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- PDB-3oe9: Crystal structure of the chemokine CXCR4 receptor in complex with... -

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Basic information

Entry
Database: PDB / ID: 3oe9
TitleCrystal structure of the chemokine CXCR4 receptor in complex with a small molecule antagonist IT1t in P1 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 / chemotaxis / 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 / telencephalon cell migration / C-X-C chemokine receptor activity / response to tacrolimus ...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 / telencephalon cell migration / C-X-C chemokine receptor activity / response to tacrolimus / 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 / endothelial tube morphogenesis / C-C chemokine receptor activity / endothelial cell differentiation / Signaling by ROBO receptors / regulation of chemotaxis / : / C-C chemokine binding / positive regulation of dendrite extension / positive regulation of chemotaxis / Formation of definitive endoderm / Chemokine receptors bind chemokines / anchoring junction / dendritic cell chemotaxis / positive regulation of oligodendrocyte differentiation / small molecule binding / epithelial cell development / cell leading edge / cellular response to cytokine stimulus / detection of temperature stimulus involved in sensory perception of pain / regulation of calcium ion transport / detection of mechanical stimulus involved in sensory perception of pain / Binding and entry of HIV virion / regulation of cell adhesion / coreceptor activity / cardiac muscle contraction / viral release from host cell by cytolysis / peptidoglycan catabolic process / neurogenesis / cell chemotaxis / ubiquitin binding / response to activity / G protein-coupled receptor activity / calcium-mediated signaling / neuron migration / brain development / response to virus / cell wall macromolecule catabolic process / late endosome / cellular response to xenobiotic stimulus / lysozyme / lysozyme activity / positive regulation of cold-induced thermogenesis / virus receptor activity / actin binding / positive regulation of cytosolic calcium ion concentration / G alpha (i) signalling events / cytoplasmic vesicle / host cell cytoplasm / lysosome / early endosome / response to hypoxia / defense response to bacterium / positive regulation of cell migration / inflammatory response / immune response / G protein-coupled receptor signaling pathway / external side of plasma membrane / ubiquitin protein ligase binding / apoptotic process / 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 ...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 / Phage lysozyme / Lysozyme domain superfamily / 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 / 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: 3.1 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_conn ...database_2 / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 9, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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


Theoretical massNumber of molelcules
Total (without water)114,1844
Polymers113,3712
Non-polymers8132
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1910 Å2
ΔGint-17 kcal/mol
Surface area43680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.497, 72.739, 84.273
Angle α, β, γ (deg.)64.66, 73.93, 61.31
Int Tables number1
Space group name H-MP1

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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: 56685.508 Da / Num. of mol.: 2
Fragment: CXCR4 residues 2-228, LYSOZYME residues 1002-1161, CXCR4 residues 231-319
Mutation: L125W, T240P, 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.: 2 / Source method: obtained synthetically / Formula: C21H34N4S2
Has protein modificationY
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 HIS228 AND GLY231 OF CXCR4, AS INDICATED AS CXCR4-3 IN THE PUBLICATION.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 9

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Sample preparation

CrystalDensity Matthews: 3.1 Å3/Da / Density % sol: 60.26 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 6
Details: Lipidic cubic phase made of monoolein and cholesterol, 27-35% PEG400, 0.27-0.33M Sodium malonate, 5mM Hexamine cobalt chloride, 0.1M MES pH 6.0, 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: 1.033 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 15, 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: 3.1→50 Å / Num. obs: 24209 / % possible obs: 96.9 % / Redundancy: 3.2 % / Biso Wilson estimate: 64.28 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 11.2
Reflection shellResolution: 3.1→3.27 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 1.5 / % possible all: 87.7

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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 / Resolution: 3.1→19.92 Å / Cor.coef. Fo:Fc: 0.8941 / Cor.coef. Fo:Fc free: 0.8834 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2841 1238 5.11 %RANDOM
Rwork0.2521 ---
obs0.2537 24209 --
Displacement parametersBiso mean: 105.21 Å2
Baniso -1Baniso -2Baniso -3
1--7.3123 Å2-0.7209 Å22.5274 Å2
2--10.8426 Å23.4738 Å2
3----3.5303 Å2
Refine analyzeLuzzati coordinate error obs: 0.821 Å
Refinement stepCycle: LAST / Resolution: 3.1→19.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6726 0 54 0 6780
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2323SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes135HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1011HARMONIC5
X-RAY DIFFRACTIONt_it6951HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion928SEMIHARMONIC5
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_contact7932SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d6951HARMONIC20.009
X-RAY DIFFRACTIONt_angle_deg9449HARMONIC21.4
X-RAY DIFFRACTIONt_omega_torsion2.41
X-RAY DIFFRACTIONt_other_torsion23.7
LS refinement shellResolution: 3.1→3.24 Å / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.2969 159 5.57 %
Rwork0.2729 2695 -
all0.2742 2854 -
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)
14.3063-0.1305-0.17571.5911.87723.93890.2796-0.12750.4144-0.2893-0.4561-0.0326-0.1982-0.27360.1765-0.3510.0846-0.03020.1647-0.0687-0.220616.47346.803512.9796
23.93971.34751.20994.09471.43151.203-0.0232-0.31730.03250.0768-0.1125-0.03530.0199-0.24590.1358-0.17270.0424-0.06990.308-0.0603-0.323514.4287-21.2173-21.6157
32.4927-0.97490.33191.12480.05963.1549-0.014-0.1143-0.2250.06610.0546-0.15010.127-0.0103-0.0405-0.231-0.0638-0.02660.12310.001-0.037417.7056-6.251918.1897
44.2595-0.1748-1.74882.1451-1.94126.10440.32540.1598-0.2068-0.2293-0.5696-0.15840.55440.31820.2442-0.09620.01920.0158-0.22560.0237-0.1974-16.6707-7.331512.0396
53.1694-0.791-0.9944.4694-0.98923.2848-0.2185-0.28260.08880.17490.4085-0.0891-0.0059-0.3252-0.19-0.21140.0340.071-0.02520.1198-0.2151-12.797820.4696-21.8853
62.4242-0.6137-1.32531.5655-2.68013.06710.0484-0.05970.11250.17020.03390.1186-0.21330.037-0.0822-0.0247-0.05160.1077-0.11180.0248-0.0226-18.58246.148316.8941
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|28 - A|228 }A28 - 228
2X-RAY DIFFRACTION2{ A|1002 - A|1161 }A1002 - 1161
3X-RAY DIFFRACTION3{ A|236 - A|303 }A236 - 303
4X-RAY DIFFRACTION4{ B|35 - B|228 }B35 - 228
5X-RAY DIFFRACTION5{ B|1002 - B|1161 }B1002 - 1161
6X-RAY DIFFRACTION6{ B|236 - B|303 }B236 - 303

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