[English] 日本語
Yorodumi
- EMDB-12172: HRV14 in complex with its receptor ICAM-1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-12172
TitleHRV14 in complex with its receptor ICAM-1
Map dataB-factor sharpened (Bf = -82) final map of HRV14-ICAM-1 complex.
Sample
  • Virus: Human rhinovirus 14
    • Complex: Rhinovirus
      • Protein or peptide: Genome polyprotein
      • Protein or peptide: Genome polyprotein
      • Protein or peptide: Genome polyprotein
      • Protein or peptide: Genome polyprotein
    • Complex: Intercellular adhesion molecule 1
      • Protein or peptide: Intercellular adhesion molecule 1
  • Ligand: water
Keywordsenterovirus / rhinovirus 14 / HRV14 / RV14 / native particle / VIRUS / receptor / virus-receptor complex / ICAM-1
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 / lysis of host organelle involved in viral entry into host cell / adhesion of symbiont to host / establishment of endothelial barrier ...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 / lysis of host organelle involved in viral entry into host cell / adhesion of symbiont to host / establishment of endothelial barrier / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / leukocyte migration / leukocyte cell-cell adhesion / cell adhesion mediated by integrin / 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 / cellular response to leukemia inhibitory factor / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / cellular response to glucose stimulus / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cellular response to amyloid-beta / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / integrin binding / transmembrane signaling receptor activity / signaling receptor activity / nucleoside-triphosphate phosphatase / virus receptor activity / channel activity / : / monoatomic ion transmembrane transport / Interleukin-4 and Interleukin-13 signaling / DNA replication / receptor-mediated virion attachment to host cell / positive regulation of ERK1 and ERK2 cascade / RNA helicase activity / cell adhesion / membrane raft / endocytosis involved in viral entry into host cell / symbiont-mediated activation of host autophagy / external side of plasma membrane / RNA-directed RNA polymerase / 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 / ATP hydrolysis activity / proteolysis / extracellular space / RNA binding / extracellular exosome / zinc ion binding / ATP binding / membrane / 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 / Picornavirus coat protein VP4 superfamily / 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 / Picornavirus coat protein VP4 superfamily / 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. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / 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
Genome polyprotein / Intercellular adhesion molecule 1
Similarity search - Component
Biological speciesHuman rhinovirus 14 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.4 Å
AuthorsHrebik D / Fuzik T
Funding support Czech Republic, 1 items
OrganizationGrant numberCountry
Czech Science Foundation19-25982X Czech Republic
CitationJournal: Proc Natl Acad Sci U S A / Year: 2021
Title: ICAM-1 induced rearrangements of capsid and genome prime rhinovirus 14 for activation and uncoating.
Authors: Dominik Hrebík / Tibor Füzik / Mária Gondová / Lenka Šmerdová / Athanassios Adamopoulos / Ondrej Šedo / Zbyněk Zdráhal / Pavel Plevka /
Abstract: Most rhinoviruses, which are the leading cause of the common cold, utilize intercellular adhesion molecule-1 (ICAM-1) as a receptor to infect cells. To release their genomes, rhinoviruses convert to ...Most rhinoviruses, which are the leading cause of the common cold, utilize intercellular adhesion molecule-1 (ICAM-1) as a receptor to infect cells. To release their genomes, rhinoviruses convert to activated particles that contain pores in the capsid, lack minor capsid protein VP4, and have an altered genome organization. The binding of rhinoviruses to ICAM-1 promotes virus activation; however, the molecular details of the process remain unknown. Here, we present the structures of virion of rhinovirus 14 and its complex with ICAM-1 determined to resolutions of 2.6 and 2.4 Å, respectively. The cryo-electron microscopy reconstruction of rhinovirus 14 virions contains the resolved density of octanucleotide segments from the RNA genome that interact with VP2 subunits. We show that the binding of ICAM-1 to rhinovirus 14 is required to prime the virus for activation and genome release at acidic pH. Formation of the rhinovirus 14-ICAM-1 complex induces conformational changes to the rhinovirus 14 capsid, including translocation of the C termini of VP4 subunits, which become poised for release through pores that open in the capsids of activated particles. VP4 subunits with altered conformation block the RNA-VP2 interactions and expose patches of positively charged residues. The conformational changes to the capsid induce the redistribution of the virus genome by altering the capsid-RNA interactions. The restructuring of the rhinovirus 14 capsid and genome prepares the virions for conversion to activated particles. The high-resolution structure of rhinovirus 14 in complex with ICAM-1 explains how the binding of uncoating receptors enables enterovirus genome release.
History
DepositionJan 6, 2021-
Header (metadata) releaseMay 19, 2021-
Map releaseMay 19, 2021-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.055
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.055
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7bg7
  • Surface level: 0.055
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7bg7
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12172.png

