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- PDB-7bin: Salmonella export gate and rod refined in focussed C1 map -

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Basic information

Entry
Database: PDB / ID: 7bin
TitleSalmonella export gate and rod refined in focussed C1 map
Components
  • (Flagellar basal-body rod protein ...) x 3
  • (Flagellar biosynthetic protein ...) x 3
  • Flagellar basal body rod protein FlgB
  • Flagellar hook-basal body complex protein FliE
KeywordsPROTEIN TRANSPORT / bacterial flagellum rod bacterial flagellum export gate basal body
Function / homology
Function and homology information


bacterial-type flagellum basal body, distal rod / bacterial-type flagellum basal body, rod / bacterial-type flagellum organization / bacterial-type flagellum basal body / bacterial-type flagellum-dependent swarming motility / bacterial-type flagellum / cytoskeletal motor activity / bacterial-type flagellum assembly / protein secretion / bacterial-type flagellum-dependent cell motility ...bacterial-type flagellum basal body, distal rod / bacterial-type flagellum basal body, rod / bacterial-type flagellum organization / bacterial-type flagellum basal body / bacterial-type flagellum-dependent swarming motility / bacterial-type flagellum / cytoskeletal motor activity / bacterial-type flagellum assembly / protein secretion / bacterial-type flagellum-dependent cell motility / protein targeting / structural molecule activity / plasma membrane
Similarity search - Function
Flagellar hook-basal body complex protein FliE / Flagellar basal-body rod FlgG / Flagellar hook-basal body complex protein FliE / Flagellar basal-body rod protein FlgC / Flagellar biosynthesis protein FliQ / Flagellar basal-body rod protein FlgB / Flagellar transport protein FliP / Flagellar biosynthesis protein FliR / Bacterial export protein family 3 / Bacterial export proteins, family 3 ...Flagellar hook-basal body complex protein FliE / Flagellar basal-body rod FlgG / Flagellar hook-basal body complex protein FliE / Flagellar basal-body rod protein FlgC / Flagellar biosynthesis protein FliQ / Flagellar basal-body rod protein FlgB / Flagellar transport protein FliP / Flagellar biosynthesis protein FliR / Bacterial export protein family 3 / Bacterial export proteins, family 3 / Flagellar hook-basal body protein, FlgE/F/G / Flagellar hook-basal body protein, FlgE/F/G-like / : / Flagellar hook protein FlgE/F/G D1 domain / Flagella transport protein fliP family signature 1. / Type III secretion system inner membrane P protein / FliP family / Flagella transport protein fliP family signature 2. / Type III secretion system inner membrane R protein / Bacterial export proteins, family 1 / Flagellar basal body rod protein, conserved site / Flagella basal body rod proteins signature. / Flagellar basal body rod protein, N-terminal / Flagellar basal-body/hook protein, C-terminal domain / Flagella basal body rod protein / Flagellar basal body rod FlgEFG protein C-terminal
Similarity search - Domain/homology
Flagellar biosynthetic protein FliR / Flagellar biosynthetic protein FliQ / Flagellar basal-body rod protein FlgC / Flagellar basal-body rod protein FlgG / Flagellar basal-body rod protein FlgF / Flagellar basal body rod protein FlgB / Flagellar hook-basal body complex protein FliE / Flagellar biosynthetic protein FliP
Similarity search - Component
Biological speciesSalmonella typhi (bacteria)
Salmonella enterica subsp. enterica serovar Typhi (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsJohnson, S. / Furlong, E. / Lea, S.M.
Funding support United Kingdom, 4items
OrganizationGrant numberCountry
Wellcome Trust219477 United Kingdom
Wellcome Trust209194 United Kingdom
Wellcome Trust201536 United Kingdom
Medical Research Council (MRC, United Kingdom)S021264 United Kingdom
CitationJournal: Nat Microbiol / Year: 2021
Title: Molecular structure of the intact bacterial flagellar basal body.
Authors: Steven Johnson / Emily J Furlong / Justin C Deme / Ashley L Nord / Joseph J E Caesar / Fabienne F V Chevance / Richard M Berry / Kelly T Hughes / Susan M Lea /
Abstract: The bacterial flagellum is a macromolecular protein complex that enables motility in many species. Bacterial flagella self-assemble a strong, multicomponent drive shaft that couples rotation in the ...The bacterial flagellum is a macromolecular protein complex that enables motility in many species. Bacterial flagella self-assemble a strong, multicomponent drive shaft that couples rotation in the inner membrane to the micrometre-long flagellar filament that powers bacterial swimming in viscous fluids. Here, we present structures of the intact Salmonella flagellar basal body, encompassing the inner membrane rotor, drive shaft and outer-membrane bushing, solved using cryo-electron microscopy to resolutions of 2.2-3.7 Å. The structures reveal molecular details of how 173 protein molecules of 13 different types assemble into a complex spanning two membranes and a cell wall. The helical drive shaft at one end is intricately interwoven with the rotor component with both the export gate complex and the proximal rod forming interactions with the MS-ring. At the other end, the drive shaft distal rod passes through the LP-ring bushing complex, which functions as a molecular bearing anchored in the outer membrane through interactions with the lipopolysaccharide. The in situ structure of a protein complex capping the drive shaft provides molecular insights into the assembly process of this molecular machine.
History
DepositionJan 12, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 5, 2021Provider: repository / Type: Initial release
Revision 1.1May 19, 2021Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jun 9, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jul 10, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_admin
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.last_update

