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- PDB-2bdn: Crystal structure of human MCP-1 bound to a blocking antibody, 11K2 -

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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 / chemokine (C-C motif) ligand 2 signaling pathway / CCR2 chemokine receptor binding / negative regulation of natural killer cell chemotaxis / astrocyte cell migration / CCR chemokine receptor binding / positive regulation of apoptotic cell clearance / ATF4 activates genes in response to endoplasmic reticulum stress / negative regulation of glial cell apoptotic process / positive regulation of glutamate receptor signaling pathway ...helper T cell extravasation / chemokine (C-C motif) ligand 2 signaling pathway / CCR2 chemokine receptor binding / negative regulation of natural killer cell chemotaxis / astrocyte cell migration / CCR chemokine receptor binding / positive regulation of apoptotic cell clearance / ATF4 activates genes in response to endoplasmic reticulum stress / negative regulation of glial cell apoptotic process / positive regulation of glutamate receptor signaling pathway / NFE2L2 regulating inflammation associated genes / chemokine-mediated signaling pathway / eosinophil chemotaxis / cellular homeostasis / chemokine activity / Chemokine receptors bind chemokines / negative regulation of vascular endothelial cell proliferation / negative regulation of G1/S transition of mitotic cell cycle / positive regulation of macrophage chemotaxis / positive regulation of calcium ion import / chemoattractant activity / macrophage chemotaxis / Interleukin-10 signaling / monocyte chemotaxis / humoral immune response / positive regulation of endothelial cell apoptotic process / cellular response to interleukin-1 / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / cell surface receptor signaling pathway via JAK-STAT / positive regulation of synaptic transmission, glutamatergic / cellular response to fibroblast growth factor stimulus / cytoskeleton organization / sensory perception of pain / viral genome replication / animal organ morphogenesis / response to bacterium / positive regulation of T cell activation / cellular response to type II interferon / cytokine-mediated signaling pathway / chemotaxis / antimicrobial humoral immune response mediated by antimicrobial peptide / 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 / protein phosphorylation / protein kinase activity / cell adhesion / positive regulation of cell migration / G protein-coupled receptor signaling pathway / inflammatory response / signaling receptor binding / positive regulation of gene expression / 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 / Beta Barrel / Immunoglobulin-like / 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
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
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.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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).

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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
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: 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

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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

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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

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