[English] 日本語
Yorodumi
- PDB-4c56: X-ray structure of the complex between staphylococcal enterotoxin... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4c56
TitleX-ray structure of the complex between staphylococcal enterotoxin B, T cell receptor and major histocompatibility complex class II
Components
  • (T CELL RECEPTOR ...) x 2
  • ENTEROTOXIN B
  • HEMAGGLUTININ
  • HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, DR ALPHA CHAIN
  • MHC CLASS II ANTIGEN
KeywordsIMMUNE SYSTEM/TOXIN / IMMUNE SYSTEM-TOXIN COMPLEX
Function / homology
Function and homology information


regulation of interleukin-4 production / regulation of interleukin-10 production / myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / autolysosome membrane / regulation of T-helper cell differentiation / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / MHC class II receptor activity / positive regulation of CD4-positive, alpha-beta T cell activation / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II ...regulation of interleukin-4 production / regulation of interleukin-10 production / myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / autolysosome membrane / regulation of T-helper cell differentiation / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / MHC class II receptor activity / positive regulation of CD4-positive, alpha-beta T cell activation / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / positive regulation of T cell mediated immune response to tumor cell / positive regulation of kinase activity / positive regulation of memory T cell differentiation / alpha-beta T cell receptor complex / positive regulation of monocyte differentiation / inflammatory response to antigenic stimulus / CD4 receptor binding / intermediate filament / T-helper 1 type immune response / transport vesicle membrane / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / polysaccharide binding / negative regulation of type II interferon production / humoral immune response / alpha-beta T cell activation / macrophage differentiation / Generation of second messenger molecules / immunological synapse / Co-inhibition by PD-1 / epidermis development / positive regulation of insulin secretion involved in cellular response to glucose stimulus / detection of bacterium / T cell receptor binding / negative regulation of T cell proliferation / MHC class II antigen presentation / viral budding from plasma membrane / trans-Golgi network membrane / lumenal side of endoplasmic reticulum membrane / response to bacterium / protein tetramerization / peptide antigen assembly with MHC class II protein complex / negative regulation of inflammatory response to antigenic stimulus / MHC class II protein complex / clathrin-coated endocytic vesicle membrane / ER to Golgi transport vesicle membrane / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / positive regulation of T cell activation / peptide antigen binding / structural constituent of cytoskeleton / positive regulation of T cell mediated cytotoxicity / cognition / positive regulation of protein phosphorylation / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / MHC class II protein complex binding / endocytic vesicle membrane / late endosome membrane / Downstream TCR signaling / T cell receptor signaling pathway / toxin activity / early endosome membrane / clathrin-dependent endocytosis of virus by host cell / adaptive immune response / positive regulation of viral entry into host cell / positive regulation of ERK1 and ERK2 cascade / lysosome / positive regulation of canonical NF-kappaB signal transduction / positive regulation of MAPK cascade / endosome membrane / host cell surface receptor binding / immune response / Golgi membrane / lysosomal membrane / fusion of virus membrane with host plasma membrane / external side of plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / positive regulation of DNA-templated transcription / virion attachment to host cell / host cell plasma membrane / virion membrane / cell surface / signal transduction / extracellular space / extracellular exosome / extracellular region / metal ion binding / membrane / plasma membrane
