[English] 日本語
Yorodumi
- PDB-1b0g: CLASS I HISTOCOMPATIBILITY ANTIGEN (HLA-A2.1)/BETA 2-MICROGLOBULI... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1b0g
TitleCLASS I HISTOCOMPATIBILITY ANTIGEN (HLA-A2.1)/BETA 2-MICROGLOBULIN/PEPTIDE P1049 COMPLEX
Components
  • BETA 2-MICROGLOBULIN
  • CLASS I HISTOCOMPATIBILITY ANTIGEN
  • PEPTIDE P1049 (ALWGFFPVL)
KeywordsHISTOCOMPATIBILITY ANTIGEN / CLASS I HISTOCOMPATIBILITY ANTIGEN (HLA-A2.1)-BETA 2-MICROGLOBULIN-PEPTIDE P1049 COMPLEX
Function / homology
Function and homology information


EMC complex / protein insertion into ER membrane by stop-transfer membrane-anchor sequence / tail-anchored membrane protein insertion into ER membrane / 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 ...EMC complex / protein insertion into ER membrane by stop-transfer membrane-anchor sequence / tail-anchored membrane protein insertion into ER membrane / 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 / positive regulation of cellular senescence / antibacterial humoral response / 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 / carbohydrate binding / 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 / signaling receptor binding / Golgi membrane / 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
Similarity search - Function
ER membrane protein complex subunit 7, beta-sandwich domain / ER membrane protein complex subunit 7 / ER membrane protein complex subunit 7, beta-sandwich domain / Carbohydrate-binding-like fold / 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 ...ER membrane protein complex subunit 7, beta-sandwich domain / ER membrane protein complex subunit 7 / ER membrane protein complex subunit 7, beta-sandwich domain / Carbohydrate-binding-like fold / 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 / Endoplasmic reticulum membrane protein complex subunit 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsZhao, R. / Collins, E.J.
CitationJournal: J.Exp.Med. / Year: 1999
Title: Structural evidence of T cell xeno-reactivity in the absence of molecular mimicry.
Authors: Zhao, R. / Loftus, D.J. / Appella, E. / Collins, E.J.
History
DepositionNov 9, 1998Deposition site: BNL / Processing site: RCSB
SupersessionNov 18, 1998ID: 1A9K
Revision 1.0Nov 18, 1998Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 10, 2013Group: Other
Revision 1.4Aug 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 1.5Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CLASS I HISTOCOMPATIBILITY ANTIGEN
B: BETA 2-MICROGLOBULIN
C: PEPTIDE P1049 (ALWGFFPVL)
D: CLASS I HISTOCOMPATIBILITY ANTIGEN
E: BETA 2-MICROGLOBULIN
F: PEPTIDE P1049 (ALWGFFPVL)


Theoretical massNumber of molelcules
Total (without water)89,5666
Polymers89,5666
Non-polymers00
Water90150
1
A: CLASS I HISTOCOMPATIBILITY ANTIGEN
B: BETA 2-MICROGLOBULIN
C: PEPTIDE P1049 (ALWGFFPVL)


Theoretical massNumber of molelcules
Total (without water)44,7833
Polymers44,7833
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4440 Å2
ΔGint-24 kcal/mol
Surface area18050 Å2
MethodPISA
2
D: CLASS I HISTOCOMPATIBILITY ANTIGEN
E: BETA 2-MICROGLOBULIN
F: PEPTIDE P1049 (ALWGFFPVL)


Theoretical massNumber of molelcules
Total (without water)44,7833
Polymers44,7833
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4380 Å2
ΔGint-22 kcal/mol
Surface area18120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.090, 62.890, 74.680
Angle α, β, γ (deg.)81.98, 76.18, 77.86
Int Tables number1
Cell settingtriclinic
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.914367, 0.404851, -0.005413), (0.404822, 0.914378, 0.005605), (0.007219, 0.002934, -0.99997)
Vector: 23.428, -47.9432, 52.4487)

-
Components

#1: Protein CLASS I HISTOCOMPATIBILITY ANTIGEN / HLA-A2.1


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


Mass: 11879.356 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PLM1 / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 PLYSS / References: UniProt: P61769
#3: Protein/peptide PEPTIDE P1049 (ALWGFFPVL)


Mass: 1049.263 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
References: UniProt: Q9NPA0*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.8 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 6.5
Details: PROTEIN WAS CRYSTALLIZED IN THE HANGING DROP VAPOR DIFFUSION METHOD. THE RESERVOIR SOLUTION CONTAINED 12-16% PEG6000, 6% DIOXANE IN 25MM MES BUFFER, PH6.5. THE HANGING DROP WAS A 1:1 MIXTURE ...Details: PROTEIN WAS CRYSTALLIZED IN THE HANGING DROP VAPOR DIFFUSION METHOD. THE RESERVOIR SOLUTION CONTAINED 12-16% PEG6000, 6% DIOXANE 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., vapor diffusion - hanging drop
Components of the solutions
IDNameCrystal-IDSol-ID
1MES BUFFER11
2PEG 600011
3DIOXANE11
4MES BUFFER12
5PEG 600012
6DIOXANE12
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
112-16 %PEG60001reservoir
26 %dioxane1reservoir
325 mMMES1reservoirpH6.5
410 mg/mlprotein1drop
525 mMMES1droppH6.5
61

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: May 15, 1997 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Protocol: MONOCHROMATIC / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. all: 29804 / Num. obs: 29804 / % possible obs: 90.9 % / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Biso Wilson estimate: 23.42 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 16.6
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.176 / Mean I/σ(I) obs: 6.5 / % possible all: 70.8
Reflection
*PLUS
Num. measured all: 77499
Reflection shell
*PLUS
Highest resolution: 2.5 Å / % possible obs: 70.8 %

-
Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HHJ

1hhj


Resolution: 2.5→30 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 3.44 / ESU R Free: 0.39
RfactorNum. reflection% reflectionSelection details
Rfree0.304 1363 5 %RANDOM
Rwork0.255 ---
all0.26 ---
obs0.26 27079 82.6 %-
Displacement parametersBiso mean: 37.06 Å2
Baniso -1Baniso -2Baniso -3
1--3.1 Å2-5.34 Å2-6.53 Å2
2--0.535 Å20.763 Å2
3---2.564 Å2
Refinement stepCycle: LAST / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6320 0 0 50 6370
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0080.02
X-RAY DIFFRACTIONp_angle_d0.0260.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0210.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.2922
X-RAY DIFFRACTIONp_mcangle_it3.7333
X-RAY DIFFRACTIONp_scbond_it3.8862
X-RAY DIFFRACTIONp_scangle_it5.9543
X-RAY DIFFRACTIONp_plane_restr0.0130.03
X-RAY DIFFRACTIONp_chiral_restr0.0980.15
X-RAY DIFFRACTIONp_singtor_nbd0.1760.3
X-RAY DIFFRACTIONp_multtor_nbd0.2620.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1260.3
X-RAY DIFFRACTIONp_planar_tor1.77
X-RAY DIFFRACTIONp_staggered_tor16.715
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor27.520
X-RAY DIFFRACTIONp_special_tor015
Refinement
*PLUS
Lowest resolution: 30 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.905
X-RAY DIFFRACTIONp_dihedral_angle_d
X-RAY DIFFRACTIONp_dihedral_angle_deg24.466
X-RAY DIFFRACTIONp_improper_angle_d
X-RAY DIFFRACTIONp_improper_angle_deg1.105

+
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