[English] 日本語
Yorodumi
- PDB-6b23: Capsid protein and C-terminal part of CpmB protein in the Staphyl... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6b23
TitleCapsid protein and C-terminal part of CpmB protein in the Staphylococcus aureus pathogenicity island 1 80alpha-derived procapsid
Components
  • Capsid morphogenesis B protein
  • Major head protein
KeywordsVIRUS / major capsid protein / HK97-like fold / scaffolding protein / procapsid
Function / homologyPathogenicity island protein gp6, Staphylococcus / Pathogenicity island protein gp6 superfamily / Pathogenicity island protein gp6 in Staphylococcus / : / Phage capsid / Phage capsid family / viral capsid / Major capsid protein / Capsid morphogenesis B protein
Function and homology information
Biological speciesStaphylococcus phage 80alpha (virus)
Staphylococcus aureus (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsKizziah, J.L. / Dearborn, A.D. / Dokland, T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI083255 United States
CitationJournal: Elife / Year: 2017
Title: Competing scaffolding proteins determine capsid size during mobilization of pathogenicity islands.
Authors: Altaira D Dearborn / Erin A Wall / James L Kizziah / Laura Klenow / Laura K Parker / Keith A Manning / Michael S Spilman / John M Spear / Gail E Christie / Terje Dokland /
Abstract: pathogenicity islands (SaPIs), such as SaPI1, exploit specific helper bacteriophages, like 80α, for their high frequency mobilization, a process termed 'molecular piracy'. SaPI1 redirects the ... pathogenicity islands (SaPIs), such as SaPI1, exploit specific helper bacteriophages, like 80α, for their high frequency mobilization, a process termed 'molecular piracy'. SaPI1 redirects the helper's assembly pathway to form small capsids that can only accommodate the smaller SaPI1 genome, but not a complete phage genome. SaPI1 encodes two proteins, CpmA and CpmB, that are responsible for this size redirection. We have determined the structures of the 80α and SaPI1 procapsids to near-atomic resolution by cryo-electron microscopy, and show that CpmB competes with the 80α scaffolding protein (SP) for a binding site on the capsid protein (CP), and works by altering the angle between capsomers. We probed these interactions genetically and identified second-site suppressors of lethal mutations in SP. Our structures show, for the first time, the detailed interactions between SP and CP in a bacteriophage, providing unique insights into macromolecular assembly processes.
History
DepositionSep 19, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 18, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2018Group: Database references / Structure summary / Category: citation / em_entity_assembly / Item: _citation.title / _em_entity_assembly.entity_id_list
Revision 1.2Mar 28, 2018Group: Data collection / Database references / Category: citation / Item: _citation.title
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list / refine
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _refine.ls_d_res_high / _refine.ls_d_res_low

-
Structure visualization

Movie
  • Biological unit as complete icosahedral assembly
  • Imaged by Jmol
  • Download
  • Biological unit as icosahedral pentamer
  • Imaged by Jmol
  • Download
  • Biological unit as icosahedral 23 hexamer
  • Imaged by Jmol
  • Download
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-7035
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Major head protein
a: Capsid morphogenesis B protein
b: Capsid morphogenesis B protein
B: Major head protein
C: Major head protein
c: Capsid morphogenesis B protein
D: Major head protein
d: Capsid morphogenesis B protein


Theoretical massNumber of molelcules
Total (without water)180,5128
Polymers180,5128
Non-polymers00
Water00
1
A: Major head protein
a: Capsid morphogenesis B protein
b: Capsid morphogenesis B protein
B: Major head protein
C: Major head protein
c: Capsid morphogenesis B protein
D: Major head protein
d: Capsid morphogenesis B protein
x 60


Theoretical massNumber of molelcules
Total (without water)10,830,748480
Polymers10,830,748480
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Major head protein
a: Capsid morphogenesis B protein
b: Capsid morphogenesis B protein
B: Major head protein
C: Major head protein
c: Capsid morphogenesis B protein
D: Major head protein
d: Capsid morphogenesis B protein
x 5


