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- PDB-3vh8: KIR3DL1 in complex with HLA-B*5701 -

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Basic information

Entry
Database: PDB / ID: 3vh8
TitleKIR3DL1 in complex with HLA-B*5701
Components
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, B-57 alpha chain
  • Killer cell immunoglobulin-like receptor 3DL1
  • peptide of Ig kappa chain C region
KeywordsIMMUNE SYSTEM / immunoglobulin fold / natural killer cell receptor
Function / homology
Function and homology information


HLA-B specific inhibitory MHC class I receptor activity / immune response-regulating signaling pathway / IgD immunoglobulin complex / IgM immunoglobulin complex / IgA immunoglobulin complex / IgE immunoglobulin complex / 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 / immune response-regulating signaling pathway / IgD immunoglobulin complex / IgM immunoglobulin complex / IgA immunoglobulin complex / IgE immunoglobulin complex / 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 / natural killer cell mediated cytotoxicity / 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 / negative regulation of receptor binding / DAP12 interactions / 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 / Regulation of Complement cascade / antigen binding / cellular response to iron ion / Endosomal/Vacuolar pathway / lumenal side of endoplasmic reticulum membrane / Cell surface interactions at the vascular wall / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / FCERI mediated MAPK activation / FCGR3A-mediated phagocytosis / 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 / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / 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 / multicellular organismal-level iron ion homeostasis / defense response / negative regulation of neurogenesis / FCERI mediated NF-kB activation / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / 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 / peptide antigen binding / positive regulation of cellular senescence / 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 / positive regulation of T cell activation / Interferon alpha/beta signaling / sensory perception of smell / negative regulation of neuron projection development / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / late endosome membrane / protein-folding chaperone binding / iron ion transport / ER-Phagosome pathway / early endosome membrane / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / adaptive immune response
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 / : ...: / 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 / Immunoglobulin subtype / Immunoglobulin / 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 / 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: 1.8 Å
AuthorsVivian, J.P. / Rossjohn, J.
CitationJournal: Nature / Year: 2011
Title: Killer cell immunoglobulin-like receptor 3DL1-mediated recognition of human leukocyte antigen B
Authors: Vivian, J.P. / Duncan, R.C. / Berry, R. / O'Connor, G.M. / Reid, H.H. / Beddoe, T. / Gras, S. / Saunders, P.M. / Olshina, M.A. / Widjaja, J.M.L. / Harpur, C.M. / Lin, J. / Maloveste, S.M. / ...Authors: Vivian, J.P. / Duncan, R.C. / Berry, R. / O'Connor, G.M. / Reid, H.H. / Beddoe, T. / Gras, S. / Saunders, P.M. / Olshina, M.A. / Widjaja, J.M.L. / Harpur, C.M. / Lin, J. / Maloveste, S.M. / Price, D.A. / Lafont, B.A.P. / McVicar, D.W. / Clements, C.S. / Brooks, A.G. / Rossjohn, J.
History
DepositionAug 24, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 26, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 7, 2011Group: Database references
Revision 1.2Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / 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_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_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
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: HLA class I histocompatibility antigen, B-57 alpha chain
B: Beta-2-microglobulin
C: peptide of Ig kappa chain C region
G: Killer cell immunoglobulin-like receptor 3DL1
D: HLA class I histocompatibility antigen, B-57 alpha chain
E: Beta-2-microglobulin
F: peptide of Ig kappa chain C region
H: Killer cell immunoglobulin-like receptor 3DL1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,88814
Polymers158,5618
Non-polymers1,3276
Water28,5721586
1
A: HLA class I histocompatibility antigen, B-57 alpha chain
B: Beta-2-microglobulin
C: peptide of Ig kappa chain C region
G: Killer cell immunoglobulin-like receptor 3DL1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,9447
Polymers79,2814
Non-polymers6643
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4340 Å2
ΔGint-18 kcal/mol
Surface area19170 Å2
2
D: HLA class I histocompatibility antigen, B-57 alpha chain
E: Beta-2-microglobulin
F: peptide of Ig kappa chain C region
H: Killer cell immunoglobulin-like receptor 3DL1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,9447
Polymers79,2814
Non-polymers6643
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.248, 66.374, 93.361
Angle α, β, γ (deg.)100.56, 92.83, 101.56
Int Tables number1
Space group name H-MP1

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Components

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Protein , 3 types, 6 molecules ADBEGH

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


Mass: 31639.059 Da / Num. of mol.: 2 / Fragment: HLA-B*5701, UNP residues 25-299
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-B*5701 / Plasmid: pET-30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P18465, UniProt: P01889*PLUS
#2: Protein Beta-2-microglobulin / Beta-2-microglobulin form pI 5.3


Mass: 11748.160 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Plasmid: pET-30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P61769
#4: Protein Killer cell immunoglobulin-like receptor 3DL1 / CD158 antigen-like family member E / HLA-BW4-specific inhibitory NK cell receptor / MHC class I NK ...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: 34927.266 Da / Num. of mol.: 2 / Fragment: KIR3DL1*001, UNP residues 22-320
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KIR3DL1*001 / Plasmid: pHLSec / Cell line (production host): HEK293S / Production host: Homo sapiens (human) / References: UniProt: P43629

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Protein/peptide / Sugars / Non-polymers , 3 types, 1594 molecules CF

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


Mass: 966.109 Da / Num. of mol.: 2 / Fragment: UNP residues 93-101 / Source method: obtained synthetically / Details: synthesised peptide / 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.: 6
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.: 1586 / 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: 2.48 Å3/Da / Density % sol: 50.47 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 16% PEG 3350, 2% tacsimate pH 5.0, 0.1M tri-sodium citrate pH 5.6., VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9536 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 10, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9536 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 136837 / % possible obs: 94.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.7 % / Rmerge(I) obs: 0.257 / Net I/σ(I): 20.8
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 3 % / Rmerge(I) obs: 0.257 / Mean I/σ(I) obs: 3 / % possible all: 87.8

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
REFMAC5.4.0077refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 2RFX and 1IM9

2rfx

1im9


Resolution: 1.8→35.85 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.947 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 2.88 / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 1.97 / ESU R: 0.152 / ESU R Free: 0.135 / Phase error: 28.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2373 6931 5.1 %random
Rwork0.2112 ---
obs0.2126 129993 96.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.215 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 70.96 Å2 / Biso mean: 29.231 Å2 / Biso min: 10.62 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å2-0.03 Å2-0.07 Å2
2---0.08 Å2-0.01 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.8→35.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10553 0 84 1586 12223
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02110968
X-RAY DIFFRACTIONr_angle_refined_deg1.2211.94714908
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.00951299
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.30222.584538
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.201151721
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1191598
X-RAY DIFFRACTIONr_chiral_restr0.0880.21546
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0218600
X-RAY DIFFRACTIONr_mcbond_it2.2191.56556
X-RAY DIFFRACTIONr_mcangle_it3.028210600
X-RAY DIFFRACTIONr_scbond_it2.80534412
X-RAY DIFFRACTIONr_scangle_it4.0064.54308
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 492 -
Rwork0.282 8863 -
all-9355 -
obs--89.97 %

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