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- EMDB-0436: Near-atomic structure of icosahedrally averaged PBCV-1 capsid -

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Basic information

Entry
Database: EMDB / ID: EMD-0436
TitleNear-atomic structure of icosahedrally averaged PBCV-1 capsid
Map dataicosahedrally averaged PBCV-1 capsid
Sample
  • Virus: Paramecium bursaria Chlorella virus 1
    • Protein or peptide: x 15 types
Function / homology
Function and homology information


viral capsid / membrane => GO:0016020 / structural molecule activity / membrane
Similarity search - Function
Protein of unknown function DUF5762 / Protein of unknown function DUF5761 / Domain of unknown function DUF5899 / Family of unknown function (DUF5761) / Family of unknown function (DUF5762) / Family of unknown function (DUF5899) / Major capsid protein, N-terminal / Major capsid protein N-terminus / Major capsid protein, C-terminal / Major capsid protein, C-terminal domain superfamily ...Protein of unknown function DUF5762 / Protein of unknown function DUF5761 / Domain of unknown function DUF5899 / Family of unknown function (DUF5761) / Family of unknown function (DUF5762) / Family of unknown function (DUF5899) / Major capsid protein, N-terminal / Major capsid protein N-terminus / Major capsid protein, C-terminal / Major capsid protein, C-terminal domain superfamily / Large eukaryotic DNA virus major capsid protein / Group II dsDNA virus coat/capsid protein
Similarity search - Domain/homology
Uncharacterized protein / Capsid protein / Major capsid protein / Uncharacterized protein / PsbP C-terminal domain-containing protein / Uncharacterized protein / Uncharacterized protein / DUF5899 domain-containing protein / Uncharacterized protein / SAYSvFN domain-containing protein ...Uncharacterized protein / Capsid protein / Major capsid protein / Uncharacterized protein / PsbP C-terminal domain-containing protein / Uncharacterized protein / Uncharacterized protein / DUF5899 domain-containing protein / Uncharacterized protein / SAYSvFN domain-containing protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Capsid protein / Uncharacterized protein
Similarity search - Component
Biological speciesPBCV-1 (virus) / Paramecium bursaria Chlorella virus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsFang Q / Rossmann MG
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI011219 United States
CitationJournal: Nat Commun / Year: 2019
Title: Near-atomic structure of a giant virus.
Authors: Qianglin Fang / Dongjie Zhu / Irina Agarkova / Jagat Adhikari / Thomas Klose / Yue Liu / Zhenguo Chen / Yingyuan Sun / Michael L Gross / James L Van Etten / Xinzheng Zhang / Michael G Rossmann /
Abstract: Although the nucleocytoplasmic large DNA viruses (NCLDVs) are one of the largest group of viruses that infect many eukaryotic hosts, the near-atomic resolution structures of these viruses have ...Although the nucleocytoplasmic large DNA viruses (NCLDVs) are one of the largest group of viruses that infect many eukaryotic hosts, the near-atomic resolution structures of these viruses have remained unknown. Here we describe a 3.5 Å resolution icosahedrally averaged capsid structure of Paramecium bursaria chlorella virus 1 (PBCV-1). This structure consists of 5040 copies of the major capsid protein, 60 copies of the penton protein and 1800 minor capsid proteins of which there are 13 different types. The minor capsid proteins form a hexagonal network below the outer capsid shell, stabilizing the capsid by binding neighboring capsomers together. The size of the viral capsid is determined by a tape-measure, minor capsid protein of which there are 60 copies in the virion. Homologs of the tape-measure protein and some of the other minor capsid proteins exist in other NCLDVs. Thus, a similar capsid assembly pathway might be used by other NCLDVs.
History
DepositionDec 11, 2018-
Header (metadata) releaseJan 30, 2019-
Map releaseJan 30, 2019-
UpdateDec 18, 2019-
Current statusDec 18, 2019Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 10
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 10
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6ncl
  • Surface level: 10
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6ncl
  • Surface level: 10
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6ncl
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_0436.map.gz / Format: CCP4 / Size: 6.4 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationicosahedrally averaged PBCV-1 capsid
Voxel sizeX=Y=Z: 1.62 Å
Density
Contour LevelBy AUTHOR: 7 / Movie #1: 10
Minimum - Maximum-56.025837 - 69.6044
Average (Standard dev.)0.028372684 (±2.7627811)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-600-600-600
Dimensions120012001200
Spacing120012001200
CellA=B=C: 1944.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.621.621.62
M x/y/z120012001200
origin x/y/z0.0000.0000.000
length x/y/z1944.0001944.0001944.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-600-600-600
NC/NR/NS120012001200
D min/max/mean-56.02669.6040.028

