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- PDB-6a22: Ternary complex of Human ROR gamma Ligand Binding Domain With Com... -

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Basic information

Entry
Database: PDB / ID: 6a22
TitleTernary complex of Human ROR gamma Ligand Binding Domain With Compound T.
Components
  • Nuclear receptor ROR-gamma
  • Nuclear receptor corepressor 2
KeywordsNUCLEAR PROTEIN/INHIBITOR / Ternary Complex / Nuclear Receptor / NUCLEAR PROTEIN / NUCLEAR PROTEIN-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 MECP2 expression and activity / regulation of glucose metabolic process / 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 / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / histone deacetylase binding / 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 / Homeobox-like domain superfamily / 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
Chem-9P6 / Nuclear receptor ROR-gamma / Nuclear receptor corepressor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsNoguchi, M. / Nomura, A. / Doi, S. / Yamaguchi, K. / Adachi, T.
CitationJournal: Sci Rep / Year: 2018
Title: Ternary crystal structure of human ROR gamma ligand-binding-domain, an inhibitor and corepressor peptide provides a new insight into corepressor interaction
Authors: Noguchi, M. / Nomura, A. / Doi, S. / Yamaguchi, K. / Hirata, K. / Shiozaki, M. / Maeda, K. / Hirashima, S. / Kotoku, M. / Yamaguchi, T. / Katsuda, Y. / Crowe, P. / Tao, H. / Thacher, S. / Adachi, T.
History
DepositionJun 8, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 12, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)131,29212
Polymers129,4178
Non-polymers1,8744
Water1,63991
1
A: Nuclear receptor ROR-gamma
B: Nuclear receptor corepressor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8233
Polymers32,3542
Non-polymers4691
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1440 Å2
ΔGint-11 kcal/mol
Surface area12840 Å2
MethodPISA
2
C: Nuclear receptor ROR-gamma
D: Nuclear receptor corepressor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8233
Polymers32,3542
Non-polymers4691
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1230 Å2
ΔGint-10 kcal/mol
Surface area12750 Å2
MethodPISA
3
E: Nuclear receptor ROR-gamma
F: Nuclear receptor corepressor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8233
Polymers32,3542
Non-polymers4691
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1140 Å2
ΔGint-11 kcal/mol
Surface area12360 Å2
MethodPISA
4
G: Nuclear receptor ROR-gamma
H: Nuclear receptor corepressor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8233
Polymers32,3542
Non-polymers4691
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1350 Å2
ΔGint-11 kcal/mol
Surface area12770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.926, 73.277, 100.204
Angle α, β, γ (deg.)90.00, 89.99, 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
16C
26E
17C
27G
18D
28F
19D
29H
110E
210G
111F
211H

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
11SERSERILEILEAA266 - 4926 - 232
21SERSERILEILECC266 - 4926 - 232
12SERSERILEILEAA266 - 4926 - 232
22SERSERILEILEEE266 - 4926 - 232
13SERSERILEILEAA266 - 4926 - 232
23SERSERILEILEGG266 - 4926 - 232
14GLYGLYMETMETBB2349 - 23594 - 14
24GLYGLYMETMETDD2349 - 23594 - 14
15GLYGLYMETMETBB2349 - 23594 - 14
25GLYGLYMETMETFF2349 - 23594 - 14
16SERSERVALVALCC266 - 4936 - 233
26SERSERVALVALEE266 - 4936 - 233
17SERSERVALVALCC266 - 4936 - 233
27SERSERVALVALGG266 - 4936 - 233
18GLYGLYGLYGLYDD2349 - 23604 - 15
28GLYGLYGLYGLYFF2349 - 23604 - 15
19GLYGLYMETMETDD2349 - 23594 - 14
29GLYGLYMETMETHH2349 - 23594 - 14
110SERSERVALVALEE266 - 4936 - 233
210SERSERVALVALGG266 - 4936 - 233
111GLYGLYMETMETFF2349 - 23594 - 14
211GLYGLYMETMETHH2349 - 23594 - 14

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

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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
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: 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: Escherichia coli (E. coli) / References: UniProt: Q9Y618
#3: Chemical
ChemComp-9P6 / 2-[2-[1-~{tert}-butyl-5-(4-methoxyphenyl)pyrazol-4-yl]-1,3-thiazol-4-yl]-~{N}-(oxan-4-ylmethyl)ethanamide


Mass: 468.612 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C25H32N4O3S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 2.21 Å3/Da / Density % sol: 44.36 %
Crystal growTemperature: 299 K / Method: vapor diffusion, sitting drop / Details: 0.1M Hepes pH6.9, 12% PEG6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9787 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 4, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.54
11-h,-k,l20.46
ReflectionResolution: 2.55→77.93 Å / Num. obs: 35566 / % possible obs: 96.2 % / Redundancy: 3.8 % / Rsym value: 0.064 / Net I/av σ(I): 8.5 / Net I/σ(I): 8.5
Reflection shellResolution: 2.55→2.62 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 2.4 / Num. unique obs: 2198 / Rsym value: 0.562 / % possible all: 79.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5X8X

5x8x


Resolution: 2.55→77.93 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.936 / SU B: 8.825 / SU ML: 0.2 / Cross valid method: THROUGHOUT / ESU R: 0.227 / ESU R Free: 0.065 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24283 1876 5.1 %RANDOM
Rwork0.21744 ---
obs0.21883 34576 98.3 %-
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: 65.332 Å2
Baniso -1Baniso -2Baniso -3
1--42 Å2-0 Å22.71 Å2
2--69.05 Å20 Å2
3----27.05 Å2
Refinement stepCycle: 1 / Resolution: 2.55→77.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7843 0 132 91 8066
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0128152
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8721.64910977
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.9035965
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.03321.176459
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.204151492
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7761568
X-RAY DIFFRACTIONr_chiral_restr0.1090.21016
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.025996
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_it7.3626.353878
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it10.5069.5024837
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it8.0486.5694274
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined14.79284.28312000
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)
11A69140.14
12C69140.14
21A69570.14
22E69570.14
31A68930.15
32G68930.15
41B2450.29
42D2450.29
51B2520.28
52F2520.28
61C69280.14
62E69280.14
71C68820.15
72G68820.15
81D2650.22
82F2650.22
91D2470.22
92H2470.22
101E69220.15
102G69220.15
111F2630.18
112H2630.18
LS refinement shellResolution: 2.55→2.616 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.624 131 -
Rwork0.527 2543 -
obs--97.63 %

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