[English] 日本語
Yorodumi
- EMDB-62912: Cryo-EM structure of bacteriophage T1 tail tip complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-62912
TitleCryo-EM structure of bacteriophage T1 tail tip complex
Map data
Sample
  • Complex: Escherichia phage T1
    • Protein or peptide: Putative tail fiber protein
    • Protein or peptide: Putative tail assembly protein
    • Protein or peptide: Putative minor tail protein
    • Protein or peptide: Putative minor tail protein
    • Protein or peptide: Tape measure protein
  • Ligand: IRON/SULFUR CLUSTER
Keywordstail tip complex / VIRAL PROTEIN
Function / homology
Function and homology information


symbiont genome ejection through host cell envelope, long flexible tail mechanism / viral tail assembly / virus tail / iron-sulfur cluster binding / host cell cytoplasm / symbiont entry into host cell / membrane
Similarity search - Function
Bacteriophage tail tape measure, C-terminal / Bacteriophage tail tape measure, N-terminal / Tape measure protein / Prophage tail length tape measure protein / Lambda phage tail tape-measure protein (Tape_meas_lam_C) / Bacteriophage lambda, Tail tip protein L / Bacteriophage lambda, Tail tip protein M / Bacteriophage lambda tail assembly I / Phage minor tail protein L / Phage minor tail protein ...Bacteriophage tail tape measure, C-terminal / Bacteriophage tail tape measure, N-terminal / Tape measure protein / Prophage tail length tape measure protein / Lambda phage tail tape-measure protein (Tape_meas_lam_C) / Bacteriophage lambda, Tail tip protein L / Bacteriophage lambda, Tail tip protein M / Bacteriophage lambda tail assembly I / Phage minor tail protein L / Phage minor tail protein / Bacteriophage lambda tail assembly protein I / Domain of unknown function DUF1983 / : / : / Bacteriophage tail tip fiber protein / Tip attachment protein J,FNIII-A domain / Tip attachment protein J / Putative phage tail protein / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Putative tail fiber protein / Putative minor tail protein / Putative tail assembly protein / Putative minor tail protein / Tape measure protein
Similarity search - Component
Biological speciesEscherichia phage T1 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsChen Y / Liu HR
Funding support China, 3 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)12034006 China
National Natural Science Foundation of China (NSFC)32430020 China
National Natural Science Foundation of China (NSFC)32071209 China
CitationJournal: To Be Published
Title: The in situ structure of T-series T1 reveals a conserved Lambda-like tail tip
Authors: Chen Y / Liu HR
History
DepositionDec 30, 2024-
Header (metadata) releaseMar 12, 2025-
Map releaseMar 12, 2025-
UpdateMar 12, 2025-
Current statusMar 12, 2025Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_62912.png

Downloads & links

-
Map

FileDownload / File: emd_62912.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.36 Å/pix.
x 240 pix.
= 326.4 Å		1.36 Å/pix.
x 240 pix.
= 326.4 Å		1.36 Å/pix.
x 240 pix.
= 326.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.36 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 4.0
Minimum - Maximum-8.842487 - 25.300173000000001
Average (Standard dev.)0.0021388608 (±0.81859267)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-120-120-120
Dimensions240240240
Spacing240240240
CellA=B=C: 326.4 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_62912_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_62912_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Escherichia phage T1

EntireName: Escherichia phage T1 (virus)
Components
  • Complex: Escherichia phage T1
    • Protein or peptide: Putative tail fiber protein
    • Protein or peptide: Putative tail assembly protein
    • Protein or peptide: Putative minor tail protein
    • Protein or peptide: Putative minor tail protein
    • Protein or peptide: Tape measure protein
  • Ligand: IRON/SULFUR CLUSTER

-
Supramolecule #1: Escherichia phage T1

SupramoleculeName: Escherichia phage T1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Escherichia phage T1 (virus)

