[English] 日本語
Yorodumi
- EMDB-43588: The base complex of the AcMNPV baculovirus nucleocapsid (Class 1,... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-43588
TitleThe base complex of the AcMNPV baculovirus nucleocapsid (Class 1, localised reconstruction)
Map datasharpened map
Sample
  • Virus: Autographa californica multiple nucleopolyhedrovirus
    • Protein or peptide: Major capsid protein
    • Protein or peptide: Capsid-associated protein VP80
    • Protein or peptide: Occlusion-derived virus envelope protein E27
    • Protein or peptide: Protein C42
    • Protein or peptide: Protein AC109
    • Protein or peptide: Protein AC142
    • Protein or peptide: 38K (AC98) protein in P143-LEF5 intergenic region
  • Ligand: ZINC ION
KeywordsNucleocapsid / Base / baculovirus / virus / AcMNPV / VP39 / VIRAL PROTEIN
Function / homology
Function and homology information


transport of viral material towards nucleus / exit of virus from host cell nucleus by nuclear egress / host cell nuclear matrix / symbiont-mediated perturbation of host cell cycle progression / nuclear capsid assembly / virion component / viral capsid / host cell / viral nucleocapsid / host cell cytoplasm ...transport of viral material towards nucleus / exit of virus from host cell nucleus by nuclear egress / host cell nuclear matrix / symbiont-mediated perturbation of host cell cycle progression / nuclear capsid assembly / virion component / viral capsid / host cell / viral nucleocapsid / host cell cytoplasm / viral envelope / host cell nucleus / virion membrane / structural molecule activity / protein homodimerization activity / DNA binding / membrane
Similarity search - Function
Protein of unknown function DUF694 / Protein of unknown function (DUF705) / Baculovirus Y142 protein / Autographa californica nuclear polyhedrosis virus (AcMNPV), Orf109 / Nucleopolyhedrovirus capsid P80/P87 / Baculovirus Y142 protein / Autographa californica nuclear polyhedrosis virus (AcMNPV) protein / Nucleopolyhedrovirus capsid protein P87 / HAD-superfamily phosphatase, subfamily IIIC / Baculovirus occlusion-derived virus envelope EC27 ...Protein of unknown function DUF694 / Protein of unknown function (DUF705) / Baculovirus Y142 protein / Autographa californica nuclear polyhedrosis virus (AcMNPV), Orf109 / Nucleopolyhedrovirus capsid P80/P87 / Baculovirus Y142 protein / Autographa californica nuclear polyhedrosis virus (AcMNPV) protein / Nucleopolyhedrovirus capsid protein P87 / HAD-superfamily phosphatase, subfamily IIIC / Baculovirus occlusion-derived virus envelope EC27 / Baculovirus occlusion-derived virus envelope protein EC27 / Autographa californica nuclear polyhedrosis virus (AcMNPV), C42 / Autographa californica nuclear polyhedrosis virus (AcMNPV), Orf101 / Baculovirus major capsid protein VP39 / Baculovirus major capsid protein VP39 / HAD superfamily / HAD-like superfamily
Similarity search - Domain/homology
Major capsid protein / Uncharacterized 38.0 kDa protein in P143-LEF5 intergenic region / Protein C42 / Protein AC109 / Protein AC142 / Occlusion-derived virus envelope protein E27 / Capsid-associated protein VP80
Similarity search - Component
Biological speciesAutographa californica multiple nucleopolyhedrovirus
Methodsingle particle reconstruction / cryo EM / Resolution: 4.71 Å
AuthorsJohnstone BA / Koszalka P / Ha J / Venugopal H / Coulibaly F
Funding support Australia, 1 items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP210103388 Australia
CitationJournal: To Be Published
Title: The baculovirus structure defines the hallmarks of a new viral realm
Authors: Johnstone BA / Hardy JM / Ha J / Butkovic A / Koszalka P / Accurso C / Venugopal H / de Marco A / Krupovic M / Coulibaly F
History
DepositionFeb 1, 2024-
Header (metadata) releaseNov 6, 2024-
Map releaseNov 6, 2024-
UpdateNov 27, 2024-
Current statusNov 27, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_43588.png

Downloads & links

-
Map

FileDownload / File: emd_43588.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.41 Å/pix.
x 384 pix.
= 541.44 Å		1.41 Å/pix.
x 384 pix.
= 541.44 Å		1.41 Å/pix.
x 384 pix.
= 541.44 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.41 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.298
Minimum - Maximum-0.8799768 - 1.5842398
Average (Standard dev.)0.00082013314 (±0.076941736)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 541.44 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_43588_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: raw unsharpened map

Fileemd_43588_additional_1.map
Annotationraw unsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half Map B