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Supplemental data

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Sample components

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Entire : Paramecium bursaria Chlorella virus 1

EntireName: Paramecium bursaria Chlorella virus 1
Components
  • Virus: Paramecium bursaria Chlorella virus 1
    • Protein or peptide: P14
    • Protein or peptide: P9
    • Protein or peptide: P10
    • Protein or peptide: P7
    • Protein or peptide: P6
    • Protein or peptide: P1
    • Protein or peptide: P12
    • Protein or peptide: P5
    • Protein or peptide: P11
    • Protein or peptide: P2
    • Protein or peptide: P4
    • Protein or peptide: P3
    • Protein or peptide: P8
    • Protein or peptide: Major capsid protein
    • Protein or peptide: P13

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Supramolecule #1: Paramecium bursaria Chlorella virus 1

SupramoleculeName: Paramecium bursaria Chlorella virus 1 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 10506 / Sci species name: Paramecium bursaria Chlorella virus 1 / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No

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Macromolecule #1: P14

MacromoleculeName: P14 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: PBCV-1 (virus)
Molecular weightTheoretical: 38.502719 KDa
SequenceString: MQTPSIIQCG LLNSFARKMT DAISDNQIIA TSRFFNIARD VADVVVSNTK LAQQYEQLSI DSLKEYLVSV AKFVAVDYSN TTSADVDDL IHKLRLFIEE ECYQYNIDKE ETCDGDVCVS DEYNEPAPKP KPKPKPKPAP KPKPAPKPKP APKPAPKPAP K PAPKPAPK ...String:
MQTPSIIQCG LLNSFARKMT DAISDNQIIA TSRFFNIARD VADVVVSNTK LAQQYEQLSI DSLKEYLVSV AKFVAVDYSN TTSADVDDL IHKLRLFIEE ECYQYNIDKE ETCDGDVCVS DEYNEPAPKP KPKPKPKPAP KPKPAPKPKP APKPAPKPAP K PAPKPAPK PAPKPAPKPA PEPAPEPAPE PAPKPAPEPA PEPAPIRPAR RCDENPSNLE TCCTNKALYG DFTDSSCDIV KK KTNWWLW GGIAILVIVL MIGGYFIYKR YFSAPKFENT GEFVNDMNFN NDVNFNNDVN FDNDMNYGNE GIDVSDLEIL NLP VPSVSP VPSASIVPSV SPIPRGSPVP SASPIK

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Macromolecule #2: P9

MacromoleculeName: P9 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: PBCV-1 (virus)
Molecular weightTheoretical: 23.407564 KDa
SequenceString: MKTETLYQDP VWFQDLSVIF KRPSEIIPTR DQSDSERINA MVRLVLYCSF AVALIRQNYL YAILGLAIIA IISLAYALGA KKTKSNEAY GNIRPYSVKR SKKSCSKSSA NNPFSNATVG ALLDNEARPP ACSYDDNDMA STMRKNFNKG LFRNLDDVYE V ENSQRQFY ...String:
MKTETLYQDP VWFQDLSVIF KRPSEIIPTR DQSDSERINA MVRLVLYCSF AVALIRQNYL YAILGLAIIA IISLAYALGA KKTKSNEAY GNIRPYSVKR SKKSCSKSSA NNPFSNATVG ALLDNEARPP ACSYDDNDMA STMRKNFNKG LFRNLDDVYE V ENSQRQFY TMPVTTAAPD LTAFGQFLYG SKGKTCKEDP SACTPAFATR DG

