5TCP

Near-atomic resolution cryo-EM structure of the periplasmic domains of PrgH and PrgK

> Summary

Summary for 5TCP

Related5TCQ 5TCR
EMDB informationEMD-8398 EMD-8399 EMD-8400 EMD-8401
DescriptorLipoprotein PrgK, Protein PrgH
Functional Keywordsbacterial, secretion, injectisome, membrane protein
Biological sourceSalmonella enterica subsp. enterica serovar Typhimurium
Cellular locationCell outer membrane ; Lipid- anchor  P41786
Cell membrane ; Single-pass membrane protein  P41783
Total number of polymer chains48
Total molecular weight1357446.24
Authors
Worrall, L.J.,Hong, C.,Vuckovic, M.,Bergeron, J.R.C.,Huang, R.K.,Yu, Z.,Strynadka, N.C.J. (deposition date: 2016-09-15, release date: 2016-12-21, modification date: 2017-01-11)
Primary citation
Worrall, L.J.,Hong, C.,Vuckovic, M.,Deng, W.,Bergeron, J.R.,Majewski, D.D.,Huang, R.K.,Spreter, T.,Finlay, B.B.,Yu, Z.,Strynadka, N.C.
Near-atomic-resolution cryo-EM analysis of the Salmonella T3S injectisome basal body.
Nature, 540:597-601, 2016
PubMed: 27974800
DOI: 10.1038/nature20576
MImport into Mendeley
Experimental method
ELECTRON MICROSCOPY
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Structure validation

ClashscoreRamachandran outliersSidechain outliers11.1%0MetricValuePercentile RanksWorseBetterPercentile relative to all structuresPercentile relative to all EM structures

More Asymmetric unit images

Molmil generated image of 5tcp
no rotation
Molmil generated image of 5tcp
rotated about x axis by 90°
Molmil generated image of 5tcp
rotated about y axis by 90°

> Structural details

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains48
Total molecular weight1357446.2
Non-Polymers*Number of molecules0
Total molecular weight0.0
All*Total molecular weight1357446.2
*Water molecules are not included.

> Experimental details

Refinement Statistics

Experimental method:ELECTRON MICROSCOPY

Cell axes1.0001.0001.000
Cell angles90.0090.0090.00
SpacegroupP 1
Resolution limits -
the highest resolution shell value -

Data Collection Statistics

Resolution limits -
the highest resolution shell value -

Crystallization Conditions

crystal IDmethodpHpH rangetemperatureunit

Crystallization Reagents

IDcrystal IDsolution IDreagent nameconcentrationdetails
Crystallization Reagents in Literatures*
IDcrystal IDsolutionreagent nameconcentration (unit)details
Annotated Information is extracted from Literature Info*

> Functional details

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Functional Information from GO Data

