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- PDB-1tvh: Crystal structure of Modified Melanoma Antigen gp100(209-T2M) Bou... -

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Basic information

Entry
Database: PDB / ID: 1tvh
TitleCrystal structure of Modified Melanoma Antigen gp100(209-T2M) Bound to Human Class I MHC HLA-A2
Components
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, A-2 alpha chain
  • epitope of Melanocyte protein Pmel 17
KeywordsIMMUNE SYSTEM / Melanoma / X-ray / modified gp100 peptide / gp100(209-T2M) peptide / MHC / HLA-A2
Function / homology
Function and homology information


cis-Golgi network membrane / positive regulation of melanin biosynthetic process / melanin biosynthetic process / melanosome membrane / melanosome organization / multivesicular body, internal vesicle / multivesicular body membrane / positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / TAP complex binding ...cis-Golgi network membrane / positive regulation of melanin biosynthetic process / melanin biosynthetic process / melanosome membrane / melanosome organization / multivesicular body, internal vesicle / multivesicular body 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 / 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
Similarity search - Function
PKD- and KLD-Associated Transmembrane / PKAT, KLD domain / PKAT, KLD domain / PKD domain / Polycystic kidney disease (PKD) domain profile. / PKD domain / PKD domain superfamily / PKD/Chitinase domain / Repeats in polycystic kidney disease 1 (PKD1) and other proteins / MHC class I, alpha chain, C-terminal ...PKD- and KLD-Associated Transmembrane / PKAT, KLD domain / PKAT, KLD domain / PKD domain / Polycystic kidney disease (PKD) domain profile. / PKD domain / PKD domain superfamily / PKD/Chitinase domain / Repeats in polycystic kidney disease 1 (PKD1) and other proteins / 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 / Melanocyte protein PMEL / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.802 Å
AuthorsBorbulevych, O.Y. / Baker, B.M.
CitationJournal: J.Immunol. / Year: 2005
Title: Increased Immunogenicity of an Anchor-Modified Tumor-Associated Antigen Is Due to the Enhanced Stability of the Peptide/MHC Complex: Implications for Vaccine Design
Authors: Borbulevych, O.Y. / Baxter, T.K. / Yu, Z. / Restifo, N.P. / Baker, B.M.
History
DepositionJun 29, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 19, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / 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_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 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HLA class I histocompatibility antigen, A-2 alpha chain
B: Beta-2-microglobulin
C: epitope of Melanocyte protein Pmel 17
D: HLA class I histocompatibility antigen, A-2 alpha chain
E: Beta-2-microglobulin
F: epitope of Melanocyte protein Pmel 17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,11634
Polymers89,5386
Non-polymers2,57928
Water13,079726
1
A: HLA class I histocompatibility antigen, A-2 alpha chain
B: Beta-2-microglobulin
C: epitope of Melanocyte protein Pmel 17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,96616
Polymers44,7693
Non-polymers1,19713
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7510 Å2
ΔGint-32 kcal/mol
Surface area19020 Å2
MethodPISA
2
D: HLA class I histocompatibility antigen, A-2 alpha chain
E: Beta-2-microglobulin
F: epitope of Melanocyte protein Pmel 17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,15018
Polymers44,7693
Non-polymers1,38115
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7860 Å2
ΔGint-31 kcal/mol
Surface area18830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.407, 84.485, 84.014
Angle α, β, γ (deg.)90.00, 90.11, 90.00
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211

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Components

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


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


Mass: 11879.356 Da / Num. of mol.: 2 / Fragment: beta-chain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M / Plasmid: pLM1 / Production host: Escherichia coli (E. coli) / Strain (production host): pHN1 / References: UniProt: P61769
#3: Protein/peptide epitope of Melanocyte protein Pmel 17


