[English] 日本語
Yorodumi
- PDB-2ypl: Structural features underlying T-cell receptor sensitivity to con... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2ypl
TitleStructural features underlying T-cell receptor sensitivity to concealed MHC class I micropolymorphisms
Components
  • (AGA T-CELL RECEPTOR ...) x 2
  • BETA-2-MICROGLOBULIN
  • HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, B-57 ALPHA CHAIN
  • KF11 P24 GAG PEPTIDE
KeywordsIMMUNE SYSTEM/VIRAL PROTEIN / IMMUNE SYSTEM-VIRAL PROTEIN COMPLEX / MICROPOLYMORPHISM
Function / homology
Function and homology information


regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / viral budding via host ESCRT complex / 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 / RNA-directed DNA polymerase activity ...regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / viral budding via host ESCRT complex / 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 / RNA-directed DNA polymerase activity / detection of bacterium / : / : / secretory granule membrane / 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 / Endosomal/Vacuolar pathway / lumenal side of endoplasmic reticulum membrane / 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 / exoribonuclease H activity / 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 / defense response / 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 / DNA integration / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / positive regulation of T cell mediated cytotoxicity / positive regulation of T cell activation / multicellular organismal-level iron ion homeostasis / cellular response to nicotine / viral genome integration into host DNA / establishment of integrated proviral latency / viral penetration into host nucleus / 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 / Interferon gamma signaling / negative regulation of epithelial cell proliferation / RNA-DNA hybrid ribonuclease activity / MHC class II protein complex binding / Modulation by Mtb of host immune system / Interferon alpha/beta signaling / late endosome membrane / sensory perception of smell / tertiary granule lumen / DAP12 signaling / positive regulation of protein binding / host cell / protein-folding chaperone binding / iron ion transport / negative regulation of neuron projection development / T cell differentiation in thymus / ER-Phagosome pathway / early endosome membrane / protein refolding / viral nucleocapsid / DNA recombination / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / adaptive immune response / aspartic-type endopeptidase activity / host cell cytoplasm / DNA-directed DNA polymerase activity / learning or memory / immune response / Amyloid fiber formation / viral translational frameshifting / endoplasmic reticulum lumen / symbiont entry into host cell / Golgi membrane / lysosomal membrane / external side of plasma membrane / signaling receptor binding / innate immune response / focal adhesion
Similarity search - Function
Gag protein p6 / Gag protein p6 / 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 / Reverse transcriptase connection / Reverse transcriptase connection domain ...Gag protein p6 / Gag protein p6 / 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 / Reverse transcriptase connection / Reverse transcriptase connection domain / 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 / 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 / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Retropepsin-like catalytic domain / MHC classes I/II-like antigen recognition protein / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / RNase H type-1 domain profile. / Ribonuclease H domain / : / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain 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 / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Ribonuclease H superfamily / Ribonuclease H-like 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
HLA class I histocompatibility antigen, B alpha chain / HLA class I histocompatibility antigen, B alpha chain / Beta-2-microglobulin / Gag polyprotein
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
HUMAN IMMUNODEFICIENCY VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsStewart-Jones, G.B. / Simpson, P. / van der Merwe, P.A. / Easterbrook, P. / McMichael, A.J. / Rowland-Jones, S.L. / Jones, E.Y. / Gillespie, G.M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Structural Features Underlying T-Cell Receptor Sensitivity to Concealed Mhc Class I Micropolymorphisms.
Authors: Stewart-Jones, G.B. / Simpson, P. / Anton Van Der Merwe, P. / Easterbrook, P. / Mcmichael, A.J. / Rowland-Jones, S.L. / Jones, E.Y. / Gillespie, G.M.
History
DepositionOct 30, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 28, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 19, 2012Group: Database references
Revision 1.2Jan 16, 2013Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, B-57 ALPHA CHAIN
B: BETA-2-MICROGLOBULIN
C: KF11 P24 GAG PEPTIDE
D: AGA T-CELL RECEPTOR ALPHA CHAIN
E: AGA T-CELL RECEPTOR BETA CHAIN


Theoretical massNumber of molelcules
Total (without water)93,7255
Polymers93,7255
Non-polymers00
Water3,513195
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10140 Å2
ΔGint-53.1 kcal/mol
Surface area39060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.348, 75.605, 241.527
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 2 types, 2 molecules AB

#1: Protein HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, B-57 ALPHA CHAIN / BW-57 / MHC CLASS I ANTIGEN B*57 / HLA-B5703


