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- PDB-5t6y: HLA-B*57:01 presenting TSTFEDVKILAF -

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Basic information

Entry
Database: PDB / ID: 5t6y
TitleHLA-B*57:01 presenting TSTFEDVKILAF
Components
  • Beta-2-microglobulin
  • Decapeptide: THR-SER-THR-PHE-GLU-ASP-VAL-LYS-ILE-LEU-ALA-PHE
  • HLA class I histocompatibility antigen, B-57 alpha chain
KeywordsIMMUNE SYSTEM / human leukocyte antigen Immunoglobulin domain antigen presentation
Function / homology
Function and homology information


tRNA nucleoside ribose methylation / adaptive thermogenesis / negative regulation of endoplasmic reticulum calcium ion concentration / tRNA modification in the nucleus and cytosol / tRNA methylation / regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / cytoplasmic side of endoplasmic reticulum membrane ...tRNA nucleoside ribose methylation / adaptive thermogenesis / negative regulation of endoplasmic reticulum calcium ion concentration / tRNA modification in the nucleus and cytosol / tRNA methylation / regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / cytoplasmic side of endoplasmic reticulum membrane / lipid homeostasis / 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 / enzyme regulator activity / secretory granule membrane / negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / 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 / MHC class II protein complex / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / regulation of erythrocyte differentiation / HFE-transferrin receptor complex / response to molecule of bacterial origin / MHC class I peptide loading complex / defense response / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / MHC class I protein complex / positive regulation of T cell activation / peptide antigen binding / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / specific granule lumen / phagocytic vesicle membrane / recycling endosome membrane / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / MHC class II protein complex binding / Interferon alpha/beta signaling / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / positive regulation of cellular senescence / tertiary granule lumen / DAP12 signaling / T cell differentiation in thymus / protein-folding chaperone binding / negative regulation of neuron projection development / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / adaptive immune response / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / immune response / endoplasmic reticulum lumen / Amyloid fiber formation / signaling receptor binding / Golgi membrane / lysosomal membrane / innate immune response / external side of plasma membrane / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / cell surface / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane
Similarity search - Function
THADA/TRM732, DUF2428 / : / : / : / THADA/TRM732, DUF2428 / Trm732, TPR repeats / Trm732, C-terminal TPR repeats / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I-like antigen recognition-like ...THADA/TRM732, DUF2428 / : / : / : / THADA/TRM732, DUF2428 / Trm732, TPR repeats / Trm732, C-terminal TPR repeats / 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 / Armadillo-type fold / 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
ACETATE ION / HLA class I histocompatibility antigen, B alpha chain / HLA class I histocompatibility antigen, B alpha chain / Beta-2-microglobulin / tRNA (32-2'-O)-methyltransferase regulator THADA
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 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 1.4Nov 20, 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-PHE-GLU-ASP-VAL-LYS-ILE-LEU-ALA-PHE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1917
Polymers44,8563
Non-polymers3354
Water5,441302
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5510 Å2
ΔGint-24 kcal/mol
Surface area19030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.707, 82.043, 110.095
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 2 molecules AB

#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

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Protein/peptide , 1 types, 1 molecules C

#3: Protein/peptide Decapeptide: THR-SER-THR-PHE-GLU-ASP-VAL-LYS-ILE-LEU-ALA-PHE


Mass: 1371.554 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: UniProt: Q6YHU6*PLUS

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Non-polymers , 3 types, 306 molecules

#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 302 / 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: 2.55 Å3/Da / Density % sol: 51.82 %
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 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 1.76→41.022 Å / Num. obs: 45709 / % possible obs: 98.5 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.122 / Net I/σ(I): 8.7
Reflection shellResolution: 1.76→1.85 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.682 / Mean I/σ(I) obs: 2.3 / % possible all: 90.6

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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: 1.76→41.022 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.87
RfactorNum. reflection% reflection
Rfree0.2189 2267 4.97 %
Rwork0.1778 --
obs0.1799 45606 98.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.76→41.022 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3162 0 22 302 3486
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073283
X-RAY DIFFRACTIONf_angle_d1.034450
X-RAY DIFFRACTIONf_dihedral_angle_d14.2911217
X-RAY DIFFRACTIONf_chiral_restr0.046456
X-RAY DIFFRACTIONf_plane_restr0.004585
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7603-1.79850.35071040.30492087X-RAY DIFFRACTION78
1.7985-1.84040.31331680.24092700X-RAY DIFFRACTION100
1.8404-1.88640.24751190.22822747X-RAY DIFFRACTION100
1.8864-1.93740.25421700.2142681X-RAY DIFFRACTION100
1.9374-1.99440.25021350.20112706X-RAY DIFFRACTION100
1.9944-2.05880.24281280.19832770X-RAY DIFFRACTION100
2.0588-2.13240.24291330.19632705X-RAY DIFFRACTION100
2.1324-2.21770.26281310.18692762X-RAY DIFFRACTION100
2.2177-2.31870.20171240.18542733X-RAY DIFFRACTION100
2.3187-2.44090.2261540.18642719X-RAY DIFFRACTION100
2.4409-2.59380.25151350.19212738X-RAY DIFFRACTION100
2.5938-2.7940.2221480.20162755X-RAY DIFFRACTION100
2.794-3.07510.27851420.19582760X-RAY DIFFRACTION100
3.0751-3.51990.211470.172775X-RAY DIFFRACTION100
3.5199-4.43390.17981640.13792806X-RAY DIFFRACTION100
4.4339-41.03260.15751650.1382895X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -12.1393 Å / Origin y: 9.1884 Å / Origin z: -18.646 Å
111213212223313233
T0.1156 Å2-0.0007 Å2-0.0136 Å2-0.091 Å20.0002 Å2--0.1396 Å2
L0.9905 °2-0.0616 °2-0.2578 °2-0.3297 °20.084 °2--0.4014 °2
S-0.0192 Å °-0.0166 Å °-0.1386 Å °0.0279 Å °-0.0182 Å °0.0201 Å °0.019 Å °-0.0209 Å °0.0309 Å °
Refinement TLS groupSelection details: all

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