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Macromolecule #3: P10

MacromoleculeName: P10 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: PBCV-1 (virus)
Molecular weightTheoretical: 31.2236 KDa
SequenceString: MMNFILVLLI VAMIGTILVS ESKYLFSKPV CKNCGVKAVT LPVDISAGKL AKVAEAVKKQ TEEIKTLLKQ KQSAPKAPEL TNPIEHIKA STTVVSGANG LENVIDEDLP FSDFKGVPVA ETTVEGMIKG IRPPTYADPR VMNPALAAAP VQFSDPTQFG T FGVTDDVS ...String:
MMNFILVLLI VAMIGTILVS ESKYLFSKPV CKNCGVKAVT LPVDISAGKL AKVAEAVKKQ TEEIKTLLKQ KQSAPKAPEL TNPIEHIKA STTVVSGANG LENVIDEDLP FSDFKGVPVA ETTVEGMIKG IRPPTYADPR VMNPALAAAP VQFSDPTQFG T FGVTDDVS PAFSTEDKIP KTNAKISSDI SVEGYENSYD ANGARLVMDG KVVKSECQLP SYQIRNSKHH TQLPMRSLNE PP PMVEDLV DESLFEGLQG YPVDEKLDLL TPPGTATPSS EWAAINYGLT NN

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Macromolecule #4: P7

MacromoleculeName: P7 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: PBCV-1 (virus)
Molecular weightTheoretical: 29.505855 KDa
SequenceString: MQIYSEYYEK IGPRKLRLLV KRRLLFASTW LYINNYILLS IIMKLQTKHM ILLGFVAVVV VFIIFMLTRK KKEGFSIGNI FGKVKGAVT GTVGKVVNVV KPQGYKPEFV NRVNFGKFWA CPEGTTDWGS EDKQCLVSQY GPMMWRNKGG NEWGWSCPAG S APNNSDDW ...String:
MQIYSEYYEK IGPRKLRLLV KRRLLFASTW LYINNYILLS IIMKLQTKHM ILLGFVAVVV VFIIFMLTRK KKEGFSIGNI FGKVKGAVT GTVGKVVNVV KPQGYKPEFV NRVNFGKFWA CPEGTTDWGS EDKQCLVSQY GPMMWRNKGG NEWGWSCPAG S APNNSDDW NQKCVQGYSM KKLIDGQWRC TDTEIDTGKD WSNSDWFTAQ QQCDRGNNKV FTRRMYIDGK WQCPDGTWDT GF TWSDGEN GGKQCKYYP

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Macromolecule #5: P6

MacromoleculeName: P6 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: PBCV-1 (virus)
Molecular weightTheoretical: 24.036729 KDa
SequenceString: MILVGIAVLI LLAVFAILYY KQKEKFVVVG KFVEPIPSNP GQDFTLLPMD QTYTFADPVP DTATAFDVVL SRFTDKKAPA DLLKGATFP EAAPYTDSEV ENISKLALSR VKGPDAPVLS FISVEYAAKG VDNKKNTHYD IAFMVYDQVK NFSLKLVLVA V LDAKNKLW ...String:
MILVGIAVLI LLAVFAILYY KQKEKFVVVG KFVEPIPSNP GQDFTLLPMD QTYTFADPVP DTATAFDVVL SRFTDKKAPA DLLKGATFP EAAPYTDSEV ENISKLALSR VKGPDAPVLS FISVEYAAKG VDNKKNTHYD IAFMVYDQVK NFSLKLVLVA V LDAKNKLW IKKFSSFNSF TPKDKGPKGV ENIDETPLAE FIPDFVQFSR LYKDNANV

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Macromolecule #6: P1

MacromoleculeName: P1 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: PBCV-1 (virus)
Molecular weightTheoretical: 18.281664 KDa
SequenceString:
MVETTQHFVS IESSNRPDPA NTTPANYSIQ LPQRYRNIWS AMLVNIALPA VSPPQKYVYL DIDKLNSIDS TSPSGGVNFA LAKIPLSIA GTGNVFFADT MTSSFPNVPL QNPVATMDKL NIKLKDANGN VLTIPAGNEH SFMIQLTCGD YIPRGGGSTI T QNGRVLGG TR

