[English] 日本語
Yorodumi
- PDB-6nwt: RORgamma Ligand Binding Domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6nwt
TitleRORgamma Ligand Binding Domain
ComponentsNuclear receptor ROR-gamma
KeywordsNUCLEAR PROTEIN / Orphan Nuclear Receptor / synthetic modulator / chemical probe
Function / homology
Function and homology information


T-helper 17 cell differentiation / ligand-activated transcription factor activity / cellular response to sterol / regulation of steroid metabolic process / Peyer's patch development / T-helper cell differentiation / positive regulation of circadian rhythm / oxysterol binding / RUNX3 Regulates Immune Response and Cell Migration / negative regulation of thymocyte apoptotic process ...T-helper 17 cell differentiation / ligand-activated transcription factor activity / cellular response to sterol / regulation of steroid metabolic process / Peyer's patch development / T-helper cell differentiation / positive regulation of circadian rhythm / oxysterol binding / RUNX3 Regulates Immune Response and Cell Migration / negative regulation of thymocyte apoptotic process / regulation of fat cell differentiation / regulation of glucose metabolic process / lymph node development / adipose tissue development / xenobiotic metabolic process / circadian regulation of gene expression / DNA-binding transcription repressor activity, RNA polymerase II-specific / Nuclear Receptor transcription pathway / nuclear receptor activity / sequence-specific double-stranded DNA binding / Interleukin-4 and Interleukin-13 signaling / nuclear body / 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 / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
Nuclear receptor ROR / Retinoid-related orphan receptors, DNA-binding domain / Retinoid X Receptor / Retinoid X 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 receptor ROR / Retinoid-related orphan receptors, DNA-binding domain / Retinoid X Receptor / Retinoid X 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-L7P / Nuclear receptor ROR-gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsStrutzenberg, T.S. / Park, H. / Griffin, P.R.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01CA206493 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)F31GM126842 United States
CitationJournal: Elife / Year: 2019
Title: HDX-MS reveals structural determinants for ROR gamma hyperactivation by synthetic agonists.
Authors: Strutzenberg, T.S. / Garcia-Ordonez, R.D. / Novick, S.J. / Park, H. / Chang, M.R. / Doebellin, C. / He, Y. / Patouret, R. / Kamenecka, T.M. / Griffin, P.R.
History
DepositionFeb 7, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Nuclear receptor ROR-gamma
C: Nuclear receptor ROR-gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,0134
Polymers56,9582
Non-polymers1,0552
Water2,054114
1
A: Nuclear receptor ROR-gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0062
Polymers28,4791
Non-polymers5271
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Nuclear receptor ROR-gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0062
Polymers28,4791
Non-polymers5271
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)99.590, 99.590, 129.600
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

-
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: 28478.979 Da / Num. of mol.: 2 / Fragment: ligand binding domain (UNP residues 265-507)
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
#2: Chemical ChemComp-L7P / 1,1,1,3,3,3-hexafluoro-2-[2-fluoro-4'-({4-[(pyridin-4-yl)methyl]piperazin-1-yl}methyl)[1,1'-biphenyl]-4-yl]propan-2-ol


Mass: 527.477 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H24F7N3O
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 114 / 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: 3.27 Å3/Da / Density % sol: 62.35 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 100-250 mM ammonium sulfate, 10-25% PEG3350, 100 mM Tris, pH 8.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97741 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 23, 2016
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
ReflectionResolution: 2.35→28.75 Å / Num. obs: 30310 / % possible obs: 99.82 % / Redundancy: 2 % / Net I/σ(I): 21.07
Reflection shellResolution: 2.35→28.75 Å

-
Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
iMOSFLMdata reduction
pointlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4QM0

4qm0


Resolution: 2.35→29.121 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2137 1563 5.16 %
Rwork0.1806 --
obs0.1823 30294 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.35→29.121 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3795 0 74 114 3983
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043951
X-RAY DIFFRACTIONf_angle_d0.6265329
X-RAY DIFFRACTIONf_dihedral_angle_d18.4262368
X-RAY DIFFRACTIONf_chiral_restr0.034572
X-RAY DIFFRACTIONf_plane_restr0.003673
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3503-2.42610.24751430.20122614X-RAY DIFFRACTION100
2.4261-2.51280.23731510.2042589X-RAY DIFFRACTION100
2.5128-2.61330.26551140.2032632X-RAY DIFFRACTION100
2.6133-2.73220.26881280.20262616X-RAY DIFFRACTION100
2.7322-2.87610.24591280.19022621X-RAY DIFFRACTION100
2.8761-3.05610.23511650.19762577X-RAY DIFFRACTION100
3.0561-3.29180.23891490.20292613X-RAY DIFFRACTION100
3.2918-3.62250.25291680.18462590X-RAY DIFFRACTION100
3.6225-4.14540.17431190.16572637X-RAY DIFFRACTION100
4.1454-5.21790.19261310.15532619X-RAY DIFFRACTION99
5.2179-29.12340.17591670.17662623X-RAY DIFFRACTION100
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)
13.30432.2165-1.58794.4474-0.53491.4134-0.1957-0.0152-0.322-0.0937-0.017-0.28610.16340.13720.18330.28860.03390.02740.28560.05070.2555-34.0652-1.831915.7613
22.10211.9194-1.89483.6418-1.22471.97560.0696-0.17960.06170.2589-0.22290.1067-0.0210.12040.14060.30110.02870.03540.34670.00580.2808-39.22850.504723.518
30.86920.8704-0.31491.5703-0.51021.1669-0.02740.55060.331-0.13230.13360.2314-0.17210.0940.01260.44330.11280.0490.76420.17390.5586-40.8126.176717.9485
43.1993-2.78773.5973.9906-2.33074.6683-0.4960.11881.50150.2375-0.7113-0.6211-0.79930.0920.91310.54690.027-0.19570.3820.0070.598-42.346112.3332-19.2475
52.995-3.21270.64576.5185-0.7970.5276-0.06170.16350.2490.2479-0.1622-0.6995-0.12330.2370.19730.3039-0.0184-0.04210.3540.05510.3369-26.0436-8.5499-9.7696
61.8746-1.58671.5482.0942-1.29351.65510.0930.0146-0.1049-0.0625-0.11140.0160.1013-0.07190.02830.2482-0.0409-0.0220.26830.03730.2554-40.4937-4.5782-17.0506
72.3596-0.72650.35491.00750.05082.3515-0.0237-0.7732-0.40740.28540.02310.32840.9748-0.3435-0.05360.7832-0.15430.0550.75150.1310.5371-42.9857-7.7946-13.1572
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 265 through 368 )
2X-RAY DIFFRACTION2chain 'A' and (resid 369 through 456 )
3X-RAY DIFFRACTION3chain 'A' and (resid 457 through 497 )
4X-RAY DIFFRACTION4chain 'C' and (resid 265 through 284 )
5X-RAY DIFFRACTION5chain 'C' and (resid 285 through 337 )
6X-RAY DIFFRACTION6chain 'C' and (resid 338 through 456 )
7X-RAY DIFFRACTION7chain 'C' and (resid 457 through 509 )

+
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