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- PDB-4pdc: Crystal structure of Cowpox virus CPXV018 (OMCP) bound to human NKG2D -

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Basic information

Entry
Database: PDB / ID: 4pdc
TitleCrystal structure of Cowpox virus CPXV018 (OMCP) bound to human NKG2D
Components
  • CPXV018 protein
  • NKG2-D type II integral membrane protein
KeywordsIMMUNE SYSTEM/VIRAL PROTEIN / secreted viral protein / immune evasion / orthopoxvirus / MHC-like fold / NK cell receptor ligand / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / IMMUNE SYSTEM-VIRAL PROTEIN complex
Function / homology
Function and homology information


negative regulation of natural killer cell chemotaxis / MHC class Ib receptor activity / positive regulation of natural killer cell mediated cytotoxicity / natural killer cell mediated cytotoxicity / natural killer cell activation / negative regulation of GTPase activity / MHC class I protein binding / stimulatory C-type lectin receptor signaling pathway / T cell costimulation / nitric oxide biosynthetic process ...negative regulation of natural killer cell chemotaxis / MHC class Ib receptor activity / positive regulation of natural killer cell mediated cytotoxicity / natural killer cell mediated cytotoxicity / natural killer cell activation / negative regulation of GTPase activity / MHC class I protein binding / stimulatory C-type lectin receptor signaling pathway / T cell costimulation / nitric oxide biosynthetic process / DAP12 interactions / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of nitric oxide biosynthetic process / positive regulation of type II interferon production / DAP12 signaling / signaling receptor activity / carbohydrate binding / cellular response to lipopolysaccharide / adaptive immune response / cell differentiation / defense response to Gram-positive bacterium / external side of plasma membrane / cell surface / signal transduction / identical protein binding / membrane / plasma membrane
Similarity search - Function
NKG2-D type II integral membrane protein / Natural killer cell receptor-like, C-type lectin-like domain / Mannose-Binding Protein A; Chain A / Mannose-Binding Protein A, subunit A / Lectin C-type domain / C-type lectin domain profile. / C-type lectin-like / C-type lectin (CTL) or carbohydrate-recognition domain (CRD) / C-type lectin-like/link domain superfamily / C-type lectin fold ...NKG2-D type II integral membrane protein / Natural killer cell receptor-like, C-type lectin-like domain / Mannose-Binding Protein A; Chain A / Mannose-Binding Protein A, subunit A / Lectin C-type domain / C-type lectin domain profile. / C-type lectin-like / C-type lectin (CTL) or carbohydrate-recognition domain (CRD) / C-type lectin-like/link domain superfamily / C-type lectin fold / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / Roll / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
NKG2-D type II integral membrane protein / CPXV018 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Cowpox virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.991 Å
Model detailsStrain Brighton Red
AuthorsLazear, E. / Nelson, C.A. / Fremont, D.H. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI073552 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI057160 United States
CitationJournal: Biorxiv / Year: 2019
Title: Structural basis of cowpox evasion of NKG2D immunosurveillance
Authors: Lazear, E. / Sun, M.M. / Wang, X. / Geurs, T.L. / Nelson, C.A. / Campbell, J.A. / Lippold, D. / Krupnick, A.S. / Davis, R.S. / Carayannopoulos, L.N. / French, A.R. / Fremont, D.H.
History
DepositionApr 17, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 21, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 30, 2014Group: Database references
Revision 1.2Aug 9, 2017Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Nov 22, 2017Group: Refinement description / Category: software
Revision 1.5Nov 6, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.6Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.7Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / refine_hist
Item: _citation.journal_id_ISSN / _database_2.pdbx_DOI ..._citation.journal_id_ISSN / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NKG2-D type II integral membrane protein
B: NKG2-D type II integral membrane protein
C: NKG2-D type II integral membrane protein
D: NKG2-D type II integral membrane protein
E: CPXV018 protein
F: CPXV018 protein


Theoretical massNumber of molelcules
Total (without water)92,7726
Polymers92,7726
Non-polymers00
Water11,890660
1
A: NKG2-D type II integral membrane protein
B: NKG2-D type II integral membrane protein
E: CPXV018 protein


Theoretical massNumber of molelcules
Total (without water)46,3863
Polymers46,3863
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: NKG2-D type II integral membrane protein
D: NKG2-D type II integral membrane protein
F: CPXV018 protein


Theoretical massNumber of molelcules
Total (without water)46,3863
Polymers46,3863
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.315, 101.110, 91.368
Angle α, β, γ (deg.)90.00, 91.63, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological unit of hNKG2D is a dimer (chains A & B and chains C & D / The biological unit of OMCP is a monomer (chains E & F / The biological unit of OMCP bound to hNKG2D is a monomer bound to a dimer (chains A, B, & E and chains C, D, & F

