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- PDB-2gtw: Human Class I MHC HLA-A2 in complex with the nonameric Melan-A/MA... -

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Basic information

Entry
Database: PDB / ID: 2gtw
TitleHuman Class I MHC HLA-A2 in complex with the nonameric Melan-A/MART-1(27-35) peptide having A27L substitution
Components
  • Beta-2-microglobulin
  • HLA-A*0201 heavy chain
  • octapeptide from Melan-A/MART-1
KeywordsIMMUNE SYSTEM / Melan-A/MART-1 peptide / nonapeptide / MHC class I / HLA-A2 / A27L mutation / melanoma / cancer vaccines
Function / homology
Function and homology information


melanosome membrane / 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 ...melanosome membrane / 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 / Regulation of MITF-M-dependent genes involved in pigmentation / 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 / Endosomal/Vacuolar pathway / lumenal side of endoplasmic reticulum membrane / 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 / trans-Golgi network / 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 / melanosome / 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
Similarity search - Function
Protein melan-A / Protein melan-A / 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 / : ...Protein melan-A / Protein melan-A / 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
FORMIC ACID / HLA class I histocompatibility antigen, A alpha chain / Beta-2-microglobulin / Melanoma antigen recognized by T-cells 1 / HLA class I histocompatibility antigen, A alpha chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.548 Å
AuthorsBorbulevych, O.Y. / Baker, B.M.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Structures of MART-1(26/27-35) Peptide/HLA-A2 Complexes Reveal a Remarkable Disconnect between Antigen Structural Homology and T Cell Recognition
Authors: Borbulevych, O.Y. / Insaidoo, F.K. / Baxter, T.K. / Powell, D.J. / Johnson, L.A. / Restifo, N.P. / Baker, B.M.
History
DepositionApr 28, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id
Revision 1.5Nov 6, 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-A*0201 heavy chain
B: Beta-2-microglobulin
C: octapeptide from Melan-A/MART-1
D: HLA-A*0201 heavy chain
E: Beta-2-microglobulin
F: octapeptide from Melan-A/MART-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,87017
Polymers89,1796
Non-polymers69111
Water12,106672
1
A: HLA-A*0201 heavy chain
B: Beta-2-microglobulin
C: octapeptide from Melan-A/MART-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,02710
Polymers44,5903
Non-polymers4377
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5730 Å2
ΔGint-36 kcal/mol
Surface area18660 Å2
MethodPISA
2
D: HLA-A*0201 heavy chain
E: Beta-2-microglobulin
F: octapeptide from Melan-A/MART-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8437
Polymers44,5903
Non-polymers2534
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5060 Å2
ΔGint-36 kcal/mol
Surface area18710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.309, 84.271, 84.293
Angle α, β, γ (deg.)90.00, 90.11, 90.00
Int Tables number4
Space group name H-MP1211
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

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Protein , 2 types, 4 molecules ADBE

#1: Protein HLA-A*0201 heavy chain / HLA class I histocompatibility antigen / A-2 alpha chain / MHC class I antigen A*2


Mass: 31854.203 Da / Num. of mol.: 2 / Fragment: heavy chain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A / Plasmid: pHN1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9TQH5, UniProt: P04439*PLUS
#2: Protein Beta-2-microglobulin / Beta-2-microglobulin variant 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 / Plasmid: pHN1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P61769

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Protein/peptide , 1 types, 2 molecules CF

#3: Protein/peptide octapeptide from Melan-A/MART-1 / Melanoma antigen recognized by T-cells 1


Mass: 856.062 Da / Num. of mol.: 2 / Fragment: residues 27-35 / Mutation: A27L / Source method: obtained synthetically / Details: Commercial synthesis for the peptide / References: UniProt: Q16655

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Non-polymers , 4 types, 683 molecules

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


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH2O2
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 672 / 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: 2.32 Å3/Da / Density % sol: 47.01 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: PEG 3350 24%, MES 0.025M, HCOOK 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: 23-ID-D / Wavelength: 1.033 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 20, 2005
RadiationMonochromator: DOUBLE CRYSTAL SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.548→20 Å / Num. all: 118490 / Num. obs: 110421 / % possible obs: 93.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.1 % / Biso Wilson estimate: 17 Å2 / Rmerge(I) obs: 0.108 / Net I/σ(I): 14.8
Reflection shellResolution: 1.548→1.61 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.354 / Mean I/σ(I) obs: 2.11 / Num. unique all: 8400 / % possible all: 71.2

