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Basic information

Entry
Database: PDB / ID: 3oe0
TitleCrystal structure of the CXCR4 chemokine receptor in complex with a cyclic peptide antagonist CVX15
Components
  • C-X-C chemokine receptor type 4, Lysozyme Chimera
  • Polyphemusin analog, CXC chemokine receptor antagonist
KeywordsSIGNALING PROTEIN / HYDROLASE/ANTIBIOTIC / Structural Genomics / PSI-2 / Protein Structure Initiative / Accelerated Technologies Center for Gene to 3D Structure / ATCG3D / 7TM / G protein-coupled receptor / GPCR / Signal transduction / Hydrolase / Cancer / HIV-1 co-receptor / chemokine / CXCL12 / Chimera / T4L fusion / Membrane protein / Transmembrane / antimicrobial / antibiotic / polyphemusin / HYDROLASE-ANTIBIOTIC complex / 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
Polyphemusin analog, CXC chemokine receptor antagonist / 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: 2.9 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 1.3Dec 12, 2012Group: Other
Revision 1.4Jul 26, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.5Oct 6, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
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.pdbx_value_order / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_validate_peptide_omega / pdbx_validate_rmsd_angle / struct_conn / struct_ref
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id / _struct_ref.pdbx_seq_one_letter_code

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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
I: Polyphemusin analog, CXC chemokine receptor antagonist


Theoretical massNumber of molelcules
Total (without water)58,8252
Polymers58,8252
Non-polymers00
Water1086
1
A: C-X-C chemokine receptor type 4, Lysozyme Chimera
I: Polyphemusin analog, CXC chemokine receptor antagonist

A: C-X-C chemokine receptor type 4, Lysozyme Chimera
I: Polyphemusin analog, CXC chemokine receptor antagonist


Theoretical massNumber of molelcules
Total (without water)117,6504
Polymers117,6504
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area7360 Å2
ΔGint-12 kcal/mol
Surface area44420 Å2
Unit cell
Length a, b, c (Å)82.080, 144.860, 73.990
Angle α, β, γ (deg.)90.00, 104.54, 90.00
Int Tables number5
Space group name H-MC121

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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.: 1
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: Protein/peptide Polyphemusin analog, CXC chemokine receptor antagonist


Type: Oligopeptide / Class: Antagonist / Mass: 2139.532 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: synthetic analog and derivative of polyphemusin from Limulus polyphemus (horseshoe crab)
References: Polyphemusin analog, CXC chemokine receptor antagonist
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O
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. THE SMALL CYCLIC PEPTIDE NAMED CVX15 IS CXC CHEMOKINE RECEPTOR (CXCR)4 ANTAGONIST, AS WELL AS ANALOG OF POLYPHEMUSIN FROM LIMULUS POLYPHEMUS (HORSESHOE CRAB). PART OF THE SEQUENCE OF THE SMALL PEPTIDE HAS SIMILARITY TO UNITPROT ENTRY P14215 WITH SEQUENCE RRWCFRVCYRGFCYRKCR

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 14

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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: 7
Details: Lipidic cubic phase made of monoolein and cholesterol, 25% PEG400, 0.3M Potassium sodium tartrate, 0.1 M Tris pH 7.0, 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: 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: 2.9→50 Å / Num. obs: 17656 / % possible obs: 94.9 % / Redundancy: 6 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 9.5
Reflection shellResolution: 2.9→3 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 1.5 / % possible all: 73.6

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
REFMAC5.5.0088refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→19.93 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.925 / SU B: 34.246 / SU ML: 0.309 / Cross valid method: THROUGHOUT / ESU R: 0.839 / ESU R Free: 0.374 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26699 898 5.1 %RANDOM
Rwork0.21463 ---
obs0.21732 16707 95.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 57.05 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20 Å20.2 Å2
2---0.41 Å20 Å2
3---0.41 Å2
Refinement stepCycle: LAST / Resolution: 2.9→19.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3634 0 0 6 3640
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0223728
X-RAY DIFFRACTIONr_bond_other_d0.0010.022530
X-RAY DIFFRACTIONr_angle_refined_deg1.1011.9565053
X-RAY DIFFRACTIONr_angle_other_deg0.85536125
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8015441
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.36622.84162
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.64615625
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9241525
X-RAY DIFFRACTIONr_chiral_restr0.060.2572
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0214046
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02822
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3851.52232
X-RAY DIFFRACTIONr_mcbond_other0.0451.5901
X-RAY DIFFRACTIONr_mcangle_it0.73323608
X-RAY DIFFRACTIONr_scbond_it0.80231496
X-RAY DIFFRACTIONr_scangle_it1.4194.51445
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.902→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.397 40 -
Rwork0.34 961 -
obs--73.6 %
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)
10.13260.29620.23341.6844-0.26761.1636-0.05940.0472-0.0348-0.1450.141-0.2135-0.02190.1337-0.08170.0526-0.01060.06570.1669-0.06960.23956.855815.00346.2863
24.4070.9320.74470.3599-0.36471.9082-0.28320.0474-0.0242-0.11040.0112-0.05910.09040.08060.2720.1686-0.0329-0.01350.08920.01870.10535.2422-20.830224.5296
30.4506-0.6918-0.47113.71150.56011.04190.0483-0.05620.01830.4368-0.140.00680.0942-0.00590.09170.1509-0.07580.0310.1712-0.02630.151150.113616.367315.7284
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A25 - 228
2X-RAY DIFFRACTION2A1002 - 1161
3X-RAY DIFFRACTION3A231 - 303

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