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- PDB-3odu: The 2.5 A structure of the CXCR4 chemokine receptor in complex wi... -

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Basic information

Entry
Database: PDB / ID: 3odu
TitleThe 2.5 A structure of the CXCR4 chemokine receptor in complex with small molecule antagonist IT1t
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 / 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 / neuron recognition / telencephalon cell migration / positive regulation of mesenchymal stem cell migration / response to tacrolimus / response to ultrasound / Specification of primordial germ cells ...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 / neuron recognition / telencephalon cell migration / positive regulation of mesenchymal stem cell migration / response to tacrolimus / response to ultrasound / Specification of primordial germ cells / CXCL12-activated CXCR4 signaling pathway / myosin light chain binding / myelin maintenance / C-X-C chemokine receptor activity / regulation of programmed cell death / positive regulation of vasculature development / endothelial tube morphogenesis / endothelial cell differentiation / Signaling by ROBO receptors / regulation of chemotaxis / positive regulation of dendrite extension / Formation of definitive endoderm / C-C chemokine receptor activity / positive regulation of chemotaxis / C-C chemokine binding / Developmental Lineage of Pancreatic Acinar Cells / Chemokine receptors bind chemokines / anchoring junction / dendritic cell chemotaxis / epithelial cell development / cellular response to cytokine stimulus / small molecule binding / cell leading edge / detection of temperature stimulus involved in sensory perception of pain / positive regulation of oligodendrocyte differentiation / regulation of calcium ion transport / Binding and entry of HIV virion / detection of mechanical stimulus involved in sensory perception of pain / regulation of cell adhesion / viral release from host cell by cytolysis / coreceptor activity / cardiac muscle contraction / neurogenesis / peptidoglycan catabolic process / ubiquitin binding / response to activity / cell chemotaxis / calcium-mediated signaling / brain development / G protein-coupled receptor activity / response to virus / neuron migration / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / late endosome / cellular response to xenobiotic stimulus / positive regulation of cold-induced thermogenesis / actin binding / virus receptor activity / positive regulation of cytosolic calcium ion concentration / cytoplasmic vesicle / G alpha (i) signalling events / host cell cytoplasm / early endosome / response to hypoxia / lysosome / defense response to bacterium / immune response / positive regulation of cell migration / G protein-coupled receptor signaling pathway / inflammatory response / 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 ...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. / Lysozyme-like domain superfamily / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-ITD / OLEIC ACID / (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: 2.5 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 11, 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
Revision 1.5Oct 16, 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)118,21615
Polymers113,9262
Non-polymers4,29113
Water2,558142
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2530 Å2
ΔGint-15 kcal/mol
Surface area49030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.540, 83.692, 119.995
Angle α, β, γ (deg.)90.00, 102.17, 90.00
Int Tables number4
Space group name H-MP1211

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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: 56962.801 Da / Num. of mol.: 2
Fragment: CXCR4 residues 2-229, LYSOZYME residues 1002-1161, CXCR4 residues 230-319
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.: 2 / 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.: 5 / Source method: obtained synthetically / Formula: C21H40O4
#4: Chemical
ChemComp-OLA / OLEIC ACID


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


Mass: 18.015 Da / Num. of mol.: 142 / Source method: isolated from a natural source / Formula: H2O
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 SER229 AND LYS230 OF CXCR4, AS INDICATED AS CXCR4-2 IN THE PUBLICATION.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.78 Å3/Da / Density % sol: 55.77 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 5.5
Details: Lipidic cubic phase made of monoolein and cholesterol, 20% PEG400, 0.3M Sodium malonate, 5mM Taurine, 0.1M Sodium citrate, pH 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: Jun 12, 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: 2.5→50 Å / Num. obs: 41569 / % possible obs: 95.8 % / Redundancy: 2.3 % / Biso Wilson estimate: 48.57 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 7.2
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 1.8 / % possible all: 89

