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- PDB-4zlt: Crystal structure of viral chemokine binding protein R17 in compl... -

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Basic information

Entry
Database: PDB / ID: 4zlt
TitleCrystal structure of viral chemokine binding protein R17 in complex with CCL3
Components
  • C-C motif chemokine 3Chemokine
  • Putative uncharacterized protein
KeywordsChemokine binding protein/Chemokine / RHVP chemokine binding protein in complex with chemokine CCL3 / Chemokine binding protein-Chemokine complex
Function / homology
Function and homology information


Chemokine receptors bind chemokines / calcium,diacylglycerol-dependent serine/threonine kinase activity / granulocyte chemotaxis / positive regulation of natural killer cell chemotaxis / signaling / astrocyte cell migration / response to xenobiotic stimulus => GO:0009410 / eosinophil degranulation / regulation of sensory perception of pain / CCR chemokine receptor binding ...Chemokine receptors bind chemokines / calcium,diacylglycerol-dependent serine/threonine kinase activity / granulocyte chemotaxis / positive regulation of natural killer cell chemotaxis / signaling / astrocyte cell migration / response to xenobiotic stimulus => GO:0009410 / eosinophil degranulation / regulation of sensory perception of pain / CCR chemokine receptor binding / lymphocyte chemotaxis / cell activation / T cell chemotaxis / positive regulation of calcium ion transport / eosinophil chemotaxis / response to cholesterol / positive regulation of osteoclast differentiation / chemokine-mediated signaling pathway / leukocyte chemotaxis / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / chemokine activity / phospholipase activator activity / macrophage chemotaxis / exocytosis / chemoattractant activity / negative regulation of osteoclast differentiation / monocyte chemotaxis / cellular response to organic cyclic compound / negative regulation by host of viral transcription / cellular response to interleukin-1 / positive regulation of calcium-mediated signaling / cytoskeleton organization / lipopolysaccharide-mediated signaling pathway / neutrophil chemotaxis / phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of interleukin-1 beta production / calcium-mediated signaling / intracellular calcium ion homeostasis / response to toxic substance / osteoblast differentiation / positive regulation of GTPase activity / positive regulation of inflammatory response / cellular response to type II interferon / positive regulation of neuron apoptotic process / calcium ion transport / chemotaxis / MAPK cascade / positive regulation of tumor necrosis factor production / cell-cell signaling / cellular response to tumor necrosis factor / kinase activity / positive regulation of cytosolic calcium ion concentration / regulation of cell shape / positive regulation of ERK1 and ERK2 cascade / protein kinase activity / positive regulation of cell migration / inflammatory response / G protein-coupled receptor signaling pathway / negative regulation of gene expression / protein phosphorylation / positive regulation of gene expression / positive regulation of transcription by RNA polymerase II / extracellular space / cytosol / cytoplasm
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) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Uncharacterized protein / C-C motif chemokine 3
Similarity search - Component
Biological speciesCricetid herpesvirus 2
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsLubman, O.Y. / Fremont, D.H.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI019687 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U54 AI057160 United States
Center for Women Infectious Disease Research United States
Washington University/Pfizer Agreement United States
CitationJournal: Structure / Year: 2016
Title: Parallel Evolution of Chemokine Binding by Structurally Related Herpesvirus Decoy Receptors.
Authors: Lubman, O.Y. / Fremont, D.H.
History
DepositionMay 1, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 18, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 30, 2015Group: Database references
Revision 1.2Jan 20, 2016Group: Database references
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Nov 1, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.5Aug 22, 2018Group: Data collection / Category: reflns_shell
Revision 1.6Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.7Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.8Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Putative uncharacterized protein
A: Putative uncharacterized protein
F: C-C motif chemokine 3
L: C-C motif chemokine 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,6268
Polymers110,7414
Non-polymers8854
Water0
1
B: Putative uncharacterized protein
F: C-C motif chemokine 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,8134
Polymers55,3712
Non-polymers4422
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3060 Å2
ΔGint-8 kcal/mol
Surface area20740 Å2
MethodPISA
2
A: Putative uncharacterized protein
L: C-C motif chemokine 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,8134
Polymers55,3712
Non-polymers4422
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3280 Å2
ΔGint-9 kcal/mol
Surface area19970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.493, 109.482, 210.956
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Detailsdimer according to multi-angle static light scattering

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Components

#1: Protein Putative uncharacterized protein


Mass: 47388.625 Da / Num. of mol.: 2 / Mutation: K333D, R335E, R336E, K337D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cricetid herpesvirus 2 / Gene: RHVP-L.R17, RHVP.R17 / Cell (production host): endothelial / Cell line (production host): 293F / Production host: Mammalian expression vector pBGSA (others) / References: UniProt: E9M5R0
#2: Protein C-C motif chemokine 3 / Chemokine / Heparin-binding chemotaxis protein / L2G25B / Macrophage inflammatory protein 1-alpha / MIP-1-alpha ...Heparin-binding chemotaxis protein / L2G25B / Macrophage inflammatory protein 1-alpha / MIP-1-alpha / SIS-alpha / Small-inducible cytokine A3 / TY-5


Mass: 7982.065 Da / Num. of mol.: 2 / Mutation: D27A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ccl3, Mip1a, Scya3 / Plasmid: pet28A / Production host: Escherichia coli (E. coli) / References: UniProt: P10855
#3: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.57 Å3/Da / Density % sol: 52.1 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / Details: 15-20% PEG 3350 0.2-0.4M MgFormate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Jun 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.761→50 Å / Num. obs: 26825 / % possible obs: 100 % / Redundancy: 4.7 % / Rsym value: 0.11 / Net I/σ(I): 7.4
Reflection shell
Resolution (Å)Redundancy (%)Diffraction-ID
2.78-3.6811
19.68-49.22

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
HKL-2000data scaling
PHASERphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZKQ and 2X6G

4zkq

2x6g


Resolution: 3→49.247 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 27.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.274 1618 7.47 %
Rwork0.2152 --
obs0.2195 21657 93.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3→49.247 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6977 0 56 0 7033
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037203
X-RAY DIFFRACTIONf_angle_d0.4629779
X-RAY DIFFRACTIONf_dihedral_angle_d10.9934342
X-RAY DIFFRACTIONf_chiral_restr0.041112
X-RAY DIFFRACTIONf_plane_restr0.0031239
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0002-3.08840.4558950.32931219X-RAY DIFFRACTION70
3.0884-3.18810.34491190.30481470X-RAY DIFFRACTION83
3.1881-3.3020.31681350.27641656X-RAY DIFFRACTION93
3.302-3.43420.34641370.24621684X-RAY DIFFRACTION96
3.4342-3.59040.26261420.25011711X-RAY DIFFRACTION96
3.5904-3.77970.28451400.22421731X-RAY DIFFRACTION97
3.7797-4.01640.26581310.2221659X-RAY DIFFRACTION93
4.0164-4.32630.26321360.20191684X-RAY DIFFRACTION95
4.3263-4.76140.22141420.17211758X-RAY DIFFRACTION97
4.7614-5.44960.24141430.17381765X-RAY DIFFRACTION98
5.4496-6.8630.26041430.22411796X-RAY DIFFRACTION99
6.863-49.25310.27981550.19881906X-RAY DIFFRACTION100

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