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Structure visualization

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  • Deposited structure unit
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  • Superimposition on EM map
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Structure viewerMolecule:
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Assembly

Deposited unit
A: Flagellar biosynthetic protein FliP
B: Flagellar biosynthetic protein FliP
C: Flagellar biosynthetic protein FliP
D: Flagellar biosynthetic protein FliP
E: Flagellar biosynthetic protein FliP
F: Flagellar biosynthetic protein FliR
G: Flagellar biosynthetic protein FliQ
H: Flagellar biosynthetic protein FliQ
I: Flagellar biosynthetic protein FliQ
J: Flagellar biosynthetic protein FliQ
K: Flagellar hook-basal body complex protein FliE
L: Flagellar hook-basal body complex protein FliE
M: Flagellar hook-basal body complex protein FliE
N: Flagellar hook-basal body complex protein FliE
O: Flagellar hook-basal body complex protein FliE
P: Flagellar hook-basal body complex protein FliE
Q: Flagellar basal body rod protein FlgB
R: Flagellar basal body rod protein FlgB
S: Flagellar basal body rod protein FlgB
T: Flagellar basal body rod protein FlgB
U: Flagellar basal body rod protein FlgB
V: Flagellar basal-body rod protein FlgC
W: Flagellar basal-body rod protein FlgC
X: Flagellar basal-body rod protein FlgC
Y: Flagellar basal-body rod protein FlgC
Z: Flagellar basal-body rod protein FlgC
a: Flagellar basal-body rod protein FlgC
b: Flagellar basal-body rod protein FlgF
c: Flagellar basal-body rod protein FlgF
d: Flagellar basal-body rod protein FlgF
e: Flagellar basal-body rod protein FlgF
f: Flagellar basal-body rod protein FlgF
g: Flagellar basal-body rod protein FlgG
h: Flagellar basal-body rod protein FlgG
i: Flagellar basal-body rod protein FlgG
j: Flagellar basal-body rod protein FlgG
k: Flagellar basal-body rod protein FlgG
l: Flagellar basal-body rod protein FlgG
m: Flagellar basal-body rod protein FlgG
n: Flagellar basal-body rod protein FlgG
o: Flagellar basal-body rod protein FlgG
p: Flagellar basal-body rod protein FlgG
q: Flagellar basal-body rod protein FlgG
r: Flagellar basal-body rod protein FlgG
s: Flagellar basal-body rod protein FlgG
t: Flagellar basal-body rod protein FlgG
u: Flagellar basal-body rod protein FlgG
v: Flagellar basal-body rod protein FlgG
w: Flagellar basal-body rod protein FlgG
x: Flagellar basal-body rod protein FlgG
y: Flagellar basal-body rod protein FlgG
z: Flagellar basal-body rod protein FlgG
1: Flagellar basal-body rod protein FlgG
2: Flagellar basal-body rod protein FlgG
3: Flagellar basal-body rod protein FlgG
4: Flagellar basal-body rod protein FlgG


