2024-03-13
REL
RCSB
RCSB
RCSB
2016-09-15
2016-12-21
2016-12-21
2024-03-13
Canadian Institutes of Health Research (CIHR)
Canada
6.3 Angstrom structure of the Salmonella SPI-1 type III secretion injectisome basal body
Worrall LJ
Hong C
Bacterial, secretion, injectisome, membrane protein
Worrall LJ
Hong C
Vuckovic M
Deng W
Bergeron JR
Majewski DD
Huang RK
Spreter T
Finlay BB
Yu Z
Strynadka NC
Near-atomic-resolution cryo-EM analysis of the Salmonella T3S injectisome basal body.
Nature
UK
540
597
601
2016
27974800
doi:10.1038/nature20576
0028-0836
0006
NATUAS
EMD-8398
other EM volume
EMD-8399
other EM volume
EMD-8401
other EM volume
5tcr
FULLOVERLAP
Type III injectisome basal body
Type III injectisome basal body
0
1
2
3
PrgH130-392 mutant
Salmonella enterica subsp. enterica serovar Typhimurium
2
Protein InvG
Salmonella enterica subsp. enterica serovar Typhimurium
0.061835559
15
LEVO
MKTHILLARVLACAALVLVTPGYSSEKIPVTGSGFVAKDDSLRTFFDAMALQLKEPVIVSKMAARKKITGNFEFHDPNAL
LEKLSLQLGLIWYFDGQAIYIYDASEMRNAVVSLRNVSLNEFNNFLKRSGLYNKNYPLRGDNRKGTFYVSGPPVYVDMVV
NAATMMDKQNDGIELGRQKIGVMRLNNTFVGDRTYNLRDQKMVIPGIATAIERLLQGEEQPLGNIVSSEPPAMPAFSANG
EKGKAANYAGGMSLQEALKQNAAAGNIKIVAYPDTNSLLVKGTAEQVHFIEMLVKALDVAKRHVELSLWIVDLNKSDLER
LGTSWSGSITIGDKLGVSLNQSSISTLDGSRFIAAVNALEEKKQATVVSRPVLLTQENVPAIFDNNRTFYTKLIGERNVA
LEHVTYGTMIRVLPRFSADGQIEMSLDIEDGNDKTPQSDTTTSVDALPEVGRTLISTIARVPHGKSLLVGGYTRDANTDT
VQSIPFLGKLPLIGSLFRYSSKNKSNVVRVFMIEPKEIVDPLTPDASESVNNILKQSGAWSGDDKLQKWVRVYLDRGQEA
IK
P35672
Lipoprotein PrgK
Salmonella enterica subsp. enterica serovar Typhimurium
0.026199723
24
LEVO
CKDKDLLKGLDQEQANEVIAVLQMHNIEANKIDSGKLGYSITVAEPDFTAAVYWIKTYQLPPRPRVEIAQMFPADSLVSS
PRAEKARLYSAIEQRLEQSLQTMEGVLSARVHISYDIDAGENGRPPKPVHLSALAVYERGSPLAHQISDIKRFLKNSFAD
VDYDNISVVLSERSDAQLQAPGTPVKRNSFATSWIVLIILLSVMSAGFGVWYYKNHYARNKKGITADDKAKSSNE
P41786
Protein PrgH
Salmonella enterica subsp. enterica serovar Typhimurium
0.030360537
24
LEVO
SAKKNEPRFKNGIVAALAGFFILGIGTVGTLWILNSPQRQAAELDSLLGQEKERFQVLPGRDKMLYVAAQNERDTLWARQ
VLARGDYDKNARVINENEENKRISIWLDTYYPQLAYYRIHFDEPRKPVFWLSRQRNTMSKKELEVLSQKLRALMPYADSV
NITLMDDVTAAGQAEAGLKQQALPYSRRNHKGGVTFVIQGALDDVEILRARQFVDSYYRTWGGRYVQFAIELKDDWLKGR
SFQYGAEGYIKMSPGHWYFPSPL
P41783
singleParticle
particle
10
8.0
10.0
C4H11NO3
Tris
500.0
NaCl
sodium chloride
0.2
LDAO
Quantifoil R1.2/1.3
GOLD
400
GLOW DISCHARGE
AIR
0.038
ETHANE
90
298
FEI VITROBOT MARK IV
FEI TITAN KRIOS
FLOOD BEAM
BRIGHT FIELD
FIELD EMISSION GUN
300
70.0
0.01
1.5
1.3
3.0
3.2
64000.0
29240.0
FEI TITAN KRIOS AUTOGRID HOLDER
NITROGEN
80.0
80.0
Gatan GIF
0
20
GATAN K2 QUANTUM (4k x 4k)
SUPER-RESOLUTION
7676
7420
1-48
1
2515
0.375
1.3
1
263900
e2initialmodel.py
C1
FOURIER SPACE
6.3
FSC 0.143 CUT-OFF
FREALIGN
Limited frequency refinement in Frealign
67800
OTHER
RELION
FREALIGN
OTHER
FREALIGN
FLEXIBLE FIT
Initial fitting was carried out with Chimera, followed by rebuilding and refinement in Rosetta, Phenix, and Coot.
REAL