Fileemd_43588_half_map_1.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half Map A

Fileemd_43588_half_map_2.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Autographa californica multiple nucleopolyhedrovirus

EntireName: Autographa californica multiple nucleopolyhedrovirus
Components
  • Virus: Autographa californica multiple nucleopolyhedrovirus
    • Protein or peptide: Major capsid protein
    • Protein or peptide: Capsid-associated protein VP80
    • Protein or peptide: Occlusion-derived virus envelope protein E27
    • Protein or peptide: Protein C42
    • Protein or peptide: Protein AC109
    • Protein or peptide: Protein AC142
    • Protein or peptide: 38K (AC98) protein in P143-LEF5 intergenic region
  • Ligand: ZINC ION

-
Supramolecule #1: Autographa californica multiple nucleopolyhedrovirus

SupramoleculeName: Autographa californica multiple nucleopolyhedrovirus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#7
Details: Recombinant AcMNPV (BacToBac, Invitrogen) viruses containing the Bombyx mori cytoplasmic virus polyhedrin gene were amplified in Sf9 cells in suspension culture.
NCBI-ID: 307456
Sci species name: Autographa californica multiple nucleopolyhedrovirus
Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: Yes / Virus empty: No
Host (natural)Organism: Lepidoptera (butterflies and moths)
Virus shellShell ID: 1 / Name: Nucleocapsid / Diameter: 500.0 Å

-
Macromolecule #1: Major capsid protein

MacromoleculeName: Major capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Autographa californica multiple nucleopolyhedrovirus
Molecular weightTheoretical: 38.991109 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MALVPVGMAP RQMRVNRCIF ASIVSFDACI TYKSPCSPDA YHDDGWFICN NHLIKRFKMS KMVLPIFDED DNQFKMTIAR HLVGNKERG IKRILIPSAT NYQDVFNLNS MMQAEQLIFH LIYNNENAVN TICDNLKYTE GFTSNTQRVI HSVYATTKSI L DTTNPNTF ...String:
MALVPVGMAP RQMRVNRCIF ASIVSFDACI TYKSPCSPDA YHDDGWFICN NHLIKRFKMS KMVLPIFDED DNQFKMTIAR HLVGNKERG IKRILIPSAT NYQDVFNLNS MMQAEQLIFH LIYNNENAVN TICDNLKYTE GFTSNTQRVI HSVYATTKSI L DTTNPNTF CSRVSRDELR FFDVTNARAL RGGAGDQLFN NYSGFLQNLI RRAVAPEYLQ IDTEELRFRN CATCIIDETG LV ASVPDGP ELYNPIRSSD IMRSQPNRLQ IRNVLKFEGD TRELDRTLSG YEEYPTYVPL FLGYQIINSE NNFLRNDFIP RAN PNATLG GGAVAGPAPG VAGEAGGGIA V

UniProtKB: Major capsid protein

-
Macromolecule #2: Capsid-associated protein VP80

MacromoleculeName: Capsid-associated protein VP80 / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Autographa californica multiple nucleopolyhedrovirus
Molecular weightTheoretical: 79.974469 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MNDSNSLLIT RLAAQILSRN MQTVDVIVDD KTLSLEEKID TLTSMVLAVN SPPQSPPRVT SSDLAASIIK NNSKMVGNDF EMRYNVLRM AVVFVKHYPK YYNETTAGLV AEIESNLLQY QNYVNQGNYQ NIEGYDSLLN KAEECYVKID RLFKESIKKI M DDTEAFER ...String:
MNDSNSLLIT RLAAQILSRN MQTVDVIVDD KTLSLEEKID TLTSMVLAVN SPPQSPPRVT SSDLAASIIK NNSKMVGNDF EMRYNVLRM AVVFVKHYPK YYNETTAGLV AEIESNLLQY QNYVNQGNYQ NIEGYDSLLN KAEECYVKID RLFKESIKKI M DDTEAFER EQEAERLRAE QTAANALLER RAQTSADDVV NRADANIPTA FSDPLPGPSA PRYMYESSES DTYMETARRT AE HYTDQDK DYNAAYTADE YNSLVKTVLL RLIEKALATL KNRLHITTID QLKKFRDYLN SDADAGEFQI FLNQEDCVIL KNL SNLASK FFNVRCVADT LEVMLEALRN NIELVQPESD AVRRIVIKMT QEIKDSSTPL YNIAMYKSDY DAIKNKNIKT LFDL YNDRL PINFLDTSAT SPVRKTSGKR SAEDDLLPTR SSKRANRPEI NVISSEDEQE DDDVEDVDYE KESKRRKLED EDFLK LKAL EFSKDIVNEK LQKIIVVTDG MKRLYEYCNC KNSLETLPSA ANYGSLLKRL NLYNLDHIEM NVNFYELLFP LTLYND NDN SDKTLSHQLV NYIFLASNYF QNCAKNFNYM RETFNVFGPF KQIDFMVMFV IKFNFLCDMR NFAKLIDELV PNKQPNM RI HSVLVMRDKI VKLAFSNLQF QTFSKKDKSR NTKHLQRLIM LMNANYNVI

