[English] 日本語
Yorodumi
- EMDB-7034: Improved cryoEM structure of human adenovirus type 5 with atomic ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-7034
TitleImproved cryoEM structure of human adenovirus type 5 with atomic details of minor proteins VI and VII
Map datahuman adenovirus type 5
SampleHuman adenovirus 5 != Human adenovirus C serotype 5

Human adenovirus 5

  • Virus: Human adenovirus C serotype 5
    • Protein or peptide: Hexon protein
    • Protein or peptide: Penton protein
    • Protein or peptide: Pre-hexon-linking protein IIIa
    • Protein or peptide: Pre-hexon-linking protein VIII
    • Protein or peptide: Hexon-interlacing protein
    • Protein or peptide: Pre-protein VI
    • Protein or peptide: Pre-histone-like nucleoprotein
    • Protein or peptide: Pre-protein VI
Function / homology
Function and homology information


hexon binding / protein transport along microtubule / viral capsid, decoration / T=25 icosahedral viral capsid / lysis of host organelle involved in viral entry into host cell / viral procapsid / host cell nucleolus / microtubule-dependent intracellular transport of viral material towards nucleus / adhesion receptor-mediated virion attachment to host cell / viral release from host cell ...hexon binding / protein transport along microtubule / viral capsid, decoration / T=25 icosahedral viral capsid / lysis of host organelle involved in viral entry into host cell / viral procapsid / host cell nucleolus / microtubule-dependent intracellular transport of viral material towards nucleus / adhesion receptor-mediated virion attachment to host cell / viral release from host cell / viral life cycle / viral penetration into host nucleus / viral capsid / clathrin-dependent endocytosis of virus by host cell / host cell cytoplasm / cell adhesion / symbiont entry into host cell / host cell nucleus / structural molecule activity / virion attachment to host cell / DNA binding / nucleus
Similarity search - Function
Adenoviral core protein VII / Adenoviral core protein VII / Pre-hexon-linking protein IIIa / Hexon-associated protein IX / Pre-hexon-linking protein IIIa, N-terminal / Hexon-associated protein (IIIa) / Adenovirus hexon-associated protein (IX) / Pre-hexon-linking protein VIII / Adenovirus hexon associated protein, protein VIII / Adenovirus Pll, hexon, subdomain 2 ...Adenoviral core protein VII / Adenoviral core protein VII / Pre-hexon-linking protein IIIa / Hexon-associated protein IX / Pre-hexon-linking protein IIIa, N-terminal / Hexon-associated protein (IIIa) / Adenovirus hexon-associated protein (IX) / Pre-hexon-linking protein VIII / Adenovirus hexon associated protein, protein VIII / Adenovirus Pll, hexon, subdomain 2 / Minor capsid protein VI / Minor capsid protein VI / Adenovirus hexon protein / Adenovirus Pll, hexon, N-terminal / Adenovirus Pll, hexon, C-terminal / Hexon, adenovirus major coat protein, N-terminal domain / Hexon, adenovirus major coat protein, C-terminal domain / Adenovirus penton base protein / Adenovirus penton base protein / Group II dsDNA virus coat/capsid protein / Adenoviral fibre protein, knob / Adenoviral fibre protein (knob domain) / Adenoviral fibre protein, repeat/shaft region / Adenoviral fibre protein (repeat/shaft region) / Adenovirus fibre protein / Attachment protein shaft domain superfamily / Adenovirus pIV-like, attachment domain
Similarity search - Domain/homology
Hexon-interlacing protein / Hexon protein / Pre-hexon-linking protein IIIa / Penton protein / Pre-hexon-linking protein VIII / Pre-protein VI / Pre-histone-like nucleoprotein / Fiber
Similarity search - Component
Biological speciesHAdV-5 (virus) / Human adenovirus C serotype 5
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsDai XH / Wu L / Sun R / Zhou ZH
Funding support United States, 7 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM071940 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI094386 United States
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)DE025567 United States
National Institutes of Health/Office of the Director1S10OD018111 United States
National Institutes of Health/National Center for Advancing Translational Sciences (NIH/NCATS)UL1TR001881 United States
National Science Foundation (NSF, United States)DBI-1338135 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1U24GM116792 United States
CitationJournal: J Virol / Year: 2017
Title: Atomic Structures of Minor Proteins VI and VII in Human Adenovirus.
Authors: Xinghong Dai / Lily Wu / Ren Sun / Z Hong Zhou /
Abstract: Human adenoviruses (Ad) are double-stranded DNA (dsDNA) viruses associated with infectious diseases, but they are better known as tools for gene delivery and oncolytic anticancer therapy. Atomic ...Human adenoviruses (Ad) are double-stranded DNA (dsDNA) viruses associated with infectious diseases, but they are better known as tools for gene delivery and oncolytic anticancer therapy. Atomic structures of Ad provide the basis for the development of antivirals and for engineering efforts toward more effective applications. Since 2010, atomic models of human Ad5 have been derived independently from photographic film cryo-electron microscopy (cryo-EM) and X-ray crystallography studies, but discrepancies exist concerning the assignment of cement proteins IIIa, VIII, and IX. To clarify these discrepancies, we employed the technology of direct electron counting to obtain a cryo-EM structure of human Ad5 at 3.2-Å resolution. Our improved structure unambiguously confirms our previous cryo-EM models of proteins IIIa, VIII, and IX and explains the likely cause of conflict in the crystallography models. The improved structure also allows the identification of three new components in the cavity of hexon-the cleaved N terminus of precursor protein VI (pVIn), the cleaved N terminus of precursor protein VII (pVIIn2), and mature protein VI. The binding of pVIIn2-and, by extension, that of genome-condensing pVII-to hexons is consistent with the previously proposed dsDNA genome-capsid coassembly for adenoviruses, which resembles that of single-stranded RNA (ssRNA) viruses but differs from the well-established mechanism of pumping dsDNA into a preformed protein capsid exemplified by tailed bacteriophages and herpesviruses. Adenovirus is a double-edged sword to humans: it is a widespread pathogen but can be used as a bioengineering tool for anticancer and gene therapies. The atomic structure of the virus provides the basis for antiviral and application developments, but conflicting atomic models for the important cement proteins IIIa, VIII, and IX from conventional/film cryo-EM and X-ray crystallography studies have caused confusion. Using cutting-edge cryo-EM technology with electron counting, we improved the structure of human adenovirus type 5 and confirmed our previous models of cement proteins IIIa, VIII, and IX, thus clarifying the inconsistent structures. The improved structure also reveals atomic details of membrane-lytic protein VI and genome-condensing protein VII and supports the previously proposed genome-capsid coassembly mechanism for adenoviruses.
History
DepositionSep 18, 2017-
Header (metadata) releaseSep 27, 2017-
Map releaseSep 27, 2017-
UpdateNov 27, 2019-
Current statusNov 27, 2019Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 3
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6b1t
  • Surface level: 3
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6b1t
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7034.png

