[English] 日本語
Yorodumi
- PDB-4wlb: Crystal structure of RORc in complex with a partial inverse agoni... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4wlb
TitleCrystal structure of RORc in complex with a partial inverse agonist compound
Components
  • Nuclear receptor ROR-gamma
  • SRC-1 peptide
KeywordsTRANSCRIPTION / NUCLEAR RECEPTOR LIGAND BINDING DOMAIN
Function / homology
Function and homology information


cellular response to sterol / T-helper 17 cell differentiation / regulation of steroid metabolic process / ligand-activated transcription factor activity / Peyer's patch development / positive regulation of circadian rhythm / T-helper cell differentiation / oxysterol binding / RUNX3 Regulates Immune Response and Cell Migration / negative regulation of thymocyte apoptotic process ...cellular response to sterol / T-helper 17 cell differentiation / regulation of steroid metabolic process / ligand-activated transcription factor activity / Peyer's patch development / positive regulation of circadian rhythm / T-helper cell differentiation / 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 / DNA-binding transcription factor activity, RNA polymerase II-specific / nuclear body / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / 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-3QQ / L(+)-TARTARIC ACID / Nuclear receptor ROR-gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.702 Å
AuthorsBoenig, G. / Hymowitz, S.G. / Kiefer, J.R.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2014
Title: A reversed sulfonamide series of selective RORc inverse agonists.
Authors: van Niel, M.B. / Fauber, B.P. / Cartwright, M. / Gaines, S. / Killen, J.C. / Rene, O. / Ward, S.I. / de Leon Boenig, G. / Deng, Y. / Eidenschenk, C. / Everett, C. / Gancia, E. / Ganguli, A. ...Authors: van Niel, M.B. / Fauber, B.P. / Cartwright, M. / Gaines, S. / Killen, J.C. / Rene, O. / Ward, S.I. / de Leon Boenig, G. / Deng, Y. / Eidenschenk, C. / Everett, C. / Gancia, E. / Ganguli, A. / Gobbi, A. / Hawkins, J. / Johnson, A.R. / Kiefer, J.R. / La, H. / Lockey, P. / Norman, M. / Ouyang, W. / Qin, A. / Wakes, N. / Waszkowycz, B. / Wong, H.
History
DepositionOct 7, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 12, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 17, 2014Group: Database references
Revision 1.2Nov 22, 2017Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_database_status / pdbx_entity_src_syn / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Nuclear receptor ROR-gamma
B: Nuclear receptor ROR-gamma
D: SRC-1 peptide
E: SRC-1 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,8678
Polymers63,5694
Non-polymers1,2974
Water7,656425
1
A: Nuclear receptor ROR-gamma
D: SRC-1 peptide
hetero molecules

B: Nuclear receptor ROR-gamma
E: SRC-1 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,8678
Polymers63,5694
Non-polymers1,2974
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_565x,y+1,z1
Buried area3590 Å2
ΔGint-27 kcal/mol
Surface area23900 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4910 Å2
ΔGint-23 kcal/mol
Surface area22570 Å2
MethodPISA
3
A: Nuclear receptor ROR-gamma
D: SRC-1 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5835
Polymers31,7852
Non-polymers7993
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1190 Å2
ΔGint-8 kcal/mol
Surface area12480 Å2
MethodPISA
4
B: Nuclear receptor ROR-gamma
E: SRC-1 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2833
Polymers31,7852
Non-polymers4991
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1090 Å2
ΔGint-9 kcal/mol
Surface area12730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.787, 86.258, 91.854
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Detailsbiological unit is the same as asym.

-
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: 30853.502 Da / Num. of mol.: 2 / Fragment: ROR-gamma ligand binding domain
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 SRC-1 peptide


Mass: 931.172 Da / Num. of mol.: 2 / Fragment: SRC-1 peptide / Source method: obtained synthetically / Details: Synthetic peptide / Source: (synth.) Homo sapiens (human)
#3: Chemical ChemComp-3QQ / N-(4-fluorobenzyl)-N-(2-methylpropyl)-6-{[1-(methylsulfonyl)piperidin-4-yl]amino}pyridine-3-sulfonamide


Mass: 498.634 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H31FN4O4S2
#4: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O6
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 425 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.23 Å3/Da / Density % sol: 44.74 %
Crystal growTemperature: 291 K / Method: vapor diffusion / Details: PEG 3350, Sodium formate

