[English] 日本語
Yorodumi
- PDB-2xn9: Crystal structure of the ternary complex between human T cell rec... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2xn9
TitleCrystal structure of the ternary complex between human T cell receptor, staphylococcal enterotoxin H and human major histocompatibility complex class II
Components
  • (T CELL RECEPTOR ...) x 2
  • ENTEROTOXIN H
  • HEMAGGLUTININ
  • HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, DR ALPHA CHAIN,
  • MAJOR HISTOCOMPATIBILITY COMPLEX CLASS II BETA CHAIN
KeywordsIMMUNE SYSTEM / SUPERANTIGEN / IMMUNORECEPTORS / TERNARY 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 / MHC class II protein binding ...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 / MHC class II protein binding / 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 / 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/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 ...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
Hemagglutinin / T cell receptor alpha chain constant / T cell receptor beta constant 1 / HLA class II histocompatibility antigen, DR alpha chain / HLA class II histocompatibility antigen, DRB1 beta chain / HLA class II histocompatibility antigen, DRB1 beta chain / Enterotoxin type H / Hemagglutinin
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
STAPHYLOCOCCUS AUREUS (bacteria)
INFLUENZA A VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsSaline, M. / Rodstrom, K.E.J. / Fischer, G. / Orekhov, V.Y. / Karlsson, B.G. / Lindkvist-Petersson, K.
CitationJournal: Nat.Commun. / Year: 2010
Title: The Structure of Superantigen Complexed with Tcr and Mhc Reveals Novel Insights Into Superantigenic T Cell Activation.
Authors: Saline, M. / Rodstrom, K.E.J. / Fischer, G. / Orekhov, V.Y. / Karlsson, B.G. / Lindkvist-Petersson, K.
History
DepositionJul 31, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 24, 2010Provider: repository / Type: Initial release
Revision 1.1Aug 3, 2011Group: Database references / Non-polymer description / Version format compliance
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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 16, 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 C REGION
B: T CELL RECEPTOR BETA-1 CHAIN C REGION
C: ENTEROTOXIN H
D: HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, DR ALPHA CHAIN,
E: MAJOR HISTOCOMPATIBILITY COMPLEX CLASS II BETA CHAIN
F: HEMAGGLUTININ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,41511
Polymers120,0236
Non-polymers3915
Water5,044280
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15320 Å2
ΔGint-94 kcal/mol
Surface area46900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)191.180, 48.890, 166.720
Angle α, β, γ (deg.)90.00, 113.55, 90.00
Int Tables number5
Space group name H-MC121

-
Components

-
T CELL RECEPTOR ... , 2 types, 2 molecules AB

#1: Protein T CELL RECEPTOR ALPHA CHAIN C REGION


Mass: 22313.818 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR DOMAIN, RESIDUES 1-95 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: VARIABLE DOMAIN TRAV27 FUSED TO CONSTANT DOMAIN / Source: (gene. exp.) HOMO SAPIENS (human) / Cell: T LYMPHOCYTE / Plasmid: PGMT7 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01848
#2: Protein T CELL RECEPTOR BETA-1 CHAIN C REGION


Mass: 27785.787 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR DOMAIN, RESIDUES 1-130 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: VARIABLE DOMAIN TRBV19 FUSED TO CONSTANT DOMAIN / Source: (gene. exp.) HOMO SAPIENS (human) / Cell: T LYMPHOCYTE / Plasmid: PGMT7 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01850

-
Protein , 3 types, 3 molecules CDE

#3: Protein ENTEROTOXIN H / SEH / STAPHYLOCOCCAL ENTEROTOXIN H


Mass: 25180.240 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STAPHYLOCOCCUS AUREUS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K-12 / Variant (production host): UL635 / References: UniProt: P0A0M0
#4: Protein HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, DR ALPHA CHAIN, / MAJOR HISTOCOMPATIBILITY COMPLEX CLASS II ALPHA / MHC CLASS II ANTIGEN DRA CHAIN


