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- PDB-6yjp: Crystal structure of a complex between glycosylated NKp30 and its... -

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Basic information

Entry
Database: PDB / ID: 6yjp
TitleCrystal structure of a complex between glycosylated NKp30 and its deglycosylated tumour ligand B7-H6
Components
  • Natural cytotoxicity triggering receptor 3
  • Natural cytotoxicity triggering receptor 3 ligand 1
KeywordsIMMUNE SYSTEM / NK CELL RECEPTOR / RECEPTOR-LIGAND COMPLEX
Function / homology
Function and homology information


cell recognition / immune response-activating cell surface receptor signaling pathway / MHC class I protein complex binding / positive regulation of natural killer cell mediated cytotoxicity / natural killer cell activation / TAP complex binding / immunoglobulin complex, circulating / immunoglobulin receptor binding / complement activation, classical pathway / antigen binding ...cell recognition / immune response-activating cell surface receptor signaling pathway / MHC class I protein complex binding / positive regulation of natural killer cell mediated cytotoxicity / natural killer cell activation / TAP complex binding / immunoglobulin complex, circulating / immunoglobulin receptor binding / complement activation, classical pathway / antigen binding / peptide antigen assembly with MHC class I protein complex / MHC class I peptide loading complex / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / antibacterial humoral response / inflammatory response / immune response / identical protein binding / plasma membrane
Similarity search - Function
Natural cytotoxicity triggering receptor 3 / Gamma-retroviral matrix domain superfamily / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Retroviral matrix protein / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type ...Natural cytotoxicity triggering receptor 3 / Gamma-retroviral matrix domain superfamily / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Retroviral matrix protein / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Natural cytotoxicity triggering receptor 3 / Natural cytotoxicity triggering receptor 3 ligand 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsSkalova, T. / Dohnalek, J. / Skorepa, O. / Kalouskova, B. / Pazicky, S. / Blaha, J. / Vanek, O.
Funding support Czech Republic, 3items
OrganizationGrant numberCountry
Czech Science Foundation18-10687S Czech Republic
Ministry of Education, Youth and Sports of the Czech RepublicLTC17065 Czech Republic
European Regional Development FundCZ.02.1.01/0.0/0.0/16_013/0001776 Czech Republic
CitationJournal: Cancers (Basel) / Year: 2020
Title: Natural Killer Cell Activation Receptor NKp30 Oligomerization Depends on Its N -Glycosylation.
Authors: Skorepa, O. / Pazicky, S. / Kalouskova, B. / Blaha, J. / Abreu, C. / Jecmen, T. / Rosulek, M. / Fish, A. / Sedivy, A. / Harlos, K. / Dohnalek, J. / Skalova, T. / Vanek, O.
History
DepositionApr 4, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 29, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 5, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Sep 30, 2020Group: Database references / Category: citation / citation_author / Item: _citation.title / _citation_author.identifier_ORCID
Revision 1.3Jan 24, 2024Group: 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Natural cytotoxicity triggering receptor 3 ligand 1
D: Natural cytotoxicity triggering receptor 3 ligand 1
A: Natural cytotoxicity triggering receptor 3
B: Natural cytotoxicity triggering receptor 3
E: Natural cytotoxicity triggering receptor 3 ligand 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,80110
Polymers106,6955
Non-polymers1,1065
Water00
1
C: Natural cytotoxicity triggering receptor 3 ligand 1
A: Natural cytotoxicity triggering receptor 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6474
Polymers40,2042
Non-polymers4422
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1700 Å2
ΔGint-3 kcal/mol
Surface area18060 Å2
2
B: Natural cytotoxicity triggering receptor 3
hetero molecules

D: Natural cytotoxicity triggering receptor 3 ligand 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6474
Polymers40,2042
Non-polymers4422
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_556x,y,z+11
Buried area1520 Å2
ΔGint-2 kcal/mol
Surface area17730 Å2
3
E: Natural cytotoxicity triggering receptor 3 ligand 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5082
Polymers26,2871
Non-polymers2211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area170 Å2
ΔGint2 kcal/mol
Surface area12680 Å2
Unit cell
Length a, b, c (Å)166.044, 86.462, 111.299
Angle α, β, γ (deg.)90.000, 97.580, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11C
21D
12C
22E
13D
23E
14A
24B

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRGLYGLYCA23 - 2452 - 224
21THRTHRGLYGLYDB23 - 2452 - 224
12ASPASPGLYGLYCA25 - 2454 - 224
22ASPASPGLYGLYEE25 - 2454 - 224
13ASPASPGLYGLYDB25 - 2454 - 224
23ASPASPGLYGLYEE25 - 2454 - 224
14GLYGLYGLUGLUAC18 - 1283 - 113
24GLYGLYGLUGLUBD18 - 1283 - 113

NCS ensembles :
ID
1
2
3
4

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Components

#1: Protein Natural cytotoxicity triggering receptor 3 ligand 1 / B7 homolog 6 / B7-H6


Mass: 26286.676 Da / Num. of mol.: 3 / Mutation: C212S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NCR3LG1, B7H6 / Plasmid: pTW5sec / Cell line (production host): HEK293S GnTI(-) / Production host: Homo sapiens (human) / References: UniProt: Q68D85
#2: Protein Natural cytotoxicity triggering receptor 3 / Activating natural killer receptor p30 / Natural killer cell p30-related protein / NKp30


Mass: 13917.621 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NCR3, 1C7, LY117 / Plasmid: pTW5sec / Cell line (production host): HEK293S GnTI(-) / Production host: Homo sapiens (human) / References: UniProt: O14931
#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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 5
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
Has ligand of interestN

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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: 3.54 Å3/Da / Density % sol: 65 %
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 6.7
Details: 0.1 M sodium citrate pH 6.7, 11.7 % PEG 6000, 10 mg/ml mixture of both proteins, micro-seeded with crushed needle-shaped crystals

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 29, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 3.1→48.95 Å / Num. obs: 27102 / % possible obs: 95 % / Redundancy: 3.7 % / Biso Wilson estimate: 105.5 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.081 / Rrim(I) all: 0.134 / Net I/σ(I): 5.7
Reflection shellResolution: 3.1→3.29 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.971 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 3968 / CC1/2: 0.645 / Rpim(I) all: 0.804 / % possible all: 87

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Processing

Software
NameVersionClassification
REFMAC5.8.0258 (LORESTR pipeline))refinement
XDSdata reduction
Aimlessdata scaling
MoRDaphasing
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PV6

3pv6


Resolution: 3.1→48.95 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.91 / SU B: 62.879 / SU ML: 0.852 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.536 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3221 1348 5 %RANDOM
Rwork0.2723 ---
obs0.2748 25738 94.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso max: 335.29 Å2 / Biso mean: 155.577 Å2 / Biso min: 74.12 Å2
Baniso -1Baniso -2Baniso -3
1-19.96 Å20 Å25.37 Å2
2---5.81 Å20 Å2
3----15.05 Å2
Refinement stepCycle: final / Resolution: 3.1→48.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6837 0 70 0 6907
Biso mean--168.91 --
Num. residues----875
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0127080
X-RAY DIFFRACTIONr_angle_refined_deg1.591.6529627
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9525868
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.71322.423359
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.118151156
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7781543
X-RAY DIFFRACTIONr_chiral_restr0.120.2935
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.025415
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11C60690.17
12D60690.17
21C59910.17
22E59910.17
31D59040.18
32E59040.18
41A31360.16
42B31360.16
LS refinement shellResolution: 3.1→3.181 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.578 87 -
Rwork0.504 1671 -
all-1758 -
obs--83.67 %

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