-
Data collection

DiffractionMean temperature: 193 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 18, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→45 Å / Num. obs: 62573 / % possible obs: 97.4 % / Redundancy: 4 % / Biso Wilson estimate: 15.93 Å2 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.047 / Rrim(I) all: 0.097 / Χ2: 1.037 / Net I/av σ(I): 14.67 / Net I/σ(I): 8.2 / Num. measured all: 248553
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.65-1.682.40.76625920.3970.5660.9590.47682.3
1.68-1.712.60.71527550.4670.5030.8820.48887.2
1.71-1.742.80.66329230.5420.4480.8070.5692.4
1.74-1.783.10.61130920.6120.3930.7320.55396.8
1.78-1.823.70.55331460.720.3210.6430.59499.5
1.82-1.864.30.53231820.7590.2880.6060.59399.8
1.86-1.93.80.50431390.9250.2870.5820.75698.6
1.9-1.963.90.37931390.8150.2090.4351.598.7
1.96-2.014.40.28431660.9220.1520.3240.81499.7
2.01-2.084.20.26631540.9150.1440.3041.2999.5
2.08-2.154.30.1832160.9720.0970.2050.82199.7
2.15-2.244.10.14931190.9810.0810.170.95398.4
2.24-2.3440.15431270.960.0860.1771.59697.1
2.34-2.464.50.09632120.9930.050.1090.8899.9
2.46-2.624.40.0932080.9910.0480.1031.00399.8
2.62-2.824.50.07332040.9940.0390.0831.0299.6
2.82-3.114.50.05532470.9970.0290.0631.01999.9
3.11-3.554.50.05432390.9960.0280.0621.66399.3
3.55-4.484.30.04432680.9970.0230.051.82399.1
4.48-454.40.03334450.9980.0170.0371.14699.4