Downloads & links

-
Map

FileDownload / File: emd_12172.map.gz / Format: CCP4 / Size: 209.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationB-factor sharpened (Bf = -82) final map of HRV14-ICAM-1 complex.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 380 pix.
= 403.94 Å		1.06 Å/pix.
x 380 pix.
= 403.94 Å		1.06 Å/pix.
x 380 pix.
= 403.94 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.063 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.055 / Movie #1: 0.055
Minimum - Maximum-0.35632035 - 0.66691226
Average (Standard dev.)0.0022133829 (±0.0408159)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-190-190-190
Dimensions380380380
Spacing380380380
CellA=B=C: 403.93997 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0631.0631.063
M x/y/z380380380
origin x/y/z0.0000.0000.000
length x/y/z403.940403.940403.940
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-190-190-190
NC/NR/NS380380380
D min/max/mean-0.3560.6670.002

-
Supplemental data

-
Mask #1

Fileemd_12172_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Locally Bfactor sharpened final map of HRV14-ICAM-1 complex...

Fileemd_12172_additional_1.map
AnnotationLocally Bfactor sharpened final map of HRV14-ICAM-1 complex by LocalDeBlur software. Better visibility of C-terminal part of VP4.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Mask used in final relion postprocess.

Fileemd_12172_additional_2.map
AnnotationMask used in final relion postprocess.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Ewald sphere corrected half map 1 used in...

Fileemd_12172_half_map_1.map
AnnotationEwald sphere corrected half map 1 used in the final relion postprocess.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Ewald sphere corrected half map 2 used in...

Fileemd_12172_half_map_2.map
AnnotationEwald sphere corrected half map 2 used in the final relion postprocess.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Human rhinovirus 14

EntireName: Human rhinovirus 14
Components
  • Virus: Human rhinovirus 14
    • Complex: Rhinovirus
      • Protein or peptide: Genome polyprotein
      • Protein or peptide: Genome polyprotein
      • Protein or peptide: Genome polyprotein
      • Protein or peptide: Genome polyprotein
    • Complex: Intercellular adhesion molecule 1
      • Protein or peptide: Intercellular adhesion molecule 1
  • Ligand: water

-
Supramolecule #1: Human rhinovirus 14

SupramoleculeName: Human rhinovirus 14 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#5 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Molecular weightTheoretical: 10.0 MDa
Virus shellShell ID: 1 / Name: HRV14-ICAM-1 complex / Diameter: 325.0 Å / T number (triangulation number): 3

-
Supramolecule #2: Rhinovirus

SupramoleculeName: Rhinovirus / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#4
Source (natural)Organism: Human rhinovirus 14 / Strain: 1059

-
Supramolecule #3: Intercellular adhesion molecule 1

SupramoleculeName: Intercellular adhesion molecule 1 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #5
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: Genome polyprotein

MacromoleculeName: Genome polyprotein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: picornain 2A
Source (natural)Organism: Human rhinovirus 14
Molecular weightTheoretical: 32.975004 KDa
SequenceString: ALTEGLGDEL EEVIVEKTKQ TVASISSGPK HTQKVPILTA NETGATMPVL PSDSIETRTT YMHFNGSETD VECFLGRAAC VHVTEIQNK DATGIDNHRE AKLFNDWKIN LSSLVQLRKK LELFTYVRFD SEYTILATAS QPDSANYSSN LVVQAMYVPP G APNPKEWD ...String:
ALTEGLGDEL EEVIVEKTKQ TVASISSGPK HTQKVPILTA NETGATMPVL PSDSIETRTT YMHFNGSETD VECFLGRAAC VHVTEIQNK DATGIDNHRE AKLFNDWKIN LSSLVQLRKK LELFTYVRFD SEYTILATAS QPDSANYSSN LVVQAMYVPP G APNPKEWD DYTWQSASNP SVFFKVGDTS RFSVPYVGLA SAYNCFYDGY SHDDAETQYG ITVLNHMGSM AFRIVNEHDE HK TLVKIRV YHRAKHVEAW IPRAPRALPY TSIGRTNYPK NTEPVIKKRK GDIKSY

UniProtKB: Genome polyprotein

-
Macromolecule #2: Genome polyprotein

MacromoleculeName: Genome polyprotein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: picornain 2A
Source (natural)Organism: Human rhinovirus 14
Molecular weightTheoretical: 28.501361 KDa
SequenceString: SPNVEACGYS DRVQQITLGN STITTQEAAN AVVCYAEWPE YLPDVDASDV NKTSKPDTSV CRFYTLDSKT WTTGSKGWCW KLPDALKDM GVFGQNMFFH SLGRSGYTVH VQCNATKFHS GCLLVVVIPE HQLASHEGGN VSVKYTFTHP GERGIDLSSA N EVGGPVKD ...String:
SPNVEACGYS DRVQQITLGN STITTQEAAN AVVCYAEWPE YLPDVDASDV NKTSKPDTSV CRFYTLDSKT WTTGSKGWCW KLPDALKDM GVFGQNMFFH SLGRSGYTVH VQCNATKFHS GCLLVVVIPE HQLASHEGGN VSVKYTFTHP GERGIDLSSA N EVGGPVKD VIYNMNGTLL GNLLIFPHQF INLRTNNTAT IVIPYINSVP IDSMTRHNNV SLMVIPIAPL TVPTGATPSL PI TVTIAPM CTEFSGIRSK SIVPQ