-
Macromolecule #1: Putative tail fiber protein

MacromoleculeName: Putative tail fiber protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage T1 (virus)
Molecular weightTheoretical: 130.265047 KDa
SequenceString: MIQKVISGSK GGSQKPHNPV EMEDNLISIN KIKILLAVSD GEIDETFSLK QLMFNSVPVQ NEDGSFNFEG VKAEFRPGTQ TQEYIKGME DSSSEVTVNR EVTTDNPYTI SVTNKTLSAI RIKMFMPRGV RIESNGDKNG VRVEYEVQQA VDGGSFETVL T DVIEGKTM ...String:
MIQKVISGSK GGSQKPHNPV EMEDNLISIN KIKILLAVSD GEIDETFSLK QLMFNSVPVQ NEDGSFNFEG VKAEFRPGTQ TQEYIKGME DSSSEVTVNR EVTTDNPYTI SVTNKTLSAI RIKMFMPRGV RIESNGDKNG VRVEYEVQQA VDGGSFETVL T DVIEGKTM SGYDRSRRVN LPNFNNQVIF RVVRKTPDSN DSNVVDAIQV KSYAEVIDAK FRYPLTGLLF VEFDSKMFPN QL PTISIRK RWKIVNVPSN YDPESRTYNG NWDGTFKKAW TNNPAWVLYD LMINQRYGLD QKELGIAVDK WALYEAAQYC DQM VPDGKG GTEPRYLCDV IIQSQTDAYK VIRDICSIFR GMSFWNGESI SVIIDRPREP AYIFTNDNVV NGDFSYTFAS EKSM YTTCN VMFDDEQNMY QQDVEPVFDR EATLRFGNNV TSITAIGCTR RSEANRRGRW ILKTNLRSTT VNFATGLEGM IPTIG DVVA IADNFWSSNL TMNLSGRLLE VSGSQIFLPF RVDARAGDFI IVNKPDGKPV KRTISSVSAD GKTIEVNIGF GFPVKP NTV FAIDRTDIAL QQYVVTKIDK GDDDEEFTYK ITAVEYDPNK YDEIDYGVNI DDRPTSIVEP DQIPRPKNVQ VSSESRI VQ GMSVETMIVS WDKVPYAVFY DVQWRKDNGN WQNVPQTANK EVYVEGIYAG NYQVRVRSVA GSGTTSGWSN IVAATLTG K QGEPGRPINL TATDDVVFGI RTKWGFSDGS GDTAYTELQQ SPDGTVDNAS LLSLIPYPQH EYYHSPMPGG NIVWYRVRT VDRIGNVSQW TDFVRGMAST NVDDIIGEIS VDIENSPGYE WLVDNATDNA AQNSANAEAA IENALANDKD AIYMKKENGK RKAEYTKSL KLIADETQAR VTAIEQLKAS FGDQISASNS ELREVIATET EALSREIDQL KAQIGDDIQA SLTDIREVIA T ETEALSRE IDQLKAQIGD DIQASLTDIR EAIANETEAR TQADLTLSAR LGNNEAALAQ KLDSWSNADS TGAMYGVKLG LK YNGQEYS AGMAMSLVGS GAAVKAQILF EASRFAIMTG MNGQTQYPFV VENGQVILSS AIIKNGFITN AMIGNFIQSN NYV FNQSGW RLDKGGTFEN YGSDGEGAMK QTNTTISVRD ASGRLRVQIG RLTGSW

UniProtKB: Putative tail fiber protein

-
Macromolecule #2: Putative tail assembly protein

MacromoleculeName: Putative tail assembly protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage T1 (virus)
Molecular weightTheoretical: 20.916922 KDa
SequenceString: MNDVKVIKLS GSLGRRFGVF HRYAVDSYPE AIRALSSQVD GFKEYMQSEV GSRSKFAIFV DGVNVGHHEE EKFKCAKEIR IVPIPTGSK TGGLFQVVLG AAIMVAAFYT GGASLALMGT MSSSLFMMGG AMVLGGVMQM ISPQPGGANF EVQSSKNKPS Y AFGGAVNT ...String:
MNDVKVIKLS GSLGRRFGVF HRYAVDSYPE AIRALSSQVD GFKEYMQSEV GSRSKFAIFV DGVNVGHHEE EKFKCAKEIR IVPIPTGSK TGGLFQVVLG AAIMVAAFYT GGASLALMGT MSSSLFMMGG AMVLGGVMQM ISPQPGGANF EVQSSKNKPS Y AFGGAVNT TAAGYPLPVP YGYRAGGGAT FSAGSYAEDM S

