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- PDB-6j1w: The structure of HLA-A*3001/RT313 -

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Basic information

Entry
Database: PDB / ID: 6j1w
TitleThe structure of HLA-A*3001/RT313
Components
  • ALA-ILE-PHE-GLN-SER-SER-MET-THR-LYS
  • Beta-2-microglobulinBeta-2 microglobulin
  • HLA-A*3001
KeywordsIMMUNE SYSTEM / HLA-A*3001
Function / homology
Function and homology information


integrase activity / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / Uncoating of the HIV Virion / 2-LTR circle formation / Vpr-mediated nuclear import of PICs / Early Phase of HIV Life Cycle / Integration of provirus ...integrase activity / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / Uncoating of the HIV Virion / 2-LTR circle formation / Vpr-mediated nuclear import of PICs / Early Phase of HIV Life Cycle / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / positive regulation of memory T cell activation / TAP complex binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / 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 / Binding and entry of HIV virion / endoplasmic reticulum exit site / beta-2-microglobulin binding / TAP binding / protection from natural killer cell mediated cytotoxicity / viral life cycle / 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 ferrous iron binding / positive regulation of transferrin receptor binding / early endosome lumen / positive regulation of receptor binding / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / Assembly Of The HIV Virion / HIV-1 retropepsin / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / : / negative regulation of forebrain neuron differentiation / Budding and maturation of HIV virion / ER to Golgi transport vesicle membrane / retroviral ribonuclease H / exoribonuclease H / response to molecule of bacterial origin / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / : / exoribonuclease H activity / HFE-transferrin receptor complex / T cell mediated cytotoxicity / cellular response to iron ion / protein processing / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / host multivesicular body / multicellular organismal-level iron ion homeostasis / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / cellular response to nicotine / RNA-directed DNA polymerase / recycling endosome membrane / phagocytic vesicle membrane / specific granule lumen / viral genome integration into host DNA / peptide antigen binding / viral penetration into host nucleus / establishment of integrated proviral latency / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / RNA-directed DNA polymerase activity / Interferon gamma signaling / positive regulation of immune response / negative regulation of epithelial cell proliferation / Modulation by Mtb of host immune system / positive regulation of T cell activation / Interferon alpha/beta signaling / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / positive regulation of type II interferon production / sensory perception of smell / RNA-DNA hybrid ribonuclease activity / negative regulation of neuron projection development / E3 ubiquitin ligases ubiquitinate target proteins / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / late endosome membrane
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 / Reverse transcriptase connection / Reverse transcriptase connection domain / MHC class I-like antigen recognition-like ...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 / Reverse transcriptase connection / Reverse transcriptase connection domain / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral / Integrase, N-terminal zinc-binding domain / Integrase, C-terminal, retroviral / Integrase DNA binding domain profile. / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / RNase H / MHC classes I/II-like antigen recognition protein / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Ribonuclease H domain / RNase H type-1 domain profile. / 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 / Retrovirus capsid, C-terminal / Retroviral matrix protein / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ribonuclease H superfamily / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / DNA/RNA polymerase superfamily / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
HLA class I histocompatibility antigen, A alpha chain / Gag-Pol polyprotein / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.501 Å
AuthorsZhu, S.Y. / Liu, K.F. / Chai, Y. / Ding, C.M. / Lv, J.X. / Gao, G.F. / Lou, Y.L. / Liu, W.J.
CitationJournal: Front Immunol / Year: 2019
Title: Divergent Peptide Presentations of HLA-A*30 Alleles Revealed by Structures With Pathogen Peptides.
Authors: Zhu, S. / Liu, K. / Chai, Y. / Wu, Y. / Lu, D. / Xiao, W. / Cheng, H. / Zhao, Y. / Ding, C. / Lyu, J. / Lou, Y. / Gao, G.F. / Liu, W.J.
History
DepositionDec 29, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 25, 2019Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HLA-A*3001
C: ALA-ILE-PHE-GLN-SER-SER-MET-THR-LYS
B: Beta-2-microglobulin


