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- PDB-3oe6: Crystal structure of the CXCR4 chemokine receptor in complex with... -

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Basic information

Entry
Database: PDB / ID: 3oe6
TitleCrystal structure of the CXCR4 chemokine receptor in complex with a small molecule antagonist IT1t in I222 spacegroup
ComponentsC-X-C chemokine receptor type 4, Lysozyme Chimera
KeywordsSIGNALING PROTEIN / HYDROLASE / Structural Genomics / PSI-2 / Protein Structure Initiative / Accelerated Technologies Center for Gene to 3D Structure / ATCG3D / 7TM / G protein-coupled receptor / GPCR / Signal transduction / Cancer / HIV-1 co-receptor / Chemokine / CXCL12 / SDF1 / isothiourea / IT1t / Chimera / T4L Fusion / Membrane protein / Transmembrane / SINGNALING PROTEIN / PSI-Biology / GPCR Network
Function / homology
Function and homology information


C-X-C motif chemokine 12 receptor activity / regulation of viral process / positive regulation of vascular wound healing / positive regulation of macrophage migration inhibitory factor signaling pathway / 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 vascular wound healing / positive regulation of macrophage migration inhibitory factor signaling pathway / 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 / C-C chemokine receptor activity / endothelial tube morphogenesis / endothelial cell differentiation / C-C chemokine binding / Signaling by ROBO receptors / regulation of chemotaxis / cellular response to organonitrogen compound / positive regulation of chemotaxis / Formation of definitive endoderm / positive regulation of dendrite extension / anchoring junction / Chemokine receptors bind chemokines / dendritic cell chemotaxis / positive regulation of oligodendrocyte differentiation / epithelial cell development / cell leading edge / cellular response to cytokine stimulus / small molecule binding / detection of temperature stimulus involved in sensory perception of pain / 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 / cell wall macromolecule catabolic process / cellular response to xenobiotic stimulus / late endosome / virus receptor activity / lysozyme / lysozyme activity / positive regulation of cold-induced thermogenesis / actin binding / 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 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 / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / Lysozyme - #40 / Endolysin T4 type / T4-type lysozyme / Glycoside hydrolase, family 24 ...CXC chemokine receptor 4 N-terminal domain / CXCR4 Chemokine receptor N terminal / CXC chemokine receptor 4/atypical chemokine receptor 2 / Chemokine receptor family / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / Lysozyme - #40 / Endolysin T4 type / T4-type lysozyme / Glycoside hydrolase, family 24 / Lysozyme domain superfamily / Phage lysozyme / 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) / Lysozyme-like domain superfamily / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-ITD / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Endolysin / C-X-C chemokine receptor type 4
Similarity search - Component
Biological speciesHomo Sapiens (human)
Enterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsWu, B. / Mol, C.D. / Han, G.W. / Katritch, V. / Chien, E.Y.T. / Liu, W. / Cherezov, V. / Stevens, R.C. / Accelerated Technologies Center for Gene to 3D Structure (ATCG3D) / GPCR Network (GPCR)
CitationJournal: Science / Year: 2010
Title: Structures of the CXCR4 chemokine GPCR with small-molecule and cyclic peptide antagonists.
Authors: Wu, B. / Chien, E.Y. / Mol, C.D. / Fenalti, G. / Liu, W. / Katritch, V. / Abagyan, R. / Brooun, A. / Wells, P. / Bi, F.C. / Hamel, D.J. / Kuhn, P. / Handel, T.M. / Cherezov, V. / Stevens, R.C.
History
DepositionAug 12, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 27, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 2, 2012Group: Structure summary
Revision 1.3Jul 26, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.4Oct 6, 2021Group: Database references / Derived calculations / Category: database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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, Lysozyme Chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,1066
Polymers57,5371
Non-polymers1,5685
Water0
1
A: C-X-C chemokine receptor type 4, Lysozyme Chimera
hetero molecules

