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- PDB-3oe8: Crystal structure of the CXCR4 chemokine receptor in complex with... -

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Basic information

Entry
Database: PDB / ID: 3oe8
TitleCrystal structure of the CXCR4 chemokine 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 / Cancer / HIV-1 co-receptor / chemotaxis / 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 / 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 1.4Jun 13, 2018Group: Advisory / Data collection ...Advisory / Data collection / Database references / Structure summary
Category: pdbx_poly_seq_scheme / pdbx_unobs_or_zero_occ_residues ...pdbx_poly_seq_scheme / pdbx_unobs_or_zero_occ_residues / struct_ref_seq / struct_ref_seq_dif
Item: _pdbx_poly_seq_scheme.pdb_seq_num / _pdbx_unobs_or_zero_occ_residues.auth_seq_id
Revision 1.5Oct 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_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Oct 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

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


Theoretical massNumber of molelcules
Total (without water)172,1086
Polymers170,8883
Non-polymers1,2203
Water00
1
B: C-X-C chemokine receptor type 4, Lysozyme Chimera
C: C-X-C chemokine receptor type 4, Lysozyme Chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,7394
Polymers113,9262
Non-polymers8132
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1320 Å2
ΔGint-16 kcal/mol
Surface area46550 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3300 Å2
ΔGint-28 kcal/mol
Surface area67690 Å2
MethodPISA
3
A: C-X-C chemokine receptor type 4, Lysozyme Chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,3692
Polymers56,9631
Non-polymers4071
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.369, 76.602, 91.719
Angle α, β, γ (deg.)96.00, 97.78, 97.38
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: 56962.801 Da / Num. of mol.: 3
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.: 3 / 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 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: 11

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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: 6
Details: Lipidic cubic phase made of monoolein and cholesterol, 26% PEG400, 0.3M Sodium malonate, 5mM Strontium 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: 28801 / % possible obs: 87.3 % / Redundancy: 3.2 % / Biso Wilson estimate: 102.46 Å2 / Rmerge(I) obs: 0.15 / Net I/σ(I): 12.7
Reflection shellResolution: 3.1→3.15 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 1.8 / % possible all: 59.3

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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→19.97 Å / Cor.coef. Fo:Fc: 0.8948 / Cor.coef. Fo:Fc free: 0.8542 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2946 1441 5.03 %RANDOM
Rwork0.2502 ---
obs0.2525 28647 --
Displacement parametersBiso mean: 103.64 Å2
Baniso -1Baniso -2Baniso -3
1-2.6845 Å2-4.1005 Å2-0.9523 Å2
2--10.3789 Å20.6612 Å2
3----13.0634 Å2
Refine analyzeLuzzati coordinate error obs: 0.838 Å
Refinement stepCycle: LAST / Resolution: 3.1→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10292 0 81 0 10373
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d3546SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes191HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1532HARMONIC5
X-RAY DIFFRACTIONt_it10545HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1410SEMIHARMONIC5
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_contact12091SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d10635HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg14450HARMONIC21.4
X-RAY DIFFRACTIONt_omega_torsion3.25
X-RAY DIFFRACTIONt_other_torsion21.6
LS refinement shellResolution: 3.1→3.22 Å / Total num. of bins used: 14
RfactorNum. reflection% reflection
Rfree0.3204 83 4.25 %
Rwork0.2558 1871 -
all0.2584 1954 -
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)
12.72440.1898-0.90182.365-0.81282.86830.02020.3570.35920.25020.0887-0.0802-0.1683-0.1644-0.1089-0.2163-0.025-0.0162-0.03390.0751-0.1883-27.15421.699835.2206
20.0242-0.0276-0.00360.0792-0.04690.0217-0.00130.00110.0033-0.00070.0015-0.0034-0.00190.0004-0.00030.11290.031-0.01060.0244-0.00940.0349-25.6706-23.088268.2627
33.5567-1.3737-1.0973.15711.06323.92140.08570.0031-0.00110.0103-0.02530.06820.07-0.1052-0.0604-0.0305-0.024-0.11830.0520.0277-0.3362-16.3508-18.814778.4237
40.82540.59710.48432.569-0.25852.54440.03880.1669-0.07630.07110.01270.2861-0.0167-0.1231-0.0515-0.1402-0.0808-0.04740.20820.0924-0.2361-33.089-8.708131.778
53.24330.20122.29491.45650.41525.6998-0.06510.074-0.0540.08670.02740.1679-0.04860.09190.0377-0.1584-0.01780.0916-0.1138-0.0136-0.1501-66.441811.385533.3222
63.30421.10381.37172.44320.88152.78260.0005-0.30850.25010.23250.1367-0.18-0.2166-0.3057-0.1372-0.0330.02740.00130.13090.1353-0.2827-45.51565.907779.2088
70.0333-0.01720.01560.00960.00070.0043-0.00020.0004-0.00210.00260.0010.00070.001-0.0015-0.00080.02170.0018-0.01460.0210.00330.0192-53.82718.777262.326
82.649-0.74682.79821.38040.27743.35520.00820.1536-0.20490.0997-0.03630.02150.1160.06660.0281-0.12290.09580.00120.0231-0.0714-0.1076-56.50483.42532.0329
92.3582-0.0202-0.12432.35210.47882.5424-0.1420.1478-0.13730.26740.0842-0.26510.34990.17780.05790.0751-0.0846-0.0136-0.0266-0.0334-0.3247-44.091738.425135.8887
103.57211.11571.0932.89850.00062.62190.0168-0.1513-0.25230.051-0.06360.10920.11790.18160.04690.02740.0845-0.0790.1349-0.0113-0.3446-67.23538.280482.7051
110.010.0134-0.02470.01720.0189-0.00180.00010.0017-0.0005-0.0020.0022-0.0040.00050.001-0.0023-0.00060.0113-0.00160.0094-0.00830.0172-55.476645.841469.5709
121.89931.1578-1.7422.2347-2.79841.7421-0.14960.24020.1150.28850.1892-0.02320.0477-0.0628-0.03960.1383-0.12710.00510.0022-0.0488-0.3215-55.001345.571633.9298
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|232 - A|305 }A232 - 305
5X-RAY DIFFRACTION5{ B|27 - B|226 }B27 - 226
6X-RAY DIFFRACTION6{ B|1002 - B|1161 }B1002 - 1161
7X-RAY DIFFRACTION7{ B|1200 - B|1201 }B1200 - 1201
8X-RAY DIFFRACTION8{ B|230 - B|304 }B230 - 304
9X-RAY DIFFRACTION9{ C|27 - C|227 }C27 - 227
10X-RAY DIFFRACTION10{ C|1002 - C|1161 }C1002 - 1161
11X-RAY DIFFRACTION11{ C|1200 - C|1201 }C1200 - 1201
12X-RAY DIFFRACTION12{ C|230 - C|305 }C230 - 305

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