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- PDB-4hx1: Structure of HLA-A68 complexed with a tumor antigen derived peptide -

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Basic information

Entry
Database: PDB / ID: 4hx1
TitleStructure of HLA-A68 complexed with a tumor antigen derived peptide
Components
  • 9-mer peptide from Tyrosinase-related protein-2
  • Beta-2-microglobulin
  • MHC class I antigen
KeywordsIMMUNE SYSTEM / HLA molecules / peptide presentation
Function / homology
Function and homology information


melanin biosynthetic process from tyrosine / Melanin biosynthesis / cell development / developmental pigmentation / ventricular zone neuroblast division / L-dopachrome isomerase / response to blue light / dopachrome isomerase activity / melanosome membrane / positive regulation of memory T cell activation ...melanin biosynthetic process from tyrosine / Melanin biosynthesis / cell development / developmental pigmentation / ventricular zone neuroblast division / L-dopachrome isomerase / response to blue light / dopachrome isomerase activity / melanosome membrane / positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / 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 / positive regulation of neuroblast proliferation / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / TAP complex binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / Golgi medial cisterna / CD8 receptor binding / Regulation of MITF-M-dependent genes involved in pigmentation / protection from natural killer cell mediated cytotoxicity / beta-2-microglobulin binding / endoplasmic reticulum exit site / TAP binding / epidermis development / detection of bacterium / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of peptide antigen via MHC class I / intracellular membrane-bounded organelle / T cell receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / Endosomal/Vacuolar pathway / T cell mediated cytotoxicity / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / lumenal side of endoplasmic reticulum membrane / regulation of iron ion transport / cellular response to iron(III) ion / negative regulation of iron ion transport / 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 erythrocyte differentiation / response to molecule of bacterial origin / HFE-transferrin receptor complex / transferrin transport / MHC class I peptide loading complex / cellular response to iron ion / negative regulation of receptor-mediated endocytosis / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / MHC class I protein complex / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / cellular response to nicotine / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / multicellular organismal-level iron ion homeostasis / positive regulation of T cell mediated cytotoxicity / specific granule lumen / positive regulation of immune response / antigen processing and presentation of exogenous peptide antigen via MHC class II / peptide antigen binding / phagocytic vesicle membrane / positive regulation of type II interferon production / recycling endosome membrane / Interferon gamma signaling / negative regulation of epithelial cell proliferation / positive regulation of T cell activation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon alpha/beta signaling / Modulation by Mtb of host immune system / sensory perception of smell / positive regulation of cellular senescence / melanosome / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / T cell differentiation in thymus / late endosome membrane / T cell receptor signaling pathway / negative regulation of neuron projection development / E3 ubiquitin ligases ubiquitinate target proteins / antibacterial humoral response / ER-Phagosome pathway / protein refolding / early endosome membrane / amyloid fibril formation / protein homotetramerization / intracellular iron ion homeostasis / learning or memory / oxidoreductase activity / defense response to Gram-positive bacterium / immune response / endoplasmic reticulum lumen / Amyloid fiber formation
Similarity search - Function
Tyrosinase CuA-binding region signature. / : / Common central domain of tyrosinase / Tyrosinase and hemocyanins CuB-binding region signature. / Tyrosinase copper-binding domain / Di-copper centre-containing domain 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 ...Tyrosinase CuA-binding region signature. / : / Common central domain of tyrosinase / Tyrosinase and hemocyanins CuB-binding region signature. / Tyrosinase copper-binding domain / Di-copper centre-containing domain 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
Tyrosinase-related protein-2 / HLA class I histocompatibility antigen, A alpha chain / L-dopachrome tautomerase / Beta-2-microglobulin / HLA class I histocompatibility antigen
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.802 Å
AuthorsNiu, L. / Cheng, H. / Zhang, S. / Tan, S. / Zhang, Y. / Qi, J. / Liu, J. / Gao, G.F.
CitationJournal: Mol.Immunol. / Year: 2013
Title: Structural basis for the differential classification of HLA-A*6802 and HLA-A*6801 into the A2 and A3 supertypes
Authors: Niu, L. / Cheng, H. / Zhang, S. / Tan, S. / Zhang, Y. / Qi, J. / Liu, J. / Gao, G.F.
History
DepositionNov 9, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 2, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 13, 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: MHC class I antigen
B: Beta-2-microglobulin
C: 9-mer peptide from Tyrosinase-related protein-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7944
Polymers44,7023
Non-polymers921
Water6,846380
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4540 Å2
ΔGint-21 kcal/mol
Surface area18710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.237, 37.857, 108.323
Angle α, β, γ (deg.)90.00, 120.04, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein MHC class I antigen


