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- PDB-4zk9: The chemokine binding protein of orf virus complexed with CCL2 -

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Basic information

Entry
Database: PDB / ID: 4zk9
TitleThe chemokine binding protein of orf virus complexed with CCL2
Components
  • C-C motif chemokine 2
  • Chemokine binding protein
KeywordsViral Protein/cytokine / Complex / Orf virus chemokine binding protein / Human C-C motif chemokine 2 / Viral Protein-cytokine complex
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 / 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 ...helper T cell extravasation / chemokine (C-C motif) ligand 2 signaling pathway / CCR2 chemokine receptor binding / negative regulation of natural killer cell chemotaxis / 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 / Chemokine receptors bind chemokines / negative regulation of vascular endothelial cell proliferation / 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 / cytoskeleton organization / sensory perception of pain / 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 / identical protein binding
Similarity search - Function
Major secreted virus protein, 35kDa / Poxvirus chemokine inhibitor superfamily / Viral chemokine binding protein / 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 / Poxvirus chemokine inhibitor superfamily / Viral chemokine binding protein / 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 2 / Chemokine binding protein
Similarity search - Component
Biological speciesOrf virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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 / _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
Revision 2.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,2144
Polymers40,0412
Non-polymers1,1732
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2190 Å2
ΔGint-9 kcal/mol
Surface area12870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.802, 78.802, 185.613
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 2 / HC11 / Monocyte chemoattractant protein 1 / Monocyte chemotactic and activating factor / MCAF / ...HC11 / Monocyte chemoattractant protein 1 / Monocyte chemotactic and activating factor / MCAF / Monocyte chemotactic protein 1 / MCP-1 / Monocyte secretory protein JE / Small-inducible cytokine A2


Mass: 9666.073 Da / Num. of mol.: 1 / Fragment: UNP residues 17-99
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCL2, MCP1, SCYA2 / Plasmid: pTT5 / Cell line (production host): HEK 293-6E / Production host: Homo sapiens (human) / References: UniProt: P13500
#3: 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.: 2
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
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: 3.63 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: 2.6→38.54 Å / Num. obs: 18835 / % possible obs: 100 % / Redundancy: 14.2 % / Biso Wilson estimate: 62.6 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 31.9
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 14.6 % / Rmerge(I) obs: 0.893 / Mean I/σ(I) obs: 3.1 / % 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: 2.6→38.54 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.901 / SU B: 19.925 / SU ML: 0.198 / Cross valid method: THROUGHOUT / ESU R: 0.294 / ESU R Free: 0.254 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28094 962 5.1 %RANDOM
Rwork0.23849 ---
obs0.24062 17803 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 77.474 Å2
Baniso -1Baniso -2Baniso -3
1-2.07 Å20 Å20 Å2
2--2.07 Å20 Å2
3----4.13 Å2
Refinement stepCycle: LAST / Resolution: 2.6→38.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1984 0 78 0 2062
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0192116
X-RAY DIFFRACTIONr_bond_other_d0.0010.021828
X-RAY DIFFRACTIONr_angle_refined_deg1.1942.0012900
X-RAY DIFFRACTIONr_angle_other_deg0.69934171
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7395276
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.01524.69181
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.45815280
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.041510
X-RAY DIFFRACTIONr_chiral_restr0.0660.2351
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212418
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02444
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_it1.484.511110
X-RAY DIFFRACTIONr_mcbond_other1.4814.5091109
X-RAY DIFFRACTIONr_mcangle_it2.5086.761384
X-RAY DIFFRACTIONr_mcangle_other2.5076.7611385
X-RAY DIFFRACTIONr_scbond_it2.2744.9481006
X-RAY DIFFRACTIONr_scbond_other2.2734.9491007
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.6787.3621517
X-RAY DIFFRACTIONr_long_range_B_refined4.60836.9022144
X-RAY DIFFRACTIONr_long_range_B_other4.60736.9112145
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.378 79 -
Rwork0.318 1277 -
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)DetailsOrigin x (Å)Origin y (Å)Origin z (Å)
12.29570.21741.17512.23051.20217.1091-0.00750.0402-0.4095-0.2865-0.05190.0440.64010.04620.05940.2121-0.00570.02510.008-0.00850.0851Chain A chemokine binding protein-14.0312-27.7463-12.3937
25.98192.5391-2.03758.27371.37384.8183-0.19020.65460.4635-1.08370.124-0.311-0.26640.8450.06630.51090.02920.14840.72130.01020.4371Human C-C motif chemokine 23.9958-23.5008-21.6598
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A11 - 269
2X-RAY DIFFRACTION2B9 - 69

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