[English] 日本語
Yorodumi
- PDB-9tif: Phage 812 baseplate in the pre-contraction state - lower arm -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9tif
TitlePhage 812 baseplate in the pre-contraction state - lower arm
Components
  • CBM-cenC domain-containing protein
  • ORF56
  • ORF57
  • ORF63
  • ORF64
  • ORF65
  • ORF67
  • ORF68
KeywordsVIRUS / phage / baseplate
Function / homology
Function and homology information


symbiont-mediated cytolysis of host cell / hydrolase activity, acting on glycosyl bonds / cysteine-type peptidase activity / proteolysis
Similarity search - Function
Protein of unknown function DUF2977 / Protein of unknown function (DUF2977) / : / Lid domain of Phi812 weld protein / : / ORF68-like, C-terminal domain / Domain of unknown function DUF4815 / Domain of unknown function (DUF4815) / : / Baseplate wedge 3 tail fiber network component ...Protein of unknown function DUF2977 / Protein of unknown function (DUF2977) / : / Lid domain of Phi812 weld protein / : / ORF68-like, C-terminal domain / Domain of unknown function DUF4815 / Domain of unknown function (DUF4815) / : / Baseplate wedge 3 tail fiber network component / CHAP domain profile. / CHAP domain / CHAP domain / NlpC/P60 domain profile. / Endopeptidase, NLPC/P60 domain / Carbohydrate-binding, CenC-like / Carbohydrate binding domain / Papain-like cysteine peptidase superfamily
Similarity search - Domain/homology
CBM-cenC domain-containing protein / ORF68 / ORF67 / ORF65 / ORF64 / ORF63 / ORF57 / ORF56
Similarity search - Component
Biological speciesStaphylococcus phage 812K1/420 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.6 Å
AuthorsBinovsky, J. / Plevka, P.
Funding supportEuropean Union, Czech Republic, 2items
OrganizationGrant numberCountry
European Research Council (ERC)101043452European Union
Other governmentLX22NP05103 Czech Republic
CitationJournal: To Be Published
Title: Conformational changes of baseplate regulating tail contraction of Staphylococcus phage 812
Authors: Binovsky, J. / Plevka, P.
History
DepositionDec 5, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 20, 2026Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CBM-cenC domain-containing protein
B: CBM-cenC domain-containing protein
D: ORF64
E: ORF64
F: ORF57
G: ORF67
H: ORF65
I: ORF64
J: CBM-cenC domain-containing protein
K: ORF64
L: ORF64
M: ORF56
N: ORF64
O: ORF64
P: ORF64
Q: ORF64
R: ORF64
S: ORF68
T: ORF68
U: ORF68
V: ORF64
b: ORF63
c: ORF64
d: ORF65
e: ORF65
f: ORF65
g: ORF65
h: ORF65


Theoretical massNumber of molelcules
Total (without water)1,633,10728
Polymers1,633,10728
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

-
Components

-
Protein , 8 types, 28 molecules ABJDEIKLNOPQRVcFGHdefghMSTUb

#1: Protein CBM-cenC domain-containing protein


Mass: 72654.742 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Staphylococcus phage 812K1/420 (virus) / References: UniProt: A0A0U1UXW5
#2: Protein
ORF64


Mass: 19259.613 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Staphylococcus phage 812K1/420 (virus) / References: UniProt: Q6Y7Q3
#3: Protein ORF57 / Putative cysteine protease


Mass: 34645.887 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus phage 812K1/420 (virus) / References: UniProt: Q6Y7R0
#4: Protein ORF67 / Putative DUF2977 domain protein


Mass: 14627.471 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus phage 812K1/420 (virus) / References: UniProt: Q6Y7Q0
#5: Protein
ORF65


Mass: 129262.961 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Staphylococcus phage 812K1/420 (virus) / References: UniProt: Q6Y7Q2
#6: Protein ORF56 / Putative CHAP domain protein


Mass: 91364.289 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus phage 812K1/420 (virus) / References: UniProt: Q6Y7R1
#7: Protein ORF68 / Putative receptor binding protein


Mass: 50474.078 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Staphylococcus phage 812K1/420 (virus) / References: UniProt: Q6Y7P9
#8: Protein ORF63


Mass: 116389.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus phage 812K1/420 (virus) / References: UniProt: Q6Y7Q4

-
Details

Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Staphylococcus phage 812K1/420 / Type: VIRUS
Details: Propagated in S. aureus SA 812 (CCM 4028) planktonic culture and purified on a CsCl gradient.
Entity ID: all / Source: NATURAL
Source (natural)Organism: Staphylococcus phage 812K1/420 (virus)
Details of virusEmpty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMtrisTris1
210 mMsodium chlorideNaCl1
310 mMcalcium chlorideCaCl21
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: 10e9 PFU/ml
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 2 sec. / Electron dose: 40.8 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 26731

-
Processing

EM software
IDNameVersionCategory
1Topazparticle selection
2SerialEMimage acquisition
4GctfCTF correction
7UCSF ChimeraX1.9model fitting
9RELION5initial Euler assignment
10RELION5final Euler assignment
12RELION53D reconstruction
13PHENIX1.21model refinement
CTF correctionType: PHASE FLIPPING ONLY
Particle selectionNum. of particles selected: 64874
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 5.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 22031 / Symmetry type: POINT
Atomic model buildingB value: 191.1 / Protocol: RIGID BODY FIT / Space: REAL
Details: Fitting of previously refined sub-models (e.g. segment A, segment B, segment C, segment DEF, uRBP1-lRBP2, lRBP1-uRBP2 from the lower arm) in ChimeraX as rigid bodies, then relaxing the model ...Details: Fitting of previously refined sub-models (e.g. segment A, segment B, segment C, segment DEF, uRBP1-lRBP2, lRBP1-uRBP2 from the lower arm) in ChimeraX as rigid bodies, then relaxing the model using ISOLDE before rigid body refinement in Phenix (rigid bodies selected: lid domain of the weld protein, cleaver domains of the hub protein, res. 95-472 of arm scaffold protein and dimers of arm segments A, B and C, dimer of arm segment D, dimer of arm segment E, dimer of arm segment F, trimer of tripod proteins, trimer of RBP1, trimer of RBP2, res. 489-752 of arm scaffold protein).

+
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