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- PDB-5uiw: Crystal Structure of CC Chemokine Receptor 5 (CCR5) in complex wi... -

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Basic information

Entry
Database: PDB / ID: 5uiw
TitleCrystal Structure of CC Chemokine Receptor 5 (CCR5) in complex with high potency HIV entry inhibitor 5P7-CCL5
Components
  • C-C chemokine receptor type 5,Rubredoxin chimera
  • C-C motif chemokine 5
KeywordsSIGNALING PROTEIN / G-protein coupled receptor / Chemokine receptor / HIV entry inhibitor / HIV-1 R5 isolates co-receptor / receptor-ligand complex
Function / homology
Function and homology information


regulation of chronic inflammatory response / CCR4 chemokine receptor binding / chemokine (C-C motif) ligand 5 signaling pathway / chemokine receptor antagonist activity / chemokine (C-C motif) ligand 5 binding / phospholipase D-activating G protein-coupled receptor signaling pathway / CCR1 chemokine receptor binding / positive regulation of natural killer cell chemotaxis / negative regulation of macrophage apoptotic process / chemokine receptor binding ...regulation of chronic inflammatory response / CCR4 chemokine receptor binding / chemokine (C-C motif) ligand 5 signaling pathway / chemokine receptor antagonist activity / chemokine (C-C motif) ligand 5 binding / phospholipase D-activating G protein-coupled receptor signaling pathway / CCR1 chemokine receptor binding / positive regulation of natural killer cell chemotaxis / negative regulation of macrophage apoptotic process / chemokine receptor binding / alkane catabolic process / receptor signaling protein tyrosine kinase activator activity / chemokine receptor activity / CCR5 chemokine receptor binding / positive regulation of receptor signaling pathway via STAT / positive regulation of T cell chemotaxis / CCR chemokine receptor binding / positive regulation of cell-cell adhesion mediated by integrin / signaling / positive regulation of homotypic cell-cell adhesion / neutrophil activation / positive regulation of G protein-coupled receptor signaling pathway / phosphatidylinositol-4,5-bisphosphate phospholipase C activity / C-C chemokine receptor activity / negative regulation of T cell apoptotic process / positive regulation of T cell apoptotic process / chemokine-mediated signaling pathway / eosinophil chemotaxis / C-C chemokine binding / response to cholesterol / positive regulation of calcium ion transport / positive regulation of monocyte chemotaxis / positive regulation of innate immune response / cell surface receptor signaling pathway via STAT / chemokine activity / regulation of T cell activation / Chemokine receptors bind chemokines / dendritic cell chemotaxis / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / positive regulation of smooth muscle cell migration / negative regulation of G protein-coupled receptor signaling pathway / phospholipase activator activity / leukocyte cell-cell adhesion / negative regulation of viral genome replication / positive regulation of macrophage chemotaxis / chemoattractant activity / macrophage chemotaxis / Interleukin-10 signaling / monocyte chemotaxis / exocytosis / positive regulation of translational initiation / cellular response to interleukin-1 / host-mediated suppression of viral transcription / positive regulation of TOR signaling / Binding and entry of HIV virion / positive regulation of T cell migration / cellular defense response / positive regulation of viral genome replication / coreceptor activity / cellular response to fibroblast growth factor stimulus / positive regulation of T cell proliferation / positive regulation of smooth muscle cell proliferation / regulation of insulin secretion / positive regulation of cell adhesion / epithelial cell proliferation / positive regulation of epithelial cell proliferation / cell chemotaxis / calcium-mediated signaling / cellular response to virus / cellular