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Macromolecule #7: P12

MacromoleculeName: P12 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: PBCV-1 (virus)
Molecular weightTheoretical: 17.715475 KDa
SequenceString:
MGNGPPMERA VSSDDILTYY NTFIFFIYFN FTNENIYIIY TIYMKVQNTI VYIVLLLIVV VIIWNFTRKE GWSDYNAPND FMKIYYSNI VEDKKLAEKY PFFGTGPFTG LRCRKPNNVG CNTTWVSGQL VELTPKLKEQ IECKFGIQYV KT

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Macromolecule #8: P5

MacromoleculeName: P5 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: PBCV-1 (virus)
Molecular weightTheoretical: 16.455834 KDa
SequenceString:
MDSRLSAAYA IRAARISMIP GGVDGLVINY AEGGEPAWVQ YPLKKQKPLP NNLCYTPTLE DIARKREAVI AKYTKQPLET GTTFTHVLN ASHLNEQYTR VKKSALPDKE FPIIETEKYP EPPILWETTI GAPSRLFDRS DGVKYVR

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Macromolecule #9: P11

MacromoleculeName: P11 / type: protein_or_peptide / ID: 9 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: PBCV-1 (virus)
Molecular weightTheoretical: 23.322656 KDa
SequenceString: MDMHMIVKVV AILAVLFLVY KLWESMNKPN ASPLKIQNPY EKYMNSAEGG EYDAEDDDIY YPETDAEDDD IYTGETDDMY DGEDDDIYV QEGDDIEDAE DEPYDDSADM EQDVPKVQQP MMPLLTPSSQ LLPKPSPEAA DFAQFAPKNL QAQNFLTATQ W IGVNTQGS ...String:
MDMHMIVKVV AILAVLFLVY KLWESMNKPN ASPLKIQNPY EKYMNSAEGG EYDAEDDDIY YPETDAEDDD IYTGETDDMY DGEDDDIYV QEGDDIEDAE DEPYDDSADM EQDVPKVQQP MMPLLTPSSQ LLPKPSPEAA DFAQFAPKNL QAQNFLTATQ W IGVNTQGS SLKNANYDLR ADPIIPKADV GPWMMSSVDP NIYQKPLFG

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Macromolecule #10: P2

MacromoleculeName: P2 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: PBCV-1 (virus)
Molecular weightTheoretical: 63.888082 KDa
SequenceString: MCNTYYKRVK FNLFLYTNSI EMELLAVASI IGYGLFSSQQ GRETRPDRNR YAEALGSGQG LDEDYDVKPT DMVRKYRKKA EKRWKKAQV PKESGIITPN MRPSEVMPYF TSGKSMNTNT DYKQRKMELF TGGVLDGHSV SGTYKHKVEA ANMFGMTPQG R VTSDGTVG ...String:
MCNTYYKRVK FNLFLYTNSI EMELLAVASI IGYGLFSSQQ GRETRPDRNR YAEALGSGQG LDEDYDVKPT DMVRKYRKKA EKRWKKAQV PKESGIITPN MRPSEVMPYF TSGKSMNTNT DYKQRKMELF TGGVLDGHSV SGTYKHKVEA ANMFGMTPQG R VTSDGTVG NAPGDTELLK ARSVNSHQYN NVLPTEQLRV GPGLGVGPEV AATGGFHQFY RQLPLNINEY KLTQLPGRLV PG GTTTGGK GEIQQIASVN HNPDALVLNY DDRPPEATPN GAILASTQYG KQPRGYAGLR PYEKNYEGIA EADVSALQAR YLD QTRGRP RTGDGDTEPI INPNGERDGT GSYVTENMCS MTLESQRGLV NRYITPPGVT GVVQQGGEMR PEFVPETTIR EQYE DIYYT GPAGTTVTPT EPMNVVELQP ESRHAKRAGQ DRAYTPGAGR VNNFAPAAQG AYGLKDHPTY NALQHVVSEP IEQTF LPAA QGDDDRFGTK SNVNNPWGNP ASLQIANNQL AANKFNRDVT NTVNLDYDAG QPMKQQNFQP KAWIPNNTDD MKMLPL WKR KQLQAQKNKQ QRK