Similarity search - Function
Staphylococcal enterotoxin/Streptococcal pyrogenic exotoxin signature 1. / Staphylococcal/streptococcal toxin, bacterial / Staphylococcal/Streptococcal toxin, OB-fold / Staphylococcal/Streptococcal toxin, OB-fold domain / Staphylococcal enterotoxin/Streptococcal pyrogenic exotoxin, conserved site / Staphyloccocal enterotoxin/Streptococcal pyrogenic exotoxin signature 2. / Ubiquitin-like (UB roll) - #120 / Superantigen, staphylococcal/streptococcal toxin, bacterial / Staphylococcal/Streptococcal toxin, beta-grasp domain / Staphylococcal/Streptococcal toxin, beta-grasp domain ...Staphylococcal enterotoxin/Streptococcal pyrogenic exotoxin signature 1. / Staphylococcal/streptococcal toxin, bacterial / Staphylococcal/Streptococcal toxin, OB-fold / Staphylococcal/Streptococcal toxin, OB-fold domain / Staphylococcal enterotoxin/Streptococcal pyrogenic exotoxin, conserved site / Staphyloccocal enterotoxin/Streptococcal pyrogenic exotoxin signature 2. / Ubiquitin-like (UB roll) - #120 / Superantigen, staphylococcal/streptococcal toxin, bacterial / Staphylococcal/Streptococcal toxin, beta-grasp domain / Staphylococcal/Streptococcal toxin, beta-grasp domain / Superantigen toxin, C-terminal / T-cell receptor alpha chain, constant domain / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / Domain of unknown function (DUF1968) / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #110 / MHC class II, beta chain, N-terminal / Class II histocompatibility antigen, beta domain / Class II histocompatibility antigen, beta domain / MHC class II, alpha chain, N-terminal / Class II histocompatibility antigen, alpha domain / Class II histocompatibility antigen, alpha domain / MHC class II, alpha/beta chain, N-terminal / Enterotoxin / Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / : / Viral capsid/haemagglutinin protein / MHC classes I/II-like antigen recognition protein / : / Ubiquitin-like (UB roll) / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / 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 / Roll / Immunoglobulin-like fold / Immunoglobulins / Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
T cell receptor beta constant 2 / MHC class II antigen / Enterotoxin type B / T cell receptor alpha chain constant / HLA class II histocompatibility antigen, DR alpha chain / HLA class II histocompatibility antigen, DRB1 beta chain / Hemagglutinin / Hemagglutinin / Enterotoxin B
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
STAPHYLOCOCCUS AUREUS (bacteria)
INFLUENZA A VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsRodstrom, K.E.J. / Elbing, K. / Lindkvist-Petersson, K.
CitationJournal: J.Immunol. / Year: 2014
Title: Structure of the Superantigen Staphylococcal Enterotoxin B in Complex with Tcr and Peptide-Mhc Demonstrates Absence of Tcr-Peptide Contacts.
Authors: Rodstrom, K.E.J. / Elbing, K. / Lindkvist-Petersson, K.
History
DepositionSep 10, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 23, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 13, 2014Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: T CELL RECEPTOR ALPHA CHAIN
B: T CELL RECEPTOR BETA CHAIN
C: ENTEROTOXIN B
D: HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, DR ALPHA CHAIN
E: MHC CLASS II ANTIGEN
F: HEMAGGLUTININ
G: T CELL RECEPTOR ALPHA CHAIN
H: T CELL RECEPTOR BETA CHAIN
I: ENTEROTOXIN B
J: HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, DR ALPHA CHAIN
K: MHC CLASS II ANTIGEN
L: HEMAGGLUTININ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)247,30913
Polymers247,21612
Non-polymers921
Water46826
1
G: T CELL RECEPTOR ALPHA CHAIN
H: T CELL RECEPTOR BETA CHAIN
I: ENTEROTOXIN B
J: HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, DR ALPHA CHAIN
K: MHC CLASS II ANTIGEN
L: HEMAGGLUTININ


