[English] 日本語
Yorodumi
- EMDB-35825: Tail tip conformation 2 of phage lambda tail -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-35825
TitleTail tip conformation 2 of phage lambda tail
Map data
Sample
  • Complex: Tail tip conformation 2 of phage lambda tail
    • Protein or peptide: Tail tip protein M
    • Protein or peptide: Tip attachment protein J
    • Protein or peptide: Tail tip protein L
    • Protein or peptide: Tape measure protein
    • Protein or peptide: Tail tip assembly protein I
    • Protein or peptide: Tail tube protein
  • Ligand: IRON/SULFUR CLUSTERIron–sulfur cluster
KeywordsBacteriophage / caudovirales / siphoviridae / tail complex / delivery device / macromolecular assembly / phage lambda / cryo-EM / VIRAL PROTEIN
Function / homology
Function and homology information


virus tail, tube / symbiont genome ejection through host cell envelope, long flexible tail mechanism / viral tail assembly / virus tail / 4 iron, 4 sulfur cluster binding / host cell cytoplasm / entry receptor-mediated virion attachment to host cell / receptor-mediated virion attachment to host cell / virion attachment to host cell / metal ion binding
Similarity search - Function
Bacteriophage tail tape measure, C-terminal / Bacteriophage lambda, Tail tip protein L / Bacteriophage tail tape measure, N-terminal / Bacteriophage lambda, Tail tip protein M / Bacteriophage lambda tail assembly I / Tape measure protein / Phage minor tail protein L / Phage minor tail protein / Prophage tail length tape measure protein / Bacteriophage lambda tail assembly protein I ...Bacteriophage tail tape measure, C-terminal / Bacteriophage lambda, Tail tip protein L / Bacteriophage tail tape measure, N-terminal / Bacteriophage lambda, Tail tip protein M / Bacteriophage lambda tail assembly I / Tape measure protein / Phage minor tail protein L / Phage minor tail protein / Prophage tail length tape measure protein / Bacteriophage lambda tail assembly protein I / Lambda phage tail tape-measure protein (Tape_meas_lam_C) / Domain of unknown function DUF1983 / Domain of unknown function DUF3672 / Domain of unknown function (DUF1983) / Fibronectin type III protein / Tip attachment protein J / Putative phage tail protein / Lambda phage tail tube protein / Lambda phage tail tube protein, TTP / Bacterial Ig-like domain (group 2) / Bacterial Ig-like domain 2 / Bacterial Ig-like domain, group 2 / Beta-grasp domain superfamily / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Tail tip assembly protein I / Tail tube protein / Tape measure protein / Tail tip protein M / Tail tip protein L / Tip attachment protein J
Similarity search - Component
Biological speciesEscherichia phage lambda (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsWang JW / Wang C
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32171190 China
CitationJournal: Structure / Year: 2024
Title: Architecture of the bacteriophage lambda tail.
Authors: Chang Wang / Jinsong Duan / Zhiwei Gu / Xiaofei Ge / Jianwei Zeng / Jiawei Wang /
Abstract: Bacteriophage lambda has a double-stranded DNA genome and a long, flexible, non-contractile tail encoded by a contiguous block of 11 genes downstream of the head genes. The tail allows host ...Bacteriophage lambda has a double-stranded DNA genome and a long, flexible, non-contractile tail encoded by a contiguous block of 11 genes downstream of the head genes. The tail allows host recognition and delivery of viral DNA from the head shell to the cytoplasm of the infected cell. Here, we present a high-resolution structure of the tail complex of bacteriophage lambda determined by cryoelectron microscopy. Most component proteins of the lambda tail were determined at the atomic scale. The structure sheds light on the molecular organization of the extensively studied tail of bacteriophage lambda.
History
DepositionApr 5, 2023-
Header (metadata) releaseOct 18, 2023-
Map releaseOct 18, 2023-
UpdateJan 24, 2024-
Current statusJan 24, 2024Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_35825.png

Downloads & links

-
Map

FileDownload / File: emd_35825.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.0742 Å
Density
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-1.5896282 - 3.4714475
Average (Standard dev.)-0.00054805074 (±0.08214874)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 515.616 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: half 1 map

Fileemd_35825_half_map_1.map
Annotationhalf 1 map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_35825_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Tail tip conformation 2 of phage lambda tail

EntireName: Tail tip conformation 2 of phage lambda tail
Components
  • Complex: Tail tip conformation 2 of phage lambda tail
    • Protein or peptide: Tail tip protein M
    • Protein or peptide: Tip attachment protein J
    • Protein or peptide: Tail tip protein L
    • Protein or peptide: Tape measure protein
    • Protein or peptide: Tail tip assembly protein I
    • Protein or peptide: Tail tube protein
  • Ligand: IRON/SULFUR CLUSTERIron–sulfur cluster

-
Supramolecule #1: Tail tip conformation 2 of phage lambda tail

SupramoleculeName: Tail tip conformation 2 of phage lambda tail / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Source (natural)Organism: Escherichia phage lambda (virus)

