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- PDB-3pwj: Human Class I MHC HLA-A2 in complex with the HuD (G2L,I9V) peptid... -

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Basic information

Entry
Database: PDB / ID: 3pwj
TitleHuman Class I MHC HLA-A2 in complex with the HuD (G2L,I9V) peptide variant
Components
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, A-2 alpha chain
  • HuD (G2L,I9V) peptide
KeywordsPROTEIN BINDING / HuD antigen / TAX peptide / nonapeptide / MHC class I / HLA-A2 / TCR A6 / cross-reactivity
Function / homology
Function and homology information


positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / TAP complex binding / 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 / antigen processing and presentation of exogenous peptide antigen via MHC class I / beta-2-microglobulin binding ...positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / TAP complex binding / 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 / antigen processing and presentation of exogenous peptide antigen via MHC class I / beta-2-microglobulin binding / endoplasmic reticulum exit site / TAP binding / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / 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 / T cell receptor binding / 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 / 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 / positive regulation of type II interferon production / 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 / antibacterial humoral response / tertiary granule lumen / DAP12 signaling / T cell differentiation in thymus / T cell receptor signaling pathway / E3 ubiquitin ligases ubiquitinate target proteins / negative regulation of neuron projection development / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / defense response to Gram-positive bacterium / 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 / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / cell surface / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / extracellular space / RNA binding / extracellular exosome
Similarity search - Function
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 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, A alpha chain / HLA class I histocompatibility antigen, A alpha chain / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsBorbulevych, O.Y. / Baker, B.M.
CitationJournal: J.Immunol. / Year: 2011
Title: Conformational Melding Permits a Conserved Binding Geometry in TCR Recognition of Foreign and Self Molecular Mimics.
Authors: Borbulevych, O.Y. / Piepenbrink, K.H. / Baker, B.M.
History
DepositionDec 8, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 13, 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
Revision 1.3Nov 27, 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, A-2 alpha chain
B: Beta-2-microglobulin
C: HuD (G2L,I9V) peptide
D: HLA class I histocompatibility antigen, A-2 alpha chain
E: Beta-2-microglobulin
F: HuD (G2L,I9V) peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,01010
Polymers89,6426
Non-polymers3684
Water12,484693
1
A: HLA class I histocompatibility antigen, A-2 alpha chain
B: Beta-2-microglobulin
C: HuD (G2L,I9V) peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0055
Polymers44,8213
Non-polymers1842
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4880 Å2
ΔGint-21 kcal/mol
Surface area19160 Å2
MethodPISA
2
D: HLA class I histocompatibility antigen, A-2 alpha chain
E: Beta-2-microglobulin
F: HuD (G2L,I9V) peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0055
Polymers44,8213
Non-polymers1842
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5110 Å2
ΔGint-25 kcal/mol
Surface area18910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.180, 62.853, 74.698
Angle α, β, γ (deg.)81.980, 76.200, 78.110
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 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 HuD (G2L,I9V) peptide


Mass: 1087.268 Da / Num. of mol.: 2 / Source method: obtained synthetically
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 693 / 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: 2.49 Å3/Da / Density % sol: 50.53 %
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: 0.9793 Å
DetectorDetector: CCD
RadiationMonochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.7→20 Å / Num. all: 95066 / Num. obs: 91454 / % possible obs: 96.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 1.9 % / Biso Wilson estimate: 21.5 Å2 / Rmerge(I) obs: 0.042 / Χ2: 0.97 / Net I/σ(I): 18
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.7-1.761.80.34987131.03492
1.76-1.831.90.28789441.07793.9
1.83-1.911.90.19290841.02595.4
1.91-2.021.90.13591240.98496
2.02-2.141.90.09891670.95496.8
2.14-2.311.90.07692540.93997.2
2.31-2.541.90.0692620.89497.2
2.54-2.91.90.04292980.87597.8
2.9-3.661.90.03193311.01898.2
3.66-2020.02292770.9397.6

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.5 Å19.86 Å
Translation3.5 Å19.86 Å

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
SBC-Collectdata collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1DUZ

1duz


Resolution: 1.7→20 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.945 / WRfactor Rfree: 0.2109 / WRfactor Rwork: 0.1756 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8522 / SU B: 5.234 / SU ML: 0.077 / SU R Cruickshank DPI: 0.1099 / SU Rfree: 0.108 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.108 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2152 4560 5 %RANDOM
Rwork0.1797 ---
all0.1814 95252 --
obs0.1814 91395 95.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 57.46 Å2 / Biso mean: 26.471 Å2 / Biso min: 2.26 Å2
Baniso -1Baniso -2Baniso -3
1-0.72 Å20.27 Å20.97 Å2
2---0.61 Å20.16 Å2
3----0.73 Å2
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6324 0 24 693 7041
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0216622
X-RAY DIFFRACTIONr_angle_refined_deg1.7731.9258995
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3485778
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.42623.168363
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.918151077
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0791558
X-RAY DIFFRACTIONr_chiral_restr0.1420.2912
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0215225
X-RAY DIFFRACTIONr_mcbond_it1.47423858
X-RAY DIFFRACTIONr_mcangle_it2.36636236
X-RAY DIFFRACTIONr_scbond_it1.97922764
X-RAY DIFFRACTIONr_scangle_it2.95132752
Refine LS restraints NCS

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

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A738MEDIUM POSITIONAL0.270.5
1A738MEDIUM THERMAL1.12
2B816MEDIUM POSITIONAL0.210.5
2B816MEDIUM THERMAL0.932
LS refinement shellResolution: 1.7→1.742 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 312 -
Rwork0.263 5919 -
all-6231 -
obs--88.79 %
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)
10.91850.16830.19581.2589-0.26192.3134-0.058-0.00920.15770.0501-0.01130.0208-0.19930.03860.06920.11110.0156-0.01160.0903-0.0080.10222.46713.9326.619
21.7784-2.0206-1.39914.47272.16352.86220.07010.145-0.0851-0.2354-0.05110.03510.17470.0395-0.01910.16540.0010.00420.0798-0.00970.07056.299-19.54-6.52
31.73181.7963-0.2984.2993-0.61951.6211-0.06950.10820.0032-0.16850.09940.27790.1577-0.1501-0.02980.0815-0.00660.00160.0940.01350.0935-11.172-4.939-7.015
40.8033-0.27230.00142.25290.31751.8152-0.07320.01130.0908-0.0340.0423-0.1078-0.13590.04390.03080.106-0.00170.00650.11980.01510.079629.516-13.43726.214
54.20621.5977-3.06272.2095-1.10393.22230.0660.0058-0.0838-0.0251-0.0773-0.020.0145-0.10080.01130.02940.0077-0.00660.0730.00980.05712.664-42.49238.945
61.0442-0.50710.16834.54730.1642.0838-0.02-0.0209-0.03890.08940.0646-0.17650.0775-0.0303-0.04470.009-0.0050.00970.0743-0.01420.054134.276-36.22639.614
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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