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- PDB-1oll: Extracellular region of the human receptor NKp46 -

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Basic information

Entry
Database: PDB / ID: 1oll
TitleExtracellular region of the human receptor NKp46
ComponentsNK RECEPTOR
KeywordsIMMUNE SYSTEM/RECEPTOR / NK CELL TRIGGERING RECEPTOR / IMMUNE SYSTEM / IG DOMAIN / CYTOTOXICITY / C2-TYPE IG-LIKE DOMAINS / IMMUNE SYSTEM-RECEPTOR complex
Function / homology
Function and homology information


regulation of natural killer cell mediated cytotoxicity / immune response-regulating signaling pathway / natural killer cell activation / SWI/SNF complex / cellular defense response / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / signal transduction / plasma membrane
Similarity search - Function
: / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Natural cytotoxicity triggering receptor 1 / Natural cytotoxicity triggering receptor 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsPonassi, M. / Cantoni, C. / Biassoni, R. / Conte, R. / Spallarossa, A. / Pesce, A. / Moretta, A. / Moretta, L. / Bolognesi, M. / Bordo, D.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2003
Title: Structure of the Human Nk Cell Triggering Receptor Nkp46 Ectodomain
Authors: Ponassi, M. / Cantoni, C. / Biassoni, R. / Conte, R. / Spallarossa, A. / Pesce, A. / Moretta, A. / Moretta, L. / Bolognesi, M. / Bordo, D.
History
DepositionAug 7, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 4, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 6, 2019Group: Advisory / Data collection ...Advisory / Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.4Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.5Dec 13, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.6Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NK RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3852
Polymers21,3231
Non-polymers621
Water2,450136
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)85.477, 85.477, 59.909
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein NK RECEPTOR / ISOFORM BNKP46 CELL RECEPTOR


Mass: 21323.410 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR DOMAIN, RESIDUES 25-212
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: VR1012-NKP46 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: O76016, UniProt: O76036*PLUS
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / Source method: isolated from a natural source / Formula: H2O
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: 2.78 Å3/Da / Density % sol: 58 %
Crystal growTemperature: 277 K / pH: 7.8
Details: 15% PEG 8000, 100 MM HEPES PH 7.8, 20% ETHANEDIOL, AT 277 K
Crystal grow
*PLUS
Temperature: 277 K / pH: 7.8 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
1100 mMHEPES1reservoirpH7.8
215 %PEG80001reservoir
320 %(v/v)ethanediol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8431
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 15, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8431 Å / Relative weight: 1
ReflectionResolution: 1.93→40 Å / Num. obs: 18944 / % possible obs: 100 % / Redundancy: 5 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 22.9
Reflection shellResolution: 1.93→1.96 Å / Redundancy: 5 % / Rmerge(I) obs: 0.765 / Mean I/σ(I) obs: 2.4 / % possible all: 100
Reflection
*PLUS
Highest resolution: 1.93 Å / Lowest resolution: 40 Å / % possible obs: 100 % / Rmerge(I) obs: 0.075
Reflection shell
*PLUS
% possible obs: 100 % / Rmerge(I) obs: 0.765 / Mean I/σ(I) obs: 2.4

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1G0X

1g0x


Resolution: 1.93→40 Å / SU B: 3.796 / SU ML: 0.108 / Cross valid method: THROUGHOUT / ESU R: 0.145 / ESU R Free: 0.154
Details: SOME ATOMS HAVE BEEN REFINED WITH AN OCCUPANCY OF 0.00 DUE TO POOR ELECTRON DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.251 968 5 %RANDOM
Rwork0.195 ---
obs0.198 18944 100 %-
Displacement parametersBiso mean: 37.7 Å2
Baniso -1Baniso -2Baniso -3
1-1.05 Å20.53 Å20 Å2
2--1.05 Å20 Å2
3----1.58 Å2
Refinement stepCycle: LAST / Resolution: 1.93→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1501 0 4 136 1641
Refinement
*PLUS
% reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbond_d0.011
X-RAY DIFFRACTIONangle_d
X-RAY DIFFRACTIONangle_deg0.952

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