-
Macromolecule #1: Tail tip protein M

MacromoleculeName: Tail tip protein M / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage lambda (virus)
Molecular weightTheoretical: 12.547373 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MKTFRWKVKP GMDVASVPSV RKVRFGDGYS QRAPAGLNAN LKTYSVTLSV PREEATVLES FLEEHGGWKS FLWTPPYEWR QIKVTCAKW SSRVSMLRVE FSAEFEQVVN

UniProtKB: Tail tip protein M

-
Macromolecule #2: Tip attachment protein J

MacromoleculeName: Tip attachment protein J / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage lambda (virus)
Molecular weightTheoretical: 124.550625 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGKGSSKGHT PREAKDNLKS TQLLSVIDAI SEGPIEGPVD GLKSVLLNST PVLDTEGNTN ISGVTVVFRA GEQEQTPPEG FESSGSETV LGTEVKYDTP ITRTITSANI DRLRFTFGVQ ALVETTSKGD RNPSEVRLLV QIQRNGGWVT EKDITIKGKT T SQYLASVV ...String:
MGKGSSKGHT PREAKDNLKS TQLLSVIDAI SEGPIEGPVD GLKSVLLNST PVLDTEGNTN ISGVTVVFRA GEQEQTPPEG FESSGSETV LGTEVKYDTP ITRTITSANI DRLRFTFGVQ ALVETTSKGD RNPSEVRLLV QIQRNGGWVT EKDITIKGKT T SQYLASVV MGNLPPRPFN IRMRRMTPDS TTDQLQNKTL WSSYTEIIDV KQCYPNTALV GVQVDSEQFG SQQVSRNYHL RG RILQVPS NYNPQTRQYS GIWDGTFKPA YSNNMAWCLW DMLTHPRYGM GKRLGAADVD KWALYVIGQY CDQSVPDGFG GTE PRITCN AYLTTQRKAW DVLSDFCSAM RCMPVWNGQT LTFVQDRPSD KTWTYNRSNV VMPDDGAPFR YSFSALKDRH NAVE VNWID PNNGWETATE LVEDTQAIAR YGRNVTKMDA FGCTSRGQAH RAGLWLIKTE LLETQTVDFS VGAEGLRHVP GDVIE ICDD DYAGISTGGR VLAVNSQTRT LTLDREITLP SSGTALISLV DGSGNPVSVE VQSVTDGVKV KVSRVPDGVA EYSVWE LKL PTLRQRLFRC VSIRENDDGT YAITAVQHVP EKEAIVDNGA HFDGEQSGTV NGVTPPAVQH LTAEVTADSG EYQVLAR WD TPKVVKGVSF LLRLTVTADD GSERLVSTAR TTETTYRFTQ LALGNYRLTV RAVNAWGQQG DPASVSFRIA APAAPSRI E LTPGYFQITA TPHLAVYDPT VQFEFWFSEK QIADIRQVET STRYLGTALY WIAASINIKP GHDYYFYIRS VNTVGKSAF VEAVGRASDD AEGYLDFFKG KITESHLGKE LLEKVELTED NASRLEEFSK EWKDASDKWN AMWAVKIEQT KDGKHYVAGI GLSMEDTEE GKLSQFLVAA NRIAFIDPAN GNETPMFVAQ GNQIFMNDVF LKRLTAPTIT SGGNPPAFSL TPDGKLTAKN A DISGSVNA NSGTLSNVTI AENCTINGTL RAEKIVGDIV KAASAAFPRQ RESSVDWPSG TRTVTVTDDH PFDRQIVVLP LT FRGSKRT VSGRTTYSMC YLKVLMNGAV IYDGAANEAV QVFSRIVDMP AGRGNVILTF TLTSTRHSAD IPPYTFASDV QVM VIKKQA LGISVV

UniProtKB: Tip attachment protein J

-
Macromolecule #3: Tail tip protein L

MacromoleculeName: Tail tip protein L / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage lambda (virus)
Molecular weightTheoretical: 25.730578 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MQDIRQETLN ECTRAEQSAS VVLWEIDLTE VGGERYFFCN EQNEKGEPVT WQGRQYQPYP IQGSGFELNG KGTSTRPTLT VSNLYGMVT GMAEDMQSLV GGTVVRRKVY ARFLDAVNFV NGNSYADPEQ EVISRWRIEQ CSELSAVSAS FVLSTPTETD G AVFPGRIM ...String:
MQDIRQETLN ECTRAEQSAS VVLWEIDLTE VGGERYFFCN EQNEKGEPVT WQGRQYQPYP IQGSGFELNG KGTSTRPTLT VSNLYGMVT GMAEDMQSLV GGTVVRRKVY ARFLDAVNFV NGNSYADPEQ EVISRWRIEQ CSELSAVSAS FVLSTPTETD G AVFPGRIM LANTCTWTYR GDECGYSGPA VADEYDQPTS DITKDKCSKC LSGCKFRNNV GNFGGFLSIN KLSQ

