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- PDB-7nvg: Salmonella flagellar basal body refined in C1 map -

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Basic information

Entry
Database: PDB / ID: 7nvg
TitleSalmonella flagellar basal body refined in C1 map
Components
  • (Flagellar basal body ...) x 2
  • (Flagellar basal-body rod protein ...) x 2
  • (Flagellar biosynthetic protein ...) x 3
  • Basal-body rod modification protein FlgD
  • Flagellar L-ring protein
  • Flagellar M-ring protein
  • Flagellar P-ring protein
  • Flagellar hook-basal body complex protein FliE
KeywordsPROTEIN TRANSPORT / bacterial flagellum / flagella / basal body
Function / homology
Function and homology information


bacterial-type flagellum basal body, distal rod, L ring / bacterial-type flagellum basal body, distal rod, P ring / bacterial-type flagellum basal body, distal rod / bacterial-type flagellum basal body, rod / bacterial-type flagellum organization / bacterial-type flagellum basal body, MS ring / bacterial-type flagellum basal body / bacterial-type flagellum-dependent swarming motility / bacterial-type flagellum assembly / cytoskeletal motor activity ...bacterial-type flagellum basal body, distal rod, L ring / bacterial-type flagellum basal body, distal rod, P ring / bacterial-type flagellum basal body, distal rod / bacterial-type flagellum basal body, rod / bacterial-type flagellum organization / bacterial-type flagellum basal body, MS ring / bacterial-type flagellum basal body / bacterial-type flagellum-dependent swarming motility / bacterial-type flagellum assembly / cytoskeletal motor activity / bacterial-type flagellum-dependent cell motility / protein secretion / protein targeting / cell outer membrane / outer membrane-bounded periplasmic space / structural molecule activity / plasma membrane
Similarity search - Function
FlgD Tudor-like domain / FlgD Tudor-like domain / Flagellar hook capping protein / Flagellar hook capping protein - N-terminal region / FlgD Ig-like domain / FlgD Ig-like domain / Flagellar L-ring protein / Flagellar L-ring protein / Flagellar P-ring protein / Flagellar P-ring protein ...FlgD Tudor-like domain / FlgD Tudor-like domain / Flagellar hook capping protein / Flagellar hook capping protein - N-terminal region / FlgD Ig-like domain / FlgD Ig-like domain / Flagellar L-ring protein / Flagellar L-ring protein / Flagellar P-ring protein / Flagellar P-ring protein / Flagellar basal-body rod protein FlgC / Flagellar basal-body rod FlgG / Flagellar hook-basal body complex protein FliE / Flagellar basal-body rod protein FlgB / Flagellar hook-basal body complex protein FliE / Flagellar biosynthesis protein FliQ / Flagellar biosynthesis protein FliR / Flagellar transport protein FliP / 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 / Type III secretion system inner membrane R protein / Bacterial export protein family 3 / Bacterial export proteins, family 1 / Bacterial export proteins, family 3 / Flagella transport protein fliP family signature 1. / Type III secretion system inner membrane P protein / FliP family / Flagella transport protein fliP family signature 2. / 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 / Flagellar M-ring protein FliF / Flagellar M-ring C-terminal / Flagellar M-ring protein C-terminal / Lipoprotein YscJ/Flagellar M-ring protein / Secretory protein of YscJ/FliF family / Flagellar M-ring , N-terminal / AMP-binding enzyme, C-terminal domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Flagellar biosynthetic protein FliR / Flagellar biosynthetic protein FliP / Flagellar hook-basal body complex protein FliE / Flagellar basal-body rod protein FlgF / Flagellar basal body rod protein FlgB / Flagellar basal-body rod protein FlgC / Flagellar P-ring protein / Flagellar biosynthetic protein FliQ / Basal-body rod modification protein FlgD / Flagellar basal-body rod protein FlgG ...Flagellar biosynthetic protein FliR / Flagellar biosynthetic protein FliP / Flagellar hook-basal body complex protein FliE / Flagellar basal-body rod protein FlgF / Flagellar basal body rod protein FlgB / Flagellar basal-body rod protein FlgC / Flagellar P-ring protein / Flagellar biosynthetic protein FliQ / Basal-body rod modification protein FlgD / Flagellar basal-body rod protein FlgG / Flagellar L-ring protein / Flagellar M-ring protein
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 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
DepositionMar 15, 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 14, 2021Group: Derived calculations
Category: pdbx_struct_sheet_hbond / struct_sheet ...pdbx_struct_sheet_hbond / struct_sheet / struct_sheet_order / struct_sheet_range
Revision 1.4Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_admin / pdbx_entry_details / pdbx_modification_feature
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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Structure viewerMolecule:
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Assembly