Mass: 1035.213 Da / Num. of mol.: 2 / Fragment: residues 209-217 / Source method: obtained synthetically / Details: a modified sequence occurs naturally in humans / References: UniProt: P40967
#4: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 726 / 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: 2.3 Å3/Da / Density % sol: 46.1 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: PEG 3350, MES, 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: 0.98731 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Apr 21, 2004
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98731 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. all: 75145 / Num. obs: 74168 / % possible obs: 98.7 % / Observed criterion σ(I): 1 / Redundancy: 2.8 % / Biso Wilson estimate: 17.58 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 16.3
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.72 / Num. unique all: 7284 / % possible all: 97

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.1.24refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 1BOR

1bor


Resolution: 1.802→10 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.904 / SU B: 3.5 / SU ML: 0.109 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.143 / ESU R Free: 0.146 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.24651 3703 5 %RANDOM
Rwork0.18489 ---
obs0.18795 70064 98.51 %-
all-74883 --
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: 14.467 Å2
Baniso -1Baniso -2Baniso -3
1--0.9 Å20 Å2-0.76 Å2
2--1.2 Å20 Å2
3----0.3 Å2
Refinement stepCycle: LAST / Resolution: 1.802→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6312 0 168 726 7206
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0216642
X-RAY DIFFRACTIONr_angle_refined_deg2.141.9348958
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6295762
X-RAY DIFFRACTIONr_chiral_restr0.1820.2898
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.025120
X-RAY DIFFRACTIONr_nbd_refined0.1680.082913
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1960.5914
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1170.0880
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1820.556
X-RAY DIFFRACTIONr_mcbond_it1.2111.53830
X-RAY DIFFRACTIONr_mcangle_it2.00826176
X-RAY DIFFRACTIONr_scbond_it3.52832812
X-RAY DIFFRACTIONr_scangle_it5.294.52782
LS refinement shellResolution: 1.802→1.847 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.303 257
Rwork0.236 4814
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)
12.3078-0.06071.29840.56270.48462.0138-0.0579-0.12330.06680.03980.0602-0.0185-0.04550.056-0.00220.0407-0.01870.0280.0709-0.01220.04155.37032.938435.4086
22.68930.0748-1.66691.14590.03834.50590.04790.15530.2174-0.15410.0505-0.0248-0.276-0.0007-0.09830.06220.0062-0.00660.001-0.00430.036736.07236.071619.0663
34.8194-0.8611.27631.6594-0.19871.86020.0502-0.0009-0.31720.0341-0.014-0.05650.14920.0864-0.03620.0594-0.0099-0.01460.01440.00240.045225.7741-11.941527.1692
412.42935.339913.24570.195.051316.45750.1441-0.98270.03850.3373-0.20920.06530.4276-0.99650.06510.23230.0431-0.01950.1868-0.01830.1777-2.28053.461838.3498
52.20180.0055-0.88330.5225-0.3291.9925-0.0315-0.1473-0.11650.05620.0273-0.01770.0286-0.130.00420.0409-0.0066-0.01360.04520.01820.043623.592937.618520.2034
62.86020.12522.15441.2727-0.05524.52940.07690.1024-0.2713-0.1503-0.01160.0060.21050.0297-0.06530.06380.01380.00730.03190.01550.0401-7.014834.52273.7703
74.1968-0.9399-0.93871.87590.16491.7204-0.0165-0.09520.17490.01150.00930.0779-0.0929-0.11990.00720.0357-0.0039-0.00160.0444-0.00140.02863.13752.511411.9642
816.63886.6627-12.59250.8089-4.122112.4148-0.0852-0.5619-0.0010.23250.0801-0.1325-0.01380.53490.00510.18370.040.01330.16820.04570.133231.112136.980323.1441
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 1821 - 182
2X-RAY DIFFRACTION2AA183 - 275183 - 275
3X-RAY DIFFRACTION3BB0 - 991 - 100
4X-RAY DIFFRACTION4CC1 - 91 - 9
5X-RAY DIFFRACTION5DD1 - 1821 - 182
6X-RAY DIFFRACTION6DD183 - 275183 - 275
7X-RAY DIFFRACTION7EE0 - 991 - 100
8X-RAY DIFFRACTION8FF1 - 91 - 9

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