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- PDB-3pv6: Crystal structure of NKp30 bound to its ligand B7-H6 -

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Basic information

Entry
Database: PDB / ID: 3pv6
TitleCrystal structure of NKp30 bound to its ligand B7-H6
Components
  • Ig-like domain-containing protein DKFZp686O24166/DKFZp686I21167
  • Natural cytotoxicity triggering receptor 3
KeywordsIMMUNE SYSTEM / NK cell receptor / receptor-ligand complex
Function / homology
Function and homology information


cell recognition / immune response-activating cell surface receptor signaling pathway / positive regulation of natural killer cell mediated cytotoxicity / natural killer cell activation / immunoglobulin complex, circulating / immunoglobulin receptor binding / complement activation, classical pathway / antigen binding / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / antibacterial humoral response ...cell recognition / immune response-activating cell surface receptor signaling pathway / positive regulation of natural killer cell mediated cytotoxicity / natural killer cell activation / immunoglobulin complex, circulating / immunoglobulin receptor binding / complement activation, classical pathway / antigen binding / 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 subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / 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 subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
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: 2.3 Å
AuthorsLi, Y.
CitationJournal: to be published
Title: Structure of the activating natural killer cell receptor NKp30 bound to its ligand B7-H6 reveals basis for tumor cell recognition in humans
Authors: Li, Y. / Wang, Q. / Mariuzza, R.A.
History
DepositionDec 6, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / 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 / struct_asym / struct_conn / struct_ref_seq_dif / 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_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ig-like domain-containing protein DKFZp686O24166/DKFZp686I21167
B: Natural cytotoxicity triggering receptor 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5435
Polymers40,6762
Non-polymers8673
Water27015
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.874, 74.868, 125.534
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Ig-like domain-containing protein DKFZp686O24166/DKFZp686I21167 / B7-H6


Mass: 27816.373 Da / Num. of mol.: 1 / Fragment: UNP residues 25-262
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pAcGP67-B / Cell line (production host): SP9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q68D85
#2: Protein Natural cytotoxicity triggering receptor 3 / Activating natural killer receptor p30 / Natural killer cell p30-related protein / NK-p30 / NKp30


Mass: 12859.525 Da / Num. of mol.: 1 / Fragment: UNP residues 19-135
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NCR3, 1C7, LY117 / Plasmid: pET26b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O14931
#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: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
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
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 15 / 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: 2.94 Å3/Da / Density % sol: 58.17 %
Crystal growTemperature: 298 K / Method: hanging drop / pH: 7
Details: PEG 3350, KF, pH 7.0, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.502 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 1, 2010 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.502 Å / Relative weight: 1
ReflectionRedundancy: 13.4 % / Number: 323809 / Rmerge(I) obs: 0.085 / Χ2: 1.07 / D res high: 2.2 Å / D res low: 50 Å / Num. obs: 24171 / % possible obs: 96
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.745099.910.0511.38413.3
3.764.7410010.0571.37514.1
3.293.7610010.0711.13814.4
2.993.2910010.1141.05914.5
2.772.9910010.1811.00214.5
2.612.7710010.2960.96414.4
2.482.6199.810.4190.92413.8
2.372.4895.610.5430.89212.6
2.282.3786.410.6080.8711.5
2.22.2877.710.6440.8689.8
ReflectionResolution: 2.3→500 Å / Num. all: 22003 / Num. obs: 21751 / % possible obs: 98.4 % / Redundancy: 14 % / Rsym value: 0.065 / Net I/σ(I): 53
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 11.8 % / Mean I/σ(I) obs: 3.3 / Num. unique all: 1909 / Rsym value: 0.485 / % possible all: 88.2

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
DENZOdata reduction
SCALEPACKdata scaling
HKL-2000data scaling
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→50 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.2887 2137 9.7 %
Rwork0.2393 --
obs-21661 98.4 %
Solvent computationBsol: 62.0383 Å2
Displacement parametersBiso max: 90.24 Å2 / Biso mean: 51.5077 Å2 / Biso min: 29.24 Å2
Baniso -1Baniso -2Baniso -3
1--15.684 Å20 Å20 Å2
2--23.439 Å20 Å2
3----7.755 Å2
Refinement stepCycle: LAST / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2540 0 56 15 2611
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.019
X-RAY DIFFRACTIONc_angle_d1.988
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:carbohydrate.param
X-RAY DIFFRACTION3CNS_TOPPAR:water.param

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