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- PDB-3v5d: HLA-A2.1 KVAELVHFL -

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Basic information

Entry
Database: PDB / ID: 3v5d
TitleHLA-A2.1 KVAELVHFL
Components
  • Beta-2-microglobulin
  • HIV peptide KVAELVHFL
  • HLA class I histocompatibility antigen, A-2 alpha chain
KeywordsIMMUNE SYSTEM / Peptide-binding groove / T cell receptor
Function / homology
Function and homology information


T cell mediated cytotoxicity directed against tumor cell target / positive regulation of memory T cell activation / TAP complex binding / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / Golgi medial cisterna / 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 / endoplasmic reticulum exit site ...T cell mediated cytotoxicity directed against tumor cell target / positive regulation of memory T cell activation / TAP complex binding / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / Golgi medial cisterna / 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 / 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 / beta-2-microglobulin binding / T cell receptor binding / detection of bacterium / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / 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 / lumenal side of endoplasmic reticulum membrane / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / regulation of erythrocyte differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / 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 / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / negative regulation of neurogenesis / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / viral genome integration into host DNA / positive regulation of T cell mediated cytotoxicity / establishment of integrated proviral latency / specific granule lumen / recycling endosome membrane / RNA stem-loop binding / phagocytic vesicle membrane / positive regulation of cellular senescence / peptide antigen binding / negative regulation of epithelial cell proliferation / antigen processing and presentation of exogenous peptide antigen via MHC class II / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / RNA-directed DNA polymerase activity / positive regulation of immune response / Modulation by Mtb of host immune system / Interferon alpha/beta signaling / positive regulation of type II interferon production / sensory perception of smell / positive regulation of T cell activation / positive regulation of protein binding / tertiary granule lumen / E3 ubiquitin ligases ubiquitinate target proteins / DAP12 signaling / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / T cell receptor signaling pathway / iron ion transport / ER-Phagosome pathway / early endosome membrane / antibacterial humoral response / T cell differentiation in thymus / protein refolding / protein homotetramerization / endonuclease activity / intracellular iron ion homeostasis / amyloid fibril formation / aspartic-type endopeptidase activity / learning or memory / defense response to Gram-positive bacterium / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / lysosomal membrane / external side of plasma membrane / Golgi membrane / innate immune response / focal adhesion / signaling receptor binding / 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 / Reverse transcriptase thumb ...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 / MHC classes I/II-like antigen recognition protein / Retropepsin-like catalytic domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / 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 / Immunoglobulins / Immunoglobulin-like fold / DNA/RNA polymerase superfamily / 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 / Resolution: 2 Å
AuthorsCollins, E.J. / Lee, H.Y.
CitationJournal: To be Published
Title: Prediction of conformation and immunogenicity of peptides bound to MHC molecules
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

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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 peptide KVAELVHFL
D: HLA class I histocompatibility antigen, A-2 alpha chain
E: Beta-2-microglobulin
F: HIV peptide KVAELVHFL


Theoretical massNumber of molelcules
Total (without water)89,5826
Polymers89,5826
Non-polymers00
Water7,314406
1
A: HLA class I histocompatibility antigen, A-2 alpha chain
B: Beta-2-microglobulin
C: HIV peptide KVAELVHFL


Theoretical massNumber of molelcules
Total (without water)44,7913
Polymers44,7913
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4620 Å2
ΔGint-21 kcal/mol
Surface area18940 Å2
MethodPISA
2
D: HLA class I histocompatibility antigen, A-2 alpha chain
E: Beta-2-microglobulin
F: HIV peptide KVAELVHFL


Theoretical massNumber of molelcules
Total (without water)44,7913
Polymers44,7913
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4610 Å2
ΔGint-19 kcal/mol
Surface area19110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.233, 90.493, 79.967
Angle α, β, γ (deg.)90.00, 90.06, 90.00
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 peptide KVAELVHFL


Mass: 1057.284 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: chemically synthesized peptide naturally found in HIV
Source: (synth.) human (human) / References: UniProt: E0YFW1*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 406 / Source method: isolated from a natural source / Formula: H2O

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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: 2.55 Å3/Da / Density % sol: 51.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 25 mM MES pH 6.5, 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: Oct 10, 2010
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 61188 / Num. obs: 60582 / % possible obs: 0.99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Biso Wilson estimate: 23.29 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 11.3
Reflection shellResolution: 2→2.1 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 4.3 / % possible all: 0.95

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
BUSTER2.10.0refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→40 Å / Cor.coef. Fo:Fc: 0.8621 / Cor.coef. Fo:Fc free: 0.822 / SU R Cruickshank DPI: 0.211 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2644 3060 5.06 %RANDOM
Rwork0.2325 ---
all0.2341 60856 --
obs0.2341 60433 99.33 %-
Displacement parametersBiso mean: 25.37 Å2
Baniso -1Baniso -2Baniso -3
1-2.7662 Å20 Å22.5179 Å2
2---7.6135 Å20 Å2
3---4.8473 Å2
Refine analyzeLuzzati coordinate error obs: 0.329 Å
Refinement stepCycle: LAST / Resolution: 2→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6318 0 0 406 6724
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0086592HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.058956HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2.832270SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes0177HARMONIC2
X-RAY DIFFRACTIONt_gen_planes0964HARMONIC5
X-RAY DIFFRACTIONt_it06592HARMONIC20
X-RAY DIFFRACTIONt_omega_torsion2.83
X-RAY DIFFRACTIONt_other_torsion17.7
X-RAY DIFFRACTIONt_chiral_improper_torsion0807SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact07472SEMIHARMONIC4
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2548 226 5.32 %
Rwork0.2242 4021 -
all0.2258 4247 -
obs--99.33 %
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)
11.89590.28430.53730.5050.48831.75850.0606-0.03540.0767-0.0342-0.02760.10730.0003-0.1556-0.033-0.09530.00520.00490.0080.0202-0.1229-6.8811-0.08116.6584
22.59440.1784-0.78920.8591-0.54453.1206-0.00170.1830.0303-0.10110.0221-0.0603-0.10980.0034-0.0205-0.07320.02170.01610.0625-0.0279-0.143524.64994.4031-0.1315
33.92930.04660.36981.03190.17051.05420.0055-0.046-0.3525-0.03320.0759-0.09550.04250.0953-0.0815-0.0556-0.00230.0167-0.01380.0034-0.077613.9907-14.20768.2663
40.45140.9130.93301.37380.002-0.0104-0.01180.01670.06730.01930.04350.009-0.0752-0.0089-0.04740.0087-0.01920.04260.02950.0269-15.17210.592220.9081
51.8042-0.25420.0970.47110.21171.1150.05320.1315-0.18170.0055-0.02030.1019-0.0332-0.0557-0.0329-0.1089-0.00270.00890.0434-0.005-0.1217-38.4719-6.768941.4953
62.6631-0.72121.86461.2659-0.67614.3454-0.0064-0.133-0.04850.20720.0828-0.06560.0657-0.0426-0.0764-0.069-0.0060.00310.0153-0.0074-0.1292-7.0222-11.102758.142
72.41970.0071-0.09371.0547-0.0060.7914-0.0528-0.02520.32430.16390.1079-0.128-0.0163-0.0217-0.0551-0.03050.0103-0.0066-0.0112-0.0112-0.0707-17.69257.508849.9374
80.00390.0139-1.057401.3-0.00220.0062-0.0227-0.0378-0.04640.03970.10750.056-0.0134-0.0459-0.08570.0263-0.01960.09860.02020.0033-46.9223-7.317637.2404
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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