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- PDB-4dn4: Crystal structure of the complex between cnto888 fab and mcp-1 mu... -

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Basic information

Entry
Database: PDB / ID: 4dn4
TitleCrystal structure of the complex between cnto888 fab and mcp-1 mutant p8a
Components
  • C-C motif chemokine 2
  • CNTO888 HEAVY CHAIN
  • CNTO888 LIGHT CHAIN
KeywordsIMMUNE SYSTEM / antibody chemokine
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
ACETATE ION / C-C motif chemokine 2
Similarity search - Component
Biological speciesHomo sapiens (human)
HOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsObmolova, G. / Teplyakov, A. / Malia, T. / Grygiel, T. / Sweet, R. / Snyder, L. / Gilliland, G.
CitationJournal: Mol.Immunol. / Year: 2012
Title: Structural basis for high selectivity of anti-CCL2 neutralizing antibody CNTO 888.
Authors: Obmolova, G. / Teplyakov, A. / Malia, T.J. / Grygiel, T.L. / Sweet, R. / Snyder, L.A. / Gilliland, G.L.
History
DepositionFeb 8, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: CNTO888 LIGHT CHAIN
H: CNTO888 HEAVY CHAIN
M: C-C motif chemokine 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,7427
Polymers56,4733
Non-polymers2694
Water1,40578
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5350 Å2
ΔGint-28 kcal/mol
Surface area21930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.010, 136.010, 109.290
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

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Protein , 1 types, 1 molecules M

#3: Protein C-C motif chemokine 2 / HC11 / Monocyte chemoattractant protein 1 / Monocyte chemotactic and activating factor / MCAF / ...HC11 / Monocyte chemoattractant protein 1 / Monocyte chemotactic and activating factor / MCAF / Monocyte chemotactic protein 1 / MCP-1 / Monocyte secretory protein JE / Small-inducible cytokine A2


Mass: 8673.009 Da / Num. of mol.: 1 / Mutation: P8A / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P13500

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Antibody , 2 types, 2 molecules LH

#1: Antibody CNTO888 LIGHT CHAIN


Mass: 23625.201 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): (HEK) 293 / Production host: HOMO SAPIENS (human)
#2: Antibody CNTO888 HEAVY CHAIN


Mass: 24175.004 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCL2, MCP1, SCYA2 / Cell line (production host): (HEK) 293 / Production host: HOMO SAPIENS (human)

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Non-polymers , 3 types, 82 molecules

#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / Source method: isolated from a natural source / Formula: H2O

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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: 2.6 Å3/Da / Density % sol: 52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 1.8 M AMMONIUM SULFATE, 0.1 M ACETATE, CRYO CONDITIONS: 2.0 M AMMONIUM SULFATE, 0.1 M ACETATE PH 5.5, 25% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Jan 6, 2009 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. all: 15133 / Num. obs: 15133 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 26.7 % / Biso Wilson estimate: 30.1 Å2 / Rmerge(I) obs: 0.149
Reflection shellResolution: 2.8→2.88 Å / Redundancy: 25.8 % / Rmerge(I) obs: 0.557 / % possible all: 98.5

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Processing

Software
NameVersionClassification
CrystalCleardata collection
MOLREPphasing
REFMAC5.5.0109refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→15 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.85 / SU B: 13.749 / SU ML: 0.274 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.393 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.26565 839 5.6 %RANDOM
Rwork0.19573 ---
all0.19955 14181 --
obs0.19955 14181 94.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 39.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.71 Å20.35 Å20 Å2
2--0.71 Å20 Å2
3----1.06 Å2
Refinement stepCycle: LAST / Resolution: 2.8→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3709 0 18 78 3805
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0223818
X-RAY DIFFRACTIONr_angle_refined_deg1.0611.9545189
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2445484
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.20624.122148
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.17815612
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.61516
X-RAY DIFFRACTIONr_chiral_restr0.070.2589
X-RAY DIFFRACTIONr_gen_planes_refined00.0212856
X-RAY DIFFRACTIONr_mcbond_it1.06422438
X-RAY DIFFRACTIONr_mcangle_it2.35843937
X-RAY DIFFRACTIONr_scbond_it26.169881380
X-RAY DIFFRACTIONr_scangle_it26.562881252
LS refinement shellResolution: 2.803→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 48 -
Rwork0.242 993 -
obs--98.5 %

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