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

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Basic information

Entry
Database: PDB / ID: 2nyz
TitleViral Chemokine Binding Protein M3 From Murine Gammaherpesvirus68 In Complex With The C- Chemokine XCL1
Components
  • Hypothetical protein GAMMAHV.M3
  • Lymphotactin
KeywordsVIRAL PROTEIN/CYTOKINE / Viral Decoy Receptor / Chemokine / Protein-Protein Complex / VIRAL PROTEIN-CYTOKINE COMPLEX
Function / homology
Function and homology information


mature natural killer cell chemotaxis / positive regulation of granzyme A production / negative regulation of T-helper 1 cell activation / positive regulation of immunoglobulin production in mucosal tissue / positive regulation of granzyme B production / positive regulation of thymocyte migration / positive regulation of B cell chemotaxis / negative regulation of T cell cytokine production / negative regulation of T-helper 1 type immune response / positive regulation of natural killer cell chemotaxis ...mature natural killer cell chemotaxis / positive regulation of granzyme A production / negative regulation of T-helper 1 cell activation / positive regulation of immunoglobulin production in mucosal tissue / positive regulation of granzyme B production / positive regulation of thymocyte migration / positive regulation of B cell chemotaxis / negative regulation of T cell cytokine production / negative regulation of T-helper 1 type immune response / positive regulation of natural killer cell chemotaxis / chemokine binding / chemokine receptor binding / positive regulation of transforming growth factor beta production / positive regulation of T-helper 1 cell cytokine production / positive regulation of T cell chemotaxis / CCR chemokine receptor binding / positive regulation of T-helper 2 cell cytokine production / positive regulation of leukocyte chemotaxis / negative regulation of CD4-positive, alpha-beta T cell proliferation / chemokine-mediated signaling pathway / positive regulation of CD4-positive, alpha-beta T cell proliferation / eosinophil chemotaxis / chemokine activity / positive regulation of neutrophil chemotaxis / Chemokine receptors bind chemokines / negative regulation of interleukin-2 production / positive regulation of CD8-positive, alpha-beta T cell proliferation / negative regulation of type II interferon production / positive regulation of interleukin-10 production / cellular response to transforming growth factor beta stimulus / release of sequestered calcium ion into cytosol / neutrophil chemotaxis / cellular response to interleukin-4 / positive regulation of release of sequestered calcium ion into cytosol / negative regulation of DNA-binding transcription factor activity / positive regulation of T cell cytokine production / response to virus / positive regulation of T cell mediated cytotoxicity / antimicrobial humoral immune response mediated by antimicrobial peptide / cell-cell signaling / regulation of inflammatory response / G alpha (q) signalling events / positive regulation of cell migration / inflammatory response / negative regulation of DNA-templated transcription / signal transduction / protein homodimerization activity / 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 / C chemokine / Chemokine beta/gamma/delta / Intercrine alpha family (small cytokine C-X-C) (chemokine CXC). ...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 / C chemokine / 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
Biological speciesMurid herpesvirus 4 (Murine herpesvirus 68)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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 21, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 2023Group: 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 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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: Lymphotactin
E: Lymphotactin


Theoretical massNumber of molelcules
Total (without water)104,2264
Polymers104,2264
Non-polymers00
Water3,495194
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.370, 103.190, 290.940
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121
Detailsasymmetric unit contains biological unit (2 monomers)

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Components

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


Mass: 41826.230 Da / Num. of mol.: 2
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 Lymphotactin / XCL1 / Cytokine SCM-1 / ATAC / Lymphotaxin / SCM-1-alpha / Small inducible cytokine C1 / XC chemokine ligand 1


Mass: 10286.789 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: The peptide was chemically synthesized. The sequence of the peptide can be naturally found in Homo sapiens (Human).
References: UniProt: P47992
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 194 / 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: 3.04 Å3/Da / Density % sol: 59.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.1
Details: 10% PEG 8000, 100 mM TRIS, pH 6.1, 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: 2.6→20 Å / Num. all: 35910 / Num. obs: 35559 / % possible obs: 90 % / Observed criterion σ(F): 0 / Redundancy: 7 % / Biso Wilson estimate: 42.8 Å2 / Rsym value: 0.01 / Net I/σ(I): 16.1
Reflection shellResolution: 2.6→2.76 Å / Redundancy: 2 % / Mean I/σ(I) obs: 2.7 / Num. unique all: 4850 / Rsym value: 0.49 / % possible all: 79.2

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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 ENTRY 1ML0

1ml0


Resolution: 2.6→19.95 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 588744.74 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.272 1771 5 %RANDOM
Rwork0.219 ---
obs0.219 35559 90 %-
all-39510 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 36.5738 Å2 / ksol: 0.324539 e/Å3
Displacement parametersBiso mean: 59.4 Å2
Baniso -1Baniso -2Baniso -3
1-17.94 Å20 Å20 Å2
2--0.98 Å20 Å2
3----18.92 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.46 Å0.36 Å
Luzzati d res low-20 Å
Luzzati sigma a0.56 Å0.46 Å
Refinement stepCycle: LAST / Resolution: 2.6→19.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6718 0 0 194 6912
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d25.3
X-RAY DIFFRACTIONc_improper_angle_d0.96
X-RAY DIFFRACTIONc_mcbond_it2.412
X-RAY DIFFRACTIONc_mcangle_it4.173
X-RAY DIFFRACTIONc_scbond_it4.924
X-RAY DIFFRACTIONc_scangle_it6.955
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.422 280 5.5 %
Rwork0.373 4850 -
obs-4850 79.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.param

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