response to type II interferon / response to toxic substance / response to virus / intracellular calcium ion homeostasis / chemotaxis / antimicrobial humoral immune response mediated by antimicrobial peptide / cellular response to tumor necrosis factor / calcium ion transport / cell-cell signaling / MAPK cascade / actin binding / cellular response to lipopolysaccharide / positive regulation of cytosolic calcium ion concentration / virus receptor activity / G alpha (i) signalling events / electron transfer activity / cell surface receptor signaling pathway / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein kinase activity / endosome / immune response / positive regulation of cell migration / G protein-coupled receptor signaling pathway / iron ion binding / inflammatory response / external side of plasma membrane / apoptotic process / cell surface / protein homodimerization activity / extracellular space / extracellular region
Similarity search - Function
CC chemokine receptor 5 / Rubredoxin / : / Rubredoxin, iron-binding site / Rubredoxin signature. / Rubredoxin domain / Rubredoxin / CC chemokine, conserved site / Small cytokines (intercrine/chemokine) C-C subfamily signature. / Rubredoxin-like domain ...CC chemokine receptor 5 / Rubredoxin / : / Rubredoxin, iron-binding site / Rubredoxin signature. / Rubredoxin domain / Rubredoxin / CC chemokine, conserved site / Small cytokines (intercrine/chemokine) C-C subfamily signature. / Rubredoxin-like domain / Rubredoxin-like domain profile. / Chemokine receptor family / : / Chemokine beta/gamma/delta / Intercrine alpha family (small cytokine C-X-C) (chemokine CXC). / Chemokine interleukin-8-like domain / Chemokine interleukin-8-like superfamily / Small cytokines (intecrine/chemokine), interleukin-8 like / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #40 / G-protein coupled receptors family 1 signature. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
OLEIC ACID / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Rubredoxin / C-C motif chemokine 5 / C-C chemokine receptor type 5
Similarity search - Component
Biological speciesHomo sapiens (human)
Clostridium pasteurianum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.204 Å
AuthorsZheng, Y. / Qin, L. / Han, G.W. / Gustavsson, M. / Kawamura, T. / Stevens, R.C. / Cherezov, V. / Kufareva, I. / Handel, T.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI118985 United States
CitationJournal: Immunity / Year: 2017
Title: Structure of CC Chemokine Receptor 5 with a Potent Chemokine Antagonist Reveals Mechanisms of Chemokine Recognition and Molecular Mimicry by HIV.
Authors: Zheng, Y. / Han, G.W. / Abagyan, R. / Wu, B. / Stevens, R.C. / Cherezov, V. / Kufareva, I. / Handel, T.M.
History
DepositionJan 15, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 28, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Apr 18, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 2.0Dec 11, 2019Group: Author supporting evidence / Polymer sequence / Category: entity_poly / pdbx_audit_support
Item: _entity_poly.pdbx_seq_one_letter_code_can / _entity_poly.pdbx_target_identifier / _pdbx_audit_support.funding_organization
Revision 2.1Oct 4, 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 / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id
Revision 2.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: C-C chemokine receptor type 5,Rubredoxin chimera
B: C-C motif chemokine 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,59111
Polymers55,8212
Non-polymers2,7709
Water79344
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4040 Å2
ΔGint-12 kcal/mol
Surface area19460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.010, 52.640, 302.670
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein C-C chemokine receptor type 5,Rubredoxin chimera / CCR5 / CHEMR13 / HIV-1 fusion coreceptor / Rd / CCR5 / CHEMR13 / HIV-1 fusion coreceptor


