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- PDB-3v5h: HLA-A2.1 KVAEIVHFL -

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Basic information

Entry
Database: PDB / ID: 3v5h
TitleHLA-A2.1 KVAEIVHFL
Components
  • Beta-2-microglobulin
  • HIV-based altered-peptide ligand KVAEIVHFL
  • HLA class I histocompatibility antigen, A-2 alpha chain
KeywordsIMMUNE SYSTEM / peptide-binding groove / T cell receptor
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 / 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 / detection of bacterium / T cell receptor binding / : / : / 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 / 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 / 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 T cell mediated cytotoxicity / positive regulation of receptor-mediated endocytosis / multicellular organismal-level iron ion homeostasis / positive regulation of T cell activation / cellular response to nicotine / viral genome integration into host DNA / establishment of integrated proviral latency / positive regulation of type II interferon production / telomerase activity / specific granule lumen / RNA stem-loop binding / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / Interferon gamma signaling / MHC class II protein complex binding / Interferon alpha/beta signaling / positive regulation of protein binding / antibacterial humoral response / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / tertiary granule lumen / DAP12 signaling / E3 ubiquitin ligases ubiquitinate target proteins / T cell receptor signaling pathway / negative regulation of neuron projection development / iron ion transport / T cell differentiation in thymus / ER-Phagosome pathway / protein refolding / early endosome membrane / endonuclease activity / protein homotetramerization / amyloid fibril formation / aspartic-type endopeptidase activity / intracellular iron ion homeostasis / learning or memory / defense response to Gram-positive bacterium / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / external side of plasma membrane / Golgi membrane / signaling receptor binding / lysosomal membrane / innate immune response / focal adhesion / Neutrophil degranulation
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 / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Retropepsin-like catalytic domain / MHC classes I/II-like antigen recognition protein / : / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Reverse transcriptase/Diguanylate cyclase domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / DNA/RNA polymerase superfamily / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Pol protein / 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)
human (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.63 Å
AuthorsCollins, E.J. / Lee, H.Y.
CitationJournal: To be Published
Title: Prediction of immunogenicity of altered-peptide ligands for HIV therapy
Authors: Collins, E.J. / Lee, H.Y.
History
DepositionDec 16, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 5, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Oct 16, 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

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Assembly

Deposited unit
A: HLA class I histocompatibility antigen, A-2 alpha chain
B: Beta-2-microglobulin
C: HIV-based altered-peptide ligand KVAEIVHFL
D: HLA class I histocompatibility antigen, A-2 alpha chain
E: Beta-2-microglobulin
F: HIV-based altered-peptide ligand KVAEIVHFL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,6747
Polymers89,5826
Non-polymers921
Water17,366964
1
A: HLA class I histocompatibility antigen, A-2 alpha chain
B: Beta-2-microglobulin
C: HIV-based altered-peptide ligand KVAEIVHFL


Theoretical massNumber of molelcules
Total (without water)44,7913
Polymers44,7913
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4500 Å2
ΔGint-20 kcal/mol
Surface area19060 Å2
MethodPISA
2
D: HLA class I histocompatibility antigen, A-2 alpha chain
E: Beta-2-microglobulin
F: HIV-based altered-peptide ligand KVAEIVHFL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8834
Polymers44,7913
Non-polymers921
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4740 Å2
ΔGint-20 kcal/mol
Surface area19210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.798, 87.604, 79.769
Angle α, β, γ (deg.)90.000, 89.960, 90.000
Int Tables number4
Space group name H-MP1211

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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*0201, HLA-A, HLAA / Plasmid: pLM1 / 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, beta-2-microglobulin, CDABP0092, HDCMA22P / Plasmid: pLM1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P61769
#3: Protein/peptide HIV-based altered-peptide ligand KVAEIVHFL


Mass: 1057.284 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: chemically synthesized peptide based on sequence from HIV
Source: (synth.) human (human) / References: UniProt: E0YFW1*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.: 964 / 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: 2.45 Å3/Da / Density % sol: 49.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 25 mM MES pH6.5, 12% PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 16, 2011
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.63→50 Å / Num. all: 107676 / Num. obs: 106085 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.049 / Χ2: 0.986 / Net I/σ(I): 17.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.63-1.663.10.36242921179.4
1.66-1.693.40.32652311.014197.6
1.69-1.723.60.28452941.034199.2
1.72-1.763.70.23352700.96199
1.76-1.793.70.19153660.99199.2
1.79-1.843.70.15953021.027199.3
1.84-1.883.70.12953521.041199.6
1.88-1.933.70.10653491.074199.9
1.93-1.993.80.08753921.029199.9
1.99-2.053.80.07353141.0491100
2.05-2.133.80.06454030.9831100
2.13-2.213.80.05654041.0981100
2.21-2.313.80.05453750.8171100
2.31-2.433.80.04953781.0171100
2.43-2.593.80.04753800.9331100
2.59-2.793.80.0553770.9531100
2.79-3.073.90.05754120.921100
3.07-3.513.90.05754160.9061100
3.51-4.423.80.03854310.905199.9
4.42-503.70.0353470.997197

