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- PDB-5t6x: HLA-B*57:01 presenting TSTTSVASSW -

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Basic information

Entry
Database: PDB / ID: 5t6x
TitleHLA-B*57:01 presenting TSTTSVASSW
Components
  • Beta-2-microglobulin
  • Decapeptide: THR-SER-THR-THR-SER-VAL-ALA-SER-SER-TRP
  • HLA class I histocompatibility antigen, B-57 alpha chain
KeywordsIMMUNE SYSTEM / human leukocyte antigen Immunoglobulin domain antigen presentation
Function / homology
Function and homology information


peptidyl-glutamic acid modification / regulation of blastocyst development / protein-glutamic acid ligase activity / tubulin-glutamic acid ligase activity / protein polyglutamylation / 9+0 non-motile cilium / Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) / Carboxyterminal post-translational modifications of tubulin / regulation of interleukin-12 production / regulation of dendritic cell differentiation ...peptidyl-glutamic acid modification / regulation of blastocyst development / protein-glutamic acid ligase activity / tubulin-glutamic acid ligase activity / protein polyglutamylation / 9+0 non-motile cilium / Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) / Carboxyterminal post-translational modifications of tubulin / 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 / tubulin 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 / cellular response to iron ion / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / MHC class II protein complex / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / response to molecule of bacterial origin / defense response / 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 / antigen processing and presentation of exogenous peptide antigen via MHC class II / MHC class I protein complex / positive regulation of immune response / peptide antigen binding / negative regulation of neurogenesis / positive regulation of T cell mediated cytotoxicity / positive regulation of receptor-mediated endocytosis / microtubule cytoskeleton organization / multicellular organismal-level iron ion homeostasis / positive regulation of T cell activation / cellular response to nicotine / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / Interferon gamma signaling / Interferon alpha/beta signaling / MHC class II protein complex binding / positive regulation of protein binding / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / tertiary granule lumen / DAP12 signaling / protein-folding chaperone binding / negative regulation of neuron projection development / iron ion transport / T cell differentiation in thymus / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / adaptive immune response / microtubule / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / ciliary basal body / immune response / cilium / Amyloid fiber formation / endoplasmic reticulum lumen / Golgi membrane / external side of plasma membrane / signaling receptor binding / lysosomal membrane / innate immune response / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / cell surface
Similarity search - Function
Tubulin-tyrosine ligase/Tubulin polyglutamylase / Tubulin-tyrosine ligase family / TTL domain profile. / 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 ...Tubulin-tyrosine ligase/Tubulin polyglutamylase / Tubulin-tyrosine ligase family / TTL domain profile. / 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 C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
HLA class I histocompatibility antigen, B alpha chain / HLA class I histocompatibility antigen, B alpha chain / Beta-2-microglobulin / Tubulin monoglutamylase TTLL4
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.686 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 1.3Oct 4, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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-THR-SER-VAL-ALA-SER-SER-TRP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,6024
Polymers44,5103
Non-polymers921
Water3,243180
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4540 Å2
ΔGint-20 kcal/mol
Surface area18670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.527, 81.667, 109.614
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#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 resiudes 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 resiudes 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/peptide Decapeptide: THR-SER-THR-THR-SER-VAL-ALA-SER-SER-TRP


Mass: 1026.056 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: UniProt: Q14679*PLUS
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / Source method: isolated from a natural source / Formula: H2O
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: 2.55 Å3/Da / Density % sol: 51.69 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 12 -20 % PEG 4000, 0.2 M ammonium acetate and 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: Apr 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 1.686→42.968 Å / Num. obs: 49434 / % possible obs: 95.7 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 15
Reflection shellResolution: 1.7→1.78 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.581 / Mean I/σ(I) obs: 3.1 / % possible all: 92.6

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2RFX

2rfx


Resolution: 1.686→42.968 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.56
RfactorNum. reflection% reflection
Rfree0.2443 1999 4.05 %
Rwork0.2085 --
obs0.21 49389 95.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.686→42.968 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3131 0 6 180 3317
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073242
X-RAY DIFFRACTIONf_angle_d1.0484404
X-RAY DIFFRACTIONf_dihedral_angle_d13.8091199
X-RAY DIFFRACTIONf_chiral_restr0.043454
X-RAY DIFFRACTIONf_plane_restr0.005579
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6859-1.7280.30421260.25783000X-RAY DIFFRACTION86
1.728-1.77480.28841460.24593459X-RAY DIFFRACTION98
1.7748-1.8270.33221460.24523451X-RAY DIFFRACTION98
1.827-1.8860.26871450.24063441X-RAY DIFFRACTION98
1.886-1.95340.26331460.2263456X-RAY DIFFRACTION98
1.9534-2.03160.25871430.22493405X-RAY DIFFRACTION97
2.0316-2.1240.26561450.22173426X-RAY DIFFRACTION97
2.124-2.2360.24381440.22453431X-RAY DIFFRACTION96
2.236-2.37610.2671420.2263373X-RAY DIFFRACTION96
2.3761-2.55950.22561440.22383396X-RAY DIFFRACTION95
2.5595-2.81710.28331440.23193399X-RAY DIFFRACTION95
2.8171-3.22460.27281410.21353353X-RAY DIFFRACTION94
3.2246-4.06220.19651420.18113375X-RAY DIFFRACTION93
4.0622-42.98210.19281450.15523425X-RAY DIFFRACTION90
Refinement TLS params.Method: refined / Origin x: 62.8002 Å / Origin y: 90.9499 Å / Origin z: 128.0198 Å
111213212223313233
T0.0617 Å2-0.0044 Å2-0.0101 Å2-0.0472 Å20.0048 Å2--0.0663 Å2
L0.6017 °20.0784 °2-0.0608 °2-0.3001 °2-0.1527 °2--0.1694 °2
S-0.0208 Å °-0.0254 Å °-0.1131 Å °-0.0053 Å °-0.0253 Å °-0.0005 Å °0.0113 Å °0.0262 Å °-0.021 Å °
Refinement TLS groupSelection details: all

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