[English] 日本語
Yorodumi
- EMDB-14090: Unique vertex of the phicrAss001 virion with C5 symmetry imposed -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-14090
TitleUnique vertex of the phicrAss001 virion with C5 symmetry imposed
Map data
Sample
  • Virus: Bacteroides phage crAss001 (virus)
    • Protein or peptide: Major capsid protein gp32
    • Protein or peptide: Auxiliary capsid protein gp36
    • Protein or peptide: Portal vertex capsid protein gp57
    • Protein or peptide: Head fiber trimer protein gp21
    • Protein or peptide: Portal protein gp20
  • Ligand: MAGNESIUM ION
Function / homology
Function and homology information


viral capsid, decoration / virion component / viral capsid / symbiont entry into host cell / virion attachment to host cell
Similarity search - Function
Bacteriophage B103, Gp8, head fibre / Head fiber protein
Similarity search - Domain/homology
Portal protein / Portal vertex auxiliary protein / Head fiber trimeric protein / Auxiliary capsid protein / Major capsid protein
Similarity search - Component
Biological speciesBacteroides phage crAss001 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.32 Å
AuthorsBayfield OW / Shkoporov AN / Yutin N / Khokhlova EV / Smith JLR / Hawkins DEDP / Koonin EV / Hill C / Antson AA
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
Citation
Journal: Nature / Year: 2023
Title: Structural atlas of a human gut crassvirus.
Authors: Oliver W Bayfield / Andrey N Shkoporov / Natalya Yutin / Ekaterina V Khokhlova / Jake L R Smith / Dorothy E D P Hawkins / Eugene V Koonin / Colin Hill / Alfred A Antson /
Abstract: CrAssphage and related viruses of the order Crassvirales (hereafter referred to as crassviruses) were originally discovered by cross-assembly of metagenomic sequences. They are the most abundant ...CrAssphage and related viruses of the order Crassvirales (hereafter referred to as crassviruses) were originally discovered by cross-assembly of metagenomic sequences. They are the most abundant viruses in the human gut, are found in the majority of individual gut viromes, and account for up to 95% of the viral sequences in some individuals. Crassviruses are likely to have major roles in shaping the composition and functionality of the human microbiome, but the structures and roles of most of the virally encoded proteins are unknown, with only generic predictions resulting from bioinformatic analyses. Here we present a cryo-electron microscopy reconstruction of Bacteroides intestinalis virus ΦcrAss001, providing the structural basis for the functional assignment of most of its virion proteins. The muzzle protein forms an assembly about 1 MDa in size at the end of the tail and exhibits a previously unknown fold that we designate the 'crass fold', that is likely to serve as a gatekeeper that controls the ejection of cargos. In addition to packing the approximately 103 kb of virus DNA, the ΦcrAss001 virion has extensive storage space for virally encoded cargo proteins in the capsid and, unusually, within the tail. One of the cargo proteins is present in both the capsid and the tail, suggesting a general mechanism for protein ejection, which involves partial unfolding of proteins during their extrusion through the tail. These findings provide a structural basis for understanding the mechanisms of assembly and infection of these highly abundant crassviruses.
#1: Journal: Res Sq / Year: 2023
Title: Structural atlas of the most abundant human gut virus
Authors: Antson A / Bayfield O / Shkoporov A / Yutin N / Khokhlova E / Smith J / Hawkins D / Koonin E / Hill C
History
DepositionDec 24, 2021-
Header (metadata) releaseMar 29, 2023-
Map releaseMar 29, 2023-
UpdateMay 24, 2023-
Current statusMay 24, 2023Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_14090.png

Downloads & links

-
Map

FileDownload / File: emd_14090.map.gz / Format: CCP4 / Size: 89.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.39 Å/pix.
x 286 pix.
= 398.712 Å		1.39 Å/pix.
x 286 pix.
= 398.712 Å		1.39 Å/pix.
x 286 pix.
= 398.712 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.3941 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.6689095 - 0.944234
Average (Standard dev.)0.004187738 (±0.028142476)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions286286286
Spacing286286286
CellA=B=C: 398.71204 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: #1

