[English] 日本語
Yorodumi
- PDB-1z7z: Cryo-em structure of human coxsackievirus A21 complexed with five... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1z7z
TitleCryo-em structure of human coxsackievirus A21 complexed with five domain icam-1kilifi
Components
  • (human coxsackievirus ...) x 5
  • Intercellular adhesion molecule-1
KeywordsVirus/Receptor / ICAM-1 / Kilifi / CD54 / Human Coxsackievirus A21 / virus-receptor complex / Icosahedral virus
Function / homology
Function and homology information


regulation of leukocyte mediated cytotoxicity / T cell extravasation / positive regulation of cellular extravasation / regulation of ruffle assembly / T cell antigen processing and presentation / membrane to membrane docking / T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / adhesion of symbiont to host / establishment of endothelial barrier / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules ...regulation of leukocyte mediated cytotoxicity / T cell extravasation / positive regulation of cellular extravasation / regulation of ruffle assembly / T cell antigen processing and presentation / membrane to membrane docking / T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / adhesion of symbiont to host / establishment of endothelial barrier / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / cell adhesion mediated by integrin / leukocyte migration / leukocyte cell-cell adhesion / Interleukin-10 signaling / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / immunological synapse / Integrin cell surface interactions / negative regulation of endothelial cell apoptotic process / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / ribonucleoside triphosphate phosphatase activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / cellular response to leukemia inhibitory factor / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / cellular response to glucose stimulus / RNA-protein covalent cross-linking / cytoplasmic vesicle membrane / host cell cytoplasmic vesicle membrane / cellular response to amyloid-beta / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / transmembrane signaling receptor activity / integrin binding / nucleoside-triphosphate phosphatase / channel activity / signaling receptor activity / virus receptor activity / monoatomic ion transmembrane transport / collagen-containing extracellular matrix / Interleukin-4 and Interleukin-13 signaling / DNA replication / positive regulation of ERK1 and ERK2 cascade / RNA helicase activity / receptor-mediated virion attachment to host cell / cell adhesion / symbiont-mediated suppression of host innate immune response / endocytosis involved in viral entry into host cell / membrane raft / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / external side of plasma membrane / cysteine-type endopeptidase activity / viral RNA genome replication / focal adhesion / RNA-directed RNA polymerase activity / : / DNA-templated transcription / host cell nucleus / virion attachment to host cell / structural molecule activity / cell surface / proteolysis / extracellular space / RNA binding / extracellular exosome / ATP binding / membrane / metal ion binding / plasma membrane
Similarity search - Function
: / ICAM-1/3/5, D2 domain / Intercellular adhesion molecule / Intercellular adhesion molecule, N-terminal / Intercellular adhesion molecule (ICAM), N-terminal domain / Intercellular adhesion molecule/vascular cell adhesion molecule, N-terminal / : / Immunoglobulin domain / Poliovirus 3A protein-like / Poliovirus 3A protein like ...: / ICAM-1/3/5, D2 domain / Intercellular adhesion molecule / Intercellular adhesion molecule, N-terminal / Intercellular adhesion molecule (ICAM), N-terminal domain / Intercellular adhesion molecule/vascular cell adhesion molecule, N-terminal / : / Immunoglobulin domain / Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Picornavirus capsid / picornavirus capsid protein / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / Immunoglobulin subtype / Immunoglobulin / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / Immunoglobulin-like domain superfamily / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Peptidase S1, PA clan, chymotrypsin-like fold / Immunoglobulin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
: / Intercellular adhesion molecule 1 / Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesHuman coxsackievirus A21
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 8 Å
AuthorsXiao, C. / Bator-Kelly, C.M. / Rieder, E. / Chipman, P.R. / Craig, A. / Kuhn, R.J. / Wimmer, E. / Rossmann, M.G.
CitationJournal: Structure / Year: 2005
Title: The crystal structure of coxsackievirus A21 and its interaction with ICAM-1.
Authors: Chuan Xiao / Carol M Bator-Kelly / Elizabeth Rieder / Paul R Chipman / Alister Craig / Richard J Kuhn / Eckard Wimmer / Michael G Rossmann /
Abstract: CVA21 and polioviruses both belong to the Enterovirus genus in the family of Picornaviridae, whereas rhinoviruses form a distinct picornavirus genus. Nevertheless, CVA21 and the major group of human ...CVA21 and polioviruses both belong to the Enterovirus genus in the family of Picornaviridae, whereas rhinoviruses form a distinct picornavirus genus. Nevertheless, CVA21 and the major group of human rhinoviruses recognize intercellular adhesion molecule-1 (ICAM-1) as their cellular receptor, whereas polioviruses use poliovirus receptor. The crystal structure of CVA21 has been determined to 3.2 A resolution. Its structure has greater similarity to poliovirus structures than to other known picornavirus structures. Cryo-electron microscopy (cryo-EM) was used to determine an 8.0 A resolution structure of CVA21 complexed with an ICAM-1 variant, ICAM-1(Kilifi). The cryo-EM map was fitted with the crystal structures of ICAM-1 and CVA21. Significant differences in the structure of CVA21 with respect to the poliovirus structures account for the inability of ICAM-1 to bind polioviruses. The interface between CVA21 and ICAM-1 has shape and electrostatic complementarity with many residues being conserved among those CVAs that bind ICAM-1.
History
DepositionMar 28, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 2, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jul 18, 2018Group: Data collection / Category: em_software / Item: _em_software.image_processing_id / _em_software.name
Revision 1.4Dec 18, 2019Group: Derived calculations / Other / Category: atom_sites / cell / struct_conn
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.length_a / _cell.length_b / _cell.length_c / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_validate_chiral / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_nonpoly_scheme.entity_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _struct_asym.entity_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_seq_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 20, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 2.2Dec 25, 2024Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_3d_fitting_list / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id ..._em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