Mass: 21155.904 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR DOMAIN, RESIDUES 26-207
Source method: isolated from a genetically manipulated source
Details: CHAIN DR 0101 / Source: (gene. exp.) HOMO SAPIENS (human) / Cell: ANTIGEN PRESENTING CELL / Plasmid: PLM1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)PLYS / References: UniProt: P01903
#5: Protein MAJOR HISTOCOMPATIBILITY COMPLEX CLASS II BETA CHAIN / MHC CLASS II ANTIGEN DRB1.1 / DR-1 / DR1


Mass: 22080.664 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR DOMAIN, RESIDUES 30-219
Source method: isolated from a genetically manipulated source
Details: CHAIN DRB1 0101 / Source: (gene. exp.) HOMO SAPIENS (human) / Cell: ANTIGEN PRESENTING CELL / Plasmid: PLM1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P04229, UniProt: P01911*PLUS

-
Protein/peptide , 1 types, 1 molecules F

#6: Protein/peptide HEMAGGLUTININ / INFLUENZA HEMAGGLUTININ PEPTIDE


Mass: 1506.807 Da / Num. of mol.: 1 / Fragment: RESIDUES 59-71 / Source method: obtained synthetically / Source: (synth.) INFLUENZA A VIRUS / References: UniProt: A8CDU0, UniProt: Q03909*PLUS

-
Non-polymers , 3 types, 285 molecules

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


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 280 / Source method: isolated from a natural source / Formula: H2O

-
Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, THR 49 TO CYS ENGINEERED RESIDUE IN CHAIN B, SER 57 TO CYS
Has protein modificationY
Sequence detailsCHAIN A RESIDUES 1-109 CONTAINS THE TCR VARIABLE DOMAIN TRAV27. ALPHA CHAIN RESIDUES 96-142 ARE ...CHAIN A RESIDUES 1-109 CONTAINS THE TCR VARIABLE DOMAIN TRAV27. ALPHA CHAIN RESIDUES 96-142 ARE EXCLUDED. CHAIN B RESIDUES 1-114 CONTAINS THE TCR VARIABLE DOMAIN TRBV19. BETA CHAIN RESIDUES 131-177 ARE EXCLUDED. SIGNAL SEQUENCES (RESIDUES B1-24, C1-25, D1-29) NOT IN CONSTRUCTS. SYNTHETIC PEPTIDE F OF 13 RESIDUES, 306-318 OF INFLUENZA HEMAGGLUTININ.

-
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: 7
Details: 15% W/V PEG 5000 MME, 0.1 M BIS-TRIS PH 7.0, 0.1 M NACL

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 23, 2009 / Details: TOROIDAL MIRRORS
RadiationMonochromator: DIAMOND (111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.3→42.72 Å / Num. obs: 61858 / % possible obs: 97.6 % / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Biso Wilson estimate: 49.17 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 10.3
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 2.1 / % possible all: 88.8

-
Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OGA CHAINS D, E AND PDB ENTRY 1HXY CHAINS A, B, D

1oga

1hxy


Resolution: 2.3→152.5 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.895 / SU B: 7.35 / SU ML: 0.181 / Cross valid method: THROUGHOUT / ESU R: 0.316 / ESU R Free: 0.248 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.27236 3148 5.1 %RANDOM
Rwork0.2215 ---
obs0.22414 58700 97.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.997 Å2
Baniso -1Baniso -2Baniso -3
1--2.75 Å20 Å2-1.62 Å2
2--2.02 Å20 Å2
3----0.56 Å2
Refinement stepCycle: LAST / Resolution: 2.3→152.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8266 0 25 280 8571
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0228646
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4431.94711751
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.67151059
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.5324.579439
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.278151435
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.711551
X-RAY DIFFRACTIONr_chiral_restr0.0960.21259
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216722
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_it0.7941.55250
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.48828514
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.87533396
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.0614.53237
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: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.358 211 -
Rwork0.293 3577 -
obs--80.97 %

+
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