[English] 日本語
Yorodumi
- EMDB-66507: Phage T4 peripheral baseplate in post-tail-contraction state (gen... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-66507
TitlePhage T4 peripheral baseplate in post-tail-contraction state (genome-full particle)
Map data
Sample
  • Virus: Escherichia phage T4 (virus)
    • Protein or peptide: Baseplate wedge protein gp8
    • Protein or peptide: Baseplate wedge protein gp7
    • Protein or peptide: Baseplate protein gp9
    • Protein or peptide: Baseplate wedge protein gp10
    • Protein or peptide: Baseplate wedge protein gp11
  • Protein or peptide: Long-tail fiber proximal subunit
KeywordsBacteriophage / Myovirus / Phage T4 / tail contraction / phage neck complex / VIRAL PROTEIN
Function / homology
Function and homology information


virus tail, baseplate / viral tail assembly / virus tail, fiber / viral release from host cell
Similarity search - Function
: / Long-tail fiber proximal subunit, C-terminal, second / : / Long-tail fiber proximal subunit, C-terminal, trimerization domain / Baseplate structural protein Gp11 / Bacteriophage T4, Gp11, C-terminal finger domain / Baseplate structural protein Gp11, N-terminal domain superfamily / Baseplate wedge protein gp7 / Baseplate structural protein Gp11 superfamily / Baseplate structural protein Gp11, C-terminal domain ...: / Long-tail fiber proximal subunit, C-terminal, second / : / Long-tail fiber proximal subunit, C-terminal, trimerization domain / Baseplate structural protein Gp11 / Bacteriophage T4, Gp11, C-terminal finger domain / Baseplate structural protein Gp11, N-terminal domain superfamily / Baseplate wedge protein gp7 / Baseplate structural protein Gp11 superfamily / Baseplate structural protein Gp11, C-terminal domain / : / : / : / GP11 baseplate wedge protein / Baseplate wedge protein gp7, domain V / Baseplate wedge protein gp7, helical domain / Baseplate wedge protein gp7, domain VI / Baseplate wedge protein gp10 / : / Baseplate wedge protein gp10 domain 3 / Baseplate structural protein Gp9 C-terminal domain superfamily / Bacteriophage T4, Gp8 / Bacteriophage T4, Gp8 superfamily / Bacteriophage T4, Gp8 / : / Baseplate structural protein Gp10, C-terminal domain / Baseplate structural protein Gp9/Gp10 / Baseplate structural protein Gp9/Gp10 middle domain superfamily / Gp9-like superfamily / : / Bacteriophage T4 gp9/10-like protein, N-terminal / Bacteriophage T4 gp9/10-like protein, C-terminal / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Baseplate protein gp9 / Baseplate wedge protein gp10 / Baseplate wedge protein gp11 / Long-tail fiber proximal subunit / Baseplate wedge protein gp7 / Baseplate wedge protein gp8
Similarity search - Component
Biological speciesEscherichia phage T4 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsShao Q / Dong J / Wang A / Hu H / Yue J / Li H / Li Y / Zhang Q / Liu J / Sun L ...Shao Q / Dong J / Wang A / Hu H / Yue J / Li H / Li Y / Zhang Q / Liu J / Sun L / Fokine A / Rao VB / Tao P / Fang Q
Funding support China, United States, 7 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32371285 China
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI175340 United States
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)DP1DA060580 United States
National Science Foundation (NSF, United States)MCB-0923873 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM124378 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM110243 United States
National Institutes of Health/Office of the Director1S10OD023603-01A1 United States
CitationJournal: J Mol Biol / Year: 2026
Title: Cryo-EM Structures of Phage T4 Infection Intermediate.
Authors: Qianqian Shao / Junhua Dong / Aohan Wang / Hongli Hu / Jian Yue / Hongmei Li / Yinyin Li / Qinfen Zhang / Jun Liu / Lei Sun / Andrei Fokine / Venigalla B Rao / Pan Tao / Qianglin Fang /
Abstract: Myophage is endowed with a sophisticated contractile tail and infection machinery. However, the mechanisms of host recognition, signal transduction, and genome delivery remain poorly understood. ...Myophage is endowed with a sophisticated contractile tail and infection machinery. However, the mechanisms of host recognition, signal transduction, and genome delivery remain poorly understood. Here, we capture a pre-genome-release intermediate of myophage T4 and determine its structure by cryo-electron microscopy. Comparative analysis of this tail-contracted, pre-genome-release intermediate structure with the mature T4 virion and the tail-contracted, post-genome-release structure reveals structural transitions in the tail, tape-measure protein (TMP), baseplate, and long tail fibers that drive genome delivery. Our findings further suggest that tail sheath contraction is coupled to a coordinated repositioning of the viral DNA-TMP complex, potentially facilitating genome translocation via charge-mediated interactions. It appears that the expelled TMP may further reorganize into a putative transmembrane complex that supports genome delivery into the host cytosol.
History
DepositionOct 9, 2025-
Header (metadata) releaseJul 22, 2026-
Map releaseJul 22, 2026-
UpdateJul 22, 2026-
Current statusJul 22, 2026Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_66507.png