Downloads & links

-
Map

FileDownload / File: emd_7034.map.gz / Format: CCP4 / Size: 7.8 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationhuman adenovirus type 5
Voxel sizeX=Y=Z: 0.85 Å
Density
Contour LevelBy AUTHOR: 3 / Movie #1: 3
Minimum - Maximum-11.581982 - 16.747877
Average (Standard dev.)0.004020501 (±0.87556183)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-640-640-640
Dimensions128012801280
Spacing128012801280
CellA=B=C: 1088.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.850.850.85
M x/y/z128012801280
origin x/y/z0.0000.0000.000
length x/y/z1088.0001088.0001088.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-640-640-640
NC/NR/NS128012801280
D min/max/mean-11.58216.7480.004

-
Supplemental data

-
Sample components

-
Entire : Human adenovirus 5

EntireName: Human adenovirus 5
Components
  • Virus: Human adenovirus C serotype 5
    • Protein or peptide: Hexon protein
    • Protein or peptide: Penton protein
    • Protein or peptide: Pre-hexon-linking protein IIIa
    • Protein or peptide: Pre-hexon-linking protein VIII
    • Protein or peptide: Hexon-interlacing protein
    • Protein or peptide: Pre-protein VI
    • Protein or peptide: Pre-histone-like nucleoprotein
    • Protein or peptide: Pre-protein VI