  • icosahedral pentamer
  • 903 kDa, 40 polymers
Theoretical massNumber of molelcules
Total (without water)902,56240
Polymers902,56240
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Major head protein
a: Capsid morphogenesis B protein
b: Capsid morphogenesis B protein
B: Major head protein
C: Major head protein
c: Capsid morphogenesis B protein
D: Major head protein
d: Capsid morphogenesis B protein
x 6


  • icosahedral 23 hexamer
  • 1.08 MDa, 48 polymers
Theoretical massNumber of molelcules
Total (without water)1,083,07548
Polymers1,083,07548
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

-
Components

#1: Protein
Major head protein / Capsid protein


Mass: 36846.883 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus phage 80alpha (virus) / Gene: orf47 / Production host: Staphylococcus aureus (bacteria) / Strain (production host): RN4220 / References: UniProt: A4ZFB3
#2: Protein
Capsid morphogenesis B protein


Mass: 8281.234 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: ERS072840_02265 / Production host: Staphylococcus aureus (bacteria) / Strain (production host): ST63 / References: UniProt: O54465

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Lysogenic 80alpha with small terminase / Type: VIRUS
Details: Lysogenic 80alpha with small terminase gene deletion
Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 10.81 MDa / Experimental value: NO
Source (natural)Organism: Staphylococcus phage 80alpha (virus)
Source (recombinant)Organism: Staphylococcus aureus (bacteria) / Strain: RN4220
Details of virusEmpty: YES / Enveloped: NO / Isolate: SPECIES / Type: VIRION
Natural hostOrganism: Staphylococcus aureus
Virus shellName: Procapsid / Diameter: 546 nm / Triangulation number (T number): 7
Buffer solutionpH: 7.8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 40 e/Å2 / Film or detector model: DIRECT ELECTRON DE-20 (5k x 3k)

-
Processing

SoftwareName: REFMAC / Version: 5.8.0088 / Classification: refinement
CTF correctionType: PHASE FLIPPING ONLY
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 14087 / Symmetry type: POINT
RefinementResolution: 3.7→3.7 Å / Cor.coef. Fo:Fc: 0.864 / SU B: 61.235 / SU ML: 0.676 / ESU R: 0.644
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rwork0.4199 --
obs0.4199 98552 100 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 238.756 Å2
Baniso -1Baniso -2Baniso -3
1--1.77 Å21.53 Å25.05 Å2
2---4.46 Å21.12 Å2
3---6.23 Å2
Refinement stepCycle: 1 / Total: 9854
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0070.0210020
ELECTRON MICROSCOPYr_bond_other_d0.0010.029716
ELECTRON MICROSCOPYr_angle_refined_deg1.0021.96613488
ELECTRON MICROSCOPYr_angle_other_deg0.845322478
ELECTRON MICROSCOPYr_dihedral_angle_1_deg5.55651224
ELECTRON MICROSCOPYr_dihedral_angle_2_deg37.08426.208480
ELECTRON MICROSCOPYr_dihedral_angle_3_deg15.303151934
ELECTRON MICROSCOPYr_dihedral_angle_4_deg11.3171532
ELECTRON MICROSCOPYr_chiral_restr0.0610.21500
ELECTRON MICROSCOPYr_gen_planes_refined0.0040.0211252
ELECTRON MICROSCOPYr_gen_planes_other0.0010.022148
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it3.06623.8884920
ELECTRON MICROSCOPYr_mcbond_other3.06623.8884919
ELECTRON MICROSCOPYr_mcangle_it5.57835.8276136
ELECTRON MICROSCOPYr_mcangle_other5.57735.8276137
ELECTRON MICROSCOPYr_scbond_it2.31524.1545100
ELECTRON MICROSCOPYr_scbond_other2.31424.1545101
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other4.59536.1637353
ELECTRON MICROSCOPYr_long_range_B_refined14.6235621
ELECTRON MICROSCOPYr_long_range_B_other14.6235622
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
LS refinement shellResolution: 3.76→3.858 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.577 7229 -
Rfree-0 -
obs--100 %

+
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