Downloads & links

-
Map

FileReleased
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.64 Å/pix.
x 256 pix.
= 419.328 Å		1.64 Å/pix.
x 256 pix.
= 419.328 Å		1.64 Å/pix.
x 256 pix.
= 419.328 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.638 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.035
Minimum - Maximum-0.1498213 - 0.23538688
Average (Standard dev.)0.00011340144 (±0.0075548175)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 419.328 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_66507_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_66507_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_66507_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Escherichia phage T4

EntireName: Escherichia phage T4 (virus)
Components
  • Virus: Escherichia phage T4 (virus)
    • Protein or peptide: Baseplate wedge protein gp8
    • Protein or peptide: Baseplate wedge protein gp7
    • Protein or peptide: Baseplate protein gp9
    • Protein or peptide: Baseplate wedge protein gp10
    • Protein or peptide: Baseplate wedge protein gp11
  • Protein or peptide: Long-tail fiber proximal subunit

-
Supramolecule #1: Escherichia phage T4

SupramoleculeName: Escherichia phage T4 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#5 / NCBI-ID: 2681598 / Sci species name: Escherichia phage T4 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Escherichia coli (E. coli)

-
Macromolecule #1: Baseplate wedge protein gp8

MacromoleculeName: Baseplate wedge protein gp8 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage T4 (virus)
Molecular weightTheoretical: 38.041668 KDa
SequenceString: MNDSSVIYRA IVTSKFRTEK MLNFYNSIGS GPDKNTIFIT FGRSEPWSSN ENEVGFAPPY PTDSVLGVTD MWTHMMGTVK VLPSMLDAV IPRRDWGDTR YPDPYTFRIN DIVVCNSAPY NATESGAGWL VYRCLDVPDT GMCSIASLTD KDECLKLGGK W TPSARSMT ...String:
MNDSSVIYRA IVTSKFRTEK MLNFYNSIGS GPDKNTIFIT FGRSEPWSSN ENEVGFAPPY PTDSVLGVTD MWTHMMGTVK VLPSMLDAV IPRRDWGDTR YPDPYTFRIN DIVVCNSAPY NATESGAGWL VYRCLDVPDT GMCSIASLTD KDECLKLGGK W TPSARSMT PPEGRGDAEG TIEPGDGYVW EYLFEIPPDV SINRCTNEYI VVPWPEELKE DPTRWGYEDN LTWQQDDFGL IY RVKANTI RFKAYLDSVY FPEAALPGNK GFRQISIITN PLEAKAHPND PNVKAEKDYY DPEDLMRHSG EMIYMENRPP IIM AMDQTE EINILFTF

