[English] 日本語
Yorodumi
- PDB-5vlz: Backbone model for phage Qbeta capsid -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5vlz
TitleBackbone model for phage Qbeta capsid
Components
  • Capsid protein
  • Maturation protein A2
KeywordsVIRUS / Qbeta / ssRNA / phage
Function / homology
Function and homology information


symbiont-mediated suppression of host cell wall biogenesis / symbiont-mediated suppression of host peptidoglycan biosynthetic process / viral release via suppression of host peptidoglycan biosynthetic process / virion attachment to host cell pilus / T=3 icosahedral viral capsid / adhesion receptor-mediated virion attachment to host cell / viral release from host cell by cytolysis / translation repressor activity / virion component / structural molecule activity / RNA binding
Similarity search - Function
Assembly protein / Phage maturation protein / Levivirus coat protein / Levivirus coat protein / Bacteriophage RNA-type, capsid
Similarity search - Domain/homology
Capsid protein / Maturation protein A2
Similarity search - Component
Biological speciesEscherichia phage Qbeta (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.4 Å
AuthorsCui, Z. / Zhang, J.
Funding support United States, 4items
OrganizationGrant numberCountry
Welch FoundationA-1863 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41GM103832 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U24GM116787 United States
Public Health ServiceGM27099 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2017
Title: Structures of Qβ virions, virus-like particles, and the Qβ-MurA complex reveal internal coat proteins and the mechanism of host lysis.
Authors: Zhicheng Cui / Karl V Gorzelnik / Jeng-Yih Chang / Carrie Langlais / Joanita Jakana / Ry Young / Junjie Zhang /
Abstract: In single-stranded RNA bacteriophages (ssRNA phages) a single copy of the maturation protein binds the genomic RNA (gRNA) and is required for attachment of the phage to the host pilus. For the ...In single-stranded RNA bacteriophages (ssRNA phages) a single copy of the maturation protein binds the genomic RNA (gRNA) and is required for attachment of the phage to the host pilus. For the canonical Qβ the maturation protein, A, has an additional role as the lysis protein, by its ability to bind and inhibit MurA, which is involved in peptidoglycan biosynthesis. Here, we determined structures of Qβ virions, virus-like particles, and the Qβ-MurA complex using single-particle cryoelectron microscopy, at 4.7-Å, 3.3-Å, and 6.1-Å resolutions, respectively. We identified the outer surface of the β-region in A as the MurA-binding interface. Moreover, the pattern of MurA mutations that block Qβ lysis and the conformational changes of MurA that facilitate A binding were found to be due to the intimate fit between A and the region encompassing the closed catalytic cleft of substrate-liganded MurA. Additionally, by comparing the Qβ virion with Qβ virus-like particles that lack a maturation protein, we observed a structural rearrangement in the capsid coat proteins that is required to package the viral gRNA in its dominant conformation. Unexpectedly, we found a coat protein dimer sequestered in the interior of the virion. This coat protein dimer binds to the gRNA and interacts with the buried α-region of A, suggesting that it is sequestered during the early stage of capsid formation to promote the gRNA condensation required for genome packaging. These internalized coat proteins are the most asymmetrically arranged major capsid proteins yet observed in virus structures.
History
DepositionApr 26, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 18, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Author supporting evidence / Other / Category: cell / pdbx_audit_support
Item: _cell.Z_PDB / _cell.length_a ..._cell.Z_PDB / _cell.length_a / _cell.length_b / _cell.length_c / _cell.volume / _pdbx_audit_support.funding_organization
Revision 1.2Apr 18, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Jul 18, 2018Group: Data collection / Experimental preparation / Category: em_sample_support / Item: _em_sample_support.grid_type
Revision 1.4Dec 18, 2019Group: Author supporting evidence / Other / Category: atom_sites / pdbx_audit_support
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _pdbx_audit_support.funding_organization
Revision 1.5Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-8709
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-8709
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
AH: Capsid protein
GN: Capsid protein
HA: Capsid protein
HB: Capsid protein
HC: Capsid protein
HD: Capsid protein
HE: Capsid protein
HF: Capsid protein
HG: Capsid protein
HH: Capsid protein
HI: Capsid protein
AI: Capsid protein
HJ: Capsid protein
HK: Capsid protein
HL: Capsid protein
HM: Capsid protein
HN: Capsid protein
IA: Capsid protein
IB: Capsid protein
IC: Capsid protein
ID: Capsid protein
IE: Capsid protein
AJ: Capsid protein
IF: Capsid protein
IG: Capsid protein
IH: Capsid protein
II: Capsid protein
IJ: Capsid protein
IK: Capsid protein
IL: Capsid protein
IM: Capsid protein
IN: Capsid protein
JA: Capsid protein
AK: Capsid protein
JB: Capsid protein
JC: Capsid protein
JD: Capsid protein
JE: Capsid protein
JF: Capsid protein
JG: Capsid protein
JH: Capsid protein
JI: Capsid protein
JJ: Capsid protein
JK: Capsid protein
AL: Capsid protein
JL: Capsid protein
JM: Capsid protein
JN: Capsid protein
KA: Capsid protein
KB: Capsid protein
KC: Capsid protein
KD: Capsid protein
KE: Capsid protein
KF: Capsid protein
KG: Capsid protein
AM: Capsid protein
KH: Capsid protein
KI: Capsid protein
KJ: Capsid protein
KK: Capsid protein
KL: Capsid protein
KM: Capsid protein
KN: Capsid protein
LA: Capsid protein
LB: Capsid protein
LC: Capsid protein
AN: Capsid protein
LD: Capsid protein
LE: Capsid protein
LF: Capsid protein
LG: Capsid protein
LH: Capsid protein
LI: Capsid protein
LJ: Capsid protein
LK: Capsid protein
LL: Capsid protein
LM: Capsid protein
BA: Capsid protein
LN: Capsid protein
MA: Capsid protein
MB: Capsid protein
MC: Capsid protein
MD: Capsid protein
ME: Capsid protein
MF: Capsid protein
MG: Capsid protein
MH: Capsid protein
MI: Capsid protein
BB: Capsid protein
MJ: Capsid protein
MK: Capsid protein
ML: Capsid protein
MM: Capsid protein
MN: Capsid protein
NA: Capsid protein
BC: Capsid protein
BD: Capsid protein
BE: Capsid protein
BF: Capsid protein
BG: Capsid protein
BH: Capsid protein
BI: Capsid protein
BJ: Capsid protein
BK: Capsid protein
BL: Capsid protein
BM: Capsid protein
AA: Capsid protein
BN: Capsid protein
CA: Capsid protein
CB: Capsid protein
CC: Capsid protein
CD: Capsid protein
CE: Capsid protein
CF: Capsid protein
CG: Capsid protein
CH: Capsid protein
CI: Capsid protein
AB: Capsid protein
CJ: Capsid protein
CK: Capsid protein
CL: Capsid protein
CM: Capsid protein
CN: Capsid protein
DA: Capsid protein
DB: Capsid protein
DC: Capsid protein
DD: Capsid protein
DE: Capsid protein
AC: Capsid protein
DF: Capsid protein
DG: Capsid protein
DH: Capsid protein
DI: Capsid protein
DJ: Capsid protein
DK: Capsid protein
DL: Capsid protein
DN: Capsid protein
EA: Capsid protein
AD: Capsid protein
EB: Capsid protein
EC: Capsid protein
ED: Capsid protein
EE: Capsid protein
EF: Capsid protein
EG: Capsid protein
EH: Capsid protein
EI: Capsid protein
EJ: Maturation protein A2
EK: Capsid protein
AE: Capsid protein
EL: Capsid protein
EM: Capsid protein
EN: Capsid protein
FA: Capsid protein
FB: Capsid protein
FC: Capsid protein
FD: Capsid protein
FE: Capsid protein
FF: Capsid protein
AF: Capsid protein
FH: Capsid protein
FI: Capsid protein
FJ: Capsid protein
FK: Capsid protein
FL: Capsid protein
FM: Capsid protein
FN: Capsid protein
GA: Capsid protein
GB: Capsid protein
GC: Capsid protein
AG: Capsid protein
GD: Capsid protein
GE: Capsid protein
GF: Capsid protein
GG: Capsid protein
GH: Capsid protein
GI: Capsid protein
GJ: Capsid protein
GK: Capsid protein
GL: Capsid protein
GM: Capsid protein