-
Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.702→39.04 Å / FOM work R set: 0.8462 / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 22.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2263 5427 10.08 %
Rwork0.1777 48387 -
obs0.1825 53814 91.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 105.39 Å2 / Biso mean: 21.63 Å2 / Biso min: 3.24 Å2
Refinement stepCycle: final / Resolution: 1.702→39.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4148 0 86 425 4659
Biso mean--24.74 27.9 -
Num. residues----512
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074396
X-RAY DIFFRACTIONf_angle_d1.0345945
X-RAY DIFFRACTIONf_chiral_restr0.037652
X-RAY DIFFRACTIONf_plane_restr0.004752
X-RAY DIFFRACTIONf_dihedral_angle_d14.8041633
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7015-1.72090.3548690.256747254128
1.7209-1.74110.302720.233869176340
1.7411-1.76230.30851110.2263954106554
1.7623-1.78460.2631290.21541169129868
1.7846-1.80810.2661770.21631438161583
1.8081-1.83290.24961810.23361652183395
1.8329-1.85910.27692130.2541667188097
1.8591-1.88680.31421820.26381697187998
1.8868-1.91630.412020.34881654185694
1.9163-1.94770.37071660.2911684185096
1.9477-1.98130.28912320.20291674190699
1.9813-2.01730.23031960.183917641960100
2.0173-2.05610.23931940.193417261920100
2.0561-2.09810.26091860.20871781196799
2.0981-2.14370.22471800.17817471927100
2.1437-2.19360.21892000.171717511951100
2.1936-2.24840.27631860.21111710189697
2.2484-2.30920.29641700.19771688185896
2.3092-2.37720.17951990.149717721971100
2.3772-2.45390.21541990.144417421941100
2.4539-2.54160.21631790.156717871966100
2.5416-2.64330.21182000.158117711971100
2.6433-2.76360.22092020.166317371939100
2.7636-2.90920.21521970.164717911988100
2.9092-3.09140.21672130.172417581971100
3.0914-3.330.1952170.163217711988100
3.33-3.66490.18591840.15461789197399
3.6649-4.19470.18721730.13711836200999
4.1947-5.28280.14822000.13181800200099
5.2828-39.050.22732180.182119142132100
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)
12.02470.2257-0.11234.3470.2190.3823-0.05220.1120.381-0.50620.0953-0.4134-0.1479-0.0064-0.01950.1363-0.01270.03180.11870.02390.1271-13.137730.2731-20.4084
20.618-0.31220.3161.0145-0.09980.7969-0.02350.0039-0.0496-0.16810.0240.19360.1925-0.10720.00470.1098-0.0285-0.00080.1077-0.02650.0836-23.88562.619-12.2264
32.01240.27560.65571.6850.32910.9799-0.05870.1374-0.07590.02260.0393-0.316-0.01370.08860.05050.049-0.0155-0.01570.0750.0090.0884-10.283217.2138-9.8263
41.06860.01480.01561.36540.30950.9534-0.05460.0222-0.022-0.00820.00690.17980.1288-0.20780.04730.0888-0.03180.02210.1159-0.03180.0859-30.15367.3783-4.3917
52.034-0.37610.43281.4143-0.17220.6217-0.1095-0.01130.2860.08050.0251-0.1479-0.0419-0.01740.06580.0895-0.0063-0.03640.0730.01420.1019-14.317127.6877-9.7864
61.7062-1.11331.3512.9251-1.92814.0707-0.1013-0.22430.24290.31980.17490.28130.0662-0.19290.06120.09530.0125-0.02340.1160.02140.1921-26.679929.4416-6.3582
70.2785-0.5215-0.15482.0630.40311.0538-0.1128-0.01010.07780.55640.1447-0.6360.36250.03070.06550.19190.041-0.05890.13610.0162-0.0233-12.45482.44490.8923
81.2527-0.75940.44364.7332-0.41321.03190.1716-0.0813-0.23580.6789-0.01810.0930.17940.0382-0.24370.2266-0.0101-0.03670.10320.0260.1159-18.5609-36.7651-4.9148
91.06050.04390.75011.9558-0.49880.8682-0.17520.04970.03350.08370.33470.6323-0.0425-0.3133-0.06390.10950.01140.04450.17870.0610.2547-28.5601-7.7739-20.9207
100.89360.44370.26763.215-1.08421.10120.0071-0.05350.04690.3070.0057-0.0536-0.0523-0.0739-0.06820.1008-0.0091-0.010.0938-0.01630.0514-14.5526-10.5586-13.6
112.3350.3767-0.04271.5235-0.03220.59870.09820.1038-0.75610.3193-0.1023-0.59630.11280.1371-0.12350.1341-0.0002-0.13470.02230.09930.2889-9.8059-24.0624-11.2264
121.31480.3990.38411.7116-0.17760.2556-0.06420.17330.0329-0.35930.13510.24320.01420.0108-0.04940.1397-0.0169-0.03240.1260.00960.091-22.2991-13.9276-27.6464
133.29650.74590.12732.3048-0.02151.1918-0.21370.0146-0.2818-0.28090.2439-0.89250.00680.1392-0.2514-0.1155-0.0189-0.07160.08870.00390.3293-12.7441-30.2357-14.9412
141.8603-0.18520.6521.6421-0.2131.5261-0.0603-0.1019-0.04680.0849-0.0124-0.78820.26910.055-0.35270.09870.012-0.06810.06510.03090.3652-13.2326-39.3696-12.1073
153.01872.2504-1.29533.1123-1.05052.13540.32260.1534-0.2381-0.41460.0287-0.3473-0.16540.13730.07190.1879-0.0080.04140.1095-0.01420.1707-19.8279-36.1496-24.2931
160.5645-0.2849-0.29751.7555-0.0111.4037-0.09250.0667-0.0914-0.090.1649-0.591-0.06990.202-0.02750.0934-0.03450.04660.1649-0.02260.1208-5.052-9.1493-21.2433
173.4258-1.09592.03244.47080.31982.88160.32570.12480.366-0.2382-0.1304-0.6216-0.10590.18790.01140.1852-0.02350.05810.1722-0.04310.2542-0.09799.4259-12.911
183.864-0.1081-1.00284.5281-0.96483.47460.169-0.3174-0.02550.4586-0.0048-0.64970.41540.09450.07580.3648-0.0226-0.13750.23190.00820.2088-3.7953-16.1074-2.8942
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 239 through 263 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 264 through 316 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 317 through 347 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 348 through 389 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 390 through 435 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 436 through 449 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 450 through 486 )A0
8X-RAY DIFFRACTION8chain 'B' and (resid 239 through 263 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 264 through 291 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 292 through 316 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 317 through 347 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 348 through 389 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 390 through 414 )B0
14X-RAY DIFFRACTION14chain 'B' and (resid 415 through 435 )B0
15X-RAY DIFFRACTION15chain 'B' and (resid 436 through 449 )B0
16X-RAY DIFFRACTION16chain 'B' and (resid 450 through 486 )B0
17X-RAY DIFFRACTION17chain 'D' and (resid 8 through 15 )D0
18X-RAY DIFFRACTION18chain 'E' and (resid 8 through 15 )E0

+
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