Fileemd_14090_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: #2

Fileemd_14090_additional_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Bacteroides phage crAss001

EntireName: Bacteroides phage crAss001 (virus)
Components
  • Virus: Bacteroides phage crAss001 (virus)
    • Protein or peptide: Major capsid protein gp32
    • Protein or peptide: Auxiliary capsid protein gp36
    • Protein or peptide: Portal vertex capsid protein gp57
    • Protein or peptide: Head fiber trimer protein gp21
    • Protein or peptide: Portal protein gp20
  • Ligand: MAGNESIUM ION

-
Supramolecule #1: Bacteroides phage crAss001

SupramoleculeName: Bacteroides phage crAss001 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#5 / NCBI-ID: 2301731 / Sci species name: Bacteroides phage crAss001 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No

-
Macromolecule #1: Major capsid protein gp32

MacromoleculeName: Major capsid protein gp32 / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Bacteroides phage crAss001 (virus)
Molecular weightTheoretical: 57.098598 KDa
SequenceString: MAGKLGKFQM LGFQHWKGLT SDNHLGAIFQ QAPQKATNLM VQLLAFYRGK SLDTFLNSFP TREFEDDNEY YWDVIGSSRR NIPLVEARD ENGVVVAANA ANVGVGTSPF YLVFPEDWFA DGEVIVGNLN QVYPFRILGD ARMEGTNAVY KVELMGGNTQ G VPAERLQQ ...String:
MAGKLGKFQM LGFQHWKGLT SDNHLGAIFQ QAPQKATNLM VQLLAFYRGK SLDTFLNSFP TREFEDDNEY YWDVIGSSRR NIPLVEARD ENGVVVAANA ANVGVGTSPF YLVFPEDWFA DGEVIVGNLN QVYPFRILGD ARMEGTNAVY KVELMGGNTQ G VPAERLQQ GERFSIEFAP VEKELSRKVG DVRFTSPVSM RNEWTTIRIQ HKVAGNKLNK KLAMGIPMVR NLESGKQVKD TA NMWMHYV DWEVELQFDE YKNNAMAWGT SNRNLNGEYM NFGKSGNAIK TGAGIFEQTE VANTMYYNTF SLKLLEDALY ELS ASKLAM DDRLFVIKTG ERGAIQFHKE VLKTVSGWTT FVLDNNSTRV VEKVQSRLHS NALSAGFQFV EYKAPNGVRV RLDV DPFYD DPVRNKILHP MGGVAFSYRY DIWYIGTMDQ PNIFKCKIKG DNEYRGYQWG IRNPFTGQKG NPYMSFDEDS AVIHR MATL GVCVLDPTRT MSLIPAILQG

-
Macromolecule #2: Auxiliary capsid protein gp36

MacromoleculeName: Auxiliary capsid protein gp36 / type: protein_or_peptide / ID: 2 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Bacteroides phage crAss001 (virus)
Molecular weightTheoretical: 36.154094 KDa
SequenceString: MVISINQVRQ LYVAKALKAN TAALTTAGDI VPKADTAKTT LYFQSMSPAG IVASDKINLK HVLYAKATPS EALAHKLVRY SVTLDADVS ATPVAGQNYI LRLAFRQYIG LSEEDQYFKY GEVIARSGMT ASDFYKKMAI SLAKNLENKT ESTPLVNIYL I SAAAASTD ...String:
MVISINQVRQ LYVAKALKAN TAALTTAGDI VPKADTAKTT LYFQSMSPAG IVASDKINLK HVLYAKATPS EALAHKLVRY SVTLDADVS ATPVAGQNYI LRLAFRQYIG LSEEDQYFKY GEVIARSGMT ASDFYKKMAI SLAKNLENKT ESTPLVNIYL I SAAAASTD VPVTSATKES DLTATDYNQI IIEETEQPWV LGMMPQAFIP FTPQFLTITV DGEDRLWGVA TVVTPTKTVP DG HLIADLE YFCMGARGDI YRGMGYPNII KTTYLVDPGA VYDVLDIHYF YTGSNESVQK SEKTITLVAV DDGSHTAMNA LIG AINTAS GLTIATL