-
Supramolecule #1: Human adenovirus C serotype 5

SupramoleculeName: Human adenovirus C serotype 5 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Cultured in HEK293T cells and purified from media / NCBI-ID: 28285 / Sci species name: Human adenovirus C serotype 5 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 150 MDa
Virus shellShell ID: 1 / Name: capsid / Diameter: 900.0 Å / T number (triangulation number): 25

-
Macromolecule #1: Hexon protein

MacromoleculeName: Hexon protein / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: HAdV-5 (virus)
Molecular weightTheoretical: 108.107617 KDa
SequenceString: MATPSMMPQW SYMHISGQDA SEYLSPGLVQ FARATETYFS LNNKFRNPTV APTHDVTTDR SQRLTLRFIP VDREDTAYSY KARFTLAVG DNRVLDMAST YFDIRGVLDR GPTFKPYSGT AYNALAPKGA PNPCEWDEAA TALEINLEEE DDDNEDEVDE Q AEQQKTHV ...String:
MATPSMMPQW SYMHISGQDA SEYLSPGLVQ FARATETYFS LNNKFRNPTV APTHDVTTDR SQRLTLRFIP VDREDTAYSY KARFTLAVG DNRVLDMAST YFDIRGVLDR GPTFKPYSGT AYNALAPKGA PNPCEWDEAA TALEINLEEE DDDNEDEVDE Q AEQQKTHV FGQAPYSGIN ITKEGIQIGV EGQTPKYADK TFQPEPQIGE SQWYETEINH AAGRVLKKTT PMKPCYGSYA KP TNENGGQ GILVKQQNGK LESQVEMQFF STTEATAGNG DNLTPKVVLY SEDVDIETPD THISYMPTIK EGNSRELMGQ QSM PNRPNY IAFRDNFIGL MYYNSTGNMG VLAGQASQLN AVVDLQDRNT ELSYQLLLDS IGDRTRYFSM WNQAVDSYDP DVRI IENHG TEDELPNYCF PLGGVINTET LTKVKPKTGQ ENGWEKDATE FSDKNEIRVG NNFAMEINLN ANLWRNFLYS NIALY LPDK LKYSPSNVKI SDNPNTYDYM NKRVVAPGLV DCYINLGARW SLDYMDNVNP FNHHRNAGLR YRSMLLGNGR YVPFHI QVP QKFFAIKNLL LLPGSYTYEW NFRKDVNMVL QSSLGNDLRV DGASIKFDSI CLYATFFPMA HNTASTLEAM LRNDTND QS FNDYLSAANM LYPIPANATN VPISIPSRNW AAFRGWAFTR LKTKETPSLG SGYDPYYTYS GSIPYLDGTF YLNHTFKK V AITFDSSVSW PGNDRLLTPN EFEIKRSVDG EGYNVAQCNM TKDWFLVQML ANYNIGYQGF YIPESYKDRM YSFFRNFQP MSRQVVDDTK YKDYQQVGIL HQHNNSGFVG YLAPTMREGQ AYPANFPYPL IGKTAVDSIT QKKFLCDRTL WRIPFSSNFM SMGALTDLG QNLLYANSAH ALDMTFEVDP MDEPTLLYVL FEVFDVVRVH RPHRGVIETV YLRTPFSAGN ATT