ChainGOidnamespacecontents
10016021cellular_componentintegral component of membrane
10005886cellular_componentplasma membrane
10009405biological_processpathogenesis
30016021cellular_componentintegral component of membrane
30005886cellular_componentplasma membrane
30009405biological_processpathogenesis
50016021cellular_componentintegral component of membrane
50005886cellular_componentplasma membrane
50009405biological_processpathogenesis
70016021cellular_componentintegral component of membrane
70005886cellular_componentplasma membrane
70009405biological_processpathogenesis
90016021cellular_componentintegral component of membrane
90005886cellular_componentplasma membrane
90009405biological_processpathogenesis
A0016021cellular_componentintegral component of membrane
A0005886cellular_componentplasma membrane
A0009405biological_processpathogenesis
C0016021cellular_componentintegral component of membrane
C0005886cellular_componentplasma membrane
C0009405biological_processpathogenesis
E0016021cellular_componentintegral component of membrane
E0005886cellular_componentplasma membrane
E0009405biological_processpathogenesis
G0016021cellular_componentintegral component of membrane
G0005886cellular_componentplasma membrane
G0009405biological_processpathogenesis
I0016021cellular_componentintegral component of membrane
I0005886cellular_componentplasma membrane
I0009405biological_processpathogenesis
K0016021cellular_componentintegral component of membrane
K0005886cellular_componentplasma membrane
K0009405biological_processpathogenesis
M0016021cellular_componentintegral component of membrane
M0005886cellular_componentplasma membrane
M0009405biological_processpathogenesis
O0016021cellular_componentintegral component of membrane
O0005886cellular_componentplasma membrane
O0009405biological_processpathogenesis
Q0016021cellular_componentintegral component of membrane
Q0005886cellular_componentplasma membrane
Q0009405biological_processpathogenesis
S0016021cellular_componentintegral component of membrane
S0005886cellular_componentplasma membrane
S0009405biological_processpathogenesis
U0016021cellular_componentintegral component of membrane
U0005886cellular_componentplasma membrane
U0009405biological_processpathogenesis
W0016021cellular_componentintegral component of membrane
W0005886cellular_componentplasma membrane
W0009405biological_processpathogenesis
Y0016021cellular_componentintegral component of membrane
Y0005886cellular_componentplasma membrane
Y0009405biological_processpathogenesis
b0016021cellular_componentintegral component of membrane
b0005886cellular_componentplasma membrane
b0009405biological_processpathogenesis
d0016021cellular_componentintegral component of membrane
d0005886cellular_componentplasma membrane
d0009405biological_processpathogenesis
f0016021cellular_componentintegral component of membrane
f0005886cellular_componentplasma membrane
f0009405biological_processpathogenesis
h0016021cellular_componentintegral component of membrane
h0005886cellular_componentplasma membrane
h0009405biological_processpathogenesis
j0016021cellular_componentintegral component of membrane
j0005886cellular_componentplasma membrane
j0009405biological_processpathogenesis
l0016021cellular_componentintegral component of membrane
l0005886cellular_componentplasma membrane
l0009405biological_processpathogenesis
00009279cellular_componentcell outer membrane
00016021cellular_componentintegral component of membrane
00009405biological_processpathogenesis
00009306biological_processprotein secretion
20009279cellular_componentcell outer membrane
20016021cellular_componentintegral component of membrane
20009405biological_processpathogenesis
20009306biological_processprotein secretion
40009279cellular_componentcell outer membrane
40016021cellular_componentintegral component of membrane
40009405biological_processpathogenesis
40009306biological_processprotein secretion
60009279cellular_componentcell outer membrane
60016021cellular_componentintegral component of membrane
60009405biological_processpathogenesis
60009306biological_processprotein secretion
80009279cellular_componentcell outer membrane
80016021cellular_componentintegral component of membrane
80009405biological_processpathogenesis
80009306biological_processprotein secretion
B0009279cellular_componentcell outer membrane
B0016021cellular_componentintegral component of membrane
B0009405biological_processpathogenesis
B0009306biological_processprotein secretion
D0009279cellular_componentcell outer membrane
D0016021cellular_componentintegral component of membrane
D0009405biological_processpathogenesis
D0009306biological_processprotein secretion
F0009279cellular_componentcell outer membrane
F0016021cellular_componentintegral component of membrane
F0009405biological_processpathogenesis
F0009306biological_processprotein secretion
H0009279cellular_componentcell outer membrane
H0016021cellular_componentintegral component of membrane
H0009405biological_processpathogenesis
H0009306biological_processprotein secretion
J0009279cellular_componentcell outer membrane
J0016021cellular_componentintegral component of membrane
J0009405biological_processpathogenesis
J0009306biological_processprotein secretion
L0009279cellular_componentcell outer membrane
L0016021cellular_componentintegral component of membrane
L0009405biological_processpathogenesis
L0009306biological_processprotein secretion
N0009279cellular_componentcell outer membrane
N0016021cellular_componentintegral component of membrane
N0009405biological_processpathogenesis
N0009306biological_processprotein secretion
P0009279cellular_componentcell outer membrane
P0016021cellular_componentintegral component of membrane
P0009405biological_processpathogenesis
P0009306biological_processprotein secretion
R0009279cellular_componentcell outer membrane
R0016021cellular_componentintegral component of membrane
R0009405biological_processpathogenesis
R0009306biological_processprotein secretion
T0009279cellular_componentcell outer membrane
T0016021cellular_componentintegral component of membrane
T0009405biological_processpathogenesis
T0009306biological_processprotein secretion
V0009279cellular_componentcell outer membrane
V0016021cellular_componentintegral component of membrane
V0009405biological_processpathogenesis
V0009306biological_processprotein secretion
X0009279cellular_componentcell outer membrane
X0016021cellular_componentintegral component of membrane
X0009405biological_processpathogenesis
X0009306biological_processprotein secretion
Z0009279cellular_componentcell outer membrane
Z0016021cellular_componentintegral component of membrane
Z0009405biological_processpathogenesis
Z0009306biological_processprotein secretion
a0009279cellular_componentcell outer membrane
a0016021cellular_componentintegral component of membrane
a0009405biological_processpathogenesis
a0009306biological_processprotein secretion
c0009279cellular_componentcell outer membrane
c0016021cellular_componentintegral component of membrane
c0009405biological_processpathogenesis
c0009306biological_processprotein secretion
e0009279cellular_componentcell outer membrane
e0016021cellular_componentintegral component of membrane
e0009405biological_processpathogenesis
e0009306biological_processprotein secretion
g0009279cellular_componentcell outer membrane
g0016021cellular_componentintegral component of membrane
g0009405biological_processpathogenesis
g0009306biological_processprotein secretion
i0009279cellular_componentcell outer membrane
i0016021cellular_componentintegral component of membrane
i0009405biological_processpathogenesis
i0009306biological_processprotein secretion
k0009279cellular_componentcell outer membrane
k0016021cellular_componentintegral component of membrane
k0009405biological_processpathogenesis
k0009306biological_processprotein secretion
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Functional Information from PDB Data

site_idNumber of ResiduesDetails
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Functional Information from PDB atom coordinates for the "HETATM" binding sites

site_idNumber of ResiduesDetails
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Functional Information from PROSITE/UniProt

site_idNumber of ResiduesDetails
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Functional Information from SwissProt/UniProt

site_idNumber of ResiduesDetails
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Catalytic Information from CSA

site_idNumber of ResiduesDetails

> Sequence Neighbor

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