UniProtKB: Capsid-associated protein VP80

-
Macromolecule #3: Occlusion-derived virus envelope protein E27

MacromoleculeName: Occlusion-derived virus envelope protein E27 / type: protein_or_peptide / ID: 3 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Autographa californica multiple nucleopolyhedrovirus
Molecular weightTheoretical: 33.568152 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MKRIKCNKVR TVTEIVNSDE KIQKTYELAE FDLKNLSSLE SYETLKIKLA LSKYMAMLST LEMTQPLLEI FRNKADTRQI AAVVFSTLA FIHNRFHPLV TNFTNKMEFV VTETNDTSIP GEPILFTENE GVLLCSVDRP SIVKMLSREF DTEALVNFEN D NCNVRIAK ...String:
MKRIKCNKVR TVTEIVNSDE KIQKTYELAE FDLKNLSSLE SYETLKIKLA LSKYMAMLST LEMTQPLLEI FRNKADTRQI AAVVFSTLA FIHNRFHPLV TNFTNKMEFV VTETNDTSIP GEPILFTENE GVLLCSVDRP SIVKMLSREF DTEALVNFEN D NCNVRIAK TFGASKRKNT TRSDDYESNK QPNYDMDLSD FSITEVEATQ YLTLLLTVEH AYLHYYIFKN YGVFEYCKSL TD HSLFTNK LRSTMSTKTS NLLLSKFKFT IEDFDKINSN SVTSGFNIYN FNK

UniProtKB: Occlusion-derived virus envelope protein E27

-
Macromolecule #4: Protein C42

MacromoleculeName: Protein C42 / type: protein_or_peptide / ID: 4 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Autographa californica multiple nucleopolyhedrovirus
Molecular weightTheoretical: 41.583594 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MSAIALYLEI NKLRLKIDEP MQLAIWPQLF PLLCDEHQSV QLNTDVLINF MMHVARKSQN TILNNNAAIA SQYAAGNADV VAAPASAQP TPRPVINLFA RANAAAPAQP SEELINMRRY RNAARKLIHH YSLNSTSSTE YKISDVVMTM IFLLRSEKYH S LFKLLETT ...String:
MSAIALYLEI NKLRLKIDEP MQLAIWPQLF PLLCDEHQSV QLNTDVLINF MMHVARKSQN TILNNNAAIA SQYAAGNADV VAAPASAQP TPRPVINLFA RANAAAPAQP SEELINMRRY RNAARKLIHH YSLNSTSSTE YKISDVVMTM IFLLRSEKYH S LFKLLETT FDDYTCRPQM TQVQTDTLLD AVRSLLEMPS TTIDLTTVDI MRSSFARCFN SPIMRYAKIV LLQNVALQRD KR TTLEELL IERGEKIQML QPQQYINSGT EIPFCDDAEF LNRLLKHIDP YPLSRMYYNA ANTMFYTTME NYAVSNCKFN IED YNNIFK VMENIRKHSN KNSNDQDELN IYLGVQSSNA KRKKY

UniProtKB: Protein C42

-
Macromolecule #5: Protein AC109

MacromoleculeName: Protein AC109 / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Autographa californica multiple nucleopolyhedrovirus
Molecular weightTheoretical: 44.851441 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MECPFQIQVC ISDRFFAFPH NLVEPQSDVG NKLIENLIVY VPTDDDRLYI DKKQFPKFNS VLVYRHEHDV NIDSRSPKKT ASATIVYWN PLVPITEIGA GETRVFSVLL TNNLFYCNTM IVHHENPKCP IEFTYPETDM QSACSALLKN RNGQSVPPPI K SNLRPIAC ...String:
MECPFQIQVC ISDRFFAFPH NLVEPQSDVG NKLIENLIVY VPTDDDRLYI DKKQFPKFNS VLVYRHEHDV NIDSRSPKKT ASATIVYWN PLVPITEIGA GETRVFSVLL TNNLFYCNTM IVHHENPKCP IEFTYPETDM QSACSALLKN RNGQSVPPPI K SNLRPIAC EIPLSHFKEL VESNDFLLCF NLETSTMVKI LSLKRIFCIF QYRKQPARYV INLPHEEIDN LYNKLNWERT RR LMKGDVP SNCATVNRSS LKYIKQAQSL LGIPDYSQTV VDFVKMFQKI IFPYQLVPNV IIKLNNFDQM VSSAPNKAEP YKK IRLFCK NDSIAISSSG IVPINMPDFS PPNTFDYSDY ANRTNINFVT QRVLTDGGFS SGITVTPVKY NYYL

