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- PDB-7qp4: Complex of a Gemini-cholesterol analogue with Retinoid-related Or... -

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Basic information

Entry
Database: PDB / ID: 7qp4
TitleComplex of a Gemini-cholesterol analogue with Retinoid-related Orphan Receptor gamma
Components
  • HIS-VAL-GLU-ARG-LEU-GLN-ILE-PHE-GLN-HIS-LEU-HIS-PRO-ILE-VAL
  • Nuclear receptor ROR-gamma
KeywordsTRANSCRIPTION / Complex / ROR / inverse agonist
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 / 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 ...Nuclear receptor ROR / Retinoid-related orphan receptors, DNA-binding domain / 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
Similarity search - Domain/homology
ACETATE ION / Chem-ECK / Nuclear receptor ROR-gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsRochel, N.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Org Chem Front / Year: 2022
Title: Development of novel Gemini-cholesterol analogues for retinoid-related orphan receptors
Authors: Gomez-Bouzo, U. / Fall, A. / Osz, J. / Fall, Y. / Rochel, N. / Santalla, H.
History
DepositionJan 2, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 14, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nuclear receptor ROR-gamma
B: Nuclear receptor ROR-gamma
P: HIS-VAL-GLU-ARG-LEU-GLN-ILE-PHE-GLN-HIS-LEU-HIS-PRO-ILE-VAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,0819
Polymers61,9003
Non-polymers1,1826
Water3,495194
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3920 Å2
ΔGint-20 kcal/mol
Surface area22860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.381, 99.381, 129.308
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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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: 30014.680 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RORC, NR1F3, RORG, RZRG / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P51449
#2: Protein/peptide HIS-VAL-GLU-ARG-LEU-GLN-ILE-PHE-GLN-HIS-LEU-HIS-PRO-ILE-VAL


Mass: 1870.202 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21(DE3) (bacteria)
#3: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-ECK / (3~{S},8~{S},9~{S},10~{R},13~{R},14~{S},17~{R})-17-[(6~{R})-2,10-dimethyl-2-oxidanyl-undecan-6-yl]-10,13-dimethyl-2,3,4,7,8,9,11,12,14,15,16,17-dodecahydro-1~{H}-cyclopenta[a]phenanthren-3-ol


Mass: 472.786 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C32H56O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 194 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.98 Å3/Da / Density % sol: 58.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.8M NH4 acetate, 0.1M Hepes pH = 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.979957 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 25, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979957 Å / Relative weight: 1
ReflectionResolution: 2.3→40.83 Å / Num. obs: 32145 / % possible obs: 99.17 % / Redundancy: 9.7 % / CC1/2: 0.97 / Net I/σ(I): 8.18
Reflection shellResolution: 2.3→2.382 Å / Num. unique obs: 3197 / CC1/2: 0.124

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Processing

Software
NameVersionClassification
PHENIX1.17_3644refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3L0L

