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- PDB-3v5k: HLA2.1 KVAELVWFL -

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Basic information

Entry
Database: PDB / ID: 3v5k
TitleHLA2.1 KVAELVWFL
Components
  • Beta-2-microglobulin
  • HIV-based altered-peptide ligand KVAELVWFL
  • 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 / molecular replacement / Resolution: 2.31 Å
AuthorsCollins, E.J. / Lee, H.Y.
CitationJournal: To be Published
Title: Prediction of Immunogenicity of altered-peptide ligands to HIV bound to MHC
Authors: Collins, E.J. / Lee, H.Y.
History
DepositionDec 16, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name

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


Theoretical massNumber of molelcules
Total (without water)89,7707
Polymers89,6786
Non-polymers921
Water5,206289
1
A: HLA class I histocompatibility antigen, A-2 alpha chain
B: Beta-2-microglobulin
C: HIV-based altered-peptide ligand KVAELVWFL


Theoretical massNumber of molelcules
Total (without water)44,8393
Polymers44,8393
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4650 Å2
ΔGint-21 kcal/mol
Surface area18880 Å2
MethodPISA
2
D: HLA class I histocompatibility antigen, A-2 alpha chain
E: Beta-2-microglobulin
F: HIV-based altered-peptide ligand KVAELVWFL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9314
Polymers44,8393
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4850 Å2
ΔGint-21 kcal/mol
Surface area18840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.773, 87.078, 79.683
Angle α, β, γ (deg.)90.000, 90.040, 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 KVAELVWFL


Mass: 1105.347 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.: 289 / 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: 2.43 Å3/Da / Density % sol: 49.35 %
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-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 12, 2011
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. all: 37378 / Num. obs: 35327 / % possible obs: 94.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Rmerge(I) obs: 0.079 / Χ2: 0.916 / Net I/σ(I): 8.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.3-2.3840.29436930.785198.6
2.38-2.4840.24536720.822198.5
2.48-2.5940.19836600.85198.7
2.59-2.7340.16137280.881198.7
2.73-2.940.12536771.012199.2
2.9-3.1240.09437041.075198.9
3.12-3.4340.07837131.019199.4
3.43-3.933.30.06619620.891152
3.93-4.953.90.05536820.881198.2
4.95-303.90.05238360.923199.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å29.39 Å
Translation2.5 Å29.39 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: 2.31→29.39 Å / Cor.coef. Fo:Fc: 0.9205 / Cor.coef. Fo:Fc free: 0.8886 / Occupancy max: 1 / Occupancy min: 1 / SU R Cruickshank DPI: 0.381 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.228 1754 4.97 %RANDOM
Rwork0.1855 ---
all0.1876 37523 --
obs0.1876 35266 93.53 %-
Displacement parametersBiso max: 135.07 Å2 / Biso mean: 38.631 Å2 / Biso min: 14.07 Å2
Baniso -1Baniso -2Baniso -3
1-2.8937 Å20 Å2-1.2817 Å2
2---12.4557 Å20 Å2
3---9.562 Å2
Refine analyzeLuzzati coordinate error obs: 0.305 Å
Refinement stepCycle: LAST / Resolution: 2.31→29.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6326 0 6 289 6621
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_dihedral_angle_d02240SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes0173HARMONIC2
X-RAY DIFFRACTIONt_gen_planes0948HARMONIC5
X-RAY DIFFRACTIONt_it06532HARMONIC20
X-RAY DIFFRACTIONt_chiral_improper_torsion0797SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact07299SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d0.0096532HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.078870HARMONIC2
X-RAY DIFFRACTIONt_omega_torsion3.41
X-RAY DIFFRACTIONt_other_torsion17.92
LS refinement shellResolution: 2.31→2.38 Å / Total num. of bins used: 18
RfactorNum. reflection% reflection
Rfree0.2664 144 5.19 %
Rwork0.2032 2629 -
all0.2066 2773 -
obs--93.53 %
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)
12.95170.24980.55040.87990.48612.32290.05740.26320.18680.0389-0.03210.13080.1281-0.2763-0.0253-0.1509-0.01790.0092-0.01190.0223-0.10645.98840.047135.8025
24.41340.735-2.28210.7814-0.2935.6927-0.06660.5443-0.0049-0.10320.1556-0.0712-0.2079-0.0356-0.0889-0.09160.02350.01710.01160.0157-0.143137.51183.875119.1282
32.4079-0.23450.16280.6918-0.19411.2237-0.00860.2085-0.3909-0.17190.0464-0.06750.22990.0421-0.0378-0.0439-0.0176-0.0144-0.046-0.0356-0.017326.5958-14.244927.2031
40.48690.3739-2.32802.91070.8385-0.0142-0.0280.0545-0.10230.0368-0.0246-0.0443-0.0283-0.0226-0.1042-0.05810.03190.08540.01460.0317-1.97970.833839.8728
52.29640.2289-0.33180.7097-0.23462.52960.12270.2324-0.06720.0435-0.0078-0.1035-0.09670.1954-0.1148-0.12350.0042-0.0133-0.037-0.0159-0.089725.403335.732119.2427
63.97210.11742.77310.85540.67268.31930.04750.4852-0.06980.00330.15230.10680.54440.1265-0.1998-0.1020.0658-0.01820.0601-0.0304-0.2137-6.155431.98052.667
71.9394-0.6679-0.23050.9022-0.14881.13940.0940.22660.1315-0.0622-0.02480.049-0.1782-0.1078-0.0693-0.0309-0.01160.02110.01490.0199-0.07774.751250.051510.7818
80.6105-1.3120.63050-2.87651.1382-0.00790.0984-0.04980.0031-0.01450.01150.08170.04790.0224-0.0478-0.012-0.03360.0509-0.0967-0.001533.457234.934222.7646
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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