Theoretical massNumber of molelcules
Total (without water)2,616,866181
Polymers2,616,866181
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

-
Components

#1: Protein ...
Capsid protein / CP / Coat protein


Mass: 14268.071 Da / Num. of mol.: 180 / Source method: isolated from a natural source / Source: (natural) Escherichia phage Qbeta (virus) / References: UniProt: P03615
#2: Protein Maturation protein A2 / MP / A2 protein


Mass: 48613.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia phage Qbeta (virus) / References: UniProt: Q8LTE2

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: Enterobacteria phage Qbeta / Type: VIRUS / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Enterobacteria phage Qbeta (virus)
Details of virusEmpty: NO / Enveloped: NO / Isolate: SPECIES / Type: VIRION
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: C-flat-1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295 K
Details: Blotted for 6s, Plunged into liquid ethane (FEI VITROBOT MARK III)

-
Electron microscopy imaging

MicroscopyModel: JEOL 3200FSC
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 30000 X
Specimen holderCryogen: NITROGEN
Image recordingAverage exposure time: 0.2 sec. / Electron dose: 1 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

-
Processing

EM software
IDNameVersionCategory
1EMAN2particle selection
2SerialEMimage acquisition
4CTFFIND4CTF correction
7UCSF Chimeramodel fitting
12RELION1.43D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 46471 / Symmetry type: POINT

+
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