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- PDB-5lwe: Crystal structure of the human CC chemokine receptor type 9 (CCR9... -

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Basic information

Entry
Database: PDB / ID: 5lwe
TitleCrystal structure of the human CC chemokine receptor type 9 (CCR9) in complex with vercirnon
ComponentsC-C chemokine receptor type 9
KeywordsMEMBRANE PROTEIN
Function / homology
Function and homology information


CD8-positive, gamma-delta intraepithelial T cell differentiation / chemokine receptor activity / C-C chemokine receptor activity / C-C chemokine binding / Chemokine receptors bind chemokines / plasma membrane => GO:0005886 / cellular defense response / viral process / cell chemotaxis / calcium-mediated signaling ...CD8-positive, gamma-delta intraepithelial T cell differentiation / chemokine receptor activity / C-C chemokine receptor activity / C-C chemokine binding / Chemokine receptors bind chemokines / plasma membrane => GO:0005886 / cellular defense response / viral process / cell chemotaxis / calcium-mediated signaling / chemotaxis / positive regulation of cytosolic calcium ion concentration / G alpha (i) signalling events / immune response / G protein-coupled receptor signaling pathway / external side of plasma membrane / cell surface / plasma membrane
Similarity search - Function
CC chemokine receptor 9 / Chemokine receptor family / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Vercirnon / CHOLESTEROL / MALONATE ION / OLEIC ACID / C-C chemokine receptor type 9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsOswald, C. / Rappas, M. / Kean, J. / Dore, A.S. / Errey, J.C. / Bennett, K. / Deflorian, F. / Christopher, J.A. / Jazayeri, A. / Mason, J.S. ...Oswald, C. / Rappas, M. / Kean, J. / Dore, A.S. / Errey, J.C. / Bennett, K. / Deflorian, F. / Christopher, J.A. / Jazayeri, A. / Mason, J.S. / Congreve, M. / Cooke, R.M. / Marshall, F.H.
CitationJournal: Nature / Year: 2016
Title: Intracellular allosteric antagonism of the CCR9 receptor.
Authors: Oswald, C. / Rappas, M. / Kean, J. / Dore, A.S. / Errey, J.C. / Bennett, K. / Deflorian, F. / Christopher, J.A. / Jazayeri, A. / Mason, J.S. / Congreve, M. / Cooke, R.M. / Marshall, F.H.
History
DepositionSep 16, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 7, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2016Group: Database references
Revision 1.2Dec 28, 2016Group: Database references
Revision 1.3Oct 16, 2019Group: Data collection / Category: reflns / Item: _reflns.pdbx_CC_half
Revision 1.4Jan 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: C-C chemokine receptor type 9
B: C-C chemokine receptor type 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,14535
Polymers75,7562
Non-polymers9,39033
Water93752
1
A: C-C chemokine receptor type 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,04819
Polymers37,8781
Non-polymers5,17118
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: C-C chemokine receptor type 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,09716
Polymers37,8781
Non-polymers4,21915
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.571, 66.197, 68.424
Angle α, β, γ (deg.)74.02, 64.72, 62.29
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein C-C chemokine receptor type 9 / CCR-9 / G-protein coupled receptor 28 / GPR-9-6


Mass: 37877.879 Da / Num. of mol.: 2
Mutation: T34E, T77A, V79A, M82A, S141C, T216A, V255A, N294A, T304A, C337A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCR9, GPR28 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P51686

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Non-polymers , 5 types, 85 molecules

#2: Chemical ChemComp-79K / Vercirnon


Mass: 444.931 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H21ClN2O4S
#3: Chemical...
ChemComp-OLA / OLEIC ACID / Oleic acid


Mass: 282.461 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: C18H34O2
#4: Chemical ChemComp-CLR / CHOLESTEROL / Cholesterol


Mass: 386.654 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H46O
#5: Chemical ChemComp-MLI / MALONATE ION / Malonic acid


Mass: 102.046 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H2O4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 10

