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- PDB-4mbs: Crystal Structure of the CCR5 Chemokine Receptor -

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Basic information

Entry
Database: PDB / ID: 4mbs
TitleCrystal Structure of the CCR5 Chemokine Receptor
ComponentsChimera protein of C-C chemokine receptor type 5 and Rubredoxin
KeywordsSIGNALING PROTEIN / Human CCR5 Chemokine Receptor / anti-HIV agent / novel protein engineering / GPCR network / membrane protein / PSI-Biology / Structural Genomics / Seven transmembrane helices / G protein-coupled receptor / membrane
Function / homology
Function and homology information


chemokine (C-C motif) ligand 5 binding / negative regulation of macrophage apoptotic process / alkane catabolic process / chemokine receptor activity / signaling / C-C chemokine receptor activity / phosphatidylinositol-4,5-bisphosphate phospholipase C activity / C-C chemokine binding / response to cholesterol / Chemokine receptors bind chemokines ...chemokine (C-C motif) ligand 5 binding / negative regulation of macrophage apoptotic process / alkane catabolic process / chemokine receptor activity / signaling / C-C chemokine receptor activity / phosphatidylinositol-4,5-bisphosphate phospholipase C activity / C-C chemokine binding / response to cholesterol / Chemokine receptors bind chemokines / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / dendritic cell chemotaxis / Interleukin-10 signaling / Binding and entry of HIV virion / cellular defense response / coreceptor activity / cell chemotaxis / calcium-mediated signaling / chemotaxis / calcium ion transport / MAPK cascade / cell-cell signaling / actin binding / virus receptor activity / positive regulation of cytosolic calcium ion concentration / cellular response to lipopolysaccharide / G alpha (i) signalling events / electron transfer activity / cell surface receptor signaling pathway / endosome / immune response / G protein-coupled receptor signaling pathway / inflammatory response / iron ion binding / external side of plasma membrane / apoptotic process / cell surface / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
CC chemokine receptor 5 / Rubredoxin / : / Rubredoxin, iron-binding site / Rubredoxin signature. / Rubredoxin domain / Rubredoxin / Chemokine receptor family / Rubredoxin-like domain / Rubredoxin-like domain profile. ...CC chemokine receptor 5 / Rubredoxin / : / Rubredoxin, iron-binding site / Rubredoxin signature. / Rubredoxin domain / Rubredoxin / Chemokine receptor family / Rubredoxin-like domain / Rubredoxin-like domain profile. / : / 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
Chem-MRV / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Rubredoxin / C-C chemokine receptor type 5
Similarity search - Component
Biological speciesHomo sapiens (human)
Clostridium pasteurianum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.71 Å
AuthorsTan, Q. / Zhu, Y. / Han, G.W. / Li, J. / Fenalti, G. / Liu, H. / Cherezov, V. / Stevens, R.C. / GPCR Network (GPCR) / Zhao, Q. / Wu, B.
CitationJournal: Science / Year: 2013
Title: Structure of the CCR5 chemokine receptor-HIV entry inhibitor maraviroc complex.
Authors: Tan, Q. / Zhu, Y. / Li, J. / Chen, Z. / Han, G.W. / Kufareva, I. / Li, T. / Ma, L. / Fenalti, G. / Li, J. / Zhang, W. / Xie, X. / Yang, H. / Jiang, H. / Cherezov, V. / Liu, H. / Stevens, R.C. / Zhao, Q. / Wu, B.
History
DepositionAug 19, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2013Group: Database references
Revision 1.2Oct 9, 2013Group: Database references
Revision 1.3Jul 26, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.4Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chimera protein of C-C chemokine receptor type 5 and Rubredoxin
B: Chimera protein of C-C chemokine receptor type 5 and Rubredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,75616
Polymers95,0332
Non-polymers4,72414
Water86548
1
A: Chimera protein of C-C chemokine receptor type 5 and Rubredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,2359
Polymers47,5161
Non-polymers2,7188
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Chimera protein of C-C chemokine receptor type 5 and Rubredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5227
Polymers47,5161
Non-polymers2,0056
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.920, 103.520, 137.470
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsAUTHORS STATE THAT THE BIOLOGICAL UNIT IS UNKNOWN.

