[English] 日本語
Yorodumi
- PDB-2bdn: Crystal structure of human MCP-1 bound to a blocking antibody, 11K2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2bdn
TitleCrystal structure of human MCP-1 bound to a blocking antibody, 11K2
Components
  • Antibody heavy chain 11K2
  • Antibody light chain 11K2
  • Small inducible cytokine A2
KeywordsIMMUNE SYSTEM / antibody-antigen complex
Function / homology
Function and homology information


helper T cell extravasation / CCR2 chemokine receptor binding / negative regulation of natural killer cell chemotaxis / positive regulation of NMDA glutamate receptor activity / negative regulation of glial cell apoptotic process / astrocyte cell migration / ATF4 activates genes in response to endoplasmic reticulum stress / positive regulation of apoptotic cell clearance / CCR chemokine receptor binding / lymphocyte chemotaxis ...helper T cell extravasation / CCR2 chemokine receptor binding / negative regulation of natural killer cell chemotaxis / positive regulation of NMDA glutamate receptor activity / negative regulation of glial cell apoptotic process / astrocyte cell migration / ATF4 activates genes in response to endoplasmic reticulum stress / positive regulation of apoptotic cell clearance / CCR chemokine receptor binding / lymphocyte chemotaxis / cellular homeostasis / positive regulation of endothelial cell apoptotic process / NFE2L2 regulating inflammation associated genes / eosinophil chemotaxis / cellular response to fibroblast growth factor stimulus / chemokine-mediated signaling pathway / Chemokine receptors bind chemokines / chemokine activity / negative regulation of vascular endothelial cell proliferation / negative regulation of G1/S transition of mitotic cell cycle / positive regulation of calcium ion import / positive regulation of nitric-oxide synthase biosynthetic process / macrophage chemotaxis / Interleukin-10 signaling / monocyte chemotaxis / cell surface receptor signaling pathway via JAK-STAT / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / humoral immune response / cellular response to interleukin-1 / sensory perception of pain / cytoskeleton organization / viral genome replication / positive regulation of synaptic transmission, glutamatergic / neutrophil chemotaxis / animal organ morphogenesis / response to bacterium / cytokine-mediated signaling pathway / cellular response to type II interferon / chemotaxis / positive regulation of T cell activation / cellular response to tumor necrosis factor / regulation of cell shape / cellular response to lipopolysaccharide / angiogenesis / Interleukin-4 and Interleukin-13 signaling / negative regulation of neuron apoptotic process / cell surface receptor signaling pathway / positive regulation of ERK1 and ERK2 cascade / cell adhesion / protein kinase activity / inflammatory response / G protein-coupled receptor signaling pathway / protein phosphorylation / signaling receptor binding / signal transduction / extracellular space / extracellular region
Similarity search - Function
CC chemokine, conserved site / Small cytokines (intercrine/chemokine) C-C subfamily signature. / Chemokine beta/gamma/delta / Intercrine alpha family (small cytokine C-X-C) (chemokine CXC). / Chemokine interleukin-8-like domain / Chemokine interleukin-8-like superfamily / Small cytokines (intecrine/chemokine), interleukin-8 like / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #40 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Immunoglobulins ...CC chemokine, conserved site / Small cytokines (intercrine/chemokine) C-C subfamily signature. / Chemokine beta/gamma/delta / Intercrine alpha family (small cytokine C-X-C) (chemokine CXC). / Chemokine interleukin-8-like domain / Chemokine interleukin-8-like superfamily / Small cytokines (intecrine/chemokine), interleukin-8 like / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #40 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Immunoglobulins / Immunoglobulin-like / Beta Barrel / Sandwich / Mainly Beta
Similarity search - Domain/homology
C-C motif chemokine 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.53 Å
AuthorsBoriack-Sjodin, P.A. / Rushe, M. / Reid, C. / Jarpe, M. / van Vlijmen, H. / Bailly, V.
CitationJournal: Protein Eng.Des.Sel. / Year: 2006
Title: Structure activity relationships of monocyte chemoattractant proteins in complex with a blocking antibody.
Authors: Reid, C. / Rushe, M. / Jarpe, M. / van Vlijmen, H. / Dolinski, B. / Qian, F. / Cachero, T.G. / Cuervo, H. / Yanachkova, M. / Nwankwo, C. / Wang, X. / Etienne, N. / Garber, E. / Bailly, V. / ...Authors: Reid, C. / Rushe, M. / Jarpe, M. / van Vlijmen, H. / Dolinski, B. / Qian, F. / Cachero, T.G. / Cuervo, H. / Yanachkova, M. / Nwankwo, C. / Wang, X. / Etienne, N. / Garber, E. / Bailly, V. / de Fougerolles, A. / Boriack-Sjodin, P.A.
History
DepositionOct 20, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Apr 3, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 999Sequence No suitable sequence database reference was available for the proteins in chains L and H ...Sequence No suitable sequence database reference was available for the proteins in chains L and H at the time of processing this file.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Small inducible cytokine A2
L: Antibody light chain 11K2
H: Antibody heavy chain 11K2