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Components

#1: Protein
NKG2-D type II integral membrane protein / Killer cell lectin-like receptor subfamily K member 1 / NK cell receptor D / NKG2-D-activating NK receptor


Mass: 14266.118 Da / Num. of mol.: 4 / Fragment: UNP residues 93-215
Source method: isolated from a genetically manipulated source
Details: refolded / Source: (gene. exp.) Homo sapiens (human) / Gene: KLRK1, D12S2489E, NKG2D / Plasmid: pET21a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: P26718
#2: Protein CPXV018 protein


Mass: 17853.852 Da / Num. of mol.: 2 / Fragment: UNP residues 20-168 / Mutation: Y23D, F95D
Source method: isolated from a genetically manipulated source
Details: refolded / Source: (gene. exp.) Cowpox virus / Gene: CPXV018 CDS / Plasmid: pET21a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: Q8QN43
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 660 / Source method: isolated from a natural source / Formula: H2O

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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: 2.16 Å3/Da / Density % sol: 42.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.75 / Details: 15% PEG 3350, 0.2M MgCl2, 0.1M Bis-Tris

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.00004 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Oct 19, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00004 Å / Relative weight: 1
ReflectionRedundancy: 6.2 % / Number: 309692 / Rmerge(I) obs: 0.118 / Χ2: 1.07 / D res high: 2 Å / D res low: 50 Å / Num. obs: 50139 / % possible obs: 93.5
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)IDRmerge(I) obsChi squaredRedundancy
4.315010.0731.1247.6
3.424.3110.0931.0567.3
2.993.4210.1141.0286.5
2.712.9910.1521.026.2
2.522.7110.1931.1245.9
2.372.5210.2390.9775.8
2.252.3710.2841.1395.7
2.152.2510.3271.0615.6
2.072.1510.371.0255.5
22.0710.4851.0975.3
ReflectionResolution: 1.991→50 Å / Num. obs: 50139 / % possible obs: 93.5 % / Redundancy: 6.2 % / Biso Wilson estimate: 21.62 Å2 / Rmerge(I) obs: 0.118 / Χ2: 1.066 / Net I/av σ(I): 14.491 / Net I/σ(I): 12.7 / Num. measured all: 309692
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2-2.075.30.48549221.09791.5
2.07-2.155.50.3748301.02590.8
2.15-2.255.60.32748071.06190.3
2.25-2.375.70.28447911.13989.5
2.37-2.525.80.23947650.97789.2
2.52-2.715.90.19348661.12490.2
2.71-2.996.20.15249681.0293.7
2.99-3.426.50.11453541.02899.2
3.42-4.317.30.09353831.056100
4.31-507.60.07354531.12499.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.5 Å45.67 Å
Translation3.5 Å45.67 Å

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-2000data scaling
PDB_EXTRACT3.14data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MPU, 4FFE

1mpu

4ffe


Resolution: 1.991→45.665 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 20.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2142 1994 3.98 %Random selection
Rwork0.166 ---
obs0.1679 50042 92.91 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: final / Resolution: 1.991→45.665 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6491 0 0 669 7160
Biso mean---33.07 -
Num. residues----791
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036687
X-RAY DIFFRACTIONf_angle_d0.7869030
X-RAY DIFFRACTIONf_dihedral_angle_d13.4232426
X-RAY DIFFRACTIONf_chiral_restr0.031933
X-RAY DIFFRACTIONf_plane_restr0.0031150
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.991-2.04080.29511230.20983147X-RAY DIFFRACTION85
2.0408-2.0960.28121450.20983341X-RAY DIFFRACTION91
2.096-2.15770.2461520.18343328X-RAY DIFFRACTION91
2.1577-2.22730.22021270.17773302X-RAY DIFFRACTION90
2.2273-2.30690.21971310.17643327X-RAY DIFFRACTION90
2.3069-2.39930.28251320.17783285X-RAY DIFFRACTION89
2.3993-2.50840.25451340.17443281X-RAY DIFFRACTION89
2.5084-2.64070.22971330.1793309X-RAY DIFFRACTION90
2.6407-2.80610.21891420.18263353X-RAY DIFFRACTION91
2.8061-3.02270.23521510.18643529X-RAY DIFFRACTION95
3.0227-3.32680.22841580.16883700X-RAY DIFFRACTION99
3.3268-3.8080.17011510.14933673X-RAY DIFFRACTION100
3.808-4.79690.1961550.12893733X-RAY DIFFRACTION100
4.7969-45.67740.17091600.16463740X-RAY DIFFRACTION100

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