-
Macromolecule #2: Penton protein

MacromoleculeName: Penton protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: HAdV-5 (virus)
Molecular weightTheoretical: 63.356602 KDa
SequenceString: MRRAAMYEEG PPPSYESVVS AAPVAAALGS PFDAPLDPPF VPPRYLRPTG GRNSIRYSEL APLFDTTRVY LVDNKSTDVA SLNYQNDHS NFLTTVIQNN DYSPGEASTQ TINLDDRSHW GGDLKTILHT NMPNVNEFMF TNKFKARVMV SRLPTKDNQV E LKYEWVEF ...String:
MRRAAMYEEG PPPSYESVVS AAPVAAALGS PFDAPLDPPF VPPRYLRPTG GRNSIRYSEL APLFDTTRVY LVDNKSTDVA SLNYQNDHS NFLTTVIQNN DYSPGEASTQ TINLDDRSHW GGDLKTILHT NMPNVNEFMF TNKFKARVMV SRLPTKDNQV E LKYEWVEF TLPEGNYSET MTIDLMNNAI VEHYLKVGRQ NGVLESDIGV KFDTRNFRLG FDPVTGLVMP GVYTNEAFHP DI ILLPGCG VDFTHSRLSN LLGIRKRQPF QEGFRITYDD LEGGNIPALL DVDAYQASLK DDTEQGGGGA GGSNSSGSGA EEN SNAAAA AMQPVEDMND HAIRGDTFAT RAEEKRAEAE AAAEAAAPAA QPEVEKPQKK PVIKPLTEDS KKRSYNLISN DSTF TQYRS WYLAYNYGDP QTGIRSWTLL CTPDVTCGSE QVYWSLPDMM QDPVTFRSTR QISNFPVVGA ELLPVHSKSF YNDQA VYSQ LIRQFTSLTH VFNRFPENQI LARPPAPTIT TVSENVPALT DHGTLPLRNS IGGVQRVTIT DARRRTCPYV YKALGI VSP RVLSSRTF

-
Macromolecule #3: Pre-hexon-linking protein IIIa

MacromoleculeName: Pre-hexon-linking protein IIIa / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: HAdV-5 (virus)
Molecular weightTheoretical: 65.322805 KDa
SequenceString: MMQDATDPAV RAALQSQPSG LNSTDDWRQV MDRIMSLTAR NPDAFRQQPQ ANRLSAILEA VVPARANPTH EKVLAIVNAL AENRAIRPD EAGLVYDALL QRVARYNSGN VQTNLDRLVG DVREAVAQRE RAQQQGNLGS MVALNAFLST QPANVPRGQE D YTNFVSAL ...String:
MMQDATDPAV RAALQSQPSG LNSTDDWRQV MDRIMSLTAR NPDAFRQQPQ ANRLSAILEA VVPARANPTH EKVLAIVNAL AENRAIRPD EAGLVYDALL QRVARYNSGN VQTNLDRLVG DVREAVAQRE RAQQQGNLGS MVALNAFLST QPANVPRGQE D YTNFVSAL RLMVTETPQS EVYQSGPDYF FQTSRQGLQT VNLSQAFKNL QGLWGVRAPT GDRATVSSLL TPNSRLLLLL IA PFTDSGS VSRDTYLGHL LTLYREAIGQ AHVDEHTFQE ITSVSRALGQ EDTGSLEATL NYLLTNRRQK IPSLHSLNSE EER ILRYVQ QSVSLNLMRD GVTPSVALDM TARNMEPGMY ASNRPFINRL MDYLHRAAAV NPEYFTNAIL NPHWLPPPGF YTGG FEVPE GNDGFLWDDI DDSVFSPQPQ TLLELQQREQ AEAALRKESF RRPSSLSDLG AAAPRSDASS PFPSLIGSLT STRTT RPRL LGEEEYLNNS LLQPQREKNL PPAFPNNGIE SLVDKMSRWK TYAQEHRDVP GPRPPTRRQR HDRQRGLVWE DDDSAD DSS VLDLGGSGNP FAHLRPRLGR MF

-
Macromolecule #4: Pre-hexon-linking protein VIII

MacromoleculeName: Pre-hexon-linking protein VIII / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: HAdV-5 (virus)
Molecular weightTheoretical: 24.71059 KDa
SequenceString: MSKEIPTPYM WSYQPQMGLA AGAAQDYSTR INYMSAGPHM ISRVNGIRAH RNRILLEQAA ITTTPRNNLN PRSWPAALVY QESPAPTTV VLPRDAQAEV QMTNSGAQLA GGFRHRVRSP GQGITHLTIR GRGIQLNDES VSSSLGLRPD GTFQIGGAGR P SFTPRQAI ...String:
MSKEIPTPYM WSYQPQMGLA AGAAQDYSTR INYMSAGPHM ISRVNGIRAH RNRILLEQAA ITTTPRNNLN PRSWPAALVY QESPAPTTV VLPRDAQAEV QMTNSGAQLA GGFRHRVRSP GQGITHLTIR GRGIQLNDES VSSSLGLRPD GTFQIGGAGR P SFTPRQAI LTLQTSSSEP RSGGIGTLQF IEEFVPSVYF NPFSGPPGHY PDQFIPNFDA VKDSADGYD