UniProtKB: Genome polyprotein

-
Macromolecule #3: Genome polyprotein

MacromoleculeName: Genome polyprotein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: picornain 2A
Source (natural)Organism: Human rhinovirus 14
Molecular weightTheoretical: 26.236754 KDa
SequenceString: GLPTTTLPGS GQFLTTDDRQ SPSALPNYEP TPRIHIPGKV HNLLEIIQVD TLIPMNNTHT KDEVNSYLIP LNANRQNEQV FGTNLFIGD GVFKTTLLGE IVQYYTHWSG SLRFSLMYTG PALSSAKLIL AYTPPGARGP QDRREAMLGT HVVWDIGLQS T IVMTIPWT ...String:
GLPTTTLPGS GQFLTTDDRQ SPSALPNYEP TPRIHIPGKV HNLLEIIQVD TLIPMNNTHT KDEVNSYLIP LNANRQNEQV FGTNLFIGD GVFKTTLLGE IVQYYTHWSG SLRFSLMYTG PALSSAKLIL AYTPPGARGP QDRREAMLGT HVVWDIGLQS T IVMTIPWT SGVQFRYTDP DTYTSAGFLS CWYQTSLILP PETTGQVYLL SFISACPDFK LRLMKDTQTI SQTVALTE

UniProtKB: Genome polyprotein

-
Macromolecule #4: Genome polyprotein

MacromoleculeName: Genome polyprotein / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO / EC number: picornain 2A
Source (natural)Organism: Human rhinovirus 14
Molecular weightTheoretical: 7.183863 KDa
SequenceString:
GAQVSTQKSG SHENQNILTN GSNQTFTVIN YYKDAASTSS AGQSLSMDPS KFTEPVKDLM LKGAPALN

UniProtKB: Genome polyprotein

-
Macromolecule #5: Intercellular adhesion molecule 1

MacromoleculeName: Intercellular adhesion molecule 1 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 49.552004 KDa
Recombinant expressionOrganism: Baculovirus expression vector pFastBac1-HM
SequenceString: QTSVSPSKVI LPRGGSVLVT CSTSCDQPKL LGIETPLPKK ELLLPGNNRK VYELSNVQED SQPMCYSNCP DGQSTAKTFL TVYWTPERV ELAPLPSWQP VGKNLTLRCQ VEGGAPRANL TVVLLRGEKE LKREPAVGEP AEVTTTVLVR RDHHGANFSC R TELDLRPQ ...String:
QTSVSPSKVI LPRGGSVLVT CSTSCDQPKL LGIETPLPKK ELLLPGNNRK VYELSNVQED SQPMCYSNCP DGQSTAKTFL TVYWTPERV ELAPLPSWQP VGKNLTLRCQ VEGGAPRANL TVVLLRGEKE LKREPAVGEP AEVTTTVLVR RDHHGANFSC R TELDLRPQ GLELFENTSA PYQLQTFVLP ATPPQLVSPR VLEVDTQGTV VCSLDGLFPV SEAQVHLALG DQRLNPTVTY GN DSFSAKA SVSVTAEDEG TQRLTCAVIL GNQSQETLQT VTIYSFPAPN VILTKPEVSE GTEVTVKCEA HPRAKVTLNG VPA QPLGPR AQLLLKATPE DNGRSFSCSA TLEVAGQLIH KNQTRELRVL YGPRLDERDC PGNWTWPENS QQTPMCQAWG NPLP ELKCL KDGTFPLPIG ESVTVTRDLE GTYLCRARST QGEVTRKVTV NVLSPRYE

UniProtKB: Intercellular adhesion molecule 1

-
Macromolecule #6: water

MacromoleculeName: water / type: ligand / ID: 6 / Number of copies: 445 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.5 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
10.0 mMNa2HPO4disodium phosphate
1.8 mMKH2PO4monopotassium phosphate
137.0 mMNaClsodium chloride
2.7 mMKClpotassium chloride

Details: PBS
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 3 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 20 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 279.15 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 4680 / Average exposure time: 1.0 sec. / Average electron dose: 83.6 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated defocus max: 3.5620000000000003 µm / Calibrated defocus min: 0.42 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 75000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 36638
Startup model#0 - Type of model: PDB ENTRY
#0 - PDB model - PDB ID:

1d3i


#1 - Type of model: PDB ENTRY
#1 - PDB model - PDB ID:

4rhv

Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: I (icosahedral) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 12085
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final 3D classificationNumber classes: 3 / Avg.num./class: 4920 / Software - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelPDB ID:

4rhv


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 9.19 / Target criteria: Correlation coefficient
Output model

PDB-7bg7:
HRV14 in complex with its receptor ICAM-1

+
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