[English] 日本語
Yorodumi
- PDB-6kva: Structure of anti-hCXCR2 abN48-2 in complex with its CXCR2 epitope -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6kva
TitleStructure of anti-hCXCR2 abN48-2 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
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: 2.2 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 3, 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 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
H: heavy chain
L: light chain
h: heavy chain
l: light chain
B: Peptide from C-X-C chemokine receptor type 2
b: Peptide from C-X-C chemokine receptor type 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,4088
Polymers98,2836
Non-polymers1242
Water7,710428
1
H: heavy chain
L: light chain
B: Peptide from C-X-C chemokine receptor type 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2665
Polymers49,1423
Non-polymers1242
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4970 Å2
ΔGint-24 kcal/mol
Surface area19640 Å2
MethodPISA
2
h: heavy chain
l: light chain
b: Peptide from C-X-C chemokine receptor type 2


Theoretical massNumber of molelcules
Total (without water)49,1423
Polymers49,1423
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4410 Å2
ΔGint-33 kcal/mol
Surface area19990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.685, 96.337, 70.783
Angle α, β, γ (deg.)90.000, 109.860, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Antibody heavy chain


Mass: 24120.109 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: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 428 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.18 Å3/Da / Density % sol: 43.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES pH 7.5, 25% w/v Polyethylene glycol 3350
PH range: 7.0-8.0

-
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: Dec 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 42603 / % possible obs: 99.2 % / Redundancy: 4.7 % / Biso Wilson estimate: 31 Å2 / CC1/2: 1 / Net I/σ(I): 12.9
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 4 % / Num. unique obs: 2473 / CC1/2: 0.83 / % possible all: 94.2

-
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: 2.2→48.56 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.925 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.328 / ESU R Free: 0.219
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2345 2159 5.1 %RANDOM
Rwork0.1939 ---
obs0.1959 40411 98.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 75.96 Å2 / Biso mean: 32 Å2 / Biso min: 16.82 Å2
Baniso -1Baniso -2Baniso -3
1-0.27 Å20 Å21.97 Å2
2---2.25 Å2-0 Å2
3---0.44 Å2
Refinement stepCycle: final / Resolution: 2.2→48.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6586 0 8 428 7022
Biso mean--37.61 35.99 -
Num. residues----876
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0146770
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175920
X-RAY DIFFRACTIONr_angle_refined_deg1.2031.6559230
X-RAY DIFFRACTIONr_angle_other_deg1.4091.63913916
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.125868
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.55422.464276
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.02151032
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7491528
X-RAY DIFFRACTIONr_chiral_restr0.0660.2890
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.027596
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021268
LS refinement shellResolution: 2.2→2.253 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.347 119 -
Rwork0.25 2779 -
obs--91.05 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more