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- PDB-3h7b: Human Class I MHC HLA-A2 in complex with the Tel1p peptide -

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Basic information

Entry
Database: PDB / ID: 3h7b
TitleHuman Class I MHC HLA-A2 in complex with the Tel1p peptide
Components
  • Beta-2-microglobulinBeta-2 microglobulin
  • HLA class I histocompatibility antigen, A-2 alpha chain
  • Tel1p peptide
KeywordsIMMUNE SYSTEM / Tel1p peptide / nonapeptide / MHC class I / HLA-A2 / TCR A6 / cross-reactivity / Disulfide bond / Glycoprotein / Host-virus interaction / Immune response / Membrane / MHC I / Phosphoprotein / Transmembrane / Disease mutation / Glycation / Immunoglobulin domain / Pyrrolidone carboxylic acid / Secreted
Function / homology
Function and homology information


Pexophagy / DNA Damage/Telomere Stress Induced Senescence / Sensing of DNA Double Strand Breaks / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / telomeric DNA binding / T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / positive regulation of memory T cell activation / TAP complex binding / antigen processing and presentation of exogenous peptide antigen via MHC class I ...Pexophagy / DNA Damage/Telomere Stress Induced Senescence / Sensing of DNA Double Strand Breaks / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / telomeric DNA binding / T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / positive regulation of memory T cell activation / TAP complex binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / endoplasmic reticulum exit site / beta-2-microglobulin binding / signal transduction in response to DNA damage / TAP binding / protection from natural killer cell mediated cytotoxicity / negative regulation of TORC1 signaling / 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 / telomere maintenance / T cell receptor binding / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / early endosome lumen / DNA damage checkpoint signaling / positive regulation of receptor binding / 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 / 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 / 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 / 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 / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / 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 / recycling endosome membrane / phagocytic vesicle membrane / specific granule lumen / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / double-strand break repair / Interferon gamma signaling / positive regulation of immune response / negative regulation of epithelial cell proliferation / Modulation by Mtb of host immune system / positive regulation of T cell activation / Interferon alpha/beta signaling / positive regulation of type II interferon production / sensory perception of smell / negative regulation of neuron projection development / E3 ubiquitin ligases ubiquitinate target proteins / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / chromatin organization / positive regulation of protein binding / ER-Phagosome pathway / antibacterial humoral response / iron ion transport / T cell receptor signaling pathway / protein refolding / early endosome membrane / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / chromosome, telomeric region / learning or memory / non-specific serine/threonine protein kinase / protein kinase activity / defense response to Gram-positive bacterium / immune response / Amyloid fiber formation
Similarity search - Function
Telomere-length maintenance and DNA damage repair / Serine/threonine-protein kinase ATM, plant / ATM, catalytic domain / Telomere-length maintenance and DNA damage repair / Telomere-length maintenance and DNA damage repair / FATC domain / FATC / FATC domain / PIK-related kinase / FAT domain profile. ...Telomere-length maintenance and DNA damage repair / Serine/threonine-protein kinase ATM, plant / ATM, catalytic domain / Telomere-length maintenance and DNA damage repair / Telomere-length maintenance and DNA damage repair / FATC domain / FATC / FATC domain / PIK-related kinase / FAT domain profile. / FATC domain profile. / Phosphatidylinositol 3- and 4-kinases signature 1. / Phosphatidylinositol 3/4-kinase, conserved site / Phosphatidylinositol 3- and 4-kinases signature 2. / Phosphatidylinositol 3-/4-kinase, catalytic domain superfamily / Phosphoinositide 3-kinase, catalytic domain / Phosphatidylinositol 3- and 4-kinase / Phosphatidylinositol 3- and 4-kinases catalytic domain profile. / Phosphatidylinositol 3-/4-kinase, catalytic 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 / 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 / Protein kinase-like domain superfamily / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
HLA class I histocompatibility antigen, A alpha chain / HLA class I histocompatibility antigen, A alpha chain / Serine/threonine-protein kinase TEL1 / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.88 Å
AuthorsBorbulevych, O.Y. / Baker, B.M.
CitationJournal: Immunity / Year: 2009
Title: T cell receptor cross-reactivity directed by antigen-dependent tuning of peptide-MHC molecular flexibility.
Authors: Borbulevych, O.Y. / Piepenbrink, K.H. / Gloor, B.E. / Scott, D.R. / Sommese, R.F. / Cole, D.K. / Sewell, A.K. / Baker, B.M.
History
DepositionApr 24, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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, A-2 alpha chain
B: Beta-2-microglobulin
C: Tel1p peptide
D: HLA class I histocompatibility antigen, A-2 alpha chain
E: Beta-2-microglobulin
F: Tel1p peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,54914
Polymers89,8126
Non-polymers7378
Water11,205622
1
A: HLA class I histocompatibility antigen, A-2 alpha chain
B: Beta-2-microglobulin
C: Tel1p peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3668
Polymers44,9063
Non-polymers4605
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6040 Å2
ΔGint-27 kcal/mol
Surface area18880 Å2
MethodPISA
2
D: HLA class I histocompatibility antigen, A-2 alpha chain
E: Beta-2-microglobulin
F: Tel1p peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1826
Polymers44,9063
Non-polymers2763
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5100 Å2
ΔGint-28 kcal/mol
Surface area18980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.324, 63.063, 74.877
Angle α, β, γ (deg.)81.950, 75.950, 77.880
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D
12B
22E

NCS domain segments:

