.pdbx_fragment / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.pdbx_seq_db_accession_code / _struct_ref_seq_dif.pdbx_seq_db_seq_num
Revision 1.3Nov 22, 2023Group: Data collection / Database references / 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
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.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Nuclear receptor ROR-gamma
B: Nuclear receptor corepressor 2
C: Nuclear receptor ROR-gamma
D: Nuclear receptor corepressor 2
E: Nuclear receptor ROR-gamma
F: Nuclear receptor corepressor 2
G: Nuclear receptor ROR-gamma
H: Nuclear receptor corepressor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,32812
Polymers129,4178
Non-polymers1,9114
Water1,26170
1
A: Nuclear receptor ROR-gamma
B: Nuclear receptor corepressor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8323
Polymers32,3542
Non-polymers4781
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1350 Å2
ΔGint-9 kcal/mol
Surface area12660 Å2
MethodPISA
2
C: Nuclear receptor ROR-gamma
D: Nuclear receptor corepressor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8323
Polymers32,3542
Non-polymers4781
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1510 Å2
ΔGint-10 kcal/mol
Surface area12540 Å2
MethodPISA
3
E: Nuclear receptor ROR-gamma
F: Nuclear receptor corepressor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8323
Polymers32,3542
Non-polymers4781
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1440 Å2
ΔGint-10 kcal/mol
Surface area12570 Å2
MethodPISA
4
G: Nuclear receptor ROR-gamma
H: Nuclear receptor corepressor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8323
Polymers32,3542
Non-polymers4781
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1440 Å2
ΔGint-10 kcal/mol
Surface area12350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.300, 72.600, 99.320
Angle α, β, γ (deg.)90.00, 89.98, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12A
22E
13A
23G
14B
24D
15B
25F
16B
26H
17C
27E
18C
28G
19D
29F
110D
210H
111E
211G
112F
212H

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERVALVALAA266 - 4936 - 233
21SERSERVALVALCC266 - 4936 - 233
12SERSERVALVALAA266 - 4936 - 233
22SERSERVALVALEE266 - 4936 - 233
13LEULEULEULEUAA267 - 4897 - 229
23LEULEULEULEUGG267 - 4897 - 229
14ASNASNLEULEUBB2347 - 23582 - 13
24ASNASNLEULEUDD2347 - 23582 - 13
15ASNASNLEULEUBB2347 - 23582 - 13
25ASNASNLEULEUFF2347 - 23582 - 13
16ASNASNLEULEUBB2347 - 23582 - 13
26ASNASNLEULEUHH2347 - 23582 - 13
17SERSERVALVALCC266 - 4936 - 233
27SERSERVALVALEE266 - 4936 - 233
18LEULEULEULEUCC267 - 4897 - 229
28LEULEULEULEUGG267 - 4897 - 229
19THRTHRLEULEUDD2346 - 23581 - 13
29THRTHRLEULEUFF2346 - 23581 - 13
110THRTHRGLYGLYDD2346 - 23601 - 15
210THRTHRGLYGLYHH2346 - 23601 - 15
111LEULEULEULEUEE267 - 4897 - 229
211LEULEULEULEUGG267 - 4897 - 229
112THRTHRLEULEUFF2346 - 23581 - 13
212THRTHRLEULEUHH2346 - 23581 - 13

NCS ensembles :
ID
2
1
3
4
5
6
7
8
9
10
11
12

-
Components

#1: Protein
Nuclear receptor ROR-gamma / Nuclear receptor RZR-gamma / Nuclear receptor subfamily 1 group F member 3 / RAR-related orphan ...Nuclear receptor RZR-gamma / Nuclear receptor subfamily 1 group F member 3 / RAR-related orphan receptor C / Retinoid-related orphan receptor-gamma


Mass: 29754.301 Da / Num. of mol.: 4 / Fragment: UNP residues 261-518 / Mutation: K469A,R473A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RORC, NR1F3, RORG, RZRG / Production host: Escherichia coli (E. coli) / References: UniProt: P51449, UniProt: G1RH57*PLUS
#2: Protein/peptide
Nuclear receptor corepressor 2 / N-CoR2 / CTG repeat protein 26 / SMAP270 / Silencing mediator of retinoic acid and thyroid hormone ...N-CoR2 / CTG repeat protein 26 / SMAP270 / Silencing mediator of retinoic acid and thyroid hormone receptor / SMRT / T3 receptor-associating factor / TRAC / Thyroid- / retinoic-acid-receptor-associated corepressor


Mass: 2599.999 Da / Num. of mol.: 4 / Fragment: UNP residues 2346-2367
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NCOR2, CTG26 / Production host: synthetic construct (others) / References: UniProt: Q9Y618
#3: Chemical
ChemComp-82O / (3R,4R)-4-[4-cyclopropyl-5-[3-(2-methylpropyl)cyclobutyl]-1,2,4-triazol-3-yl]-N-(2,4-dimethylphenyl)-1-ethanoyl-pyrrolidine-3-carboxamide


Mass: 477.642 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C28H39N5O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44.32 %
Crystal growTemperature: 299 K / Method: vapor diffusion, sitting drop / Details: 0.1M Hepes pH6.9, 12% PEG6000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jan 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.58
11-h,-k,l20.42
ReflectionResolution: 2.6→29.3 Å / Num. obs: 33867 / % possible obs: 97.2 % / Redundancy: 3.5 % / CC1/2: 0.996 / Rmerge(I) obs: 0.069 / Net I/σ(I): 9.1
Reflection shellResolution: 2.6→2.67 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.588 / Mean I/σ(I) obs: 2 / Num. unique obs: 2475 / CC1/2: 0.787 / % possible all: 97.4

-
Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3L0L

3l0l


Resolution: 2.6→29.31 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.951 / SU B: 8.438 / SU ML: 0.191 / Cross valid method: THROUGHOUT / ESU R Free: 0.066 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2331 1698 5.1 %RANDOM
Rwork0.19864 ---
obs0.20042 31889 95.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 64.673 Å2
Baniso -1Baniso -2Baniso -3
1--38.74 Å2-0 Å2-1.7 Å2
2--61.97 Å20 Å2
3----23.23 Å2
Refinement stepCycle: 1 / Resolution: 2.6→29.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7819 0 140 70 8029
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0198122
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.651.97210943
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6695957
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.75823.163392
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.68151491
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0541568
X-RAY DIFFRACTIONr_chiral_restr0.1160.21190
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026036
X-RAY DIFFRACTIONr_gen_planes_other
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_it7.1496.2123852
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it10.0299.3044801
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it7.9936.564270
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined15.34932378
X-RAY DIFFRACTIONr_long_range_B_other
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)
11A144160.08
12C144160.08
21A145540.09
22E145540.09
31A142480.07
32G142480.07
41B6040.17
42D6040.17
51B6240.1
52F6240.1
61B6180.13
62H6180.13
71C143940.09
72E143940.09
81C141940.08
82G141940.08
91D6440.13
92F6440.13
101D7360.13
102H7360.13
111E143440.08
112G143440.08
121F6500.11
122H6500.11
LS refinement shellResolution: 2.599→2.666 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.55 127 -
Rwork0.566 2304 -
obs--95.26 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more