Mass: 31598.096 Da / Num. of mol.: 1 / Fragment: RESIDUES 25-298
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): DE3 / References: UniProt: P18465, UniProt: P01889*PLUS
#2: Protein BETA-2-MICROGLOBULIN / BETA-2-MICROGLOBULIN FORM PI 5.3


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 (E. coli) / Strain (production host): DE3 / References: UniProt: P61769

-
AGA T-CELL RECEPTOR ... , 2 types, 2 molecules DE

#4: Protein AGA T-CELL RECEPTOR ALPHA CHAIN


Mass: 22307.789 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): DE3
#5: Protein AGA T-CELL RECEPTOR BETA CHAIN


Mass: 26804.928 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): DE3

-
Protein/peptide / Non-polymers , 2 types, 196 molecules C

#3: Protein/peptide KF11 P24 GAG PEPTIDE


Mass: 1266.526 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) HUMAN IMMUNODEFICIENCY VIRUS / References: UniProt: Q70XD7*PLUS
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 195 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.74 Å3/Da / Density % sol: 55.18 % / Description: NONE
Crystal growpH: 7.3 / Details: pH 7.3

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. obs: 41023 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 13.1 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 40.1
Reflection shellResolution: 2.4→2.51 Å / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 5.5 / % possible all: 94.7

-
Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BVO

2bvo


Resolution: 2.4→29.77 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.916 / SU B: 21.049 / SU ML: 0.236 / Cross valid method: THROUGHOUT / ESU R: 0.412 / ESU R Free: 0.284 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.27746 2054 5 %RANDOM
Rwork0.22072 ---
obs0.22358 38896 98.68 %-
Displacement parametersBiso mean: 66.1 Å2
Baniso -1Baniso -2Baniso -3
1-3.21 Å20 Å20 Å2
2--0.07 Å20 Å2
3----3.29 Å2
Refinement stepCycle: LAST / Resolution: 2.4→29.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6601 0 0 195 6796
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0196778
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2221.949208
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5725816
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.62723.848343
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.836151107
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.941549
X-RAY DIFFRACTIONr_chiral_restr0.0910.2969
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215292
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.399→2.46 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.425 157 -
Rwork0.346 2603 -
obs--91.24 %
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)
10.39990.0524-0.38970.1154-0.33991.8377-0.01470.09740.04140.01910.1205-0.0540.0313-0.2812-0.10570.0850.13090.09270.29550.12720.3684-3.4308-33.301431.6149
21.67430.8449-0.42471.0529-1.63393.6736-0.24030.37980.1051-0.0790.27260.07910.09170.015-0.03220.16620.0050.07030.36860.08280.30339.9511-28.5795-1.6937
30.9074-0.5916-0.01940.8720.39782.8225-0.0268-0.2032-0.151-0.13160.4694-0.03330.3665-0.6143-0.44250.1462-0.25910.0020.59980.11470.2449-8.1969-39.93765.8727
40.38-0.33711.0850.3175-0.99313.15340.1567-0.3897-0.1462-0.24150.25370.07390.6946-1.0663-0.41040.2744-0.10270.09040.52430.34340.4076-5.8941-32.699140.4108
50.75180.1884-0.48480.10990.31795.29360.1723-0.11880.06760.0217-0.06090.00210.09240.5249-0.11140.1380.10840.06350.27080.09640.33155.6309-34.638462.857
60.4871-0.1409-0.43561.9482-0.44483.1870.1037-0.2039-0.03120.2409-0.0941-0.08680.21950.4802-0.00960.2236-0.00170.01110.19060.02970.2749-0.4277-38.367396.595
73.48351.0295-2.81280.4018-0.76124.18160.23410.8233-0.08390.13780.016-0.13420.2663-1.1625-0.25010.1907-0.1789-0.05130.70380.15220.3074-18.1527-42.044461.0613
80.92691.1526-0.16651.4775-0.15921.6830.00020.09780.08490.08410.09560.08330.0092-0.2426-0.09580.1794-0.06070.05570.1705-0.01340.3336-15.2213-34.794390.3973
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 181
2X-RAY DIFFRACTION2A182 - 274
3X-RAY DIFFRACTION3B1 - 99
4X-RAY DIFFRACTION4C1 - 11
5X-RAY DIFFRACTION5D1 - 115
6X-RAY DIFFRACTION6D116 - 199
7X-RAY DIFFRACTION7E4 - 115
8X-RAY DIFFRACTION8E116 - 241

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more