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Sample preparation

CrystalDensity Matthews: 2.98 Å3/Da / Density % sol: 58.81 % / Description: ROD SHAPED
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 8 / Details: 0.1 M BICINE 0.2 M SODIUM MALONATE 28-43% PEG400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96863 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 24, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96863 Å / Relative weight: 1
ReflectionResolution: 2.8→58.34 Å / Num. obs: 21320 / % possible obs: 98.9 % / Redundancy: 3.7 % / Biso Wilson estimate: 49.97 Å2 / CC1/2: 0.98 / Rsym value: 0.162 / Net I/σ(I): 5.6
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.887 / Mean I/σ(I) obs: 1.7 / CC1/2: 0.51 / % possible all: 98.3

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MBS

4mbs


Resolution: 2.8→19.974 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 24.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2427 1133 5.33 %Random selection
Rwork0.2153 ---
obs0.2167 21254 98.89 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→19.974 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4453 0 536 52 5041
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025090
X-RAY DIFFRACTIONf_angle_d0.496787
X-RAY DIFFRACTIONf_dihedral_angle_d10.5462744
X-RAY DIFFRACTIONf_chiral_restr0.035767
X-RAY DIFFRACTIONf_plane_restr0.003794
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8004-2.92750.30521450.28462507X-RAY DIFFRACTION98
2.9275-3.08130.29141660.26022514X-RAY DIFFRACTION100
3.0813-3.27360.26421190.24172548X-RAY DIFFRACTION99
3.2736-3.5250.28311640.22062506X-RAY DIFFRACTION99
3.525-3.87740.24161460.20682521X-RAY DIFFRACTION99
3.8774-4.43320.19991260.18822529X-RAY DIFFRACTION99
4.4332-5.56520.21371110.19912532X-RAY DIFFRACTION99
5.5652-19.97420.2331560.20872464X-RAY DIFFRACTION98
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)
10.88650.4659-0.04070.39810.21970.8429-0.02580.1617-0.0207-0.03190.2161-0.00940.3744-0.44160.36890.2929-0.0304-0.01010.1613-0.00330.13169.356461.695556.1198
22.4957-0.4075-1.63340.11120.32481.76460.89830.65610.61010.1360.62740.70590.6072-0.35051.06470.7195-0.168-0.49510.44090.23150.3722164.712375.004441.4694
3-0.03020.00820.0213-0.0172-0.00540.0116-0.037-0.073-0.20960.0969-0.1010.1431-0.0269-0.1765-0.00011.587-0.0787-0.16210.6694-0.27440.8578169.035844.724539.3328
40.5576-0.10640.01080.1589-0.16060.1022-0.11540.0075-0.0765-0.43240.0888-0.32180.39810.3367-0.01830.46990.10350.10470.3003-0.06750.3441181.490257.762747.5534
50.12230.04290.20490.30060.21640.42680.08550.21840.4437-0.07410.1939-0.3715-0.68210.20870.01290.4160.0558-0.00530.2178-0.01120.3324168.531179.695464.9367
60.0141-0.007-0.0013-0.00460.00170.00010.2139-0.1461-0.0081-0.1678-0.1165-0.0245-0.13310.1404-0.00010.9255-0.0195-0.09650.75330.14980.8328136.53224.309829.8271
70.7080.45420.0320.7382-0.33821.14840.0481-0.12880.0654-0.08320.128-0.27270.16310.25570.0170.2366-0.0104-0.02510.2784-0.0210.2713147.568862.289527.0598
80.6854-0.14350.45040.86520.38970.64840.0088-0.073-0.0550.06730.13020.196-0.0358-0.1530.00040.26730.00820.00680.2750.01930.2852138.81960.096730.5965
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 44 through 149 )
2X-RAY DIFFRACTION2chain 'A' and (resid 150 through 179 )
3X-RAY DIFFRACTION3chain 'A' and (resid 180 through 223 )
4X-RAY DIFFRACTION4chain 'A' and (resid 224 through 311 )
5X-RAY DIFFRACTION5chain 'A' and (resid 312 through 345 )
6X-RAY DIFFRACTION6chain 'B' and (resid 32 through 41 )
7X-RAY DIFFRACTION7chain 'B' and (resid 42 through 184 )
8X-RAY DIFFRACTION8chain 'B' and (resid 185 through 344 )

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