Deposited unit
A1: Flagellar M-ring protein
B1: Flagellar M-ring protein
C1: Flagellar M-ring protein
D1: Flagellar M-ring protein
E1: Flagellar M-ring protein
F1: Flagellar M-ring protein
G1: Flagellar M-ring protein
H1: Flagellar M-ring protein
I1: Flagellar M-ring protein
J1: Flagellar M-ring protein
K1: Flagellar M-ring protein
L1: Flagellar M-ring protein
M1: Flagellar M-ring protein
N1: Flagellar M-ring protein
O1: Flagellar M-ring protein
P1: Flagellar M-ring protein
Q1: Flagellar M-ring protein
R1: Flagellar M-ring protein
S1: Flagellar M-ring protein
T1: Flagellar M-ring protein
U1: Flagellar M-ring protein
V1: Flagellar M-ring protein
W1: Flagellar M-ring protein
X1: Flagellar M-ring protein
Y1: Flagellar M-ring protein
Z1: Flagellar M-ring protein
a1: Flagellar M-ring protein
b1: Flagellar M-ring protein
c1: Flagellar M-ring protein
d1: Flagellar M-ring protein
e1: Flagellar M-ring protein
f1: Flagellar M-ring protein
g1: Flagellar M-ring protein
h1: Flagellar M-ring protein
A2: Flagellar biosynthetic protein FliP
B2: Flagellar biosynthetic protein FliP
C2: Flagellar biosynthetic protein FliP
D2: Flagellar biosynthetic protein FliP
E2: Flagellar biosynthetic protein FliP
F2: Flagellar biosynthetic protein FliR
G2: Flagellar biosynthetic protein FliQ
H2: Flagellar biosynthetic protein FliQ
I2: Flagellar biosynthetic protein FliQ
J2: Flagellar biosynthetic protein FliQ
K2: Flagellar hook-basal body complex protein FliE
L2: Flagellar hook-basal body complex protein FliE
M2: Flagellar hook-basal body complex protein FliE
N2: Flagellar hook-basal body complex protein FliE
O2: Flagellar hook-basal body complex protein FliE
P2: Flagellar hook-basal body complex protein FliE
Q2: Flagellar basal body rod protein FlgB
R2: Flagellar basal body rod protein FlgB
S2: Flagellar basal body rod protein FlgB
T2: Flagellar basal body rod protein FlgB
U2: Flagellar basal body rod protein FlgB
V2: Flagellar basal-body rod protein FlgC
W2: Flagellar basal-body rod protein FlgC
X2: Flagellar basal-body rod protein FlgC
Y2: Flagellar basal-body rod protein FlgC
Z2: Flagellar basal-body rod protein FlgC
a2: Flagellar basal-body rod protein FlgC
b2: Flagellar basal body protein
c2: Flagellar basal body protein
d2: Flagellar basal body protein
e2: Flagellar basal body protein
f2: Flagellar basal body protein
g2: Flagellar basal-body rod protein FlgG
h2: Flagellar basal-body rod protein FlgG
i2: Flagellar basal-body rod protein FlgG
j2: Flagellar basal-body rod protein FlgG
k2: Flagellar basal-body rod protein FlgG
l2: Flagellar basal-body rod protein FlgG
m2: Flagellar basal-body rod protein FlgG
n2: Flagellar basal-body rod protein FlgG
o2: Flagellar basal-body rod protein FlgG
p2: Flagellar basal-body rod protein FlgG
q2: Flagellar basal-body rod protein FlgG
r2: Flagellar basal-body rod protein FlgG
s2: Flagellar basal-body rod protein FlgG
t2: Flagellar basal-body rod protein FlgG
u2: Flagellar basal-body rod protein FlgG
v2: Flagellar basal-body rod protein FlgG
w2: Flagellar basal-body rod protein FlgG
x2: Flagellar basal-body rod protein FlgG
y2: Flagellar basal-body rod protein FlgG
z2: Flagellar basal-body rod protein FlgG
12: Flagellar basal-body rod protein FlgG
22: Flagellar basal-body rod protein FlgG
32: Flagellar basal-body rod protein FlgG
42: Flagellar basal-body rod protein FlgG
A3: Flagellar L-ring protein
B3: Flagellar L-ring protein
C3: Flagellar L-ring protein
D3: Flagellar L-ring protein
E3: Flagellar L-ring protein
F3: Flagellar L-ring protein
G3: Flagellar L-ring protein
H3: Flagellar L-ring protein
I3: Flagellar L-ring protein
J3: Flagellar L-ring protein
K3: Flagellar L-ring protein
L3: Flagellar L-ring protein
M3: Flagellar L-ring protein
N3: Flagellar L-ring protein
O3: Flagellar L-ring protein
P3: Flagellar L-ring protein
Q3: Flagellar L-ring protein
R3: Flagellar L-ring protein
S3: Flagellar L-ring protein
T3: Flagellar L-ring protein
U3: Flagellar L-ring protein
V3: Flagellar L-ring protein
W3: Flagellar L-ring protein
X3: Flagellar L-ring protein
Y3: Flagellar L-ring protein
Z3: Flagellar L-ring protein
a3: Flagellar P-ring protein
b3: Flagellar P-ring protein
c3: Flagellar P-ring protein
d3: Flagellar P-ring protein
e3: Flagellar P-ring protein
f3: Flagellar P-ring protein
g3: Flagellar P-ring protein
h3: Flagellar P-ring protein
i3: Flagellar P-ring protein
j3: Flagellar P-ring protein
k3: Flagellar P-ring protein
l3: Flagellar P-ring protein
m3: Flagellar P-ring protein
n3: Flagellar P-ring protein
o3: Flagellar P-ring protein
p3: Flagellar P-ring protein
q3: Flagellar P-ring protein
r3: Flagellar P-ring protein
s3: Flagellar P-ring protein
t3: Flagellar P-ring protein
u3: Flagellar P-ring protein
v3: Flagellar P-ring protein
w3: Flagellar P-ring protein
x3: Flagellar P-ring protein
y3: Flagellar P-ring protein
z3: Flagellar P-ring protein
A4: Basal-body rod modification protein FlgD
B4: Basal-body rod modification protein FlgD
C4: Basal-body rod modification protein FlgD
D4: Basal-body rod modification protein FlgD
E4: Basal-body rod modification protein FlgD