-
Structure visualization

Movie
  • Biological unit as complete icosahedral assembly
  • Imaged by Jmol
  • Download
  • Biological unit as icosahedral pentamer
  • Imaged by Jmol
  • Download
  • Biological unit as icosahedral 23 hexamer
  • Imaged by Jmol
  • Download
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-1114
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-1114
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
1: human coxsackievirus A21
2: human coxsackievirus A21
3: human coxsackievirus A21
4: human coxsackievirus A21
5: human coxsackievirus A21
I: Intercellular adhesion molecule-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,66214
Polymers138,8926
Non-polymers1,7708
Water00
1
1: human coxsackievirus A21
2: human coxsackievirus A21
3: human coxsackievirus A21
4: human coxsackievirus A21
5: human coxsackievirus A21
I: Intercellular adhesion molecule-1
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)8,439,700840
Polymers8,333,520360
Non-polymers106,180480
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
1: human coxsackievirus A21
2: human coxsackievirus A21
3: human coxsackievirus A21
4: human coxsackievirus A21
5: human coxsackievirus A21
I: Intercellular adhesion molecule-1
hetero molecules
x 5


  • icosahedral pentamer
  • 703 kDa, 30 polymers
Theoretical massNumber of molelcules
Total (without water)703,30870
Polymers694,46030
Non-polymers8,84840
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
1: human coxsackievirus A21
2: human coxsackievirus A21
3: human coxsackievirus A21
4: human coxsackievirus A21
5: human coxsackievirus A21
I: Intercellular adhesion molecule-1
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 844 kDa, 36 polymers
Theoretical massNumber of molelcules
Total (without water)843,97084
Polymers833,35236
Non-polymers10,61848
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral))