Component-ID: 1 / Refine code: 4

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPGLUGLUAA183 - 275183 - 275
21ASPASPGLUGLUDD183 - 275183 - 275
12METMETMETMETBB0 - 991 - 100
22METMETMETMETEE0 - 991 - 100

NCS ensembles :
ID
1
2

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Components

#1: Protein HLA class I histocompatibility antigen, A-2 alpha chain / MHC class I antigen A*2


Mass: 31854.203 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A, HLAA / Plasmid: pHN1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P01892, UniProt: P04439*PLUS
#2: Protein Beta-2-microglobulin / Beta-2 microglobulin / Beta-2-microglobulin form pI 5.3


Mass: 11879.356 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Plasmid: pHN1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P61769
#3: Protein/peptide Tel1p peptide


Mass: 1172.395 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Peptide synthesis / References: UniProt: P38110*PLUS
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 622 / 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: 2.5 Å3/Da / Density % sol: 50.77 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: PEG3350 24%, MES 0.025M, NaCl 0.1M, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.98494 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Jun 29, 2007
RadiationMonochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98494 Å / Relative weight: 1
ReflectionResolution: 1.88→20 Å / Num. all: 69668 / Num. obs: 67439 / % possible obs: 96.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 1.9 % / Biso Wilson estimate: 22.7 Å2 / Rmerge(I) obs: 0.066 / Χ2: 1.088 / Net I/σ(I): 11.766
Reflection shellResolution: 1.88→1.97 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.356 / Mean I/σ(I) obs: 1.99 / Num. unique all: 6629 / Χ2: 0.968 / % possible all: 94.4

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.5 Å19.89 Å
Translation3.5 Å19.89 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
SBC-Collectdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2AV1

2av1


Resolution: 1.88→20 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.926 / WRfactor Rfree: 0.234 / WRfactor Rwork: 0.186 / Occupancy max: 1 / Occupancy min: 0.33 / FOM work R set: 0.804 / SU B: 8.597 / SU ML: 0.128 / SU R Cruickshank DPI: 0.168 / SU Rfree: 0.157 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.166 / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.242 3396 5 %RANDOM
Rwork0.192 ---
all0.195 70539 --
obs0.195 67422 95.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 51.82 Å2 / Biso mean: 26.217 Å2 / Biso min: 12.46 Å2
Baniso -1Baniso -2Baniso -3
1-0.97 Å20.59 Å21.78 Å2
2---0.69 Å20.16 Å2
3----1.44 Å2
Refinement stepCycle: LAST / Resolution: 1.88→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6334 0 48 622 7004
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0216654
X-RAY DIFFRACTIONr_angle_refined_deg1.7171.9289046
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6965793
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.19623.183355
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.477151078
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7341556
X-RAY DIFFRACTIONr_chiral_restr0.1270.2914
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025246
X-RAY DIFFRACTIONr_nbd_refined0.1450.082872
X-RAY DIFFRACTIONr_nbtor_refined0.3110.54391
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2110.5951
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0980.0845
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1960.541
X-RAY DIFFRACTIONr_mcbond_it1.49323997
X-RAY DIFFRACTIONr_mcangle_it2.18436289
X-RAY DIFFRACTIONr_scbond_it1.54823113
X-RAY DIFFRACTIONr_scangle_it2.29932747
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A740MEDIUM POSITIONAL0.30.5
1A740MEDIUM THERMAL0.912
2B830MEDIUM POSITIONAL0.310.5
2B830MEDIUM THERMAL0.922
LS refinement shellResolution: 1.88→1.93 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 207 -
Rwork0.271 3902 -
all-4109 -
obs--78.73 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.32070.120.05891.7268-0.3482.9829-0.0548-0.02380.17940.1057-0.01190.0374-0.22920.05550.0667-0.1056-0.0053-0.0311-0.0688-0.0233-0.06232.563613.82326.6563
21.8996-2.4766-1.81835.3972.45833.72570.0840.1037-0.1009-0.3991-0.1111-0.00670.16610.02480.0271-0.0555-0.0184-0.0204-0.0988-0.0149-0.08166.1603-19.7061-6.4332
32.30882.1566-0.76545.2572-1.18742.135-0.05970.1315-0.0143-0.14260.11960.2950.1561-0.2116-0.0599-0.1272-0.015-0.0358-0.0636-0.0009-0.0888-11.2603-5.003-7.0015
41.0722-0.2335-0.21493.11860.71952.6442-0.03570.02040.091-0.066-0.0199-0.067-0.18770.0250.0556-0.0896-0.0056-0.0015-0.06190.0158-0.078429.6947-13.579226.3069
54.61911.711-3.57762.1706-1.04623.96160.04990.0248-0.12730.052-0.0358-0.05220.0389-0.179-0.0141-0.1340.0042-0.0211-0.09190.0165-0.095712.6899-42.699339.0862
61.1382-0.39050.18655.62440.72422.3922-0.0279-0.0433-0.0460.09120.0465-0.15790.11510.0067-0.0186-0.1992-0.008-0.0081-0.0792-0.0004-0.120734.4028-36.433339.7724
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 182
2X-RAY DIFFRACTION1C1 - 9
3X-RAY DIFFRACTION2A183 - 275
4X-RAY DIFFRACTION3B0 - 99
5X-RAY DIFFRACTION4D1 - 182
6X-RAY DIFFRACTION4F1 - 9
7X-RAY DIFFRACTION5D183 - 275
8X-RAY DIFFRACTION6E0 - 99

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