UniProtKB: Baseplate wedge protein gp8

-
Macromolecule #2: Baseplate wedge protein gp7

MacromoleculeName: Baseplate wedge protein gp7 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage T4 (virus)
Molecular weightTheoretical: 119.336516 KDa
SequenceString: MTVKAPSVTS LRISKLSANQ VQVRWDDVGA NFYYFVEIAE TKTNSGENLP SNQYRWINLG YTANNSFFFD DADPLTTYII RVATAAQDF EQSDWIYTEE FETFATNAYT FQNMIEMQLA NKFIQEKFTL NNSDYVNFNN DTIMAALMNE SFQFSPSYVD V SSISNFII ...String:
MTVKAPSVTS LRISKLSANQ VQVRWDDVGA NFYYFVEIAE TKTNSGENLP SNQYRWINLG YTANNSFFFD DADPLTTYII RVATAAQDF EQSDWIYTEE FETFATNAYT FQNMIEMQLA NKFIQEKFTL NNSDYVNFNN DTIMAALMNE SFQFSPSYVD V SSISNFII GENEYHEIQG SIQQVCKDIN RVYLMESEGI LYLFERYQPV VKVSNDKGQT WKAVKLFNDR VGYPLSKTVY YQ SANTTYV LGYDKIFYGR KSTDVRWSAD DVRFSSQDIT FAKLGDQLHL GFDVEIFATY ATLPANVYRI AEAITCTDDY IYV VARDKV RYIKTSNALI DFDPLSPTYS ERLFEPDTMT ITGNPKAVCY KMDSICDKVF ALIIGEVETL NANPRTSKII DSAD KGIYV LNHDEKTWKR VFGNTEEERR RIQPGYANMS TDGKLVSLSS SNFKFLSDNV VNDPETAAKY QLIGAVKYEF PREWL ADKH YHMMAFIADE TSDWETFTPQ PMKYYAEPFF NWSKKSNTRC WINNSDRAVV VYADLKYTKV IENIPETSPD RLVHEY WDD GDCTIVMPNV KFTGFKKYAS GMLFYKASGE IISYYDFNYR VRDTVEIIWK PTEVFLKAFL QNQEHETPWS PEEERGL AD PDLRPLIGTM MPDSYLLQDS NFEAFCEAYI QYLSDGYGTQ YNNLRNLIRN QYPREEHAWE YLWSEIYKRN IYLNADKR D AVARFFESRS YDFYSTKGIE ASYKFLFKVL YNEEVEIEIE SGAGTEYDII VQSDSLTEDL VGQTIYTATG RCNVTYIER SYSNGKLQWT VTIHNLLGRL IAGQEVKAER LPSFEGEIIR GVKGKDLLQN NIDYINRSRS YYVMKIKSNL PSSRWKSDVI RFVHPVGFG FIAITLLTMF INVGLTLKHT ETIINKYKNY KWDSGLPTEY ADRIAKLTPT GEIEHDSVTG EAIYEPGPMA G VKYPLPDD YNAENNNSIF QGQLPSERRK LMSPLFDASG TTFAQFRDLV NKRLKDNIGN PRDPENPTQV KIDE

UniProtKB: Baseplate wedge protein gp7

-
Macromolecule #3: Baseplate protein gp9

MacromoleculeName: Baseplate protein gp9 / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage T4 (virus)
Molecular weightTheoretical: 31.024725 KDa
SequenceString: MFIQEPKKLI DTGEIGNAST GDILFDGGNK INSDFNAIYN AFGDQRKMAV ANGTGADGQI IHATGYYQKH SITEYATPVK VGTRHDIDT STVGVKVIIE RGELGDCVEF INSNGSISVT NPLTIQAIDS IKGVSGNLVV TSPYSKVTLR CISSDNSTSV W NYSIESMF ...String:
MFIQEPKKLI DTGEIGNAST GDILFDGGNK INSDFNAIYN AFGDQRKMAV ANGTGADGQI IHATGYYQKH SITEYATPVK VGTRHDIDT STVGVKVIIE RGELGDCVEF INSNGSISVT NPLTIQAIDS IKGVSGNLVV TSPYSKVTLR CISSDNSTSV W NYSIESMF GQKESPAEGT WNISTSGSVD IPLFHRTEYN MAKLLVTCQS VDGRKIKTAE INILVDTVNS EVISSEYAVM RV GNETEED EIANIAFSIK ENYVTATISS STVGMRAAVK VIATQKIGVA Q

