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- PDB-1i1f: Crystal structure of human class i mhc (hla-a2.1) complexed with ... -

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Basic information

Entry
Database: PDB / ID: 1i1f
TitleCrystal structure of human class i mhc (hla-a2.1) complexed with beta 2-microglobulin and hiv-rt variant peptide i1y
Components
  • PROTEIN (BETA 2-MICROGLOBULIN)
  • PROTEIN (CLASS I HISTOCOMPATIBILITY ANTIGEN, GOGO-A0201 ALPHA CHAIN)
  • PROTEIN (HIV-RT VARIANT PEPTIDE I1F (FLKEPVHGV))
KeywordsIMMUNE SYSTEM / HUMAN CLASS I MHC / HIV
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 / TAP binding / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / 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 / negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / 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 / MHC class II protein complex / 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 iron ion transport / regulation of erythrocyte differentiation / HFE-transferrin receptor complex / response to molecule of bacterial origin / MHC class I peptide loading complex / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / MHC class I protein complex / positive regulation of T cell activation / peptide antigen binding / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / specific granule lumen / positive regulation of type II interferon production / phagocytic vesicle membrane / recycling endosome membrane / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / MHC class II protein complex binding / Interferon alpha/beta signaling / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / antibacterial humoral response / positive regulation of cellular senescence / tertiary granule lumen / DAP12 signaling / T cell differentiation in thymus / T cell receptor signaling pathway / E3 ubiquitin ligases ubiquitinate target proteins / negative regulation of neuron projection development / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / defense response to Gram-positive bacterium / immune response / endoplasmic reticulum lumen / Amyloid fiber formation / Golgi membrane / signaling receptor binding / lysosomal membrane / innate immune response / external side of plasma membrane / focal adhesion / Neutrophil degranulation / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / cell surface / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / extracellular space / RNA binding / extracellular exosome
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 / 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
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)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsKirksey, T.J. / Pogue-Caley, R.R. / Frelinger, J.A. / Collins, E.J.
CitationJournal: J.Biol.Chem. / Year: 1999
Title: The structural basis for the increased immunogenicity of two HIV-reverse transcriptase peptide variant/class I major histocompatibility complexes.
Authors: Kirksey, T.J. / Pogue-Caley, R.R. / Frelinger, J.A. / Collins, E.J.
History
DepositionApr 16, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Jan 12, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (CLASS I HISTOCOMPATIBILITY ANTIGEN, GOGO-A0201 ALPHA CHAIN)
B: PROTEIN (BETA 2-MICROGLOBULIN)
C: PROTEIN (HIV-RT VARIANT PEPTIDE I1F (FLKEPVHGV))
D: PROTEIN (CLASS I HISTOCOMPATIBILITY ANTIGEN, GOGO-A0201 ALPHA CHAIN)
E: PROTEIN (BETA 2-MICROGLOBULIN)
F: PROTEIN (HIV-RT VARIANT PEPTIDE I1F (FLKEPVHGV))


Theoretical massNumber of molelcules
Total (without water)89,5226
Polymers89,5226
Non-polymers00
Water00
1
A: PROTEIN (CLASS I HISTOCOMPATIBILITY ANTIGEN, GOGO-A0201 ALPHA CHAIN)
B: PROTEIN (BETA 2-MICROGLOBULIN)
C: PROTEIN (HIV-RT VARIANT PEPTIDE I1F (FLKEPVHGV))


Theoretical massNumber of molelcules
Total (without water)44,7613
Polymers44,7613
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4400 Å2
ΔGint-19 kcal/mol
Surface area18800 Å2
MethodPISA
2
D: PROTEIN (CLASS I HISTOCOMPATIBILITY ANTIGEN, GOGO-A0201 ALPHA CHAIN)
E: PROTEIN (BETA 2-MICROGLOBULIN)
F: PROTEIN (HIV-RT VARIANT PEPTIDE I1F (FLKEPVHGV))


Theoretical massNumber of molelcules
Total (without water)44,7613
Polymers44,7613
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4350 Å2
ΔGint-19 kcal/mol
Surface area18890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.574, 62.970, 74.559
Angle α, β, γ (deg.)82.09, 76.47, 77.78
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.91, 0.4146, 0.0008), (0.4146, 0.91, 0.0037), (0.0008, 0.0037, -1)
Vector: 22.8431, -48.119, 39.2622)

