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- PDB-5t6w: HLA-B*57:01 presenting SSTRGISQLW -

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Basic information

Entry
Database: PDB / ID: 5t6w
TitleHLA-B*57:01 presenting SSTRGISQLW
Components
  • Beta-2-microglobulin
  • Decapeptide: SER-SER-THR-ARG-GLY-ILE-SER-GLN-LEU-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


Nuclear Pore Complex (NPC) Disassembly / Transport of Ribonucleoproteins into the Host Nucleus / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / NS1 Mediated Effects on Host Pathways / SUMOylation of SUMOylation proteins / Transport of Mature mRNA Derived from an Intronless Transcript / regulation of interleukin-12 production ...Nuclear Pore Complex (NPC) Disassembly / Transport of Ribonucleoproteins into the Host Nucleus / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / NS1 Mediated Effects on Host Pathways / SUMOylation of SUMOylation proteins / Transport of Mature mRNA Derived from an Intronless Transcript / regulation of interleukin-12 production / regulation of dendritic cell differentiation / Rev-mediated nuclear export of HIV RNA / structural constituent of nuclear pore / nuclear outer membrane / SUMOylation of RNA binding proteins / Nuclear import of Rev protein / regulation of T cell anergy / Transport of Mature mRNA derived from an Intron-Containing Transcript / NEP/NS2 Interacts with the Cellular Export Machinery / tRNA processing in the nucleus / RNA export from nucleus / Postmitotic nuclear pore complex (NPC) reformation / regulation of interleukin-6 production / nuclear inner membrane / Viral Messenger RNA Synthesis / nuclear localization sequence binding / SUMOylation of ubiquitinylation proteins / Vpr-mediated nuclear import of PICs / SUMOylation of DNA replication proteins / TAP binding / protection from natural killer cell mediated cytotoxicity / Regulation of HSF1-mediated heat shock response / mRNA transport / SUMOylation of DNA damage response and repair proteins / nuclear pore / detection of bacterium / SUMOylation of chromatin organization proteins / HCMV Late Events / 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 / 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 / lumenal side of endoplasmic reticulum membrane / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / Transcriptional regulation by small RNAs / 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 / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / 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 / ISG15 antiviral mechanism / MHC class I protein complex / defense response / multicellular organismal-level iron ion homeostasis / negative regulation of neurogenesis / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / HCMV Early Events / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / specific granule lumen / recycling endosome membrane / protein import into nucleus / phagocytic vesicle membrane / positive regulation of cellular senescence / peptide antigen binding / 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 / Interferon alpha/beta signaling / sensory perception of smell / positive regulation of T cell activation / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / nuclear envelope / snRNP Assembly
Similarity search - Function
Nuclear pore protein POM121 / Nuclear pore complex protein / 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 ...Nuclear pore protein POM121 / Nuclear pore complex protein / 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 / Immunoglobulins / Immunoglobulin-like fold / 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 / Nuclear envelope pore membrane protein POM 121
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 1, 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

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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: SER-SER-THR-ARG-GLY-ILE-SER-GLN-LEU-TRP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7124
Polymers44,6203
Non-polymers921
Water3,729207
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4720 Å2
ΔGint-19 kcal/mol
Surface area18840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.790, 81.180, 109.790
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 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
#3: Protein/peptide Decapeptide: SER-SER-THR-ARG-GLY-ILE-SER-GLN-LEU-TRP


Mass: 1135.252 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: UniProt: Q96HA1*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.: 207 / 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: 2.54 Å3/Da / Density % sol: 51.61 %
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 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 1.9→32.637 Å / Num. obs: 36411 / % possible obs: 99.6 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.197 / Net I/σ(I): 4.7
Reflection shellResolution: 1.9→2 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.553 / Mean I/σ(I) obs: 2.3 / % possible all: 99.8

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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: 1.9→32.637 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.65
RfactorNum. reflection% reflection
Rfree0.263 1799 4.95 %
Rwork0.2114 --
obs0.2139 36352 99.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→32.637 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3139 0 6 207 3352
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073232
X-RAY DIFFRACTIONf_angle_d1.0444383
X-RAY DIFFRACTIONf_dihedral_angle_d14.0481194
X-RAY DIFFRACTIONf_chiral_restr0.041448
X-RAY DIFFRACTIONf_plane_restr0.005577
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.95140.40681440.29762628X-RAY DIFFRACTION99
1.9514-2.00880.33251240.27672608X-RAY DIFFRACTION100
2.0088-2.07360.28031370.24722621X-RAY DIFFRACTION99
2.0736-2.14770.26631460.23682597X-RAY DIFFRACTION99
2.1477-2.23370.30411430.22872644X-RAY DIFFRACTION100
2.2337-2.33530.29971170.22742658X-RAY DIFFRACTION100
2.3353-2.45840.29021430.22492640X-RAY DIFFRACTION100
2.4584-2.61240.30391480.22732628X-RAY DIFFRACTION100
2.6124-2.8140.30111540.24542656X-RAY DIFFRACTION100
2.814-3.0970.29081190.23022686X-RAY DIFFRACTION100
3.097-3.54460.24651530.19932663X-RAY DIFFRACTION99
3.5446-4.4640.21691330.16932704X-RAY DIFFRACTION99
4.464-32.64190.18641380.16872820X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: -12.3275 Å / Origin y: 9.1785 Å / Origin z: -18.4472 Å
111213212223313233
T0.1316 Å2-0.0053 Å2-0.0191 Å2-0.1359 Å2-0.0082 Å2--0.2257 Å2
L1.0161 °2-0.1526 °2-0.3224 °2-0.5304 °20.1767 °2--0.4719 °2
S-0.051 Å °0.0181 Å °-0.1867 Å °0.0168 Å °-0.0235 Å °0.0502 Å °0.0476 Å °-0.0339 Å °0.0628 Å °
Refinement TLS groupSelection details: all

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