-
Components

-
Human coxsackievirus ... , 5 types, 5 molecules 12345

#1: Protein human coxsackievirus A21


Mass: 31946.727 Da / Num. of mol.: 1 / Fragment: Viral Protein 1 residues 1073-1286 / Source method: isolated from a natural source / Details: THE NATURE HOST OF THIS VIRUS IS HUMAN / Source: (natural) Human coxsackievirus A21 / Genus: Enterovirus / Cell line: Hela / Species: Human enterovirus C / Strain: KUYKENDALL / References: GenBank: 33304569, UniProt: Q7T7N6*PLUS
#2: Protein human coxsackievirus A21


Mass: 29918.537 Da / Num. of mol.: 1 / Fragment: Viral Protein 2 residues 2010-2272 / Source method: isolated from a natural source / Details: THE NATURE HOST OF THIS VIRUS IS HUMAN / Source: (natural) Human coxsackievirus A21 / Genus: Enterovirus / Cell line: Hela / Species: Human enterovirus C / Strain: KUYKENDALL / References: GenBank: 33304569, UniProt: Q7T7N6*PLUS
#3: Protein human coxsackievirus A21


Mass: 25898.895 Da / Num. of mol.: 1 / Fragment: Viral Protein 3 residues 3043-3234 / Source method: isolated from a natural source / Details: THE NATURE HOST OF THIS VIRUS IS HUMAN / Source: (natural) Human coxsackievirus A21 / Genus: Enterovirus / Cell line: Hela / Species: Human enterovirus C / Strain: KUYKENDALL / References: GenBank: 33304569, UniProt: Q7T7N6*PLUS
#4: Protein/peptide human coxsackievirus A21


Mass: 1335.565 Da / Num. of mol.: 1 / Fragment: Viral Protein 1 residues 1287-1298 / Source method: isolated from a natural source / Details: THE NATURE HOST OF THIS VIRUS IS HUMAN / Source: (natural) Human coxsackievirus A21 / Genus: Enterovirus / Cell line: Hela / Species: Human enterovirus C / Strain: KUYKENDALL / References: GenBank: 33304569, UniProt: P22055*PLUS
#5: Protein/peptide human coxsackievirus A21


Mass: 687.809 Da / Num. of mol.: 1 / Fragment: Viral Protein 3 residues 3035-3239 / Source method: isolated from a natural source / Details: THE NATURE HOST OF THIS VIRUS IS HUMAN / Source: (natural) Human coxsackievirus A21 / Genus: Enterovirus / Cell line: Hela / Species: Human enterovirus C / Strain: KUYKENDALL / References: GenBank: 33304569

-
Protein / Sugars , 2 types, 9 molecules I

#6: Protein Intercellular adhesion molecule-1 / ICAM-1 / Major group rhinovirus receptor / CD54


Mass: 49104.473 Da / Num. of mol.: 1 / Fragment: ICAM-1 EXTRACELLULAR DOMAIN 1-5 / Mutation: K29M / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: COS7 / References: UniProt: P05362
#7: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

Component
IDNameTypeDetailsParent-ID
1COXSACKIEVIRUS A21/ICAM- 1KILIFI COMPLEXVIRUSTHIS STRUCTURE IS MODELED BASED ON CRYO-EM DENSITY AT 8A RESOLUTION.0
2HUMAN COXSACKIEVIRUS A21 VP1 1073-1286Apply 60 icoshedral symmetry operation as MATRIX to obtain the whole complex1
3human coxsackievirus A21 VP2 2010-2272Apply 60 icoshedral symmetry operation as MATRIX to obtain the whole complex1
4human coxsackievirus A21 VP3 3043-3234Apply 60 icoshedral symmetry operation as MATRIX to obtain the whole complex1
5human coxsackievirus A21 VP1 1287-1298Apply 60 icoshedral symmetry operation as MATRIX to obtain the whole complex1
6human coxsackievirus A21 VP3 3035-3239Apply 60 icoshedral symmetry operation as MATRIX to obtain the whole complex1
7ICAM-1KILIFIApply 60 icoshedral symmetry operation as MATRIX to obtain the whole complex1
Details of virusHost category: MAMMALIAN / Type: VIRION
Natural hostOrganism: Homo sapiens / Strain: Hela
Buffer solutionName: TRIS / pH: 7.2 / Details: TRIS
SpecimenConc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationInstrument: REICHERT-JUNG PLUNGER / Cryogen name: ETHANE / Details: PLUNGED INTO ETHANE AT LIQUID NITROGEN TEMPERATURE