A: C-X-C chemokine receptor type 4, Lysozyme Chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,21212
Polymers115,0752
Non-polymers3,13710
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area2640 Å2
ΔGint-20 kcal/mol
Surface area47890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.121, 78.711, 240.592
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, Lysozyme Chimera / 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: 57537.426 Da / Num. of mol.: 1
Fragment: CXCR4 residues 2-228, LYSOZYME residues 1002-1161, CXCR4 residues 231-325
Mutation: L125W, C1054T, C1097T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo Sapiens (human), (gene. exp.) Enterobacteria phage T4 (virus)
Gene: CXCR4, CXCR4_HUMAN,E / Plasmid: pFastBac / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9 / References: UniProt: P61073, UniProt: P00720, lysozyme
#2: Chemical ChemComp-ITD / (6,6-dimethyl-5,6-dihydroimidazo[2,1-b][1,3]thiazol-3-yl)methyl N,N'-dicyclohexylimidothiocarbamate


Mass: 406.651 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H34N4S2
#3: Chemical ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H40O4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
Sequence detailsTHE PROTEIN IS A FUSION PROTEIN WITH RESIDUES ASN1002-TYR1161 OF T4 LYSOZYME INSERTED BETWEEN ...THE PROTEIN IS A FUSION PROTEIN WITH RESIDUES ASN1002-TYR1161 OF T4 LYSOZYME INSERTED BETWEEN SER229 AND LYS230 OF CXCR4, AS INDICATED AS CXCR4-1 IN THE PUBLICATION.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 4

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Sample preparation

CrystalDensity Matthews: 2.93 Å3/Da / Density % sol: 57.96 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 5.5
Details: Lipidic cubic phase made of monoolein and cholesterol, 20-26% PEG400, 0.3M Sodium malonate, 5mM Nickel chloride, 0.1M Sodium citrate pH 5.0-5.5, 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: 1.033 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 25, 2010 / Details: mirrors
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 10233 / % possible obs: 94.4 % / Redundancy: 3.6 % / Biso Wilson estimate: 89.11 Å2 / Rmerge(I) obs: 0.136 / Net I/σ(I): 10.2
Reflection shellResolution: 3.3→3.42 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 1.5 / % possible all: 78.2

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
BUSTER2.8.0refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Cor.coef. Fo:Fc: 0.8474 / Cor.coef. Fo:Fc free: 0.7467 / Highest resolution: 3.2 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.3063 406 4.89 %RANDOM
Rwork0.2319 ---
obs0.2355 8310 --
Displacement parametersBiso mean: 69.12 Å2
Baniso -1Baniso -2Baniso -3
1--1.4805 Å20 Å20 Å2
2--5.0282 Å20 Å2
3----3.5476 Å2
Refine analyzeLuzzati coordinate error obs: 0.578 Å
Refinement stepCycle: LAST / Highest resolution: 3.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3356 0 79 0 3435
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1170SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes61HARMONIC2
X-RAY DIFFRACTIONt_gen_planes501HARMONIC5
X-RAY DIFFRACTIONt_it3448HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion463SEMIHARMONIC5
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_contact3940SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3521HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg4767HARMONIC21.31
X-RAY DIFFRACTIONt_omega_torsion2.92
X-RAY DIFFRACTIONt_other_torsion22.48
LS refinement shellResolution: 3.2→3.58 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.2797 117 5.11 %
Rwork0.2415 2172 -
all0.2434 2289 -
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)
11.7894-0.2014-0.0232.3820.76732.72130.01410.07830.24350.0109-0.0029-0.20.25320.1668-0.0112-0.16560.0343-0.0383-0.15930.0039-0.039216.64931.60257.3607
200.2535-0.76420.81590.07772.9429-0.0079-0.02050.01950.0870.20470.06390.40210.0755-0.1969-0.02430.1520.02250.22270.0184-0.3041.494823.520511.2511
31.5458-0.44520.32270.96850.518800.0855-0.1813-0.211-0.0025-0.0681-0.08970.1624-0.0264-0.0174-0.0082-0.0193-0.0115-0.07290.00740.005610.158519.88960.4589
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|35 - A|226 }A35 - 226
2X-RAY DIFFRACTION2{ A|1010 - A|1159 }A1010 - 1159
3X-RAY DIFFRACTION3{ A|235 - A|312 }A235 - 312

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