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- PDB-4zkb: The chemokine binding protein of orf virus complexed with CCL3 -

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Basic information

Entry
Database: PDB / ID: 4zkb
TitleThe chemokine binding protein of orf virus complexed with CCL3
Components
  • C-C motif chemokine 3Chemokine
  • Chemokine binding protein
KeywordsViral Protein/cytokine / Complex / Orf chemokine binding protein / CCL3 / Viral Protein-cytokine complex
Function / homology
Function and homology information


granulocyte chemotaxis / CCR1 chemokine receptor binding / positive regulation of microglial cell migration / positive regulation of natural killer cell chemotaxis / regulation of behavior / signaling / astrocyte cell migration / eosinophil degranulation / CCR5 chemokine receptor binding / negative regulation of bone mineralization ...granulocyte chemotaxis / CCR1 chemokine receptor binding / positive regulation of microglial cell migration / positive regulation of natural killer cell chemotaxis / regulation of behavior / signaling / astrocyte cell migration / eosinophil degranulation / CCR5 chemokine receptor binding / negative regulation of bone mineralization / regulation of sensory perception of pain / CCR chemokine receptor binding / positive regulation of microglial cell activation / lymphocyte chemotaxis / cell activation / T cell chemotaxis / positive regulation of calcium ion transport / eosinophil chemotaxis / response to cholesterol / chemokine-mediated signaling pathway / Chemokine receptors bind chemokines / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / chemokine activity / phospholipase activator activity / macrophage chemotaxis / positive regulation of calcium ion import / exocytosis / chemoattractant activity / negative regulation of osteoclast differentiation / Interleukin-10 signaling / monocyte chemotaxis / negative regulation by host of viral transcription / cellular response to interleukin-1 / positive regulation of calcium-mediated signaling / cytoskeleton organization / neutrophil chemotaxis / positive regulation of interleukin-1 beta production / calcium-mediated signaling / intracellular calcium ion homeostasis / response to toxic substance / osteoblast differentiation / 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 / regulation of cell shape / positive regulation of ERK1 and ERK2 cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein kinase activity / positive regulation of cell migration / inflammatory response / G protein-coupled receptor signaling pathway / negative regulation of gene expression / positive regulation of gene expression / extracellular space / extracellular region / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Major secreted virus protein, 35kDa / 35kD major secreted virus protein / Poxvirus chemokine inhibitor superfamily / 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 ...Major secreted virus protein, 35kDa / 35kD major secreted virus protein / Poxvirus chemokine inhibitor superfamily / 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
C-C motif chemokine 3 / Chemokine binding protein
Similarity search - Component
Biological speciesOrf virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsKnapp, K.M. / Nakatani, Y. / Krause, K.L.
CitationJournal: Structure / Year: 2015
Title: Structures of Orf Virus Chemokine Binding Protein in Complex with Host Chemokines Reveal Clues to Broad Binding Specificity.
Authors: Counago, R.M. / Knapp, K.M. / Nakatani, Y. / Fleming, S.B. / Corbett, M. / Wise, L.M. / Mercer, A.A. / Krause, K.L.
History
DepositionApr 30, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 15, 2015Group: Database references
Revision 1.2Jun 13, 2018Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: citation / diffrn_source ...citation / diffrn_source / entity_src_gen / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct / struct_keywords
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site ..._citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _struct.title / _struct_keywords.text
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_mod_residue / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_mod_residue.auth_asym_id / _pdbx_struct_mod_residue.auth_seq_id / _pdbx_struct_mod_residue.label_asym_id / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 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
A: Chemokine binding protein
B: C-C motif chemokine 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9374
Polymers38,9262
Non-polymers1,0112
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1540 Å2
ΔGint-4 kcal/mol
Surface area13080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.000, 78.000, 186.020
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Chemokine binding protein


Mass: 30374.613 Da / Num. of mol.: 1 / Fragment: UNP residues 17-286
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Orf virus (strain NZ2) / Plasmid: PTT5 / Cell line (production host): HEK 293-6E / Production host: Homo sapiens (human) / References: UniProt: Q2F862
#2: Protein C-C motif chemokine 3 / Chemokine / G0/G1 switch regulatory protein 19-1 / Macrophage inflammatory protein 1-alpha / MIP-1-alpha / PAT ...G0/G1 switch regulatory protein 19-1 / Macrophage inflammatory protein 1-alpha / MIP-1-alpha / PAT 464.1 / SIS-beta / Small-inducible cytokine A3 / Tonsillar lymphocyte LD78 alpha protein


Mass: 8551.468 Da / Num. of mol.: 1 / Fragment: UNP residues 24-92
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCL3, G0S19-1, MIP1A, SCYA3 / Plasmid: pTT5 / Cell line (production host): HEK 293-6E / Production host: Homo sapiens (human) / References: UniProt: P10147
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.63 Å3/Da / Density % sol: 66.16 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.2M potassium sodium tartrate tetrahydrate, 0.1M sodium citrate tribasic dihydrate pH5.6, 2.0M ammonium citrate

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Data collection

DiffractionMean temperature: 93.2 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.95369 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Mar 10, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95369 Å / Relative weight: 1
ReflectionResolution: 2.9→47.44 Å / Num. obs: 13416 / % possible obs: 99.8 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.117 / Net I/σ(I): 8.4
Reflection shellResolution: 2.9→3.06 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.757 / Mean I/σ(I) obs: 1.8 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4P5I

4p5i


Resolution: 2.9→47.44 Å / Cor.coef. Fo:Fc: 0.903 / Cor.coef. Fo:Fc free: 0.837 / SU B: 41.375 / SU ML: 0.353 / Cross valid method: THROUGHOUT / ESU R: 0.492 / ESU R Free: 0.372 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.32302 692 5.2 %RANDOM
Rwork0.26769 ---
obs0.27041 12641 99.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 78.862 Å2
Baniso -1Baniso -2Baniso -3
1-2.08 Å20 Å20 Å2
2--2.08 Å20 Å2
3----4.16 Å2
Refinement stepCycle: LAST / Resolution: 2.9→47.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1852 0 67 0 1919
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0191959
X-RAY DIFFRACTIONr_bond_other_d0.0010.021675
X-RAY DIFFRACTIONr_angle_refined_deg1.4442.0042684
X-RAY DIFFRACTIONr_angle_other_deg0.79533811
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4845262
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.42624.32867
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.64915241
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.997159
X-RAY DIFFRACTIONr_chiral_restr0.0680.2328
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212247
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02406
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5874.3021063
X-RAY DIFFRACTIONr_mcbond_other1.5874.31062
X-RAY DIFFRACTIONr_mcangle_it2.6356.4491320
X-RAY DIFFRACTIONr_mcangle_other2.6346.4511321
X-RAY DIFFRACTIONr_scbond_it2.6594.73896
X-RAY DIFFRACTIONr_scbond_other2.6574.731897
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.2857.0121364
X-RAY DIFFRACTIONr_long_range_B_refined5.33536.5412176
X-RAY DIFFRACTIONr_long_range_B_other5.33436.5522177
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.424 53 -
Rwork0.375 902 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.09540.3791-1.1722.4897-1.01957.99930.0397-0.43710.0142-0.1541-0.02690.4306-0.1817-0.6727-0.01280.02730.0475-0.03040.3164-0.00450.0789-27.4148-13.671512.0863
26.69211.6936-2.04565.70280.5487.79060.1814-1.01551.14180.2215-0.6392-0.1688-1.6641-0.15580.45780.89620.1602-0.07280.7882-0.20880.4088-24.61065.482619.8154
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A11 - 269
2X-RAY DIFFRACTION2B8 - 64

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