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- PDB-3wyr: Crystal structure of Killer cell immunoglobulin-like receptor 2DL4 -

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Basic information

Entry
Database: PDB / ID: 3wyr
TitleCrystal structure of Killer cell immunoglobulin-like receptor 2DL4
ComponentsKiller cell immunoglobulin-like receptor 2DL4
KeywordsIMMUNE SYSTEM / Immunoglobulin domains / Immune receptor
Function / homology
Function and homology information


MHC class Ib receptor activity / positive regulation of natural killer cell cytokine production / negative regulation of natural killer cell mediated cytotoxicity / plasma membrane => GO:0005886 / regulation of immune response / cellular defense response / positive regulation of cellular senescence / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / transmembrane signaling receptor activity / early endosome membrane ...MHC class Ib receptor activity / positive regulation of natural killer cell cytokine production / negative regulation of natural killer cell mediated cytotoxicity / plasma membrane => GO:0005886 / regulation of immune response / cellular defense response / positive regulation of cellular senescence / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / transmembrane signaling receptor activity / early endosome membrane / signal transduction / membrane / plasma membrane
Similarity search - Function
Immunoglobulin / Immunoglobulin domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Killer cell immunoglobulin-like receptor 2DL4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsVivian, J.P. / Moradi, S. / Rossjohn, J.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: The structure of the atypical killer cell immunoglobulin-like receptor, KIR2DL4.
Authors: Moradi, S. / Berry, R. / Pymm, P. / Hitchen, C. / Beckham, S.A. / Wilce, M.C. / Walpole, N.G. / Clements, C.S. / Reid, H.H. / Perugini, M.A. / Brooks, A.G. / Rossjohn, J. / Vivian, J.P.
History
DepositionSep 7, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 18, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / struct_conn / struct_ref_seq_dif
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Nov 8, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Killer cell immunoglobulin-like receptor 2DL4
B: Killer cell immunoglobulin-like receptor 2DL4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,2734
Polymers45,8312
Non-polymers4422
Water64936
1
A: Killer cell immunoglobulin-like receptor 2DL4
B: Killer cell immunoglobulin-like receptor 2DL4
hetero molecules

A: Killer cell immunoglobulin-like receptor 2DL4
B: Killer cell immunoglobulin-like receptor 2DL4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,5478
Polymers91,6624
Non-polymers8854
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Unit cell
Length a, b, c (Å)87.836, 87.836, 105.996
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212

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Components

#1: Protein Killer cell immunoglobulin-like receptor 2DL4 / CD158 antigen-like family member D / G9P / Killer cell inhibitory receptor 103AS / KIR-103AS / MHC ...CD158 antigen-like family member D / G9P / Killer cell inhibitory receptor 103AS / KIR-103AS / MHC class I NK cell receptor KIR103AS


Mass: 22915.498 Da / Num. of mol.: 2 / Fragment: extracellular domain, UNP residues 24-218
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KIR2DL4, CD158D, KIR103AS / Plasmid: pHLSec / Cell line (production host): HEK 293S / Production host: Homo sapiens (human) / References: UniProt: Q99706
#2: 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 / 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
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHESE RESIDUES ARE NATURAL VARIANT.

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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: 2.23 Å3/Da / Density % sol: 44.85 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 16% PEG 3350, 4% tacsimate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9546 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 6, 2012
RadiationMonochromator: synchrotron / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9546 Å / Relative weight: 1
ReflectionResolution: 2.8→67.632 Å / Num. all: 10753 / Num. obs: 10753 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2 % / Biso Wilson estimate: 49.1 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 10.8
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 2 % / Rmerge(I) obs: 0.333 / Mean I/σ(I) obs: 2.2 / Num. unique all: 1034 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.9_1690)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: KIR2DS4 PDB code 3H8N

3h8n


Resolution: 2.8→67.632 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 25.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2434 490 4.56 %random
Rwork0.2108 ---
obs0.2124 10746 99.95 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 142.17 Å2 / Biso mean: 53.3422 Å2 / Biso min: 14.88 Å2
Refinement stepCycle: LAST / Resolution: 2.8→67.632 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2944 0 28 36 3008
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033089
X-RAY DIFFRACTIONf_angle_d0.7174228
X-RAY DIFFRACTIONf_chiral_restr0.031447
X-RAY DIFFRACTIONf_plane_restr0.004552
X-RAY DIFFRACTIONf_dihedral_angle_d13.5521092
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.8002-3.0820.35951220.27624832605
3.082-3.5280.23481150.226925342649
3.528-4.44480.22281320.182225362668
4.4448-67.65190.22341210.205627032824
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)Origin x (Å)Origin y (Å)Origin z (Å)
13.91170.9096-1.23673.1542-0.75222.5239-0.004-0.0163-0.0511-0.12340.085-0.36390.09860.3265-0.11110.20190.0035-0.0180.2147-0.05350.245620.205634.726617.7923
22.36430.0925-2.4281.9573-1.15568.6640.0147-0.3427-0.1604-0.1299-0.1125-0.0745-0.06710.5618-0.02810.31810.0712-0.01340.267-0.0590.319938.678222.1424.0084
33.956-0.0035-1.02032.851-0.44834.23640.2821-0.79240.11581.0058-0.1809-0.20290.53110.2699-0.14060.5964-0.0852-0.14540.53560.08910.37037.11523.960140.8369
42.8112-0.14890.31122.06370.23672.0915-0.135-0.427-0.21180.73950.3124-0.11590.6124-0.4752-0.07460.72450.1060.00660.59040.09230.409530.86215.377732.1958
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 7 through 97)
2X-RAY DIFFRACTION2(chain B and resid 7 through 97)
3X-RAY DIFFRACTION3(chain A and resid 98 through 195)
4X-RAY DIFFRACTION4(chain B and resid 98 through 195)

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