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- PDB-4rws: Crystal structure of CXCR4 and viral chemokine antagonist vMIP-II... -

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Basic information

Entry
Database: PDB / ID: 4rws
TitleCrystal structure of CXCR4 and viral chemokine antagonist vMIP-II complex (PSI Community Target)
Components
  • C-X-C chemokine receptor type 4/Endolysin chimeric protein
  • Viral macrophage inflammatory protein 2
KeywordsSIGNALING PROTEIN / HYDROLASE / Human chemokine-chemokine receptor complex / GPCR signaling / PSI-Biology / GPCR network / membrane protein / GPCR / CXCR4 / viral antagonist chemokine vMIP-II / membrane / lipidic cubic phase / T4L / Structural Genomics
Function / homology
Function and homology information


C-X-C motif chemokine 12 receptor activity / regulation of viral process / positive regulation of macrophage migration inhibitory factor signaling pathway / positive regulation of vascular wound healing / positive regulation of mesenchymal stem cell migration / neuron recognition / response to ultrasound / response to tacrolimus / telencephalon cell migration / C-X-C chemokine receptor activity ...C-X-C motif chemokine 12 receptor activity / regulation of viral process / positive regulation of macrophage migration inhibitory factor signaling pathway / positive regulation of vascular wound healing / positive regulation of mesenchymal stem cell migration / neuron recognition / response to ultrasound / response to tacrolimus / telencephalon cell migration / C-X-C chemokine receptor activity / Specification of primordial germ cells / CXCL12-activated CXCR4 signaling pathway / myosin light chain binding / myelin maintenance / positive regulation of vasculature development / regulation of programmed cell death / CXCR chemokine receptor binding / C-C chemokine receptor activity / endothelial tube morphogenesis / endothelial cell differentiation / C-C chemokine binding / Signaling by ROBO receptors / positive regulation of chemotaxis / regulation of chemotaxis / cellular response to organonitrogen compound / Formation of definitive endoderm / positive regulation of dendrite extension / anchoring junction / Chemokine receptors bind chemokines / chemokine activity / dendritic cell chemotaxis / positive regulation of oligodendrocyte differentiation / epithelial cell development / cellular response to cytokine stimulus / cell leading edge / detection of temperature stimulus involved in sensory perception of pain / small molecule binding / regulation of calcium ion transport / Binding and entry of HIV virion / coreceptor activity / detection of mechanical stimulus involved in sensory perception of pain / regulation of cell adhesion / cardiac muscle contraction / viral release from host cell by cytolysis / neurogenesis / cell chemotaxis / peptidoglycan catabolic process / response to activity / ubiquitin binding / G protein-coupled receptor activity / calcium-mediated signaling / brain development / neuron migration / response to virus / cellular response to xenobiotic stimulus / cell wall macromolecule catabolic process / late endosome / virus receptor activity / lysozyme / lysozyme activity / actin binding / positive regulation of cold-induced thermogenesis / positive regulation of cytosolic calcium ion concentration / G alpha (i) signalling events / cytoplasmic vesicle / host cell cytoplasm / lysosome / response to hypoxia / early endosome / positive regulation of cell migration / defense response to bacterium / immune response / inflammatory response / G protein-coupled receptor signaling pathway / external side of plasma membrane / apoptotic process / ubiquitin protein ligase binding / cell surface / protein-containing complex / extracellular space / extracellular exosome / plasma membrane / cytoplasm
Similarity search - Function
CXC chemokine receptor 4 N-terminal domain / CXCR4 Chemokine receptor N terminal / CXC chemokine receptor 4/atypical chemokine receptor 2 / Chemokine receptor family / CC chemokine, conserved site / Small cytokines (intercrine/chemokine) C-C subfamily signature. / Chemokine beta/gamma/delta / Intercrine alpha family (small cytokine C-X-C) (chemokine CXC). / Chemokine interleukin-8-like domain / Chemokine interleukin-8-like superfamily ...CXC chemokine receptor 4 N-terminal domain / CXCR4 Chemokine receptor N terminal / CXC chemokine receptor 4/atypical chemokine receptor 2 / Chemokine receptor family / CC chemokine, conserved site / Small cytokines (intercrine/chemokine) C-C subfamily signature. / 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 / Endolysin T4 type / T4-type lysozyme / Glycoside hydrolase, family 24 / Lysozyme domain superfamily / Phage lysozyme / 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) / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Lysozyme-like domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Endolysin / C-X-C chemokine receptor type 4 / Viral macrophage inflammatory protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Enterobacteria phage T4 (virus)
Human herpesvirus 8 strain GK18
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsQin, L. / Kufareva, I. / Holden, L. / Wang, C. / Zheng, Y. / Wu, H. / Fenalti, G. / Han, G.W. / Cherezov, V. / Abagyan, R. ...Qin, L. / Kufareva, I. / Holden, L. / Wang, C. / Zheng, Y. / Wu, H. / Fenalti, G. / Han, G.W. / Cherezov, V. / Abagyan, R. / Stevens, R.C. / Handel, T.M. / GPCR Network (GPCR)
CitationJournal: Science / Year: 2015
Title: Structural biology. Crystal structure of the chemokine receptor CXCR4 in complex with a viral chemokine.
Authors: Qin, L. / Kufareva, I. / Holden, L.G. / Wang, C. / Zheng, Y. / Zhao, C. / Fenalti, G. / Wu, H. / Han, G.W. / Cherezov, V. / Abagyan, R. / Stevens, R.C. / Handel, T.M.
History
DepositionDec 5, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 11, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 25, 2015Group: Database references
Revision 1.2Apr 15, 2015Group: Database references
Revision 1.3Aug 2, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.4Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.5Sep 20, 2023Group: 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: C-X-C chemokine receptor type 4/Endolysin chimeric protein
C: Viral macrophage inflammatory protein 2