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Macromolecule #11: P4

MacromoleculeName: P4 / type: protein_or_peptide / ID: 11 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: PBCV-1 (virus)
Molecular weightTheoretical: 20.637311 KDa
SequenceString:
MFSAFRDTAS IGFSDTHQDE KTLRFLKKQI SQFIKHLKEY YPNNELTKKL VMKYSDVQLL PYTKGATKDT YTSGLFDHTT GVIKIAPRD GLGNVRDEQS LNKSICHELA HGTRVKYPGE SSHSDEWKDA WKTFLKIAAD ELGWKIEVPC SSVSFYGLTK D DCENCVWD QDPETCPKTA KLA

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Macromolecule #12: P3

MacromoleculeName: P3 / type: protein_or_peptide / ID: 12 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: PBCV-1 (virus)
Molecular weightTheoretical: 19.116688 KDa
SequenceString:
MAMKTQRKEN VLFQNVKPRE IPLVDNPFST YPYKHVITET QPTQAKNQAI WGLVQMGLSG EAAAMYGDVV VQKTTRACRK SEGGFKDVN TELWGTSPYL GRGDGEVYNM PASNQLLRGF ESSLRGSRVR TQIDDKSFIP YTWQMIDVPL AAAKTSFIAG L DTRQQLAY GNP

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Macromolecule #13: P8

MacromoleculeName: P8 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: PBCV-1 (virus)
Molecular weightTheoretical: 19.226947 KDa
SequenceString:
METIGNFIQN MAFPTENPYK LSGDFGNSTL EPTVTAALRI LHESPAPFNT EFFSRKNVDF IQKKLISETK RYTSFDIGPQ NEDELIMMM AGIYVQDSTF DGNIKAGLRK LNTLVITECL KQILPGVRAY ALYVRDASLP FSGGGEEAFK RPELATLKGS K VLSGFLPL DRNAS

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Macromolecule #14: Major capsid protein

MacromoleculeName: Major capsid protein / type: protein_or_peptide / ID: 14 / Number of copies: 84 / Enantiomer: LEVO
Source (natural)Organism: PBCV-1 (virus)
Molecular weightTheoretical: 48.199625 KDa
SequenceString: MAGGLSQLVA YGAQDVYLTG NPQITFFKTV YRRYTNFAIE SIQQTINGSV GFGNKVSTQI SRNGDLITDI VVEFVLTKGG NGGTTYYPA EELLQDVELE IGGQRIDKHY NDWFRTYDAL FRMNDDRYNY RRMTDWVNNE LVGAQKRFYV PLIFFFNQTP G LALPLIAL ...String:
MAGGLSQLVA YGAQDVYLTG NPQITFFKTV YRRYTNFAIE SIQQTINGSV GFGNKVSTQI SRNGDLITDI VVEFVLTKGG NGGTTYYPA EELLQDVELE IGGQRIDKHY NDWFRTYDAL FRMNDDRYNY RRMTDWVNNE LVGAQKRFYV PLIFFFNQTP G LALPLIAL QYHEVKLYFT LASQVQGVNY NGSSAIAGAA QPTMSVWVDY IFLDTQERTR FAQLPHEYLI EQLQFTGSET AT PSATTQA SQNIRLNFNH PTKYLAWNFN NPTNYGQYTA LANIPGACSG AGTAAATVTT PDYGNTGTYN EQLAVLDSAK IQL NGQDRF ATRKGSYFNK VQPYQSIGGV TPAGVYLYSF ALKPAGRQPS GTCNFSRIDN ATLSLTYKTC SIDATSPAAV LGNT ETVTA NTATLLTALN IYAKNYNVLR IMSGMGGLAY AN

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Macromolecule #15: P13

MacromoleculeName: P13 / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: PBCV-1 (virus)
Molecular weightTheoretical: 11.07083 KDa
SequenceString:
MHKITPFLIA AVVAVIVLAV WLFKKDNKKE TWFSRDLNYG KANSKIWNAT VAKGLKGIAN ENAEIRKMYP YLGYGDFTGA ICKGPNNQG CTYYANYTR

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.8
GridSupport film - Material: CARBON / Support film - topology: LACEY / Details: unspecified
VitrificationCryogen name: ETHANE / Chamber humidity: 85 % / Instrument: GATAN CRYOPLUNGE 3

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 24.4 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 13000

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