[English] 日本語
Yorodumi
- PDB-5ntn: Structural states of RORgt: X-ray elucidation of molecular mechan... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ntn
TitleStructural states of RORgt: X-ray elucidation of molecular mechanisms and binding interactions for natural and synthetic compounds
Components
  • Nuclear receptor ROR-gamma
  • Nuclear receptor-interacting protein 1
KeywordsSIGNALING PROTEIN / nuclear hormone receptor / ligand-binding domain / agonist
Function / homology
Function and homology information


ovarian follicle rupture / NR1H2 & NR1H3 regulate gene expression linked to gluconeogenesis / nuclear glucocorticoid receptor binding / cellular response to sterol / T-helper 17 cell differentiation / ligand-activated transcription factor activity / regulation of steroid metabolic process / NR1H2 & NR1H3 regulate gene expression linked to lipogenesis / lipid storage / Peyer's patch development ...ovarian follicle rupture / NR1H2 & NR1H3 regulate gene expression linked to gluconeogenesis / nuclear glucocorticoid receptor binding / cellular response to sterol / T-helper 17 cell differentiation / ligand-activated transcription factor activity / regulation of steroid metabolic process / NR1H2 & NR1H3 regulate gene expression linked to lipogenesis / lipid storage / Peyer's patch development / positive regulation of circadian rhythm / T-helper cell differentiation / RUNX3 Regulates Immune Response and Cell Migration / oxysterol binding / negative regulation of thymocyte apoptotic process / regulation of fat cell differentiation / histone deacetylase complex / regulation of glucose metabolic process / lymph node development / adipose tissue development / nuclear retinoid X receptor binding / xenobiotic metabolic process / SUMOylation of transcription cofactors / cellular response to estradiol stimulus / nuclear receptor binding / nuclear estrogen receptor binding / circadian regulation of gene expression / Heme signaling / DNA-binding transcription repressor activity, RNA polymerase II-specific / fibrillar center / histone deacetylase binding / Nuclear Receptor transcription pathway / circadian rhythm / nuclear receptor activity / transcription corepressor activity / sequence-specific double-stranded DNA binding / Circadian Clock / Interleukin-4 and Interleukin-13 signaling / Estrogen-dependent gene expression / transcription coactivator activity / nuclear body / DNA-binding transcription factor activity, RNA polymerase II-specific / nuclear speck / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / signaling receptor binding / chromatin / regulation of transcription by RNA polymerase II / nucleolus / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / 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 / Nuclear receptor ROR ...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 / 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-98H / Nuclear receptor-interacting protein 1 / Nuclear receptor ROR-gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsKallen, J.
CitationJournal: ChemMedChem / Year: 2017
Title: Structural States of ROR gamma t: X-ray Elucidation of Molecular Mechanisms and Binding Interactions for Natural and Synthetic Compounds.
Authors: Kallen, J. / Izaac, A. / Be, C. / Arista, L. / Orain, D. / Kaupmann, K. / Guntermann, C. / Hoegenauer, K. / Hintermann, S.
History
DepositionApr 28, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 21, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 19, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_volume ..._citation.country / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Jan 17, 2024Group: 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
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
B: Nuclear receptor ROR-gamma
C: Nuclear receptor ROR-gamma
D: Nuclear receptor ROR-gamma
P: Nuclear receptor-interacting protein 1
Q: Nuclear receptor-interacting protein 1
R: Nuclear receptor-interacting protein 1
S: Nuclear receptor-interacting protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,05412
Polymers128,2368
Non-polymers1,8194
Water11,764653
1
A: Nuclear receptor ROR-gamma
P: Nuclear receptor-interacting protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5143
Polymers32,0592
Non-polymers4551
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area890 Å2
ΔGint-9 kcal/mol
Surface area12570 Å2
MethodPISA
2
B: Nuclear receptor ROR-gamma
Q: Nuclear receptor-interacting protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5143
Polymers32,0592
Non-polymers4551
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area940 Å2
ΔGint-8 kcal/mol
Surface area12600 Å2
MethodPISA
3
C: Nuclear receptor ROR-gamma
R: Nuclear receptor-interacting protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5143
Polymers32,0592
Non-polymers4551
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area910 Å2
ΔGint-8 kcal/mol
Surface area12580 Å2
MethodPISA
4
D: Nuclear receptor ROR-gamma
S: Nuclear receptor-interacting protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5143
Polymers32,0592
Non-polymers4551
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area970 Å2
ΔGint-8 kcal/mol
Surface area12660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.238, 69.684, 97.208
Angle α, β, γ (deg.)90.000, 107.940, 90.000
Int Tables number4
Space group name H-MP1211

-
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: 29739.316 Da / Num. of mol.: 4 / Fragment: C-terminal domain, ligand binding domain / Mutation: C455S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RORC, NR1F3, RORG, RZRG / Plasmid: pET28-derived vector / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P51449
#2: Protein/peptide
Nuclear receptor-interacting protein 1 / Nuclear factor RIP140 / Receptor-interacting protein 140


Mass: 2319.615 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P48552
#3: Chemical
ChemComp-98H / (5R,10S,13R,14R,17R)-17-((R,E)-7-hydroxy-6-methylhept-5-en-2-yl)-4,4,10,13,14-pentamethyl-1,2,5,6,10,11,12,13,14,15,16,17-dodecahydro-3H-cyclopenta[a]phenanthrene-3,7(4H)-dione


Mass: 454.684 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C30H46O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 653 / 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: 2.17 Å3/Da / Density % sol: 43.24 % / Mosaicity: 0.584 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 14% PEG 3350, 0.04M NaFormate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.90013 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 28, 2008
RadiationMonochromator: SI 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.90013 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 77514 / % possible obs: 89.2 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.058 / Χ2: 1.048 / Net I/σ(I): 13.4 / Num. measured all: 280258
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsΧ2Diffraction-ID% possible all
1.9-1.972.20.2490.647143
1.97-2.052.50.2220.711165.7
2.05-2.142.90.1910.784187.8
2.14-2.253.40.160.818198.4
2.25-2.393.90.1310.791199.8
2.39-2.584.10.0990.7991100
2.58-2.844.10.0830.997199.9
2.84-3.254.10.0661.279199.8
3.25-4.083.90.0381.317199.2
4.08-203.70.0291.669197.9

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHASERphasing
REFMAC5refinement
PDB_EXTRACT3.22data extraction
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1s0x

1s0x


Resolution: 1.9→19.92 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.934 / SU B: 3.339 / SU ML: 0.099 / SU R Cruickshank DPI: 0.1982 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.198 / ESU R Free: 0.159
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2253 3880 5 %RANDOM
Rwork0.2 ---
obs0.2013 73461 89.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 71.61 Å2 / Biso mean: 28.5 Å2 / Biso min: 12.31 Å2
Baniso -1Baniso -2Baniso -3
1--1.92 Å20 Å20.4 Å2
2--1.19 Å20 Å2
3---0.49 Å2
Refinement stepCycle: final / Resolution: 1.9→19.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8256 0 132 653 9041
Biso mean--22.97 35.65 -
Num. residues----1011
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0218608
X-RAY DIFFRACTIONr_angle_refined_deg0.9311.97611652
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.151019
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.81523.116414
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.759151563
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7011568
X-RAY DIFFRACTIONr_chiral_restr0.0620.21298
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.026394
LS refinement shellResolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 134 -
Rwork0.269 2468 -
all-2602 -
obs--41.2 %

+
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