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- PDB-6kvf: Structure of anti-hCXCR2 abN48 in complex with its CXCR2 epitope -

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Basic information

Entry
Database: PDB / ID: 6kvf
TitleStructure of anti-hCXCR2 abN48 in complex with its CXCR2 epitope
Components
  • Peptide from C-X-C chemokine receptor type 2
  • heavy chain
  • light chain
KeywordsIMMUNE SYSTEM / Antibody-Antigen complex / CXCR2
Function / homology
Function and homology information


interleukin-8-mediated signaling pathway / interleukin-8 receptor activity / mast cell granule / interleukin-8 binding / C-X-C chemokine receptor activity / neutrophil activation / C-C chemokine receptor activity / C-C chemokine binding / Chemokine receptors bind chemokines / dendritic cell chemotaxis ...interleukin-8-mediated signaling pathway / interleukin-8 receptor activity / mast cell granule / interleukin-8 binding / C-X-C chemokine receptor activity / neutrophil activation / C-C chemokine receptor activity / C-C chemokine binding / Chemokine receptors bind chemokines / dendritic cell chemotaxis / cellular defense response / neutrophil chemotaxis / secretory granule membrane / calcium-mediated signaling / G protein-coupled receptor activity / receptor internalization / chemotaxis / mitotic spindle / microtubule cytoskeleton / positive regulation of cytosolic calcium ion concentration / G alpha (i) signalling events / phospholipase C-activating G protein-coupled receptor signaling pathway / cell surface receptor signaling pathway / immune response / inflammatory response / external side of plasma membrane / positive regulation of cell population proliferation / Neutrophil degranulation / negative regulation of apoptotic process / cell surface / signal transduction / nucleoplasm / membrane / plasma membrane
Similarity search - Function
CXC chemokine receptor 2 / CXC chemokine receptor 1/2 / : / 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) / Immunoglobulins / Immunoglobulin-like ...CXC chemokine receptor 2 / CXC chemokine receptor 1/2 / : / 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) / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
C-X-C chemokine receptor type 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.79 Å
AuthorsXiang, J.C. / Yan, L. / Yang, B. / Wilson, I.A.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31600619 China
CitationJournal: Nat Commun / Year: 2021
Title: Selection of a picomolar antibody that targets CXCR2-mediated neutrophil activation and alleviates EAE symptoms.
Authors: Shi, X. / Wan, Y. / Wang, N. / Xiang, J. / Wang, T. / Yang, X. / Wang, J. / Dong, X. / Dong, L. / Yan, L. / Li, Y. / Liu, L. / Hou, S. / Zhong, Z. / Wilson, I.A. / Yang, B. / Yang, G. / Lerner, R.A.
History
DepositionSep 4, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 9, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 22, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 22, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: heavy chain
A: heavy chain
L: light chain
C: light chain
b: Peptide from C-X-C chemokine receptor type 2
B: Peptide from C-X-C chemokine receptor type 2


Theoretical massNumber of molelcules
Total (without water)98,0036
Polymers98,0036
Non-polymers00
Water23413
1
H: heavy chain
L: light chain
b: Peptide from C-X-C chemokine receptor type 2


Theoretical massNumber of molelcules
Total (without water)49,0013
Polymers49,0013
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4470 Å2
ΔGint-33 kcal/mol
Surface area19740 Å2
MethodPISA
2
A: heavy chain
C: light chain
B: Peptide from C-X-C chemokine receptor type 2


Theoretical massNumber of molelcules
Total (without water)49,0013
Polymers49,0013
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3810 Å2
ΔGint-31 kcal/mol
Surface area19670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)159.509, 76.082, 85.364
Angle α, β, γ (deg.)90.000, 108.530, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody heavy chain


Mass: 23979.877 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody light chain


Mass: 23646.229 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Protein/peptide Peptide from C-X-C chemokine receptor type 2 / CXCR2 peptide


Mass: 1375.373 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P25025
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 53.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES sodium pH 7.5, 2% v/v Polyethylene glycol 400, 2.0M Ammonium sulfate
PH range: 7.0-8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.79→50 Å / Num. obs: 24116 / % possible obs: 99.7 % / Redundancy: 6.7 % / Biso Wilson estimate: 67 Å2 / CC1/2: 1 / Net I/σ(I): 14.2
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 6.5 % / Num. unique obs: 2817 / CC1/2: 0.75 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XCN

4xcn


Resolution: 2.79→39.42 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.892 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.4 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2644 1174 4.9 %RANDOM
Rwork0.2283 ---
obs0.23 22942 99.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 117.25 Å2 / Biso mean: 65.432 Å2 / Biso min: 28.65 Å2
Baniso -1Baniso -2Baniso -3
1--2.63 Å20 Å20.81 Å2
2--0.39 Å20 Å2
3---1.39 Å2
Refinement stepCycle: final / Resolution: 2.79→39.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6465 0 25 13 6503
Biso mean--101.93 39.34 -
Num. residues----860
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0146640
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175803
X-RAY DIFFRACTIONr_angle_refined_deg0.7621.6549055
X-RAY DIFFRACTIONr_angle_other_deg1.381.63713638
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5875852
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.33822.738263
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.469151006
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1331524
X-RAY DIFFRACTIONr_chiral_restr0.0330.2878
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.027413
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021243
LS refinement shellResolution: 2.794→2.867 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 79 -
Rwork0.327 1645 -
all-1724 -
obs--97.46 %

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