-
Macromolecule #5: Hexon-interlacing protein

MacromoleculeName: Hexon-interlacing protein / type: protein_or_peptide / ID: 5 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: HAdV-5 (virus)
Molecular weightTheoretical: 14.468134 KDa
SequenceString:
MSTNSFDGSI VSSYLTTRMP PWAGVRQNVM GSSIDGRPVL PANSTTLTYE TVSGTPLETA ASAAASAAAA TARGIVTDFA FLSPLASSA ASRSSARDDK LTALLAQLDS LTRELNVVSQ QLLDLRQQVS ALKASSPPNA V

-
Macromolecule #6: Pre-protein VI

MacromoleculeName: Pre-protein VI / type: protein_or_peptide / ID: 6 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: HAdV-5 (virus)
Molecular weightTheoretical: 3.584953 KDa
SequenceString:
MEDINFASLA PRHGSRPFMG NWQDIGTSNM SGG

-
Macromolecule #7: Pre-histone-like nucleoprotein

MacromoleculeName: Pre-histone-like nucleoprotein / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: HAdV-5 (virus)
Molecular weightTheoretical: 1.198438 KDa
SequenceString:
GLRFPSKMFG G

-
Macromolecule #8: Pre-protein VI

MacromoleculeName: Pre-protein VI / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: HAdV-5 (virus)
Molecular weightTheoretical: 23.460559 KDa
SequenceString: AFSWGSLWSG IKNFGSTVKN YGSKAWNSST GQMLRDKLKE QNFQQKVVDG LASGISGVVD LANQAVQNKI NSKLDPRPPV EEPPPAVET VSPEGRGEKR PRPDREETLV TQIDEPPSYE EALKQGLPTT RPIAPMATGV LGQHTPVTLD LPPPADTQQK P VLPGPTAV ...String:
AFSWGSLWSG IKNFGSTVKN YGSKAWNSST GQMLRDKLKE QNFQQKVVDG LASGISGVVD LANQAVQNKI NSKLDPRPPV EEPPPAVET VSPEGRGEKR PRPDREETLV TQIDEPPSYE EALKQGLPTT RPIAPMATGV LGQHTPVTLD LPPPADTQQK P VLPGPTAV VVTRPSRASL RRAASGPRSL RPVASGNWQS TLNSIVGLGV QSLKRRRCF

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
Component:
ConcentrationFormulaName
20.0 mMC4H11NO3Tris-HClTris
150.0 mMNaClSodium chloridesodium chloride
1.0 mMMgCl2magnesium chloride
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK II
DetailsPurified virion

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 81000
Specialist opticsEnergy filter - Name: Gatan Image Filter / Energy filter - Lower energy threshold: 0 eV / Energy filter - Upper energy threshold: 20 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
TemperatureMin: 80.0 K
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Dimensions - Width: 7676 pixel / Digitization - Dimensions - Height: 7420 pixel / Digitization - Sampling interval: 2.5 µm / Digitization - Frames/image: 2-32 / Number grids imaged: 1 / Number real images: 5608 / Average exposure time: 9.0 sec. / Average electron dose: 25.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Particle selectionNumber selected: 96375
CTF correctionSoftware - Name: CTFFIND3
Startup modelType of model: EMDB MAP
EMDB ID:

5172
EMDB Unreleased entry

Initial angle assignmentType: COMMON LINE / Software - Name: IMIRS
Final angle assignmentType: COMMON LINE / Software - Name: IMIRS
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: eLite3D / Number images used: 53000

-
Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: Correlation coefficient
Output model

PDB-3izo:
Model of the fiber tail and its interactions with the penton base of human adenovirus by cryo-electron microscopy

PDB-6b1t:
Improved cryoEM structure of human adenovirus type 5 with atomic details of minor proteins VI and VII

+
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