Theoretical massNumber of molelcules
Total (without water)55,3973
Polymers55,3973
Non-polymers00
Water77543
1
A: Small inducible cytokine A2
L: Antibody light chain 11K2
H: Antibody heavy chain 11K2

A: Small inducible cytokine A2
L: Antibody light chain 11K2
H: Antibody heavy chain 11K2


Theoretical massNumber of molelcules
Total (without water)110,7946
Polymers110,7946
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556x,-y,-z+11
Unit cell
Length a, b, c (Å)86.36, 89.10, 176.24
Angle α, β, γ (deg.)90, 90, 90
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-84-

HOH

DetailsThe MCP-1 dimer is generated by the symmetry operator x, -y, -z and translation of the resulting symmetry protein by 0 0 1 fractional (ie, translation along the Z axis by 1 unit cell length).

-
Components

#1: Protein Small inducible cytokine A2 / CCL2 / Monocyte chemotactic protein 1 / MCP-1 / Monocyte chemoattractant protein 1 / Monocyte ...CCL2 / Monocyte chemotactic protein 1 / MCP-1 / Monocyte chemoattractant protein 1 / Monocyte chemotactic and activating factor / MCAF / Monocyte secretory protein JE / HC11


Mass: 8699.045 Da / Num. of mol.: 1 / Fragment: monocyte chemotactic protein -1 / Source method: obtained synthetically
Details: Chemically synthesized. This sequence occurs naturally in humans
References: UniProt: P13500
#2: Antibody Antibody light chain 11K2


Mass: 23574.939 Da / Num. of mol.: 1 / Fragment: fab fragment
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell (production host): murine hybridoma cells / Production host: Mus musculus (house mouse)
#3: Antibody Antibody heavy chain 11K2


Mass: 23122.873 Da / Num. of mol.: 1 / Fragment: fab fragment
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell (production host): murine hybridoma cells / Production host: Mus musculus (house mouse)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.11 Å3/Da / Density % sol: 60.44 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 13% PEG 4000, 100 mM Hepes, pH 7.5, 30 mM glycl-glycl-glycine, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97945 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 19, 2002
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 2.53→50 Å / Num. all: 22774 / Num. obs: 22774 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 21.2
Reflection shellResolution: 2.53→2.59 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.436 / Mean I/σ(I) obs: 3.3 / % possible all: 99.9

-
Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT1.7data extraction
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNXrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 11K2 fab model from Modeler

11k2


Resolution: 2.53→35 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.277 1106 4.6 %Random
Rwork0.219 ---
all0.22 23911 --
obs0.22 22739 95.1 %-
Displacement parametersBiso mean: 47.124 Å2
Baniso -1Baniso -2Baniso -3
1-17.498 Å20 Å20 Å2
2---17.173 Å20 Å2
3----0.326 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.49 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.75 Å0.52 Å
Refinement stepCycle: LAST / Resolution: 2.53→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3826 0 0 43 3869
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg0.007
X-RAY DIFFRACTIONc_bond_d1.376
X-RAY DIFFRACTIONc_dihedral_angle_d26.47
X-RAY DIFFRACTIONc_improper_angle_d0.85
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param

+
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://pdbjlvh1.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