Theoretical massNumber of molelcules
Total (without water)123,6086
Polymers123,6086
Non-polymers00
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17600 Å2
ΔGint-111.3 kcal/mol
Surface area55760 Å2
MethodPISA
2
A: T CELL RECEPTOR ALPHA CHAIN
B: T CELL RECEPTOR BETA CHAIN
C: ENTEROTOXIN B
D: HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, DR ALPHA CHAIN
E: MHC CLASS II ANTIGEN
F: HEMAGGLUTININ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,7007
Polymers123,6086
Non-polymers921
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17040 Å2
ΔGint-109 kcal/mol
Surface area57120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.350, 217.650, 101.410
Angle α, β, γ (deg.)90.00, 99.82, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
T CELL RECEPTOR ... , 2 types, 4 molecules AGBH

#1: Protein T CELL RECEPTOR ALPHA CHAIN


Mass: 22812.125 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell: T-LYMPHOCYTE / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR / References: UniProt: P01848*PLUS
#2: Protein T CELL RECEPTOR BETA CHAIN


Mass: 27770.773 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell: T-LYMPHOCYTE / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR / References: UniProt: A0A5B9*PLUS

-
Protein , 3 types, 6 molecules CIDJEK

#3: Protein ENTEROTOXIN B


Mass: 28281.953 Da / Num. of mol.: 2 / Fragment: OB-DOMAIN AND BETA-GRASP DOMAIN, RESIDUES 13-250
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STAPHYLOCOCCUS AUREUS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K12 / Variant (production host): UL635 / References: UniProt: Q5MAA8, UniProt: P01552*PLUS
#4: Protein HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, DR ALPHA CHAIN / MAJOR HISTOCOMPATIBILITY COMPLEX CLASS II ALPHA CHAIN


Mass: 21155.904 Da / Num. of mol.: 2 / Fragment: IMMUNOGLOBULIN DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR / References: UniProt: P01903
#5: Protein MHC CLASS II ANTIGEN / MAJOR HISTOCOMPATIBILITY COMPLEX CLASS II BETA CHAIN


Mass: 22080.664 Da / Num. of mol.: 2 / Fragment: IMMUNOGLOBULIN DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR / References: UniProt: A9JJF6, UniProt: P01911*PLUS

-
Protein/peptide , 1 types, 2 molecules FL

#6: Protein/peptide HEMAGGLUTININ


Mass: 1506.807 Da / Num. of mol.: 2 / Fragment: HA PEPTIDE, RESIDUES 327-339 / Source method: obtained synthetically / Source: (synth.) INFLUENZA A VIRUS / References: UniProt: Q03909, UniProt: P03437*PLUS

-
Non-polymers , 2 types, 27 molecules

#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY
Sequence detailsIMGT ACCESSION NUMBERS FOR CHAINS A,G TRAV22 01 01 (AE000660), TRAJ40 01 (M35620) AND TRAC 01 ...IMGT ACCESSION NUMBERS FOR CHAINS A,G TRAV22 01 01 (AE000660), TRAJ40 01 (M35620) AND TRAC 01 (X02883). PRODUCT OF SOMATIC RECOMBINATION. EXTRACELLULAR DOMAIN ONLY. IMGT ACCESSION NUMBERS FOR CHAINS B,H TRBV19 01 (L36092), TRBJ2-7 01 (M14159), AND TRBC2 01 (M12888). PRODUCT OF SOMATIC RECOMBINATION. EXTRACELLULAR DOMAIN ONLY.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.9 Å3/Da / Density % sol: 58 % / Description: NONE
Crystal growpH: 5.5
Details: 8% PEG 20000, 0.1 M SODIUM CITRATE PH 5.5, 0.09 M MAGNESIUM CHLORIDE

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.07227
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 10, 2011
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07227 Å / Relative weight: 1
ReflectionResolution: 2.9→48.7 Å / Num. obs: 61924 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Biso Wilson estimate: 82.8 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 13.1
Reflection shellResolution: 2.9→3.06 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 2.3 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1OGA CHAINS D AND E, 2IAL CHAIN A, 1SEB CHAINS A, B AND C

1oga

2ial

1seb


Resolution: 2.9→29.23 Å / Cor.coef. Fo:Fc: 0.8907 / Cor.coef. Fo:Fc free: 0.8727 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 3.964 / SU Rfree Blow DPI: 0.357
RfactorNum. reflection% reflectionSelection details
Rfree0.2511 3134 5.07 %RANDOM
Rwork0.2329 ---
obs0.2338 61848 98.98 %-
Displacement parametersBiso mean: 65.03 Å2
Baniso -1Baniso -2Baniso -3
1--4.7586 Å20 Å2-11.4009 Å2
2--5.0533 Å20 Å2
3----0.2947 Å2
Refine analyzeLuzzati coordinate error obs: 0.494 Å
Refinement stepCycle: LAST / Resolution: 2.9→29.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16279 0 6 26 16311
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00716719HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.8722807HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d5443SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes435HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2436HARMONIC5
X-RAY DIFFRACTIONt_it16719HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion1.47
X-RAY DIFFRACTIONt_other_torsion20.84
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion2178SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact17183SEMIHARMONIC4
LS refinement shellResolution: 2.9→2.98 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3055 215 4.7 %
Rwork0.2804 4359 -
all0.2816 4574 -
obs--98.98 %

+
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