UniProtKB: Tail tip protein L

-
Macromolecule #4: Tape measure protein

MacromoleculeName: Tape measure protein / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage lambda (virus)
Molecular weightTheoretical: 92.39343 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAEPVGDLVV DLSLDAARFD EQMARVRRHF SGTESDAKKT AAVVEQSLSR QALAAQKAGI SVGQYKAAMR MLPAQFTDVA TQLAGGQSP WLILLQQGGQ VKDSFGGMIP MFRGLAGAIT LPMVGATSLA VATGALAYAW YQGNSTLSDF NKTLVLSGNQ A GLTADRML ...String:
MAEPVGDLVV DLSLDAARFD EQMARVRRHF SGTESDAKKT AAVVEQSLSR QALAAQKAGI SVGQYKAAMR MLPAQFTDVA TQLAGGQSP WLILLQQGGQ VKDSFGGMIP MFRGLAGAIT LPMVGATSLA VATGALAYAW YQGNSTLSDF NKTLVLSGNQ A GLTADRML VLSRAGQAAG LTFNQTSESL SALVKAGVSG EAQIASISQS VARFSSASGV EVDKVAEAFG KLTTDPTSGL TA MARQFHN VSAEQIAYVA QLQRSGDEAG ALQAANEAAT KGFDDQTRRL KENMGTLETW ADRTARAFKS MWDAVLDIGR PDT AQEMLI KAEAAYKKAD DIWNLRKDDY FVNDEARARY WDDREKARLA LEAARKKAEQ QTQQDKNAQQ QSDTEASRLK YTEE AQKAY ERLQTPLEKY TARQEELNKA LKDGKILQAD YNTLMAAAKK DYEATLKKPK QSSVKVSAGD RQEDSAHAAL LTLQA ELRT LEKHAGANEK ISQQRRDLWK AESQFAVLEE AAQRRQLSAQ EKSLLAHKDE TLEYKRQLAA LGDKVTYQER LNALAQ QAD KFAQQQRAKR AAIDAKSRGL TDRQAEREAT EQRLKEQYGD NPLALNNVMS EQKKTWAAED QLRGNWMAGL KSGWSEW EE SATDSMSQVK SAATQTFDGI AQNMAAMLTG SEQNWRSFTR SVLSMMTEIL LKQAMVGIVG SIGSAIGGAV GGGASASG G TAIQAAAAKF HFATGGFTGT GGKYEPAGIV HRGEFVFTKE ATSRIGVGNL YRLMRGYATG GYVGTPGSMA DSRSQASGT FEQNNHVVIN NDGTNGQIGP AALKAVYDMA RKGARDEIQT QMRDGGLFSG GGR

UniProtKB: Tape measure protein

-
Macromolecule #5: Tail tip assembly protein I

MacromoleculeName: Tail tip assembly protein I / type: protein_or_peptide / ID: 5 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage lambda (virus)
Molecular weightTheoretical: 23.14659 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAATHTLPLA SPGMARICLY GDLQRFGRRI DLRVKTGAEA IRALATQLPA FRQKLSDGWY QVRIAGRDVS TSGLTAQLHE TLPDGAVIH IVPRVAGAKS GGVFQIVLGA AAIAGSFFTA GATLAAWGAA IGAGGMTGIL FSLGASMVLG GVAQMLAPKA R TPRIQTTD ...String:
MAATHTLPLA SPGMARICLY GDLQRFGRRI DLRVKTGAEA IRALATQLPA FRQKLSDGWY QVRIAGRDVS TSGLTAQLHE TLPDGAVIH IVPRVAGAKS GGVFQIVLGA AAIAGSFFTA GATLAAWGAA IGAGGMTGIL FSLGASMVLG GVAQMLAPKA R TPRIQTTD NGKQNTYFSS LDNMVAQGNV LPVLYGEMRV GSRVVSQEIS TADEGDGGQV VVIGR

UniProtKB: Tail tip assembly protein I

-
Macromolecule #6: Tail tube protein

MacromoleculeName: Tail tube protein / type: protein_or_peptide / ID: 6 / Number of copies: 24 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage lambda (virus)
Molecular weightTheoretical: 25.831779 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MPVPNPTMPV KGAGTTLWVY KGSGDPYANP LSDVDWSRLA KVKDLTPGEL TAESYDDSYL DDEDADWTAT GQGQKSAGDT SFTLAWMPG EQGQQALLAW FNEGDTRAYK IRFPNGTVDV FRGWVSSIGK AVTAKEVITR TVKVTNVGRP SMAEDRSTVT A ATGMTVTP ...String:
MPVPNPTMPV KGAGTTLWVY KGSGDPYANP LSDVDWSRLA KVKDLTPGEL TAESYDDSYL DDEDADWTAT GQGQKSAGDT SFTLAWMPG EQGQQALLAW FNEGDTRAYK IRFPNGTVDV FRGWVSSIGK AVTAKEVITR TVKVTNVGRP SMAEDRSTVT A ATGMTVTP ASTSVVKGQS TTLTVAFQPE GVTDKSFRAV SADKTKATVS VSGMTITVNG VAAGKVNIPV VSGNGEFAAV AE ITVTAS

UniProtKB: Tail tube protein

-
Macromolecule #7: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 7 / Number of copies: 3 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER / Iron–sulfur cluster

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: NITROGEN

-
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 / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: NONE
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 54547
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