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- PDB-5t70: KIR3DL1 in complex with HLA-B*57:01 presenting TSNLQEQIGW -

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Basic information

Entry
Database: PDB / ID: 5t70
TitleKIR3DL1 in complex with HLA-B*57:01 presenting TSNLQEQIGW
Components
  • Beta-2-microglobulinBeta-2 microglobulin
  • Decapeptide: THR-SER-ASN-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 / natural killer cell mediated cytotoxicity / regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / TAP binding / protection from natural killer cell mediated cytotoxicity / 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 ...HLA-B specific inhibitory MHC class I receptor activity / natural killer cell mediated cytotoxicity / regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / TAP binding / protection from natural killer cell mediated cytotoxicity / 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 / detection of bacterium / secretory granule membrane / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / 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 / : / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / : / HIV-1 retropepsin / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / retroviral ribonuclease H / exoribonuclease H / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / exoribonuclease H activity / HFE-transferrin receptor complex / T cell mediated cytotoxicity / cellular response to iron ion / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / defense response / MHC class I protein complex / host multivesicular body / multicellular organismal-level iron ion homeostasis / DNA integration / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / cellular response to nicotine / RNA-directed DNA polymerase / viral penetration into host nucleus / recycling endosome membrane / viral genome integration into host DNA / specific granule lumen / phagocytic vesicle membrane / peptide antigen binding / establishment of integrated proviral latency / positive regulation of cellular senescence / 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 / Modulation by Mtb of host immune system / positive regulation of T cell activation / Interferon alpha/beta signaling / RNA-DNA hybrid ribonuclease activity / sensory perception of smell / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / negative regulation of neuron projection development / tertiary granule lumen / DAP12 signaling / positive regulation of protein binding / MHC class II protein complex binding / T cell differentiation in thymus / late endosome membrane / ER-Phagosome pathway / iron ion transport / protein-folding chaperone binding / protein refolding / early endosome membrane / viral nucleocapsid / protein homotetramerization / DNA recombination / intracellular iron ion homeostasis / amyloid fibril formation / adaptive immune response / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / learning or memory / molecular adaptor activity / DNA-directed DNA polymerase activity / immune response / symbiont entry into host cell
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 / Reverse transcriptase connection domain ...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 / MHC classes I/II-like antigen recognition protein / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Ribonuclease H domain / RNase H type-1 domain profile. / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Retrovirus capsid, C-terminal / Retroviral matrix protein / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / 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 / 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: 2.1 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 / Structure summary / Category: diffrn_source / struct / Item: _diffrn_source.pdbx_synchrotron_site / _struct.title
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_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
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

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


Theoretical massNumber of molelcules
Total (without water)78,4007
Polymers77,7364
Non-polymers6643
Water6,017334
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6970 Å2
ΔGint-28 kcal/mol
Surface area33860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.726, 61.209, 65.186
Angle α, β, γ (deg.)96.04, 97.46, 108.72
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 / 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
#3: 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, 338 molecules C

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


Mass: 1175.248 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 / N-Acetylglucosamine


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 / Water


Mass: 18.015 Da / Num. of mol.: 334 / 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: 2.47 Å3/Da / Density % sol: 50.11 %
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: Apr 4, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 2.1→63.84 Å / Num. obs: 39560 / % possible obs: 91.4 % / Redundancy: 3.8 % / Biso Wilson estimate: 34.45 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 12.7
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.579 / Mean I/σ(I) obs: 2.4 / % possible all: 91.7

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Processing

Software
NameVersionClassification
BUSTER2.8.0refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VH8

3vh8


Resolution: 2.1→63.84 Å / Cor.coef. Fo:Fc: 0.9549 / Cor.coef. Fo:Fc free: 0.9263 / Cross valid method: FREE R-VALUE / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2245 1983 5.01 %RANDOM
Rwork0.1742 ---
obs0.1767 39559 91.7 %-
Displacement parametersBiso mean: 36.65 Å2
Baniso -1Baniso -2Baniso -3
1--0.3714 Å2-0.0844 Å2-0.021 Å2
2---0.0776 Å2-0.2863 Å2
3---0.4491 Å2
Refinement stepCycle: 1 / Resolution: 2.1→63.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5377 0 42 334 5753
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.015577HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.097579HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1859SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes129HARMONIC2
X-RAY DIFFRACTIONt_gen_planes822HARMONIC5
X-RAY DIFFRACTIONt_it5577HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.6
X-RAY DIFFRACTIONt_other_torsion18.57
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion702SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact6048SEMIHARMONIC4
LS refinement shellResolution: 2.1→2.15 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2539 151 5.14 %
Rwork0.2123 2786 -
all0.2144 2937 -

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