-
Macromolecule #3: Portal vertex capsid protein gp57

MacromoleculeName: Portal vertex capsid protein gp57 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Bacteroides phage crAss001 (virus)
Molecular weightTheoretical: 11.32708 KDa
SequenceString:
MAGQQGIYCA PDNIVPNRDR VDVGCAPDGA MQLWVMEYEV TGIGKGCAMC KAINPQQAEM LLKSNGIYNG SSYLYKVTRI EQVIVPPCN GLMAEQVVTY KDVVS

-
Macromolecule #4: Head fiber trimer protein gp21

MacromoleculeName: Head fiber trimer protein gp21 / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Bacteroides phage crAss001 (virus)
Molecular weightTheoretical: 10.294763 KDa
SequenceString:
MKTLRTLKIS PNAPDINSVW LYKGTMKYFN NGEWETIGGE SEPYVLPAAT TSTIGGVKKA TNVGNLATGA ELATVVTKVN AILSALKVA DIMVEDAN

-
Macromolecule #5: Portal protein gp20

MacromoleculeName: Portal protein gp20 / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Bacteroides phage crAss001 (virus)
Molecular weightTheoretical: 93.122211 KDa
SequenceString: MADFLNFPRQ MLPFSKKTKQ WRKDCLLWAN QKTFFNYSLV RKSVIHKKIN YDLLNGRLHM SDLELVLNPD GIKAAYIPDR LQHYPIMNS KLNVLRGEES KRVFDFKVVV TNPNAISEIE DNKKNELLQR LQEMITDTSI SEDEYNIKLE KLNDYYTYEW Q DIREVRAN ...String:
MADFLNFPRQ MLPFSKKTKQ WRKDCLLWAN QKTFFNYSLV RKSVIHKKIN YDLLNGRLHM SDLELVLNPD GIKAAYIPDR LQHYPIMNS KLNVLRGEES KRVFDFKVVV TNPNAISEIE DNKKNELLQR LQEMITDTSI SEDEYNIKLE KLNDYYTYEW Q DIREVRAN ELLNHYIKEY DIPLIFNNGF MDAMTCGEEI YQCDIVGGEP VIERVNPLKI RIFKSGYSNK VEDADMIILE DY WSPGRVI DTYYDVLSPK DIKYIETMPD YIGQGAVDQM DNIDERYGFV NQNMIGDEIT VRDGTYFFDP ANLFTEGIAN SLL PYDLAG NLRVLRLYWK SKRKILKVKS YDPETGEEEW NFYPENYVVN KEAGEEVQSF WVNEAWEGTM IGNEIFVNMR PRLI QYNRL NNPSRCHFGI VGSIYNLNDS RPFSLVDMMK PYNYLYDAIH DRLNKAIASN WGSILELDLS KVPKGWDVGK WMYYA RVNH IAVIDSFKEG TIGASTGKLA GALNNAGKGM IETNIGNYIQ QQINLLEFIK MEMADVAGIS KQREGQISQR ETVGGV ERA TLQSSHITEW LFTIHDDVKK RALECFLETA KVALKGRNKK FQYILSDTST RVMEIDGDEF AEADYGLVVD NSNGTQE LQ QKLDTLAQAA LQTQTLSFST ITKLYTSSSL AEKQRLIEKD EKQIRERQAQ AQKEQLEAQQ QIAAMQQQQK EAELLQKE E ANIRDNQTKI IIAQIQSEGG PDEEDGIMID DYSPEAKANL AEKIREFDEK LKLDKDKLKL DKKKAETDAS IKRQALRKK SSTTNK

-
Macromolecule #6: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 6 / Number of copies: 6 / Formula: MG
Molecular weightTheoretical: 24.305 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
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: 1.5 µm / Nominal defocus min: 0.3 µm
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Average electron dose: 51.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER / Software - Name: RELION (ver. 3.1)
Final reconstructionApplied symmetry - Point group: C5 (5 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.32 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 122709
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL / Overall B value: 157
Output model

PDB-7qoh:
Unique vertex of the phicrAss001 virion with C5 symmetry imposed

+
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