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- PDB-5t6z: KIR3DL1 in complex with HLA-B*57:01-TW10 -

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Basic information

Entry
Database: PDB / ID: 5t6z
TitleKIR3DL1 in complex with HLA-B*57:01-TW10
Components
  • Beta-2-microglobulin
  • Decapeptide: THR-SER-THR-LEU-GLN-GLU-GLN-ILE-GLY-TRP
  • HLA class I histocompatibility antigen, B-57 alpha chain
  • Killer cell immunoglobulin-like receptor 3DL1
KeywordsIMMUNE SYSTEM / human leukocyte antigen Immunoglobulin domain antigen presentation
Function / homology
Function and homology information


HLA-B specific inhibitory MHC class I receptor activity / immune response-regulating signaling pathway / regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / natural killer cell mediated cytotoxicity / TAP binding / protection from natural killer cell mediated cytotoxicity / detection of bacterium ...HLA-B specific inhibitory MHC class I receptor activity / immune response-regulating signaling pathway / regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / natural killer cell mediated cytotoxicity / TAP binding / protection from natural killer cell mediated cytotoxicity / detection of bacterium / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / secretory granule membrane / 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 Ib / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / lumenal side of endoplasmic reticulum membrane / HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / retroviral ribonuclease H / negative regulation of forebrain neuron differentiation / exoribonuclease H / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / regulation of iron ion transport / exoribonuclease H activity / response to molecule of bacterial origin / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / host multivesicular body / MHC class I protein complex / defense response / DNA integration / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / viral genome integration into host DNA / peptide antigen assembly with MHC class II protein complex / multicellular organismal-level iron ion homeostasis / RNA-directed DNA polymerase / establishment of integrated proviral latency / MHC class II protein complex / cellular response to nicotine / specific granule lumen / symbiont-mediated suppression of host gene expression / viral penetration into host nucleus / positive regulation of cellular senescence / positive regulation of T cell mediated cytotoxicity / RNA stem-loop binding / recycling endosome membrane / phagocytic vesicle membrane / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / RNA-directed DNA polymerase activity / negative regulation of epithelial cell proliferation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of immune response / Interferon gamma signaling / RNA-DNA hybrid ribonuclease activity / Modulation by Mtb of host immune system / positive regulation of T cell activation / Interferon alpha/beta signaling / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / sensory perception of smell / host cell / 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 / T cell differentiation in thymus / early endosome membrane / protein refolding / viral nucleocapsid / DNA recombination / protein homotetramerization / intracellular iron ion homeostasis / adaptive immune response / amyloid fibril formation / DNA-directed DNA polymerase / molecular adaptor activity / Hydrolases; Acting on ester bonds / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity
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 / Reverse transcriptase connection ...: / 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 / Reverse transcriptase connection / Reverse transcriptase connection domain / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral / Integrase, N-terminal zinc-binding domain / Integrase, C-terminal, retroviral / Integrase DNA binding domain profile. / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / MHC classes I/II-like antigen recognition protein / Retropepsin-like catalytic domain / RNase H type-1 domain profile. / Ribonuclease H domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Reverse transcriptase (RNA-dependent DNA polymerase) / Retroviral matrix protein / Retrovirus capsid, C-terminal / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / : / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / 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 / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Ribonuclease H superfamily / Aspartic peptidase domain superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / DNA/RNA polymerase superfamily / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
HLA class I histocompatibility antigen, B alpha chain / Gag-Pol polyprotein / HLA class I histocompatibility antigen, B alpha chain / Killer cell immunoglobulin-like receptor 3DL1 / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsPymm, P. / Rossjohn, J. / Vivian, J.P.
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2017
Title: MHC-I peptides get out of the groove and enable a novel mechanism of HIV-1 escape.
Authors: Pymm, P. / Illing, P.T. / Ramarathinam, S.H. / O'Connor, G.M. / Hughes, V.A. / Hitchen, C. / Price, D.A. / Ho, B.K. / McVicar, D.W. / Brooks, A.G. / Purcell, A.W. / Rossjohn, J. / Vivian, J.P.
History
DepositionSep 2, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 1, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 19, 2017Group: Database references
Revision 1.2Aug 9, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Jul 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_leaving_atom_flag / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Oct 4, 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
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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: Decapeptide: THR-SER-THR-LEU-GLN-GLU-GLN-ILE-GLY-TRP
G: Killer cell immunoglobulin-like receptor 3DL1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,3877
Polymers77,7234
Non-polymers6643
Water11,728651
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7360 Å2
ΔGint-15 kcal/mol
Surface area32940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.812, 61.382, 65.359
Angle α, β, γ (deg.)95.31, 98.02, 109.23
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 / 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 / Plasmid: pET-30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P18465, UniProt: P01889*PLUS
#2: Protein Beta-2-microglobulin


