[English] 日本語
Yorodumi
- PDB-9n4v: Azotobacter vinelandii extended type VI secretion system sheath t... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9n4v
TitleAzotobacter vinelandii extended type VI secretion system sheath tube complex
Components
  • DUF877 family protein
  • Type VI secretion system contractile sheath small subunit
KeywordsTRANSPORT PROTEIN / secretion system
Function / homologyType VI secretion system TssC-like / TssC1, N-terminal / TssC1, C-terminal / EvpB/VC_A0108, tail sheath N-terminal domain / EvpB/VC_A0108, tail sheath gpW/gp25-like domain / Type VI secretion system sheath protein TssB1 / Type VI secretion system, VipA, VC_A0107 or Hcp2 / Type VI secretion system contractile sheath small subunit / DUF877 family protein
Function and homology information
Biological speciesAzotobacter vinelandii (bacteria)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 1.85 Å
AuthorsWarmack, R.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM143836-01 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM152765 United States
CitationJournal: To Be Published
Title: CryoEM-enabled visual proteomics reveals de novo structures of oligomeric protein complexes
Authors: Warmack, R.A.
History
DepositionFeb 3, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 16, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DUF877 family protein
B: Type VI secretion system contractile sheath small subunit
C: DUF877 family protein
D: Type VI secretion system contractile sheath small subunit
E: DUF877 family protein
F: Type VI secretion system contractile sheath small subunit
G: DUF877 family protein
H: Type VI secretion system contractile sheath small subunit
I: DUF877 family protein
J: Type VI secretion system contractile sheath small subunit
K: DUF877 family protein
L: Type VI secretion system contractile sheath small subunit
M: DUF877 family protein
N: Type VI secretion system contractile sheath small subunit
O: DUF877 family protein
P: Type VI secretion system contractile sheath small subunit
Q: DUF877 family protein
R: Type VI secretion system contractile sheath small subunit
S: DUF877 family protein
T: Type VI secretion system contractile sheath small subunit
U: DUF877 family protein
V: Type VI secretion system contractile sheath small subunit
W: DUF877 family protein
X: Type VI secretion system contractile sheath small subunit
Y: DUF877 family protein
Z: Type VI secretion system contractile sheath small subunit
a: DUF877 family protein
b: Type VI secretion system contractile sheath small subunit
c: DUF877 family protein
d: Type VI secretion system contractile sheath small subunit
e: DUF877 family protein
f: Type VI secretion system contractile sheath small subunit
g: DUF877 family protein
h: Type VI secretion system contractile sheath small subunit
i: DUF877 family protein
j: Type VI secretion system contractile sheath small subunit
k: DUF877 family protein
l: Type VI secretion system contractile sheath small subunit
m: DUF877 family protein
n: Type VI secretion system contractile sheath small subunit
o: DUF877 family protein
p: Type VI secretion system contractile sheath small subunit
q: DUF877 family protein
r: Type VI secretion system contractile sheath small subunit
s: DUF877 family protein
t: Type VI secretion system contractile sheath small subunit
u: DUF877 family protein
v: Type VI secretion system contractile sheath small subunit


Theoretical massNumber of molelcules
Total (without water)1,821,16348
Polymers1,821,16348
Non-polymers00
Water110,7926150
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

#1: Protein ...
DUF877 family protein


Mass: 55032.344 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Source: (natural) Azotobacter vinelandii (bacteria) / Strain: DJ / References: UniProt: C1DM91
#2: Protein ...
Type VI secretion system contractile sheath small subunit


Mass: 20849.465 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Source: (natural) Azotobacter vinelandii (bacteria) / Strain: DJ / References: UniProt: C1DM90
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6150 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: HELICAL ARRAY / 3D reconstruction method: helical reconstruction

-
Sample preparation

ComponentName: Filamentous assembly of the extended type VI secretion system sheath tube complex
Type: COMPLEX / Entity ID: #1-#2 / Source: NATURAL
Source (natural)Organism: Azotobacter vinelandii (bacteria) / Strain: DJ
Buffer solutionpH: 7.5
SpecimenConc.: 0.75 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE-PROPANE

-
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 defocus max: -2500 nm / Nominal defocus min: -800 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

-
Processing

EM softwareName: PHENIX / Version: 1.20.1_4487 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 22.12 ° / Axial rise/subunit: 30.58 Å / Axial symmetry: C6
3D reconstructionResolution: 1.85 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 265571 / Symmetry type: HELICAL
RefinementHighest resolution: 1.85 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00483664
ELECTRON MICROSCOPYf_angle_d0.609113352
ELECTRON MICROSCOPYf_dihedral_angle_d4.70611280
ELECTRON MICROSCOPYf_chiral_restr0.04112672
ELECTRON MICROSCOPYf_plane_restr0.00514664

+
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