Theoretical massNumber of molelcules
Total (without water)44,4443
Polymers44,4443
Non-polymers00
Water8,179454
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4130 Å2
ΔGint-20 kcal/mol
Surface area19090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.268, 72.025, 78.011
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-511-

HOH

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Components

#1: Protein HLA-A*3001


Mass: 31682.865 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: P04439*PLUS
#2: Protein/peptide ALA-ILE-PHE-GLN-SER-SER-MET-THR-LYS / RT313


Mass: 1013.188 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: P04585*PLUS
#3: Protein Beta-2-microglobulin / Beta-2 microglobulin / hB2m / FcRn light chain


Mass: 11748.160 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: P61769
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 454 / 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: 2.51 Å3/Da / Density % sol: 50.9 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.1 M sodium citrate tribasic dehydrate (pH 5.5)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97774 Å
DetectorType: SDMS / Detector: IMAGE PLATE / Date: Feb 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97774 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 71391 / % possible obs: 99.1 % / Redundancy: 12.7 % / Net I/σ(I): 50
Reflection shellResolution: 1.5→1.55 Å

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementResolution: 1.501→44.012 Å / SU ML: 0.13 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 19.24
RfactorNum. reflection% reflection
Rfree0.2055 3576 5.04 %
Rwork0.1882 --
obs0.1891 70951 98.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.501→44.012 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3132 0 0 454 3586
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0133219
X-RAY DIFFRACTIONf_angle_d1.2084369
X-RAY DIFFRACTIONf_dihedral_angle_d28.5761196
X-RAY DIFFRACTIONf_chiral_restr0.08445
X-RAY DIFFRACTIONf_plane_restr0.009575
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5008-1.52050.22581030.22242084X-RAY DIFFRACTION80
1.5205-1.54140.28571190.20822314X-RAY DIFFRACTION89
1.5414-1.56340.22591310.20492480X-RAY DIFFRACTION95
1.5634-1.58670.2331350.20142547X-RAY DIFFRACTION99
1.5867-1.61150.24511400.19632597X-RAY DIFFRACTION100
1.6115-1.63790.24071300.1922617X-RAY DIFFRACTION100
1.6379-1.66620.21991150.19622613X-RAY DIFFRACTION100
1.6662-1.69650.2251200.19922625X-RAY DIFFRACTION100
1.6965-1.72910.22331610.19722581X-RAY DIFFRACTION100
1.7291-1.76440.21841440.20082628X-RAY DIFFRACTION100
1.7644-1.80280.21371320.2012594X-RAY DIFFRACTION100
1.8028-1.84470.24011360.19592609X-RAY DIFFRACTION100
1.8447-1.89080.2341620.20062602X-RAY DIFFRACTION100
1.8908-1.9420.1961450.19842593X-RAY DIFFRACTION100
1.942-1.99910.25431460.1952614X-RAY DIFFRACTION100
1.9991-2.06360.19981500.19612594X-RAY DIFFRACTION100
2.0636-2.13740.19851270.19432637X-RAY DIFFRACTION100
2.1374-2.2230.19971920.19422575X-RAY DIFFRACTION100
2.223-2.32410.18671770.18982613X-RAY DIFFRACTION100
2.3241-2.44660.18681510.19662607X-RAY DIFFRACTION100
2.4466-2.59990.20831470.2042654X-RAY DIFFRACTION100
2.5999-2.80060.22521640.20262601X-RAY DIFFRACTION100
2.8006-3.08240.19821170.18912687X-RAY DIFFRACTION100
3.0824-3.52830.19191120.18732702X-RAY DIFFRACTION100
3.5283-4.44460.1821850.15492778X-RAY DIFFRACTION99
4.4446-44.03140.17051350.16462829X-RAY DIFFRACTION99

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