-
Electron microscopy imaging

MicroscopyModel: FEI/PHILIPS CM300FEG/T / Date: Mar 15, 2001
Details: SAMPLES WERE MAINTAINED AT LIQUID NITROGEN TEMPERATURES IN THE ELECTRON MICROSCOPE.
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal magnification: 45000 X / Calibrated magnification: 47000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 700 nm / Cs: 2 mm
Specimen holderTemperature: 100 K / Tilt angle max: 0 ° / Tilt angle min: 0 °
Image recordingElectron dose: 26 e/Å2 / Film or detector model: KODAK SO-163 FILM
Image scansNum. digital images: 33
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

-
Processing

EM software
IDNameCategory
1EMfitmodel fitting
2EM3DR3D reconstruction
3PFT3D reconstruction
CTF correctionDetails: REVERSED CTF WITH WEINER FACTOR FOR EACH PARTICLE
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionMethod: POLAR FOURIER TRANSFORM METHOD AND FOURIER-BESSEL RECONSTRUCTION
Resolution: 8 Å / Num. of particles: 4704 / Nominal pixel size: 2.98 Å / Actual pixel size: 2.85 Å
Magnification calibration: THE PIXEL SIZE OF THE CRYO-EM MAP WAS CALIBRATED AGAINST THE ATOMIC MODEL OF THE VIRUS CAPSID. DENSITIES WERE COMPARED BY CROSS- CORRELATION WITHIN A SPHERICAL SHELL OF ...Magnification calibration: THE PIXEL SIZE OF THE CRYO-EM MAP WAS CALIBRATED AGAINST THE ATOMIC MODEL OF THE VIRUS CAPSID. DENSITIES WERE COMPARED BY CROSS- CORRELATION WITHIN A SPHERICAL SHELL OF INTERNAL RADIUS 104 ANGSTROMS AND EXTERNAL RADIUS 177 ANGSTROMS.
Details: A B-FACTOR OF 589.46 WAS SET FOR ALL THE ATOMS BASED ON THE EQUATION OF -4*LN(0.1*RESOLUTION2) TO MIMIC A 8 ANGSTROM RESOLUTION CRYOEM STRUCTURE. OCCUPANCY OF 1.0 WAS SET FOR ALL ATOMS OF ...Details: A B-FACTOR OF 589.46 WAS SET FOR ALL THE ATOMS BASED ON THE EQUATION OF -4*LN(0.1*RESOLUTION2) TO MIMIC A 8 ANGSTROM RESOLUTION CRYOEM STRUCTURE. OCCUPANCY OF 1.0 WAS SET FOR ALL ATOMS OF THE VIRAL CAPSID. OCCUPANCY OF 0.80, 0.56, 0.24, 0.16, AND 0.08 WAS SET FOR ATOMS OF ICAM-1 DOMAIN 1, 2, 3, 4, AND 5, RESPECTIVELY, BASED ON THE FITTING RESULTS. SEE DETAILS IN THE CITATION.
Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Target criteria: BEST SUMF VALUE FIT USING THE PROGRAM EMFIT
Details: REFINEMENT PROTOCOL--RIGID BODY
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
11IAM

1iam

11IAM1PDBexperimental model
21Z7S

1z7s

11Z7S2PDBexperimental model
RefinementHighest resolution: 8 Å
Refinement stepCycle: LAST / Highest resolution: 8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8712 0 112 0 8824

+
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