Mass: 31778.119 Da / Num. of mol.: 1 / Fragment: UNP residues 25-298
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A / Production host: Escherichia coli (E. coli) / References: UniProt: Q1ELT0, UniProt: P04439*PLUS
#2: Protein Beta-2-microglobulin / Beta-2-microglobulin form pI 5.3


Mass: 11748.160 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M / Production host: Escherichia coli (E. coli) / References: UniProt: P61769
#3: Protein/peptide 9-mer peptide from Tyrosinase-related protein-2 / tumor antigen derived peptide


Mass: 1175.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: peptide dirived from tumor antigen / Source: (synth.) Homo sapiens (human) / References: UniProt: O75767, UniProt: P40126*PLUS
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 380 / 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: 2.57 Å3/Da / Density % sol: 52.06 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 100mM Tris, 8% PEG8000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 1, 2012
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 41016 / % possible obs: 95.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 21.59 Å2
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 4 % / Rmerge(I) obs: 0.271 / Mean I/σ(I) obs: 4.906 / Num. unique all: 155862 / Rsym value: 0.271 / % possible all: 99.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
CNSrefinement
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.802→31.461 Å / Occupancy max: 1 / Occupancy min: 0.41 / FOM work R set: 0.8397 / SU ML: 0.21 / σ(F): 1.34 / Phase error: 22.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2261 2053 5.07 %
Rwork0.19 --
all0.2261 --
obs0.1918 40466 95.21 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 28.832 Å2 / ksol: 0.335 e/Å3
Displacement parametersBiso max: 91.55 Å2 / Biso mean: 29.0756 Å2 / Biso min: 11.54 Å2
Baniso -1Baniso -2Baniso -3
1-2.0051 Å20 Å2-9.4175 Å2
2--0.3305 Å20 Å2
3----2.3355 Å2
Refinement stepCycle: LAST / Resolution: 1.802→31.461 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3154 0 6 380 3540
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053262
X-RAY DIFFRACTIONf_angle_d0.9584423
X-RAY DIFFRACTIONf_chiral_restr0.069446
X-RAY DIFFRACTIONf_plane_restr0.004578
X-RAY DIFFRACTIONf_dihedral_angle_d15.4071191
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8019-1.84380.28821550.24612546270197
1.8438-1.890.29411220.235326852807100
1.89-1.9410.36471170.25952623274098
1.941-1.99820.22641270.205327062833100
1.9982-2.06260.23021500.18826122762100
2.0626-2.13630.20291520.186126652817100
2.1363-2.22190.22161480.19242626277498
2.2219-2.32290.26311040.20981823192768
2.3229-2.44540.24331540.198926732827100
2.4454-2.59850.24291310.193226862817100
2.5985-2.7990.21341130.196127322845100
2.799-3.08050.23461610.18926772838100
3.0805-3.52570.19091450.1852652279798
3.5257-4.44010.19781340.15941957209173
4.4401-31.46620.23251400.17752750289097
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)
10.597-0.13960.41190.80390.19660.30540.0372-0.0111-0.0538-0.0182-0.03040.12360.1554-0.0542-00.1709-0.0210.00960.12830.00320.1618.6511-21.6052-15.4246
20.1285-0.19070.06090.2607-0.12070.1788-0.0169-0.0377-0.02470.03170.04360.05130.10510.024700.1788-0.0047-0.00910.15290.00830.190926.5906-20.6964-7.0671
30.5390.11360.26920.71140.43990.3695-0.01410.08160.067-0.03860.0070.0077-0.0915-0.0355-00.1381-0.00170.01240.13650.01480.136827.2962-6.8705-14.1552
