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- PDB-1ml0: VIRAL CHEMOKINE BINDING PROTEIN M3 FROM MURINE GAMMAHERPESVIRUS68... -

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Basic information

Entry
Database: PDB / ID: 1ml0
TitleVIRAL CHEMOKINE BINDING PROTEIN M3 FROM MURINE GAMMAHERPESVIRUS68 IN COMPLEX WITH THE P8A VARIANT OF CC-CHEMOKINE MCP-1
Components
  • M3 Protein
  • Small Inducible Cytokine
KeywordsIMMUNE SYSTEM / HERPESVIRUS / VIRAL IMMUNE EVASION / CHEMOKINE BINDING PROTEIN / DECOY RECEPTOR
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 / chemokine binding / 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 ...helper T cell extravasation / chemokine (C-C motif) ligand 2 signaling pathway / CCR2 chemokine receptor binding / negative regulation of natural killer cell chemotaxis / chemokine binding / 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 / negative regulation of vascular endothelial cell proliferation / Chemokine receptors bind chemokines / 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 / sensory perception of pain / cytoskeleton organization / 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
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) / Beta Barrel / Immunoglobulin-like / 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 / MAD, MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsAlexander, J.M. / Fremont, D.H.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2002
Title: Structural Basis of Chemokine Sequestration by a Herpesvirus Decoy Receptor
Authors: Alexander, J.M. / Nelson, C.A. / van Berkel, V. / Lau, E.K. / Studts, J.M. / Brett, T.J. / Speck, S.H. / Handel, T.M. / Virgin, H.W. / Fremont, D.H.
History
DepositionAug 29, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 27, 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 1.4Nov 6, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: M3 Protein
D: Small Inducible Cytokine


Theoretical massNumber of molelcules
Total (without water)50,4812
Polymers50,4812
Non-polymers00
Water77543
1
A: M3 Protein
D: Small Inducible Cytokine

A: M3 Protein
D: Small Inducible Cytokine


Theoretical massNumber of molelcules
Total (without water)100,9624
Polymers100,9624
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_556x-y,-y,-z+11
Buried area6840 Å2
ΔGint-41 kcal/mol
Surface area37310 Å2
MethodPISA
2
A: M3 Protein
D: Small Inducible Cytokine
x 6


Theoretical massNumber of molelcules
Total (without water)302,88712
Polymers302,88712
Non-polymers00
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_556y,x,-z+11
crystal symmetry operation5_556x-y,-y,-z+11
crystal symmetry operation6_556-x,-x+y,-z+11
MethodPQS
Unit cell
Length a, b, c (Å)99.200, 99.200, 78.900
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11A-409-

HOH

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Components

#1: Protein M3 Protein


Mass: 41826.230 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Murid herpesvirus 4 (Murine herpesvirus 68)
Genus: Rhadinovirus / Gene: M3 / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O41925
#2: Protein Small Inducible Cytokine / CCL2 / Monocyte chemotactic protein 1 / MCP-1 / Monocyte chemotactic protein 1 / MCP-1 / Monocyte ...CCL2 / Monocyte chemotactic protein 1 / MCP-1 / Monocyte chemotactic protein 1 / MCP-1 / Monocyte chemoattractant protein-1 / Monocyte chemotactic and activating factor / MCAF / Monocyte secretory protein JE / HC11


Mass: 8654.971 Da / Num. of mol.: 1 / Mutation: P8A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MONOCYTE CHEMOATTRACTANT PROTEIN 1 / Plasmid: PAED-4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 PLYS S / References: UniProt: P13500
#3: 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: 2.21 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.1
Details: 14% PEG4000 200MM, SODIUM ACETATE, 100MM MAGNESIUM CHLORIDE, pH 4.10, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
pH: 4.1
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
115 mg/mlprotein1drop
214 %PEG40001reservoir
3200 mMsodium acetate1reservoirpH4.1
4100 mM1reservoirMgCl2

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 / Wavelength: 1.000, 0.9796, 0.9789, 0.9599
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 1, 2000
RadiationMonochromator: SI 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.11
211
30.97961
40.97891
50.95991
ReflectionResolution: 2.8→20 Å / Num. all: 11156 / Num. obs: 11156 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 13.4 % / Biso Wilson estimate: 70.9 Å2 / Rsym value: 0.088 / Net I/σ(I): 14.5
Reflection shellResolution: 2.8→2.97 Å / Mean I/σ(I) obs: 4.8 / Rsym value: 0.422 / % possible all: 97.9
Reflection
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 20 Å / Num. obs: 16718 / % possible obs: 96.3 % / Num. measured all: 41932 / Rmerge(I) obs: 0.08
Reflection shell
*PLUS
Highest resolution: 3 Å / Lowest resolution: 3.19 Å / % possible obs: 94.4 % / Rmerge(I) obs: 0.286 / Mean I/σ(I) obs: 3.2

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MAD, MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1MKF

1mkf


Resolution: 2.8→19.37 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 36852.37 / Data cutoff high rms absF: 36852.37 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.282 569 5.2 %RANDOM
Rwork0.201 ---
all-10904 --
obs-10904 96 %-
Solvent computationBsol: 43.4831 Å2 / ksol: 0.316929 e/Å3
Displacement parametersBiso mean: 62.8 Å2
Baniso -1Baniso -2Baniso -3
1--14.22 Å25.3 Å20 Å2
2---14.22 Å20 Å2
3---28.43 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.33 Å
Luzzati d res low-6 Å
Luzzati sigma a0.6 Å0.46 Å
Refinement stepCycle: LAST / Resolution: 2.8→19.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3368 0 0 43 3411
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONo_bond_d0.008
X-RAY DIFFRACTIONo_angle_deg1.4
X-RAY DIFFRACTIONo_dihedral_angle_d25.7
X-RAY DIFFRACTIONo_improper_angle_d0.87
X-RAY DIFFRACTIONo_mcbond_it1.361.5
X-RAY DIFFRACTIONo_mcangle_it2.422
X-RAY DIFFRACTIONo_scbond_it1.82
X-RAY DIFFRACTIONo_scangle_it2.792.5
LS refinement shellResolution: 2.8→2.97 Å / Rfactor Rfree error: 0.039 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.371 91 5.5 %
Rwork0.324 1564 -
obs-1564 89.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
Lowest resolution: 19.37 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_dihedral_angle_d
X-RAY DIFFRACTIONo_dihedral_angle_deg25.7
X-RAY DIFFRACTIONo_improper_angle_d
X-RAY DIFFRACTIONo_improper_angle_deg0.87
LS refinement shell
*PLUS
Highest resolution: 2.8 Å

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