UniProtKB: Putative tail assembly protein

-
Macromolecule #3: Putative minor tail protein

MacromoleculeName: Putative minor tail protein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage T1 (virus)
Molecular weightTheoretical: 29.058648 KDa
SequenceString: MSENKKLYDE ESGKSLFHNC LQSLYPGEII TLIEVDGSKF GAQVYRFHGE NIQYTPEEIM QAQQTGTLPP KEITFRGEKY GARPFGISG ISFDSSGKAT KPQLTVANID SRVSAMIRAY NGLMQAKVTI WITQRELINS DGSIADGAYR KLVYYIERPN Y VDKSVARF ...String:
MSENKKLYDE ESGKSLFHNC LQSLYPGEII TLIEVDGSKF GAQVYRFHGE NIQYTPEEIM QAQQTGTLPP KEITFRGEKY GARPFGISG ISFDSSGKAT KPQLTVANID SRVSAMIRAY NGLMQAKVTI WITQRELINS DGSIADGAYR KLVYYIERPN Y VDKSVARF DLTSPYDMDG IMIPSRLTQS VCYFAQRGWY KTGKGCGYNG QNGYFDKDNN PVDDPSLDFC PGTVTACRLR FG ANNELDF GGCAVASLQR KNQ

UniProtKB: Putative minor tail protein

-
Macromolecule #4: Putative minor tail protein

MacromoleculeName: Putative minor tail protein / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage T1 (virus)
Molecular weightTheoretical: 12.992562 KDa
SequenceString:
MATLDTFGWC TQVQGGGGSL TTTNSDRSIQ FGNGYMQLAS SGFNTTRREY SVVYAGEDFM AVYDFCNSHR IKPFAWTPPD GKIGIWVVK PNSLGAKPVS RDVMEINVTF MEQFTSME

UniProtKB: Putative minor tail protein

-
Macromolecule #5: Tape measure protein

MacromoleculeName: Tape measure protein / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage T1 (virus)
Molecular weightTheoretical: 103.784391 KDa
SequenceString: MVDKVAGLSL DVDVSTVQRA VKSLKEFSKA NDQAADSMGS LINESEVAKQ KAKEHAEQLR RQRKEYEAVE KAIDPTVSKM ERLKIASQQ LDKLWQQGVV PDETFFRLGE MLDLQNAKLA RSRAMLTEEG QAALQEAKAK EQAAVRSKAF MDALNGQVNA I GKTHAELM ...String:
MVDKVAGLSL DVDVSTVQRA VKSLKEFSKA NDQAADSMGS LINESEVAKQ KAKEHAEQLR RQRKEYEAVE KAIDPTVSKM ERLKIASQQ LDKLWQQGVV PDETFFRLGE MLDLQNAKLA RSRAMLTEEG QAALQEAKAK EQAAVRSKAF MDALNGQVNA I GKTHAELM ELKAAELGLS KEAAPLIAKL KDQGRAMNAA GISAGEYRQA MRMLPAQITD VVTSLASGMP VWMVAIQQGG QI KDSFGGI GNTFKVLLSY INPVTAGVGV LVGSLGILAK AGYDSYKSIT DIQNALIETG GYAGVTAEEL DSVSKKIAQT SNS TIGSIR EIVTELASSG KYTREQIQNI TKATAEWSAS TGKSASQIIS EFEKIASDPV KGLKKLNEQY NFLEKGQLTY IDTL SRTKG ETEAVSEATK LFADVMEKRM KSIADNATPL EKMWSDIKQW ASDAWGWVGD HTLGALNLII DVVQGTVIQV KMILA KGDE YISNFIASAI KATQSLPGMS DFGADVLKEQ ENIVKSSRDN YDQLASDLDA INARVEKGEM GYIEAMRQRR TLEKQY SEE TKEAIRKEAE EIEKRNRERN KQSKIVRSPT EQFDKELISL RAQLKVLQEH KEIGQKLSAQ RKALFTTEAT IAVLREA SS KRQLSAEEKA LLASQERVIE LAKQKAEIGD QIVKQQQLND LTDKSLKFVN EMTAATEQLN ASRGLSTRDM ERQAELAK I TTDYINSGGS EGDEKLQNMI KAQNDYYAAE DAKRADWLAG AESAFADYGD AAMDMYGNVN EIASSALNGM SDMMVQFLT TGKANFEDFA KNIIGMIIKM IAQMVIFNTI SGMMGGKTWS FAGGASSGAS AASQATPTPA ASVFRSVSSG GAAVSLAAAA GSVATSGFN ASNSAPKVVN HSGGGTVVDV SGMEVKVDNG SDPRGISQGV EMMFKKMIRE SCSQGGEVYN YIQEKTGG

UniProtKB: Tape measure protein

-
Macromolecule #6: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 6 / Number of copies: 1 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.6
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 32.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.0 µm / Nominal defocus min: 2.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 4467
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: COMMON LINE

+
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