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- PDB-5b38: KIR3DL1*005 in complex with HLA-B*57:01 -

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Basic information

Entry
Database: PDB / ID: 5b38
TitleKIR3DL1*005 in complex with HLA-B*57:01
Components
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, B-57 alpha chain
  • Killer cell immunoglobulin-like receptor 3DL1
  • peptide from Ig kappa chain C region
KeywordsIMMUNE SYSTEM / Innate Immune Receptor / KIR / Natural Killer Cell
Function / homology
Function and homology information


HLA-B specific inhibitory MHC class I receptor activity / IgD immunoglobulin complex / IgM immunoglobulin complex / IgA immunoglobulin complex / IgE immunoglobulin complex / natural killer cell mediated cytotoxicity / CD22 mediated BCR regulation / regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy ...HLA-B specific inhibitory MHC class I receptor activity / IgD immunoglobulin complex / IgM immunoglobulin complex / IgA immunoglobulin complex / IgE immunoglobulin complex / natural killer cell mediated cytotoxicity / CD22 mediated BCR regulation / regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / IgG immunoglobulin complex / Fc epsilon receptor (FCERI) signaling / regulation of interleukin-6 production / Classical antibody-mediated complement activation / Initial triggering of complement / TAP binding / FCGR activation / protection from natural killer cell mediated cytotoxicity / immunoglobulin mediated immune response / Role of phospholipids in phagocytosis / Role of LAT2/NTAL/LAB on calcium mobilization / Scavenging of heme from plasma / detection of bacterium / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / secretory granule membrane / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / Regulation of Complement cascade / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / lumenal side of endoplasmic reticulum membrane / cellular response to iron ion / Endosomal/Vacuolar pathway / Cell surface interactions at the vascular wall / FCERI mediated MAPK activation / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / FCGR3A-mediated phagocytosis / antigen binding / B cell receptor signaling pathway / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / regulation of erythrocyte differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / Regulation of actin dynamics for phagocytic cup formation / MHC class I protein complex / defense response / multicellular organismal-level iron ion homeostasis / FCERI mediated NF-kB activation / negative regulation of neurogenesis / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / peptide antigen binding / negative regulation of epithelial cell proliferation / antigen processing and presentation of exogenous peptide antigen via MHC class II / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / Modulation by Mtb of host immune system / Interferon alpha/beta signaling / sensory perception of smell / positive regulation of T cell activation / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / iron ion transport / ER-Phagosome pathway / early endosome membrane / protein-folding chaperone binding / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / adaptive immune response / amyloid fibril formation
Similarity search - Function
Immunoglobulin / Immunoglobulin domain / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / MHC class I-like antigen recognition-like ...Immunoglobulin / Immunoglobulin domain / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Immunoglobulin kappa constant / HLA class I histocompatibility antigen, B alpha chain / HLA class I histocompatibility antigen, B alpha chain / Killer cell immunoglobulin-like receptor 3DL1 / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsVivian, J.P. / Rossjohn, J.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (Australia)1099814 Australia
CitationJournal: J.Exp.Med. / Year: 2016
Title: Killer cell immunoglobulin-like receptor 3DL1 polymorphism defines distinct hierarchies of HLA class I recognition
Authors: Saunders, P.M. / Pymm, P. / Pietra, G. / Hughes, V.A. / Hitchen, C. / O'Connor, G.M. / Loiacono, F. / Widjaja, J. / Price, D.A. / Falco, M. / Mingari, M.C. / Moretta, L. / McVicar, D.W. / ...Authors: Saunders, P.M. / Pymm, P. / Pietra, G. / Hughes, V.A. / Hitchen, C. / O'Connor, G.M. / Loiacono, F. / Widjaja, J. / Price, D.A. / Falco, M. / Mingari, M.C. / Moretta, L. / McVicar, D.W. / Rossjohn, J. / Brooks, A.G. / Vivian, J.P.
History
DepositionFeb 12, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 30, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 20, 2016Group: Database references
Revision 1.2May 18, 2016Group: Database references
Revision 1.3Oct 18, 2017Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Derived calculations
Category: citation / diffrn_source ...citation / diffrn_source / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site ..._citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Jul 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_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Nov 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: HLA class I histocompatibility antigen, B-57 alpha chain
B: Beta-2-microglobulin
C: peptide from Ig kappa chain C region
G: Killer cell immunoglobulin-like receptor 3DL1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,1077
Polymers77,4444
Non-polymers6643
Water4,234235
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7150 Å2
ΔGint-22 kcal/mol
Surface area32720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.557, 61.271, 66.365
Angle α, β, γ (deg.)95.20, 100.25, 108.22
Int Tables number1
Space group name H-MP1