UniProtKB: Baseplate protein gp9

-
Macromolecule #4: Baseplate wedge protein gp10

MacromoleculeName: Baseplate wedge protein gp10 / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage T4 (virus)
Molecular weightTheoretical: 66.28168 KDa
SequenceString: MKQNINIGNV VDDGTGDYLR KGGIKINENF DELYYELGDG DVPYSAGAWK TYNASSGQTL TAEWGKSYAI NTSSGRVTIN LPKGTVNDY NKVIRARDVF ATWNVNPVTL VAASGDTIKG SAVPVEINVR FSDLELVYCA PGRWEYVKNK QIDKITSSDI S NVARKEFL ...String:
MKQNINIGNV VDDGTGDYLR KGGIKINENF DELYYELGDG DVPYSAGAWK TYNASSGQTL TAEWGKSYAI NTSSGRVTIN LPKGTVNDY NKVIRARDVF ATWNVNPVTL VAASGDTIKG SAVPVEINVR FSDLELVYCA PGRWEYVKNK QIDKITSSDI S NVARKEFL VEVQGQTDFL DVFRGTSYNV NNIRVKHRGN ELYYGDVFSE NSDFGSPGEN EGELVPLDGF NIRLRQPCNI GD TVQIETF MDGVSQWRSS YTRRQIRLLD SKLTSKTSLE GSIYVTDLST MKSIPFSAFG LIPGEPINPN SLEVRFNGIL QEL AGTVGM PLFHCVGADS DDEVECSVLG GTWEQSHTDY SVETDENGIP EILHFDSVFE HGDIINITWF NNDLGTLLTK DEII DETDN LYVSQGPGVD ISGDVNLTDF DKIGWPNVEA VQSYQRAFNA VSNIFDTIYP IGTIYENAVN PNNPVTYMGF GSWKL FGQG KVLVGWNEDI SDPNFALNNN DLDSGGNPSH TAGGTGGSTS VTLENANLPA TETDEEVLIV DENGSVIVGG CQYDPD ESG PIYTKYREAK ASTNSTHTPP TSITNIQPYI TVYRWIRIA

UniProtKB: Baseplate wedge protein gp10

-
Macromolecule #5: Baseplate wedge protein gp11

MacromoleculeName: Baseplate wedge protein gp11 / type: protein_or_peptide / ID: 5 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage T4 (virus)
Molecular weightTheoretical: 23.725523 KDa
SequenceString: MSLLNNKAGV ISRLADFLGF RPKTGDIDVM NRQSVGSVTI SQLAKGFYEP NIESAINDVH NFSIKDVGTI ITNKTGVSPE GVSQTDYWA FSGTVTDDSL PPGSPITVLV FGLPVSATTG MTAIEFVAKV RVALQEAIAS FTAINSYKDH PTDGSKLEVT Y LDNQKHVL ...String:
MSLLNNKAGV ISRLADFLGF RPKTGDIDVM NRQSVGSVTI SQLAKGFYEP NIESAINDVH NFSIKDVGTI ITNKTGVSPE GVSQTDYWA FSGTVTDDSL PPGSPITVLV FGLPVSATTG MTAIEFVAKV RVALQEAIAS FTAINSYKDH PTDGSKLEVT Y LDNQKHVL STYSTYGITI SQEIISESKP GYGTWNLLGA QTVTLDNQQT PTVFYHFERT A