UniProtKB: Protein AC109

-
Macromolecule #6: Protein AC142

MacromoleculeName: Protein AC142 / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Autographa californica multiple nucleopolyhedrovirus
Molecular weightTheoretical: 55.480898 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MSGGGNLLTL ERDHFKYLFL TSYFDLKDNE HVPSEPMAFI RNYLNCTFDL LDDAVLMNYF NYLQSMQLKH LVGSTSTNIF KFVKPQFRF VCDRTTVDIL EFDTRMYIKP GTPVYATNLF TSNPRKMMAF LYAEFGKVFK NKIFVNINNY GCVLAGSAGF L FDDAYVDW ...String:
MSGGGNLLTL ERDHFKYLFL TSYFDLKDNE HVPSEPMAFI RNYLNCTFDL LDDAVLMNYF NYLQSMQLKH LVGSTSTNIF KFVKPQFRF VCDRTTVDIL EFDTRMYIKP GTPVYATNLF TSNPRKMMAF LYAEFGKVFK NKIFVNINNY GCVLAGSAGF L FDDAYVDW NGVRMCAAPR LDNNMHPFRL YLLGEDMAKH FVDNNILPPH PSNAKTRKIN NSMFMLKNFY KGLPLFKSKY TV VNSTKIV TRKPNDIFNE IDKELNGNCP FIKFIQRDYI FDAQFPPDLL DLLNEYMTKS SIMKIITKFV IEENPAMSGE MSR EIILDR YSVDNYRKLY IKMEITNQFP VMYDHESSYI FVSKDFLQLK GTMNAFYAPK QRILSILAVN RLFGATETID FHPN LLVYR QSSPPVRLTG DVYVVDKNEK VFLVKHVFSN TVPAYLLIRG DYESSSDLKS LRDLNPWVQN TLLKLLIPDS VQ

UniProtKB: Protein AC142

-
Macromolecule #7: 38K (AC98) protein in P143-LEF5 intergenic region

MacromoleculeName: 38K (AC98) protein in P143-LEF5 intergenic region / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Autographa californica multiple nucleopolyhedrovirus
Molecular weightTheoretical: 38.0705 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MASSLQSKWI CLRLNDAIIK RHVLVLSEYA DLKYLGFEKY KFFEYVIFQF CNDPQLCKII ENNYNYCMQI FKAPADDMRD IRHNIKRAF KTPVLGHMCV LSNKPPMYSF LKEWFLLPHY KVVSLKSESL TWGFPHVVVF DLDSTLITEE EQVEIRDPFV Y DSLQELHE ...String:
MASSLQSKWI CLRLNDAIIK RHVLVLSEYA DLKYLGFEKY KFFEYVIFQF CNDPQLCKII ENNYNYCMQI FKAPADDMRD IRHNIKRAF KTPVLGHMCV LSNKPPMYSF LKEWFLLPHY KVVSLKSESL TWGFPHVVVF DLDSTLITEE EQVEIRDPFV Y DSLQELHE MGCVLVLWSY GSRDHVAHSM RDVDLEGYFD IIISEGSTVQ EERSDLVQNS HNAIVDYNLK KRFIENKFVF DI HNHRSDN NIPKSPKIVI KYLSDKNVNF FKSITLVDDL PTNNYAYDFY VKVKRCPTPV QDWEHYHNEI IQNIMDYEQY FIK

UniProtKB: Uncharacterized 38.0 kDa protein in P143-LEF5 intergenic region

-
Macromolecule #8: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 8 / Number of copies: 12 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4 / Details: 10 mM HEPES pH 7.4, 500 mM potassium chloride
GridModel: Quantifoil R2/2 / Material: GOLD / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV
DetailsA suspension of AcMNPV viruses was purified from cell culture supernatant using sucrose gradient ultracentrifugation. Sucrose was removed after purification through dialysis.

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 11439 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.4000000000000001 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 64000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 143933
Details: Particles were picked using a trained Topaz model, trained using manual picking of nucleocapsid ends from 700 micrographs
Startup modelType of model: OTHER / Details: Ab initio model
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.71 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.1.2) / Number images used: 53750
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.1.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.1.2)
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
Output model

PDB-8vwi:
The base complex of the AcMNPV baculovirus nucleocapsid (Class 1, localised reconstruction)

+
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