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Components

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Protein , 3 types, 3 molecules ABG

#1: Protein HLA class I histocompatibility antigen, B-57 alpha chain / HLA-B*57:01 / Bw-57 / MHC class I antigen B*57


Mass: 31736.172 Da / Num. of mol.: 1 / Fragment: UNP residues 25-300
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-B, HLAB / Production host: Enterobacteria phage L1 (virus) / References: UniProt: P18465, UniProt: P01889*PLUS
#2: Protein Beta-2-microglobulin


Mass: 11748.160 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: Enterobacteria phage L1 (virus) / References: UniProt: P61769
#4: Protein Killer cell immunoglobulin-like receptor 3DL1 / KIR3DL1*005 / CD158 antigen-like family member E / HLA-BW4-specific inhibitory NK cell receptor / ...KIR3DL1*005 / CD158 antigen-like family member E / HLA-BW4-specific inhibitory NK cell receptor / MHC class I NK cell receptor / Natural killer-associated transcript 3 / NKAT-3 / p70 natural killer cell receptor clones CL-2/CL-11 / p70 NK receptor CL-2/CL-11


Mass: 32993.367 Da / Num. of mol.: 1 / Fragment: UNP residues 22-320
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KIR3DL1, CD158E, NKAT3, NKB1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P43629

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Protein/peptide / Sugars / Non-polymers , 3 types, 239 molecules C

#3: Protein/peptide peptide from Ig kappa chain C region


Mass: 966.109 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P01834
#5: 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.: 3
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
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 235 / 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: 2.5 Å3/Da / Density % sol: 50.78 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 14 to 18% PEG 3350, 2% tacsimate pH 5.0, 0.1 M tri-sodium citrate pH 5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.954 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 2, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 61910 / % possible obs: 92.9 % / Redundancy: 4.5 % / Net I/σ(I): 6.9
Reflection shellResolution: 2.3→2.42 Å

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Processing

Software
NameVersionClassification
PHENIX1.9_1690refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VH8

3vh8


Resolution: 2.3→35.496 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 0.65 / Phase error: 28.13
Details: the entry contains Friedel pairs in F_Plus/Minus columns
RfactorNum. reflection% reflection
Rfree0.2506 3068 5.01 %
Rwork0.1955 --
obs0.1984 61236 91.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.3→35.496 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5255 0 42 235 5532
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035468
X-RAY DIFFRACTIONf_angle_d0.7027412
X-RAY DIFFRACTIONf_dihedral_angle_d12.7711989
X-RAY DIFFRACTIONf_chiral_restr0.03777
X-RAY DIFFRACTIONf_plane_restr0.003963
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.33590.28781100.25242684X-RAY DIFFRACTION93
2.3359-2.37420.31171400.24142742X-RAY DIFFRACTION95
2.3742-2.41520.29841390.24542671X-RAY DIFFRACTION95
2.4152-2.45910.30681460.23362815X-RAY DIFFRACTION93
2.4591-2.50630.32131220.24062581X-RAY DIFFRACTION95
2.5063-2.55750.31711210.23222846X-RAY DIFFRACTION95
2.5575-2.61310.30581520.23622660X-RAY DIFFRACTION94
2.6131-2.67390.32841520.22222753X-RAY DIFFRACTION95
2.6739-2.74070.28531380.22952655X-RAY DIFFRACTION94
2.7407-2.81480.27881410.22652709X-RAY DIFFRACTION94
2.8148-2.89760.34971450.2232703X-RAY DIFFRACTION93
2.8976-2.9910.23931320.2072635X-RAY DIFFRACTION93
2.991-3.09790.28231400.19972684X-RAY DIFFRACTION93
3.0979-3.22180.24181790.20512647X-RAY DIFFRACTION92
3.2218-3.36840.24041650.1912623X-RAY DIFFRACTION92
3.3684-3.54580.25271460.1942608X-RAY DIFFRACTION93
3.5458-3.76770.32911250.22522648X-RAY DIFFRACTION90
3.7677-4.05830.20031200.18122514X-RAY DIFFRACTION88
4.0583-4.46590.19251410.15342599X-RAY DIFFRACTION89
4.4659-5.11050.17021330.13882303X-RAY DIFFRACTION80
5.1105-6.43250.21031560.16462705X-RAY DIFFRACTION95
6.4325-35.50020.22691250.17272383X-RAY DIFFRACTION83

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