3l0l


Resolution: 2.3→40.83 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 27.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2373 1053 3.3 %random
Rwork0.178 30838 --
obs0.18 31891 99.19 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 187.23 Å2 / Biso mean: 67.4463 Å2 / Biso min: 28.81 Å2
Refinement stepCycle: final / Resolution: 2.3→40.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3836 0 84 194 4114
Biso mean--81.35 67.73 -
Num. residues----468
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3-2.40.381210.3141363494
2.4-2.530.33091320.29053873100
2.53-2.690.29821340.26163897100
2.69-2.90.27731300.22113848100
2.9-3.190.27761270.20123884100
3.19-3.650.24121360.15563889100
3.65-4.60.1961380.13123881100
4.6-40.830.20981350.16213932100
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)
14.01785.1292-3.87578.7401-4.46833.92-0.4831-0.0842-1.1287-0.368-0.229-0.37230.65170.46920.8320.54670.01790.07260.4596-0.00280.5231-40.174-17.0467-3.7403
23.66774.8975-0.1768.647-0.62511.3249-0.07520.2318-0.2443-0.20360.0855-0.6784-0.02260.30510.00840.3480.04070.10870.4316-0.00660.3778-26.36495.4094-13.8512
35.08960.98540.71686.4563-1.39365.0734-0.17950.5255-0.0233-0.39330.09370.51420.1326-0.24780.10630.3767-0.0040.10110.4724-0.04380.3841-44.0797-3.8327-13.2869
45.85610.3142-1.68959.1186-4.99658.62730.1172-0.4750.34120.7180.0611-0.1593-0.3503-0.2435-0.17510.4136-0.0842-0.02170.3572-0.05670.3567-28.904211.9891-5.1522
58.5420.34153.45984.0248-1.19049.1775-0.03540.128-0.052-0.03170.07280.45890.2001-0.6636-0.02820.33820.02620.08980.3328-0.05010.3284-47.7422-7.9222-3.6719
62.93090.9256-1.73147.141-4.88723.669-0.15080.67290.4926-0.53080.53440.4257-0.2299-0.882-0.34020.66130.0711-0.06080.6635-0.04490.5749-40.77196.5461-10.0997
75.5159-4.76326.09944.1765-5.26236.7229-0.5314-0.69181.1670.0831-0.1197-0.7652-0.6352-0.58530.6920.4880.0055-0.08270.4849-0.04750.4481-42.926711.9674-47.41
86.8247-3.06421.1247.3554-2.56444.14630.36460.58140.7957-0.6109-0.8883-1.79460.03480.73080.51760.358-0.02470.04290.5210.11310.5991-19.2411-9.7226-42.4609
98.7858-6.00263.22674.9934-4.29165.8813-0.5701-0.73410.60780.88860.4962-0.7843-0.1774-0.13630.01390.4574-0.0358-0.0280.3636-0.0110.396-32.6128-7.589-32.6682
108.2495-2.2313-2.89114.0327-0.6439.0017-0.1461-0.1330.31360.16760.17040.2854-0.2367-0.68690.01530.3314-0.0376-0.09710.3697-0.00580.3839-44.2631-1.7119-38.1672
118.0539-3.4682.36586.655-5.28248.18940.29140.6753-0.1853-1.0098-0.21590.10030.7106-0.0837-0.07220.52510.055-0.02220.338-0.0320.3946-27.5886-15.1699-46.5549
127.7057-0.9106-1.7353.7552-0.84137.8987-0.01060.1232-0.0616-0.0983-0.02780.2350.0976-0.75660.04560.3145-0.0853-0.04680.3633-0.01630.2836-48.49831.7516-47.6705
132.68250.98440.42322.5848-2.34252.8509-0.0623-0.5524-0.06410.22250.160.77071.1522-0.4472-0.0080.7931-0.1176-0.00530.56170.07120.7121-42.7345-3.1963-58.6926
149.8023-3.93336.00255.985-5.17035.383-0.1498-1.6189-1.3724-0.2510.5570.08610.0153-0.7368-0.31420.9607-0.1653-0.00211.10180.17840.9774-41.8601-17.1745-39.2878
157.19217.31374.82129.01622.76596.06840.8452-1.67890.4271.2616-1.50981.79112.6868-1.52120.39161.2197-0.29220.06971.29460.15620.644-43.3084-3.5052-26.8369
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 265 through 284 )A265 - 284
2X-RAY DIFFRACTION2chain 'A' and (resid 285 through 337 )A285 - 337
3X-RAY DIFFRACTION3chain 'A' and (resid 338 through 368 )A338 - 368
4X-RAY DIFFRACTION4chain 'A' and (resid 369 through 410 )A369 - 410
5X-RAY DIFFRACTION5chain 'A' and (resid 411 through 456 )A411 - 456
6X-RAY DIFFRACTION6chain 'A' and (resid 457 through 497 )A457 - 497
7X-RAY DIFFRACTION7chain 'B' and (resid 264 through 284 )B264 - 284
8X-RAY DIFFRACTION8chain 'B' and (resid 285 through 312 )B285 - 312
9X-RAY DIFFRACTION9chain 'B' and (resid 313 through 337 )B313 - 337
10X-RAY DIFFRACTION10chain 'B' and (resid 338 through 368 )B338 - 368
11X-RAY DIFFRACTION11chain 'B' and (resid 369 through 410 )B369 - 410
12X-RAY DIFFRACTION12chain 'B' and (resid 411 through 456 )B411 - 456
13X-RAY DIFFRACTION13chain 'B' and (resid 457 through 470 )B457 - 470
14X-RAY DIFFRACTION14chain 'B' and (resid 471 through 484 )B471 - 484
15X-RAY DIFFRACTION15chain 'P' and (resid 479 through 493 )P479 - 493

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