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Components

#1: Protein Chimera protein of C-C chemokine receptor type 5 and Rubredoxin / C-C CKR-5 / CC-CKR-5 / CCR-5 / CCR5 / CHEMR13 / HIV-1 fusion coreceptor


Mass: 47516.281 Da / Num. of mol.: 2
Fragment: Rubredoxin inserted into CCR5 between residue 223 and 227
Mutation: C58Y, G163N, A233D, K303E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Clostridium pasteurianum (bacteria)
Gene: CCR5, CCR5_HUMAN, CMKBR5, Rd / Plasmid: pFastBac / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): sf9 / References: UniProt: P51681, UniProt: P00268
#2: Chemical ChemComp-MRV / 4,4-difluoro-N-[(1S)-3-{(3-exo)-3-[3-methyl-5-(propan-2-yl)-4H-1,2,4-triazol-4-yl]-8-azabicyclo[3.2.1]oct-8-yl}-1-phenylpropyl]cyclohexanecarboxamide


Mass: 513.666 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C29H41F2N5O / Comment: medication, antiretroviral*YM
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C21H40O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.73 Å3/Da / Density % sol: 54.94 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 7
Details: 32% PEG 400, 0.1M HEPES, 0.1M sodium chloride, pH 7.0, Lipidic cubic phase, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 20, 2013 / Details: mirrors
RadiationMonochromator: Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. all: 28947 / Num. obs: 27674 / % possible obs: 95.6 % / Redundancy: 6 % / Biso Wilson estimate: 67.63 Å2 / Rmerge(I) obs: 0.144 / Net I/σ(I): 14.5
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.853 / Mean I/σ(I) obs: 2 / % possible all: 92.3

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
BUSTER2.10.0refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3ODU

3odu


Resolution: 2.71→36.33 Å / Cor.coef. Fo:Fc: 0.9383 / Cor.coef. Fo:Fc free: 0.903 / SU R Cruickshank DPI: 0.664 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2632 1416 5.12 %RANDOM
Rwork0.2156 ---
obs0.2181 27630 95.47 %-
all-28941 --
Displacement parametersBiso mean: 72.95 Å2
Baniso -1Baniso -2Baniso -3
1-5.7134 Å20 Å20 Å2
2---3.7025 Å20 Å2
3----2.0109 Å2
Refine analyzeLuzzati coordinate error obs: 0.417 Å
Refinement stepCycle: LAST / Resolution: 2.71→36.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5486 0 230 48 5764
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.015871HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.997980HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2586SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes99HARMONIC2
X-RAY DIFFRACTIONt_gen_planes845HARMONIC5
X-RAY DIFFRACTIONt_it5871HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.47
X-RAY DIFFRACTIONt_other_torsion3.24
X-RAY DIFFRACTIONt_chiral_improper_torsion758SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact6545SEMIHARMONIC4
LS refinement shellResolution: 2.71→2.81 Å / Total num. of bins used: 14
RfactorNum. reflection% reflection
Rfree0.2411 145 5.36 %
Rwork0.2191 2561 -
all0.2203 2706 -
obs--95.47 %
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)
11.7832-0.08970.18851.57331.30453.1921-0.07290.1339-0.1459-0.01370.00640.0202-0.0063-0.00320.0665-0.2472-0.0412-0.01980.0671-0.0554-0.262147.597107.79833.5432
27.74360.32541.19475.45590.5886.8399-0.09030.14690.2164-0.0811-0.0964-0.0847-0.01470.03450.1867-0.048-0.0226-0.02530.04690.0346-0.3032152.514140.22866.1547
31.71310.47730.79251.0260.71184.7541-0.06110.26320.06160.03450.0885-0.095-0.17950.0955-0.0274-0.1915-0.0636-0.02380.1028-0.0128-0.2434155.465116.42336.0787
41.6630.38010.52161.83571.40663.6221-0.0950.1137-0.0904-0.04980.04140.0302-0.0932-0.06270.0536-0.2691-0.0432-0.02270.0635-0.036-0.2734183.232111.22233.9726
56.5090.44080.91188.3076-2.1646.1615-0.02520.15890.20730.2778-0.2121-0.3643-0.0418-0.04180.2373-0.0785-0.016-0.04580.04610.0411-0.304189.455143.73666.0225
61.58740.3267-0.251.72880.80222.7532-0.16250.27380.1139-0.10670.2318-0.0961-0.30250.1312-0.0693-0.178-0.12170.00750.1782-0.0474-0.304191.37119.44736.1572
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA19 - 22319 - 223
2X-RAY DIFFRACTION2AA1001 - 10541001 - 1054
3X-RAY DIFFRACTION3AA227 - 313227 - 313
4X-RAY DIFFRACTION4BB19 - 22319 - 223
5X-RAY DIFFRACTION5BB1001 - 10541001 - 1054
6X-RAY DIFFRACTION6BB227 - 313227 - 313

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