Mass: 47158.828 Da / Num. of mol.: 1 / Mutation: C58Y, G163N, A233D, K303E
Source method: isolated from a genetically manipulated source
Details: Rubredoxin fusion sequence P00268; in between CCR5 residue 223 and 227 MKKYTCTVCGYIYNPEDGDPDNGVNPGTDFKDIPDDWVCPLCGVGKDQFEEVEE
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Clostridium pasteurianum (bacteria)
Gene: CCR5, CMKBR5 / Plasmid: pfastbac-1 / Cell line (production host): sf9 / Organ (production host): Ovary / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P51681, UniProt: P00268
#2: Protein C-C motif chemokine 5 / EoCP / Eosinophil chemotactic cytokine / SIS-delta / Small-inducible cytokine A5 / T cell-specific ...EoCP / Eosinophil chemotactic cytokine / SIS-delta / Small-inducible cytokine A5 / T cell-specific protein P228 / TCP228 / T-cell-specific protein RANTES


Mass: 8662.117 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Sequence before CC motif "QGPPLMALQS" (where the first residue Q is PCA as glutamine is cyclized into pyroglutamic acid residue) is artificial to replace native sequence "SPYSSDTTP". As the ...Details: Sequence before CC motif "QGPPLMALQS" (where the first residue Q is PCA as glutamine is cyclized into pyroglutamic acid residue) is artificial to replace native sequence "SPYSSDTTP". As the register 0 for PCA, all the rest of residue numbers are consistent for chemokine residues.
Source: (gene. exp.) Homo sapiens (human) / Gene: CCL5, D17S136E, SCYA5 / Plasmid: pfastbac-1 / Cell line (production host): sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P13501

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Non-polymers , 4 types, 53 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / 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.: 6 / Source method: obtained synthetically / Formula: C21H40O4
#5: Chemical ChemComp-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H34O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.71 Å3/Da / Density % sol: 54.65 %
Crystal growTemperature: 295.5 K / Method: lipidic cubic phase / pH: 6.3
Details: 29% (v/v) PEG 400, 120 mM lithium citrate, 1.2% (w/v) 1,5-Diaminopentane dihydrochloride, 100 mM 2-(N-morpholino)ethanesulfonic acid

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Type: OTHER / Wavelength: 1.0332 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 5, 2016 / Details: K-B pair of biomorph 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: 2.18→29.472 Å / Num. obs: 32803 / % possible obs: 99.2 % / Redundancy: 13.7 % / Biso Wilson estimate: 28.07 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.145 / Rpim(I) all: 0.039 / Rrim(I) all: 0.151 / Net I/av σ(I): 9.4 / Net I/σ(I): 9.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.18-2.257.42.2920.625750.6440.7992.43791.3
8.99-46.6711.60.05136.55790.9990.0160.05499.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.9refinement
Aimless0.1.29data scaling
PHASERphasing
PDB_EXTRACT3.22data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MBS

4mbs


Resolution: 2.204→29.472 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 27.72
RfactorNum. reflection% reflectionSelection details
Rfree0.2502 1196 5.1 %Random selection
Rwork0.2158 ---
obs0.2176 23465 73.44 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 109.87 Å2 / Biso mean: 42.3057 Å2 / Biso min: 5.5 Å2
Refinement stepCycle: final / Resolution: 2.204→29.472 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3269 0 124 44 3437
Biso mean--59.43 33.79 -
Num. residues----420
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063491
X-RAY DIFFRACTIONf_angle_d0.9694722
X-RAY DIFFRACTIONf_chiral_restr0.035539
X-RAY DIFFRACTIONf_plane_restr0.005582
X-RAY DIFFRACTIONf_dihedral_angle_d15.1021218
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2036-2.29180.329260.270732435010
2.2918-2.39610.3529650.26871165123035
2.3961-2.52230.27651080.2541772188054
2.5223-2.68030.29371270.25692315244271
2.6803-2.8870.30311330.24852945307887
2.887-3.17730.28381750.25213349352499
3.1773-3.63630.24871680.216433623530100
3.6363-4.57860.24731770.185934353612100
4.5786-29.47460.20222170.192936023819100
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)
11.8342-0.0167-1.23911.65471.91513.02540.07230.62940.3912-0.48360.0168-0.0362-0.5779-0.0707-0.24810.1809-0.04130.00450.57470.08140.1637-132.3783-94.8877611.2836
21.1851-0.1183-0.13591.08230.51611.5743-0.21340.01070.00440.33150.03730.07660.14710.004-0.08890.12910.04860.02670.286-0.04630.1217-133.5119-97.4485642.3796
30.92350.901-0.61382.6023-2.78133.2562-0.18270.2252-0.3645-1.1064-0.1435-0.43231.24920.14160.2980.9807-0.03080.13170.38490.09360.3185-140.0878-122.1137683.0264
42.15610.04540.24611.4603-0.53681.664-0.1376-0.1311-0.01790.42650.06290.24390.4221-0.32620.11960.2582-0.05120.11370.231-0.01480.1808-141.3603-104.9308644.9275
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 0 through 67 )B0 - 67
2X-RAY DIFFRACTION2chain 'A' and (resid 16 through 223 )A16 - 223
3X-RAY DIFFRACTION3chain 'A' and (resid 1001 through 1054 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 227 through 316 )A227 - 316

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