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å49.36 Å
Translation2.5 Å49.36 Å

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASER2.3.0phasing
BUSTER-TNTrefinement
PDB_EXTRACT3.1data extraction
MAR345dtbdata collection
DENZOdata reduction
BUSTER2.10.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.63→16.43 Å / Cor.coef. Fo:Fc: 0.9486 / Cor.coef. Fo:Fc free: 0.9351 / Occupancy max: 1 / Occupancy min: 0.3 / SU R Cruickshank DPI: 0.093 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2144 5285 4.99 %RANDOM
Rwork0.1838 ---
all0.1853 107454 --
obs0.1853 105970 98.59 %-
Displacement parametersBiso max: 173.25 Å2 / Biso mean: 29.7528 Å2 / Biso min: 10.36 Å2
Baniso -1Baniso -2Baniso -3
1-1.3315 Å20 Å21.1245 Å2
2---4.0291 Å20 Å2
3---2.6977 Å2
Refine analyzeLuzzati coordinate error obs: 0.207 Å
Refinement stepCycle: LAST / Resolution: 1.63→16.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6318 0 6 964 7288
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_dihedral_angle_d02242SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes0173HARMONIC2
X-RAY DIFFRACTIONt_gen_planes0914HARMONIC5
X-RAY DIFFRACTIONt_it06495HARMONIC20
X-RAY DIFFRACTIONt_nbd096SEMIHARMONIC5
X-RAY DIFFRACTIONt_chiral_improper_torsion0800SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact07858SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d0.0096495HARMONIC2
X-RAY DIFFRACTIONt_angle_deg18796HARMONIC2
X-RAY DIFFRACTIONt_omega_torsion4.11
X-RAY DIFFRACTIONt_other_torsion15.23
LS refinement shellResolution: 1.63→1.67 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2626 305 4.47 %
Rwork0.2163 6521 -
all0.2183 6826 -
obs--98.59 %
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)
12.04530.14090.27240.59950.3611.66240.02590.06870.1728-0.0423-0.01860.16460.0952-0.1936-0.0073-0.0752-0.01960.0119-0.08520.0177-0.04365.90470.0625-4.1588
22.61250.7762-1.46421.1161-0.49543.65710.00820.3919-0.0308-0.15440.0934-0.1081-0.05780.102-0.1016-0.05810.00730.04880.0157-0.0122-0.083637.36344.0376-20.9364
32.17740.01240.16180.6342-0.07420.78890.00510.1758-0.2896-0.08640.0479-0.04660.0883-0.001-0.053-0.0098-0.0012-0.0014-0.0569-0.0381-0.011826.5246-14.1819-12.8473
40.06111.79480.096501.34120.0087-0.01780.05470.01030.09230.06540.0956-0.062-0.1595-0.0476-0.0623-0.02220.03240.03910.00760.0381-2.1210.3562-0.6055
51.6121-0.0396-0.50020.5620.50132.21580.0228-0.0322-0.08760.0638-0.04370.14940.0176-0.21470.0209-0.06630.00090.0313-0.09210.0063-0.0433-25.4202-7.778420.3584
62.0408-0.37221.5340.9955-0.52324.40380.1038-0.17-0.04390.0907-0.0059-0.08240.20680.205-0.0979-0.046-0.018-0.0068-0.00670.0046-0.07945.9085-11.430937.0883
71.73780.1146-0.02380.66340.15280.74910.0413-0.15340.16490.04530.0213-0.0421-0.06480.0606-0.0626-0.0079-0.01530.0434-0.0328-0.0182-0.0249-4.68956.664229.0223
81.0076-1.09980.76010.0002-0.33820.6151-0.0127-0.0881-0.0629-0.04280.09490.0970.004-0.1495-0.0822-0.0458-0.01950.02870.0201-0.01070.0359-33.4476-8.219216.8102
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|1 - 183}A1 - 183
2X-RAY DIFFRACTION2{A|184 - 275}A184 - 275
3X-RAY DIFFRACTION3{B|0 - 99}B0 - 99
4X-RAY DIFFRACTION4{C|1 - 9}C1 - 9
5X-RAY DIFFRACTION5{D|1 - 183}D1 - 183
6X-RAY DIFFRACTION6{D|184 - 275}D184 - 275
7X-RAY DIFFRACTION7{E|0 - 99}E0 - 99
8X-RAY DIFFRACTION8{F|1 - 9}F1 - 9

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