40.2834-0.06930.19250.02920.0180.1318-0.08040.04390.09420.07060.0569-0.1913-0.07180.177-00.1719-0.00370.00710.17810.00030.212637.1659-7.6187-11.4719
50.1981-0.196-0.19190.1710.06350.22040.17670.1211-0.0602-0.1617-0.10250.02750.18540.00880.00010.22030.03750.01310.175-0.00180.183224.1362-22.6375-32.4106
60.5823-0.10040.17540.1898-0.37020.6813-0.03260.10530.02690.0189-0.0387-0.0584-0.1095-0.067-00.20810.011-0.03120.1929-0.00110.1709-1.308-3.768-37.5443
70.08890.0482-0.05570.15690.16760.19340.03070.06360.1609-0.1184-0.0332-0.02480.08870.0971-00.21790.0012-0.04760.22820.02290.19995.4291-8.8086-45.5639
80.16240.0551-0.18530.1326-0.11160.1819-0.0994-0.03990.03370.03070.1112-0.0996-0.1870.000700.1872-0.0166-0.00370.238-0.0210.23253.567-6.7304-17.081
90.02880.0275-0.0690.0415-0.0860.1799-0.09960.2425-0.1327-0.58050.24730.11310.21570.0305-0.00010.3385-0.25460.02440.4793-0.36740.612-7.2417-22.0132-31.7668
100.178-0.1121-0.05610.087-0.0620.1515-0.0125-0.054-0.29460.04920.0864-0.06270.1278-0.07990.00010.179-0.05020.00280.2233-0.00360.24351.141-15.6541-21.1034
110.4710.18460.08160.40160.10870.01960.2385-0.47120.04710.3744-0.21060.16730.2403-0.2950.06420.2045-0.07470.04240.40730.04270.25330.8948-13.7102-10.6264
120.01470.0083-0.02220.0241-0.0050.0203-0.2073-0.084-0.02750.561-0.0670.10070.1877-0.3099-0.00020.2711-0.01130.03820.45620.00910.3867-11.2282-20.2295-12.2967
130.32270.1293-0.03530.0513-0.01880.0862-0.22230.0375-0.3662-0.0284-0.1262-0.0620.35120.1547-0.02170.2867-0.00660.12170.27840.12340.525-0.0482-24.6909-14.0899
140.00960.01190.00730.01010.0065-0.0003-0.1751-0.0682-0.12290.31270.2140.0333-0.25760.0935-00.20070.00360.03210.19050.03440.213713.2775-15.7607-15.967
150.2471-0.2852-0.04810.26810.05280.0368-0.0169-0.1085-0.16470.0673-0.0113-0.00410.1279-0.0015-00.1725-0.01940.01350.1920.02720.21966.612-14.7334-18.5568
160.12280.0601-0.08070.0439-0.04040.0545-0.11720.01880.158-0.3270.00630.3568-0.0039-0.186-0.00960.2961-0.14640.02390.62540.030.4173-16.977-19.3102-24.7046
170.5328-0.13120.27790.0207-0.0190.1402-0.1101-0.54530.09490.03890.09290.2164-0.0398-0.6370.02370.1793-0.04440.0250.4613-0.01370.2385-3.3029-8.6724-10.2695
180.11270.0024-0.04390.03170.00580.01120.103-0.02670.2144-0.2150.09140.0298-0.2612-0.3618-00.2216-0.0364-0.01310.35710.00650.2451-8.6509-10.3688-23.5258
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 1:56)A1 - 56
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 57:84)A57 - 84
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 85:137)A85 - 137
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 138:162)A138 - 162
5X-RAY DIFFRACTION5CHAIN A AND (RESSEQ 163:185)A163 - 185
6X-RAY DIFFRACTION6CHAIN A AND (RESSEQ 186:262)A186 - 262
7X-RAY DIFFRACTION7CHAIN A AND (RESSEQ 263:274)A263 - 274
8X-RAY DIFFRACTION8CHAIN B AND (RESSEQ 2:12)B2 - 12
9X-RAY DIFFRACTION9CHAIN B AND (RESSEQ 13:20)B13 - 20
10X-RAY DIFFRACTION10CHAIN B AND (RESSEQ 21:31)B21 - 31
11X-RAY DIFFRACTION11CHAIN B AND (RESSEQ 32:42)B32 - 42
12X-RAY DIFFRACTION12CHAIN B AND (RESSEQ 43:47)B43 - 47
13X-RAY DIFFRACTION13CHAIN B AND (RESSEQ 48:52)B48 - 52
14X-RAY DIFFRACTION14CHAIN B AND (RESSEQ 53:57)B53 - 57
15X-RAY DIFFRACTION15CHAIN B AND (RESSEQ 58:72)B58 - 72
16X-RAY DIFFRACTION16CHAIN B AND (RESSEQ 73:78)B73 - 78
17X-RAY DIFFRACTION17CHAIN B AND (RESSEQ 79:91)B79 - 91
18X-RAY DIFFRACTION18CHAIN B AND (RESSEQ 92:100)B92 - 100

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