Theoretical massNumber of molelcules
Total (without water)5,065,017147
Polymers5,065,017147
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 5 types, 97 molecules A1B1C1D1E1F1G1H1I1J1K1L1M1N1O1P1Q1R1S1T1U1V1W1X1Y1Z1a1b1c1d1...

#1: Protein ...
Flagellar M-ring protein


Mass: 61295.645 Da / Num. of mol.: 34 / Source method: isolated from a natural source
Source: (natural) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
References: UniProt: P15928
#5: 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 Typhimurium (bacteria)
References: UniProt: A0A0D6FLN2
#10: Protein ...
Flagellar L-ring protein / Basal body L-ring protein


Mass: 24726.666 Da / Num. of mol.: 26 / Source method: isolated from a natural source
Source: (natural) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
References: UniProt: A0A0J5DWE9
#11: Protein ...
Flagellar P-ring protein / Basal body P-ring protein


Mass: 38194.176 Da / Num. of mol.: 26 / Source method: isolated from a natural source
Source: (natural) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
References: UniProt: A0A0F7J5J5
#12: Protein
Basal-body rod modification protein FlgD


Mass: 24001.637 Da / Num. of mol.: 5 / Source method: isolated from a natural source
Source: (natural) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
References: UniProt: A0A0F7J820

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Flagellar biosynthetic protein ... , 3 types, 10 molecules A2B2C2D2E2F2G2H2I2J2

#2: Protein
Flagellar biosynthetic protein FliP


Mass: 26801.086 Da / Num. of mol.: 5 / Source method: isolated from a natural source
Source: (natural) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
References: UniProt: A0A0D6FLD2
#3: 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 Typhimurium (bacteria)
References: UniProt: A0A0D6FLB3
#4: 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 Typhimurium (bacteria)
References: UniProt: A0A0F7J7J8

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Flagellar basal body ... , 2 types, 10 molecules Q2R2S2T2U2b2c2d2e2f2

#6: Protein
Flagellar basal body rod protein FlgB


Mass: 15145.061 Da / Num. of mol.: 5 / Source method: isolated from a natural source
Source: (natural) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
References: UniProt: A0A0D6GKK7
#8: Protein
Flagellar basal body protein


Mass: 26121.223 Da / Num. of mol.: 5 / Source method: isolated from a natural source
Source: (natural) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
References: UniProt: A0A0D6GIC9

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Flagellar basal-body rod protein ... , 2 types, 30 molecules V2W2X2Y2Z2a2g2h2i2j2k2l2m2n2o2p2q2r2s2t2u2v2w2x2y2z212223242

#7: Protein
Flagellar basal-body rod protein FlgC


Mass: 13991.889 Da / Num. of mol.: 6 / Source method: isolated from a natural source
Source: (natural) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
References: UniProt: A0A0F7J5J2
#9: 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 Typhimurium (bacteria)
References: UniProt: A0A0F7J893

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Details

Has protein modificationY

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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: Salmonella flagellar basal body / Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium (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

EM software
IDNameVersionCategory
4SIMPLE3CTF correction
5RELION3.1CTF correction
11RELION3.1initial Euler assignment
12RELION3.1final Euler assignment
14RELION3.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 60497 / Symmetry type: POINT

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