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Components

#1: Protein PROTEIN (CLASS I HISTOCOMPATIBILITY ANTIGEN, GOGO-A0201 ALPHA CHAIN) / HLA-A2.1


Mass: 31854.203 Da / Num. of mol.: 2 / Fragment: PEPTIDE-BINDING DOMAIN + ALPHA3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cellular location: CYTOPLASM / Plasmid: PLM1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 PLYSS / References: UniProt: P01892, UniProt: P04439*PLUS
#2: Protein PROTEIN (BETA 2-MICROGLOBULIN)


Mass: 11879.356 Da / Num. of mol.: 2 / Fragment: BETA 2-MICROGLOBULIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cellular location: CYTOPLASM / Plasmid: PLM1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 PLYSS / References: UniProt: P61769
#3: Protein/peptide PROTEIN (HIV-RT VARIANT PEPTIDE I1F (FLKEPVHGV)) / I1F


Mass: 1027.215 Da / Num. of mol.: 2 / Fragment: RESIDUES 309-317 / Mutation: I1F / Source method: obtained synthetically
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: 2.5 Å3/Da / Density % sol: 46 %
Crystal growpH: 6.5
Details: PROTEIN WAS CRYSTALLIZED IN THE HANGING DROP VAPOR DIFFUSION METHOD. THE RESERVOIR SOLUTION CONTAINED 16% PEG8000 IN 25MM MES BUFFER, PH6.5. THE HANGING DROP WAS A 1:1 MIXTURE OF THE ...Details: PROTEIN WAS CRYSTALLIZED IN THE HANGING DROP VAPOR DIFFUSION METHOD. THE RESERVOIR SOLUTION CONTAINED 16% PEG8000 IN 25MM MES BUFFER, PH6.5. THE HANGING DROP WAS A 1:1 MIXTURE OF THE RESERVOIR SOLUTION AND THE PROTEIN SOLUTION WHICH CONTAINED 10MG/ML PROTEIN IN 25MM MES BUFFER, PH6.5.
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Details: drop consists of 1:1 mixture of well and protein solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotease1drop
225 mMMES1drop
320 %PEG80001reservoir
425 mMMES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Dec 1, 1997 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. obs: 21030 / % possible obs: 99.2 % / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 45.5 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 13.2
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 3 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 4.2 / % possible all: 98.6
Reflection
*PLUS
Num. measured all: 148065

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREIN CCP4phasing
REFMACrefinement
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HHH

1hhh


Resolution: 2.8→15 Å / SU B: 0.2 / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.53
RfactorNum. reflection% reflectionSelection details
Rfree0.315 2102 8 %RANDOM
Rwork0.26 ---
obs0.274 18619 99 %-
Displacement parametersBiso mean: 43.2 Å2
Refinement stepCycle: LAST / Resolution: 2.8→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6311 0 0 0 6311
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.010.02
X-RAY DIFFRACTIONp_angle_d0.0450.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0730.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.8112
X-RAY DIFFRACTIONp_mcangle_it1.0063
X-RAY DIFFRACTIONp_scbond_it1.0462
X-RAY DIFFRACTIONp_scangle_it1.5263
X-RAY DIFFRACTIONp_plane_restr0.0203
X-RAY DIFFRACTIONp_chiral_restr0.1050.15
X-RAY DIFFRACTIONp_singtor_nbd0.1890.3
X-RAY DIFFRACTIONp_multtor_nbd0.2710.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.2280.3
X-RAY DIFFRACTIONp_planar_tor7.47
X-RAY DIFFRACTIONp_staggered_tor20.115
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor26.220
X-RAY DIFFRACTIONp_special_tor015
Software
*PLUS
Name: REFMAC / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.009
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg2.493
X-RAY DIFFRACTIONp_dihedral_angle_d
X-RAY DIFFRACTIONp_dihedral_angle_deg26.095
X-RAY DIFFRACTIONp_improper_angle_d
X-RAY DIFFRACTIONp_improper_angle_deg1.907

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