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- PDB-1tvb: Crystal structure of Melanoma Antigen gp100(209-217) Bound to Hum... -

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Basic information

Entry
Database: PDB / ID: 1tvb
TitleCrystal structure of Melanoma Antigen gp100(209-217) 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 / gp100 / peptide / MHC / HLA-A2
Function / homology
Function and homology information


cis-Golgi network membrane / positive regulation of melanin biosynthetic process / melanin biosynthetic process / multivesicular body, internal vesicle / melanosome membrane / melanosome organization / 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 / multivesicular body, internal vesicle / melanosome membrane / melanosome organization / 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 / Regulation of MITF-M-dependent genes involved in pigmentation / endoplasmic reticulum exit site / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / TAP binding / 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 / T cell receptor binding / detection of bacterium / : / : / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / negative regulation of receptor binding / DAP12 interactions / 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 / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / MHC class II protein complex / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / response to molecule of bacterial origin / 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 / antigen processing and presentation of exogenous peptide antigen via MHC class II / MHC class I protein complex / positive regulation of immune response / peptide antigen binding / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / positive regulation of T cell mediated cytotoxicity / positive regulation of T cell activation / multicellular organismal-level iron ion homeostasis / cellular response to nicotine / specific granule lumen / positive regulation of type II interferon production / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / negative regulation of epithelial cell proliferation / MHC class II protein complex binding / Modulation by Mtb of host immune system / Interferon alpha/beta signaling / late endosome membrane / sensory perception of smell / antibacterial humoral response / tertiary granule lumen / melanosome / DAP12 signaling / positive regulation of protein binding / E3 ubiquitin ligases ubiquitinate target proteins / T cell receptor signaling pathway / iron ion transport / negative regulation of neuron projection development / T cell differentiation in thymus / ER-Phagosome pathway / early endosome membrane / protein refolding / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / defense response to Gram-positive bacterium / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / Golgi membrane / lysosomal membrane / external side of plasma membrane / signaling receptor binding
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: 1.8 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 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

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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: 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)91,50328
Polymers89,4776
Non-polymers2,02622
Water16,754930
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)45,56812
Polymers44,7393
Non-polymers8299
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6930 Å2
ΔGint-21 kcal/mol
Surface area18120 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)45,93616
Polymers44,7393
Non-polymers1,19713
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7920 Å2
ΔGint-29 kcal/mol
Surface area18110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.388, 84.452, 84.016
Angle α, β, γ (deg.)90.00, 90.01, 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: 1005.121 Da / Num. of mol.: 2 / Fragment: residues 209-217 / Source method: obtained synthetically / Details: 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.: 22 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 930 / 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: 0.97951 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: 0.97951 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. all: 75417 / Num. obs: 74663 / % possible obs: 99 % / Observed criterion σ(I): 1 / Redundancy: 3.9 % / Biso Wilson estimate: 13.5 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 16.8
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.344 / Mean I/σ(I) obs: 3.7 / % possible all: 98.2

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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 / Resolution: 1.8→10 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.923 / SU B: 2.619 / SU ML: 0.082 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.129 / ESU R Free: 0.129 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.21618 3748 5 %RANDOM
Rwork0.16486 ---
obs0.16743 70516 98.96 %-
all-75044 --
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: 12.691 Å2
Baniso -1Baniso -2Baniso -3
1--0.69 Å20 Å2-0.35 Å2
2--1.14 Å20 Å2
3----0.44 Å2
Refinement stepCycle: LAST / Resolution: 1.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6310 0 132 930 7372
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0216610
X-RAY DIFFRACTIONr_angle_refined_deg1.9461.938928
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2935762
X-RAY DIFFRACTIONr_chiral_restr0.1760.2900
X-RAY DIFFRACTIONr_gen_planes_refined0.010.025120
X-RAY DIFFRACTIONr_nbd_refined0.1620.0753069
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1890.51254
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1210.07573
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2160.594
X-RAY DIFFRACTIONr_mcbond_it1.0111.53830
X-RAY DIFFRACTIONr_mcangle_it1.80826178
X-RAY DIFFRACTIONr_scbond_it3.13732780
X-RAY DIFFRACTIONr_scangle_it4.9374.52750
LS refinement shellResolution: 1.8→1.845 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.238 249
Rwork0.202 4981
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)
12.1032-0.07221.29570.34620.41831.9568-0.0509-0.0860.05970.07040.050.011-0.05110.06050.00080.0776-0.01630.03430.0827-0.00120.06385.43162.914135.3806
22.07680.4287-0.85280.9683-0.52193.8911-0.00970.07690.1179-0.06430.0560.0014-0.2005-0.0335-0.04630.0620.00640.00560.001-0.00340.048736.04746.103919.0263
33.867-0.51880.65671.2341-0.22571.21860.0763-0.0369-0.30730.0178-0.0217-0.04330.16020.001-0.05460.0917-0.0139-0.01240.03530.00650.066225.8646-11.916927.1352
415.4616.59516.14513.55584.902115.03520.1417-0.8527-0.17360.261-0.07280.10170.2744-0.598-0.06890.14740.04220.02240.1452-0.0270.1325-2.31423.483138.1286
51.8969-0.033-0.68440.4404-0.19641.6057-0.0105-0.1662-0.12220.06340.0088-0.00590.0385-0.17590.00160.0727-0.0181-0.01810.09920.02880.080823.65637.605820.1476
62.74220.12911.80371.07890.18453.9650.08310.0824-0.2096-0.10130.00330.03340.17330.1621-0.08640.06770.01210.00860.04350.00480.0595-6.959534.47273.7529
73.4104-0.6723-0.42761.64120.22831.41210.0172-0.10190.21020.0566-0.02430.0315-0.0864-0.13110.0070.0646-0.01380.0090.0905-0.01530.05343.102452.496311.8988
815.29048.8553-16.17355.2358-7.824923.40870.1429-0.38990.30810.28850.11250.1322-0.24160.3036-0.25540.11110.0347-0.02170.05230.0370.154831.285536.880923.0647
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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