Theoretical massNumber of molelcules
Total (without water)1,225,01556
Polymers1,225,01556
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area344170 Å2
ΔGint-2301 kcal/mol
Surface area321740 Å2
MethodPISA

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Components

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Flagellar biosynthetic protein ... , 3 types, 10 molecules ABCDEFGHIJ

#1: Protein
Flagellar biosynthetic protein FliP


Mass: 26801.086 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Salmonella typhi (bacteria) / References: UniProt: Q8Z5R3
#2: Protein Flagellar biosynthetic protein FliR


Mass: 28938.865 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Salmonella enterica subsp. enterica serovar Typhi (bacteria)
References: UniProt: A0A3U0BCQ2
#3: Protein
Flagellar biosynthetic protein FliQ


Mass: 9606.758 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Source: (natural) Salmonella enterica subsp. enterica serovar Typhi (bacteria)
References: UniProt: A0A3Y0WXN7

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Protein , 2 types, 11 molecules KLMNOPQRSTU

#4: Protein
Flagellar hook-basal body complex protein FliE


Mass: 11087.662 Da / Num. of mol.: 6 / Source method: isolated from a natural source
Source: (natural) Salmonella enterica subsp. enterica serovar Typhi (bacteria)
Strain: LT2 / SGSC1412 / ATCC 700720 / References: UniProt: P26462
#5: Protein
Flagellar basal body rod protein FlgB / Putative proximal rod protein


Mass: 15145.061 Da / Num. of mol.: 5 / Source method: isolated from a natural source
Source: (natural) Salmonella enterica subsp. enterica serovar Typhi (bacteria)
Strain: LT2 / SGSC1412 / ATCC 700720 / References: UniProt: P16437

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Flagellar basal-body rod protein ... , 3 types, 35 molecules VWXYZabcdefghijklmnopqrstuvwxy...

#6: Protein
Flagellar basal-body rod protein FlgC / Putative proximal rod protein


Mass: 13991.889 Da / Num. of mol.: 6 / Source method: isolated from a natural source
Source: (natural) Salmonella enterica subsp. enterica serovar Typhi (bacteria)
Strain: LT2 / SGSC1412 / ATCC 700720 / References: UniProt: P0A1I7
#7: Protein
Flagellar basal-body rod protein FlgF / Putative proximal rod protein


Mass: 26121.223 Da / Num. of mol.: 5 / Source method: isolated from a natural source
Source: (natural) Salmonella enterica subsp. enterica serovar Typhi (bacteria)
Strain: LT2 / SGSC1412 / ATCC 700720 / References: UniProt: P16323
#8: Protein ...
Flagellar basal-body rod protein FlgG / Distal rod protein


Mass: 27784.807 Da / Num. of mol.: 24 / Source method: isolated from a natural source
Source: (natural) Salmonella enterica subsp. enterica serovar Typhi (bacteria)
Strain: LT2 / SGSC1412 / ATCC 700720 / References: UniProt: P0A1J3

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Flagellar LP ring / Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhi (bacteria)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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: 59 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

Software
NameVersionClassification
phenix.real_space_refine1.18.2_3874refinement
PHENIX1.18.2_3874refinement
EM software
IDNameVersionCategory
4SIMPLE3CTF correction
10RELION3.1initial Euler assignment
11RELION3.1final Euler assignment
12RELION3.1classification
13RELION3.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 60497 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 74.76 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.010182837
ELECTRON MICROSCOPYf_angle_d0.8967112567
ELECTRON MICROSCOPYf_chiral_restr0.050713422
ELECTRON MICROSCOPYf_plane_restr0.00614862
ELECTRON MICROSCOPYf_dihedral_angle_d17.762830356

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