Mass: 11748.160 Da / Num. of mol.: 1 / Fragment: UNP residues 21-119
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: 33076.461 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 / Plasmid: pHLSEC / Cell line (production host): HEK 293S / Production host: Homo sapiens (human) / References: UniProt: P43629

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Protein/peptide / Sugars / Non-polymers , 3 types, 655 molecules C

#3: Protein/peptide Decapeptide: THR-SER-THR-LEU-GLN-GLU-GLN-ILE-GLY-TRP


Mass: 1162.249 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: UniProt: P03366*PLUS
#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.: 651 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.48 Å3/Da / Density % sol: 50.32 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 16% PEG 3350, 2% tacsimate pH 5.0 and 0.1M 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: May 11, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 2→39.867 Å / Num. obs: 47511 / % possible obs: 94.4 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 11.2
Reflection shellResolution: 2→2.11 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.218 / Mean I/σ(I) obs: 11.2 / % possible all: 94.2

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Processing

Software
NameVersionClassification
PHENIX1.7.2_869refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VH8

3vh8


Resolution: 2→39.87 Å / SU ML: 0.57 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 23.69
RfactorNum. reflection% reflection
Rfree0.24 2393 5.06 %
Rwork0.203 --
obs0.205 47284 94 %
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Bsol: 40.55 Å2 / ksol: 0.37 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.4479 Å2-4.7816 Å2-4.1205 Å2
2--0.5983 Å24.3741 Å2
3----0.1504 Å2
Refinement stepCycle: LAST / Resolution: 2→39.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5360 0 42 651 6053
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055567
X-RAY DIFFRACTIONf_angle_d1.1427554
X-RAY DIFFRACTIONf_dihedral_angle_d13.6442053
X-RAY DIFFRACTIONf_chiral_restr0.079785
X-RAY DIFFRACTIONf_plane_restr0.005987
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.04080.26791440.20512660X-RAY DIFFRACTION94
2.0408-2.08520.22821440.19342622X-RAY DIFFRACTION94
2.0852-2.13370.26051450.19952649X-RAY DIFFRACTION95
2.1337-2.18710.27421450.222669X-RAY DIFFRACTION94
2.1871-2.24620.50021170.39852543X-RAY DIFFRACTION90
2.2462-2.31230.37941270.34832502X-RAY DIFFRACTION90
2.3123-2.38690.2591390.2192668X-RAY DIFFRACTION95
2.3869-2.47220.2621440.20432682X-RAY DIFFRACTION95
2.4722-2.57120.26571470.20792629X-RAY DIFFRACTION95
2.5712-2.68820.31211350.22092699X-RAY DIFFRACTION95
2.6882-2.82980.23181200.20652680X-RAY DIFFRACTION95
2.8298-3.00710.25661590.2042649X-RAY DIFFRACTION95
3.0071-3.23920.23221560.19162676X-RAY DIFFRACTION95
3.2392-3.5650.18431380.17842650X-RAY DIFFRACTION95
3.565-4.08040.17231470.16542684X-RAY DIFFRACTION95
4.0804-5.13910.18741460.1452652X-RAY DIFFRACTION95
5.1391-39.87470.21181400.19252577X-RAY DIFFRACTION92

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