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Processing

Software
NameVersionClassification
Blu-Ice(GM/CA)data collection
HKL-2000data reduction
MOLREPphasing
REFMAC5.2refinement
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1TVB

1tvb


Resolution: 1.548→20 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.944 / SU B: 3.217 / SU ML: 0.058 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.089 / ESU R Free: 0.091 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.21768 5541 5 %RANDOM
Rwork0.18135 ---
all0.18317 118485 --
obs0.18317 104852 93.17 %-
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 mean: 22.072 Å2
Baniso -1Baniso -2Baniso -3
1--0.84 Å20 Å20.39 Å2
2--1.08 Å20 Å2
3----0.23 Å2
Refinement stepCycle: LAST / Resolution: 1.548→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6288 0 44 672 7004
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0216580
X-RAY DIFFRACTIONr_angle_refined_deg1.731.9278912
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2055765
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.49123.114350
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.348151083
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1771558
X-RAY DIFFRACTIONr_chiral_restr0.1580.2920
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.025118
X-RAY DIFFRACTIONr_nbd_refined0.1640.082718
X-RAY DIFFRACTIONr_nbtor_refined0.3110.54429
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1840.51026
X-RAY DIFFRACTIONr_metal_ion_refined0.0810.52
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1390.0867
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2120.562
X-RAY DIFFRACTIONr_mcbond_it1.0651.53860
X-RAY DIFFRACTIONr_mcangle_it1.88426220
X-RAY DIFFRACTIONr_scbond_it3.03532871
X-RAY DIFFRACTIONr_scangle_it4.8824.52691
Refine LS restraints NCS

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

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A745medium positional0.260.5
2B834medium positional0.340.5
1A745medium thermal0.772
2B834medium thermal0.812
LS refinement shellResolution: 1.548→1.588 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 306 -
Rwork0.225 5603 -
obs--67.84 %
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)
12.4523-0.1898-1.26170.2757-0.19951.7852-0.0425-0.2109-0.0940.06080.0147-0.01620.04890.02850.0278-0.0386-0.0136-0.0245-0.05920.0042-0.062524.140217.190635.4625
21.86580.19631.12451.05330.60723.530.02950.0897-0.1203-0.04760.0312-0.00590.14060.0396-0.0607-0.06260.0036-0.0099-0.10630.0082-0.0798-6.871914.087619.0798
33.8247-0.5204-0.67031.28920.2551.44720.0762-0.00890.36240.0445-0.02720.0512-0.1359-0.0816-0.049-0.0394-0.00150.0105-0.0952-0.0031-0.06133.348332.110327.1678
42.223-0.02160.71920.36370.11581.5585-0.0003-0.27570.15430.0467-0.01140.0327-0.0120.0550.0117-0.0386-0.00860.0115-0.0446-0.0291-0.04065.1359-17.35620.305
52.50090.2557-1.74920.9444-0.35953.68770.08540.05480.1708-0.08-0.0125-0.0024-0.1551-0.0643-0.0729-0.05210.0102-0.004-0.0903-0.0101-0.069636.0916-14.25263.8015
63.1648-0.49740.35111.5295-0.1531.55030.0167-0.1142-0.23570.0444-0.0274-0.06010.08580.13710.0107-0.0545-0.0023-0.0083-0.06080.0112-0.076226.0472-32.255411.9625
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 1821 - 182
2X-RAY DIFFRACTION1CC1 - 91 - 9
3X-RAY DIFFRACTION2AA183 - 275183 - 275
4X-RAY DIFFRACTION3BB0 - 991 - 100
5X-RAY DIFFRACTION4DD1 - 1821 - 182
6X-RAY DIFFRACTION4FF1 - 91 - 9
7X-RAY DIFFRACTION5DD183 - 275183 - 275
8X-RAY DIFFRACTION6EE0 - 991 - 100

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