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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: 2.5→19.98 Å / Cor.coef. Fo:Fc: 0.8957 / Cor.coef. Fo:Fc free: 0.8559 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2818 2079 5.02 %RANDOM
Rwork0.2374 ---
obs0.2396 41455 --
Displacement parametersBiso mean: 43.79 Å2
Baniso -1Baniso -2Baniso -3
1--0.5243 Å20 Å20.0403 Å2
2---0.4989 Å20 Å2
3---1.0233 Å2
Refine analyzeLuzzati coordinate error obs: 0.375 Å
Refinement stepCycle: LAST / Resolution: 2.5→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7393 0 242 142 7777
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0147843HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.310596HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2598SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes144HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1126HARMONIC5
X-RAY DIFFRACTIONt_it7606HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion6.46
X-RAY DIFFRACTIONt_other_torsion19.4
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1019SEMIHARMONIC5
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_contact9337SEMIHARMONIC4
LS refinement shellResolution: 2.5→2.56 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2902 126 4.56 %
Rwork0.2511 2639 -
all0.253 2765 -
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)
10.8188-0.12770.3250.76960.13021.2852-0.01560.05110.0076-0.01530.0417-0.0670.01020.117-0.0261-0.09940.00040.0032-0.05050.0185-0.052418.0031-5.800756.0337
2-0.01090.05620.02390-0.01970.0124-0.0005-0.00390.00190.0033-0.00020.00310.00240.00150.0007-0.029-0.03670.0298-0.0153-0.01980.00771.1966-8.540624.2529
31.58051.7319-0.27172.7047-0.12220.69370.0105-0.04480.0669-0.0232-0.05130.1089-0.0372-0.24760.0408-0.0020.0204-0.0921-0.0307-0.0259-0.1619-5.6476-2.70311.4639
4-0.002-0.01230.00310-0.00830.0149-0.00060.00050.00110.0009-0.0008-0.00050.00070.00180.00140.0140.01080.00230.00930.0039-0.00076.0277-13.963622.6564
50.2882-0.08420.06440.83570.36980.01440.00810.02010.01890.01040.02870.03140.1131-0.0465-0.0368-0.05750.0093-0.0208-0.02110.0231-0.039812.8482-21.317553.1576
61.316-0.1484-0.27150.9931-0.13580.9347-0.02250.0227-0.0936-0.00070.01550.097-0.0253-0.07430.0069-0.11360.0205-0.0261-0.0683-0.0111-0.0386-10.967412.362856.0292
70.01420.02780.00440.0079-0.01290.00120.00090.0026-0.0021-0.0004-0.00050.0025-0.0008-0.0015-0.00040.00380.048-0.0665-0.0118-0.0098-0.008314.075126.646327.0151
82.4466-0.91931.04141.4877-0.41382.23650.04440.28630.0149-0.0285-0.0553-0.0263-0.13060.17170.0108-0.0354-0.0094-0.0576-0.09640.0476-0.191912.273332.67914.5479
90.0142-0.01430.00590.0174-0.01320.0132-0.00030.001-0.0015-0.00070.0010.00110.00310.0006-0.00070.0199-0.0003-0.01180.01090.0070.0269-1.169320.312423.1779
100.15640.1857-0.1240.56180.2114-0.0606-0.002-0.04310.05490.00090.0196-0.0202-0.04210.0747-0.0177-0.11130.02220.0135-0.025-0.0148-0.0279-5.631225.460355.6226
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|27 - A|229 }A27 - 229
2X-RAY DIFFRACTION2{ A|900 - A|901 }A900 - 901
3X-RAY DIFFRACTION3{ A|1002 - A|1161 }A1002 - 1161
4X-RAY DIFFRACTION4{ A|1200 - A|1201 }A1200 - 1201
5X-RAY DIFFRACTION5{ A|230 - A|328 }A230 - 328
6X-RAY DIFFRACTION6{ B|28 - B|229 }B28 - 229
7X-RAY DIFFRACTION7{ B|900 - B|901 }B900 - 901
8X-RAY DIFFRACTION8{ B|1002 - B|1161 }B1002 - 1161
9X-RAY DIFFRACTION9{ B|1200 - B|1201 }B1200 - 1201
10X-RAY DIFFRACTION10{ B|230 - B|319 }B230 - 319

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