Theoretical massNumber of molelcules
Total (without water)65,7462
Polymers65,7462
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2600 Å2
ΔGint-14 kcal/mol
Surface area25900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.320, 121.827, 189.766
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein C-X-C chemokine receptor type 4/Endolysin chimeric protein / CXC-R4 / CXCR-4 / Stromal cell-derived factor 1 receptor / SDF-1 receptor / Fusin / Leukocyte- ...CXC-R4 / CXCR-4 / Stromal cell-derived factor 1 receptor / SDF-1 receptor / Fusin / Leukocyte-derived seven transmembrane domain receptor / LESTR / LCR1 / FB22 / NPYRL / HM89 / Lysis protein / Muramidase / Endolysin


Mass: 56602.484 Da / Num. of mol.: 1
Fragment: CXCR4 residues 2-228, LYSOZYME residues 1002-1161, CXCR4 residues 231-319
Mutation: L125W, T240P, D187C, C1054T, C1097T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Enterobacteria phage T4 (virus)
Plasmid: pFASTBAC / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): sf9 / References: UniProt: P61073, UniProt: P00720, lysozyme
#2: Protein Viral macrophage inflammatory protein 2 / Viral macrophage inflammatory protein II / vMIP-II / vMIP-1B


Mass: 9143.729 Da / Num. of mol.: 1 / Mutation: W5C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human herpesvirus 8 strain GK18 / Gene: ORF K4 / Plasmid: pFASTBAC / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): sf9 / References: UniProt: Q98157

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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: 3.62 Å3/Da / Density % sol: 66.01 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 5.5
Details: 100 mM sodium citrate pH 5.5, 28% PEG 400, 120 mM ammonium phosphate dibasic, 2-6% polypropylene P400, Lipidic cubic phase, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 23-ID-B11.0332
SYNCHROTRONAPS 23-ID-D21.0332
Detector
TypeIDDetectorDateDetails
MARMOSAIC 300 mm CCD1CCDMar 9, 2014mirrors
PSI PILATUS 6M2PIXELFeb 21, 2014
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1double crystalSINGLE WAVELENGTHMx-ray1
2ACCEL Fixed Exit Double CrystalSINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 3.1→30 Å / Num. obs: 16747 / % possible obs: 95.8 % / Redundancy: 8.8 % / Biso Wilson estimate: 82.26 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 17.8
Reflection shellResolution: 3.1→3.21 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 2 / % possible all: 80.7

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Processing

Software
NameVersionClassification
Blu-IceIcedata collection
PHASERphasing
PHENIXrefinement
BUSTER2.10.0refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3Oe0, PDB entry 2FHT

3oe0

2fht


Resolution: 3.1→30 Å / Cor.coef. Fo:Fc: 0.8369 / Cor.coef. Fo:Fc free: 0.7998 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2739 767 5.06 %RANDOM
Rwork0.2493 ---
obs0.2505 15153 85.58 %-
Displacement parametersBiso mean: 84.16 Å2
Baniso -1Baniso -2Baniso -3
1-12.8215 Å20 Å20 Å2
2---1.4795 Å20 Å2
3----11.342 Å2
Refine analyzeLuzzati coordinate error obs: 0.819 Å
Refinement stepCycle: LAST / Resolution: 3.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3953 0 0 0 3953
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0094057HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.945535HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1806SINUSOIDAL6
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes73HARMONIC2
X-RAY DIFFRACTIONt_gen_planes594HARMONIC5
X-RAY DIFFRACTIONt_it4057HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion1.99
X-RAY DIFFRACTIONt_other_torsion2.21
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion548SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4597SEMIHARMONIC4
LS refinement shellResolution: 3.1→3.31 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.2421 79 4.94 %
Rwork0.2504 1520 -
all0.25 1599 -
obs--85.58 %
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)
11.3098-0.0287-1.56032.85541.37446.97620.0272-0.1203-0.0917-0.0130.071-0.30340.02350.5794-0.09810.2549-0.0538-0.0028-0.2657-0.0361-0.426999.78942.494947.9252
25.9286-1.36410.9965.49910.54083.55940.10150.2827-0.015-0.76530.0573-0.2909-0.89460.4631-0.15870.6079-0.0860.1059-0.3399-0.055-0.607986.770525.2582.4686
30.96620.1236-0.37829.11265.11558.86860.02630.0019-0.01160.1181-0.05860.2515-0.0536-0.2730.03230.589-0.15260.1134-0.25390.0386-0.4969100.468.097510.0361
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|23 - A|303 }A23 - 303
2X-RAY DIFFRACTION2{ A|1002 - A|1164 }A1002 - 1164
3X-RAY DIFFRACTION3{ C|1 - C|70 }C1 - 70

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