UniProtKB: Baseplate wedge protein gp11

-
Macromolecule #6: Long-tail fiber proximal subunit

MacromoleculeName: Long-tail fiber proximal subunit / type: protein_or_peptide / ID: 6 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage T4 (virus)
Molecular weightTheoretical: 140.530922 KDa
SequenceString: MAEIKREFRA EDGLDAGGDK IINVALADRT VGTDGVNVDY LIQENTVQQY DPTRGYLKDF VIIYDNRFWA AINDIPKPAG AFNSGRWRA LRTDANWITV SSGSYQLKSG EAISVNTAAG NDITFTLPSS PIDGDTIVLQ DIGGKPGVNQ VLIVAPVQSI V NFRGEQVR ...String:
MAEIKREFRA EDGLDAGGDK IINVALADRT VGTDGVNVDY LIQENTVQQY DPTRGYLKDF VIIYDNRFWA AINDIPKPAG AFNSGRWRA LRTDANWITV SSGSYQLKSG EAISVNTAAG NDITFTLPSS PIDGDTIVLQ DIGGKPGVNQ VLIVAPVQSI V NFRGEQVR SVLMTHPKSQ LVLIFSNRLW QMYVADYSRE AIVVTPANTY QAQSNDFIVR RFTSAAPINV KLPRFANHGD II NFVDLDK LNPLYHTIVT TYDETTSVQE VGTHSIEGRT SIDGFLMFDD NEKLWRLFDG DSKARLRIIT TNSNIRPNEE VMV FGANNG TTQTIELKLP TNISVGDTVK ISMNYMRKGQ TVKIKAADED KIASSVQLLQ FPKRSEYPPE AEWVTVQELV FNDE TNYVP VLELAYIEDS DGKYWVVQQN VPTVERVDSL NDSTRARLGV IALATQAQAN VDLENSPQKE LAITPETLAN RTATE TRRG IARIATTAQV NQNTTFSFAD DIIITPKKLN ERTATETRRG VAEIATQQET NAGTDDTTII TPKKLQARQG SESLSG IVT FVSTAGATPA SSRELNGTNV YNKNTDNLVV SPKALDQYKA TPTQQGAVIL AVESEVIAGQ SQQGWANAVV TPETLHK KT STDGRIGLIE IATQSEVNTG TDYTRAVTPK TLNDRRATES LSGIAEIATQ VEFDAGVDDT RISTPLKIKT RFNSTDRT S VVALSGLVES GTLWDHYTLN ILEANETQRG TLRVATQVEA AAGTLDNVLI TPKKLLGTKS TEAQEGVIKV ATQSETVTG TSANTAVSPK NLKWIAQSEP TWAATTAIRG FVKTSSGSIT FVGNDTVGST QDLELYEKNS YAVSPYELNR VLANYLPLKA KAADTNLLD GLDSSQFIRR DIAQTVNGSL TLTQQTNLSA PLVSSSTGEF GGSLAANRTF TIRNTGAPTS IVFEKGPASG A NPAQSMSI RVWGNQFGGG SDTTRSTVFE VGDDTSHHFY SQRNKDGNIA FNINGTVMPI NINASGLMNV NGTATFGRSV TA NGEFISK SANAFRAING DYGFFIRNDA SNTYFLLTAA GDQTGGFNGL RPLLINNQSG QITIGEGLII AKGVTINSGG LTV NSRIRS QGTKTSDLYT RAPTSDTVGF WSIDINDSAT YNQFPGYFKM VEKTNEVTGL PYLERGEEVK SPGTLTQFGN TLDS LYQDW ITYPTTPEAR TTRWTRTWQK TKNSWSSFVQ VFDGGNPPQP SDIGALPSDN ATMGNLTIRD FLRIGNVRIV PDPVN KTVK FEWVE

UniProtKB: Long-tail fiber proximal subunit

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
GridModel: C-flat-1.2/1.3 / Material: COPPER / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum
Image recording#0 - Image recording ID: 1 / #0 - Film or detector model: GATAN K2 SUMMIT (4k x 4k) / #0 - Detector mode: SUPER-RESOLUTION / #0 - Number real images: 2276 / #0 - Average exposure time: 8.0 sec. / #0 - Average electron dose: 40.0 e/Å2 / #1 - Image recording ID: 2 / #1 - Film or detector model: GATAN K3 (6k x 4k) / #1 - Number real images: 5090 / #1 - Average exposure time: 8.0 sec. / #1 - Average electron dose: 59.6 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: 3.0 µm / Nominal defocus min: 1.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Image recording ID1
Particle selectionNumber selected: 116671
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 235806
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

+
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