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- PDB-2nz1: Viral Chemokine Binding Protein M3 From Murine Gammaherpesvirus68... -

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Basic information

Entry
Database: PDB / ID: 2nz1
TitleViral Chemokine Binding Protein M3 From Murine Gammaherpesvirus68 In Complex With The CC-Chemokine CCL2/MCP-1
Components
  • Hypothetical protein GAMMAHV.M3Hypothesis
  • Small inducible cytokine A2
KeywordsVIRAL PROTEIN/CYTOKINE / Viral Decoy Receptor / Chemokine / Protein-Protein Complex / VIRAL PROTEIN-CYTOKINE 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 / chemokine binding / 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 ...helper T cell extravasation / CCR2 chemokine receptor binding / negative regulation of natural killer cell chemotaxis / positive regulation of NMDA glutamate receptor activity / chemokine binding / 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 / NFE2L2 regulating inflammation associated genes / eosinophil chemotaxis / positive regulation of endothelial cell apoptotic process / 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 / macrophage chemotaxis / positive regulation of nitric-oxide synthase biosynthetic process / 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 / Interleukin-4 and Interleukin-13 signaling / angiogenesis / cellular response to lipopolysaccharide / 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
Immunoglobulin-like - #1330 / Chemokine-binding protein M3-like / Chemokine-binding M3, viral / Chemokine-binding M3, subdomain 1, viral / Chemokine-binding M3, subdomain 2, viral / Chemokine-binding M3 superfamily / M3 / CC chemokine, conserved site / Small cytokines (intercrine/chemokine) C-C subfamily signature. / Chemokine beta/gamma/delta ...Immunoglobulin-like - #1330 / Chemokine-binding protein M3-like / Chemokine-binding M3, viral / Chemokine-binding M3, subdomain 1, viral / Chemokine-binding M3, subdomain 2, viral / Chemokine-binding M3 superfamily / M3 / 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) / Immunoglobulin-like / Beta Barrel / Sandwich / Mainly Beta
Similarity search - Domain/homology
M3 / C-C motif chemokine 2
Similarity search - Component
Biological speciesMurid herpesvirus 4 (Murine herpesvirus 68)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsAlexander-Brett, J.M. / Fremont, D.H.
CitationJournal: J.Exp.Med. / Year: 2007
Title: Dual GPCR and GAG mimicry by the M3 chemokine decoy receptor.
Authors: Alexander-Brett, J.M. / Fremont, D.H.
History
DepositionNov 22, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hypothetical protein GAMMAHV.M3
B: Hypothetical protein GAMMAHV.M3
D: Small inducible cytokine A2
E: Small inducible cytokine A2
X: Hypothetical protein GAMMAHV.M3
Y: Small inducible cytokine A2


Theoretical massNumber of molelcules
Total (without water)151,5226
Polymers151,5226
Non-polymers00
Water10,124562
1
A: Hypothetical protein GAMMAHV.M3
B: Hypothetical protein GAMMAHV.M3
D: Small inducible cytokine A2
E: Small inducible cytokine A2


Theoretical massNumber of molelcules
Total (without water)101,0144
Polymers101,0144
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7050 Å2
ΔGint-39 kcal/mol
Surface area37450 Å2
MethodPISA, PQS
2
X: Hypothetical protein GAMMAHV.M3
Y: Small inducible cytokine A2

X: Hypothetical protein GAMMAHV.M3
Y: Small inducible cytokine A2


Theoretical massNumber of molelcules
Total (without water)101,0144
Polymers101,0144
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
MethodPQS
Unit cell
Length a, b, c (Å)99.240, 99.240, 243.460
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Hypothetical protein GAMMAHV.M3 / Hypothesis / M3 protein


Mass: 41826.230 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Murid herpesvirus 4 (Murine herpesvirus 68)
Genus: Rhadinovirus / Gene: GAMMAHV.M3, M3 / Plasmid: PFB-1 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O41925
#2: 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: 8681.007 Da / Num. of mol.: 3 / Mutation: M87I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCL2, MCP1, SCYA2 / Plasmid: Paed-4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 PLys S / References: UniProt: P13500
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 562 / 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: 2.28 Å3/Da / Density % sol: 46.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.1
Details: 12% PEG 4000, 100 mM sodium acetate, 200 mM magnesium chloride, pH 4.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 22, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. all: 49106 / Num. obs: 45669 / % possible obs: 93.4 % / Observed criterion σ(F): 0 / Redundancy: 6 % / Biso Wilson estimate: 32.7 Å2 / Rsym value: 0.139 / Net I/σ(I): 11.7
Reflection shellResolution: 2.5→2.61 Å / Redundancy: 6 % / Mean I/σ(I) obs: 4.1 / Num. unique all: 6652 / Rsym value: 0.412 / % possible all: 87.3

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB CODE 1ML0

1ml0


Resolution: 2.5→19.75 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 445022.33 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.3 2258 4.9 %RANDOM
Rwork0.231 ---
obs0.231 45669 93.4 %-
all-49106 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.4868 Å2 / ksol: 0.334325 e/Å3
Displacement parametersBiso mean: 37.4 Å2
Baniso -1Baniso -2Baniso -3
1--5.08 Å22.85 Å20 Å2
2---5.08 Å20 Å2
3---10.16 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.34 Å
Luzzati d res low-20 Å
Luzzati sigma a0.41 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 2.5→19.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10110 0 0 562 10672
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d25.4
X-RAY DIFFRACTIONc_improper_angle_d0.87
X-RAY DIFFRACTIONc_mcbond_it2.332
X-RAY DIFFRACTIONc_mcangle_it3.843
X-RAY DIFFRACTIONc_scbond_it5.014
X-RAY DIFFRACTIONc_scangle_it6.635
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.358 342 4.9 %
Rwork0.275 6652 -
obs-6652 87.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.param

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