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- PDB-7bgl: Salmonella LP ring 26 mer refined in C26 map -

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Basic information

Entry
Database: PDB / ID: 7bgl
TitleSalmonella LP ring 26 mer refined in C26 map
Components
  • Flagellar L-ring protein
  • Flagellar P-ring protein
  • YecR
KeywordsMEMBRANE PROTEIN / bacterial flagellum LP ring salmonella
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-dependent cell motility / motor activity / cell outer membrane / outer membrane-bounded periplasmic space / structural molecule activity
Similarity search - Function
YecR-like lipoprotein / YecR-like lipoprotein / Flagellar L-ring protein / Flagellar L-ring protein / Flagellar P-ring protein / Flagellar P-ring protein / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Flagellar L-ring protein / Chem-TLW / Uncharacterized protein / Chem-TQN / Flagellar P-ring protein
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.2 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 7, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 5, 2021Provider: repository / Type: Initial release
Revision 2.0May 19, 2021Group: Database references / Non-polymer description / Category: chem_comp / citation / citation_author
Item: _chem_comp.formula / _citation.pdbx_database_id_DOI ..._chem_comp.formula / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 2.1Jun 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

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Structure visualization

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Assembly

Deposited unit
A: Flagellar L-ring protein
a: Flagellar P-ring protein
1: YecR
b: Flagellar P-ring protein
c: Flagellar P-ring protein
d: Flagellar P-ring protein
e: Flagellar P-ring protein
f: Flagellar P-ring protein
g: Flagellar P-ring protein
h: Flagellar P-ring protein
i: Flagellar P-ring protein
j: Flagellar P-ring protein
k: Flagellar P-ring protein
l: Flagellar P-ring protein
m: Flagellar P-ring protein
n: Flagellar P-ring protein
o: Flagellar P-ring protein
p: Flagellar P-ring protein
q: Flagellar P-ring protein
r: Flagellar P-ring protein
s: Flagellar P-ring protein
t: Flagellar P-ring protein
u: Flagellar P-ring protein
v: Flagellar P-ring protein
w: Flagellar P-ring protein
x: Flagellar P-ring protein
y: Flagellar P-ring protein
z: Flagellar P-ring protein
2: YecR
3: YecR
4: YecR
5: YecR
6: YecR
7: YecR
8: YecR
9: YecR
10: YecR
11: YecR
12: YecR
13: YecR
14: YecR
15: YecR
16: YecR
17: YecR
18: YecR
19: YecR
20: YecR
21: YecR
22: YecR
23: YecR
24: YecR
25: YecR
26: YecR
B: Flagellar L-ring protein
C: Flagellar L-ring protein
D: Flagellar L-ring protein
E: Flagellar L-ring protein
F: Flagellar L-ring protein
G: Flagellar L-ring protein
H: Flagellar L-ring protein
I: Flagellar L-ring protein
J: Flagellar L-ring protein
K: Flagellar L-ring protein
L: Flagellar L-ring protein
M: Flagellar L-ring protein
N: Flagellar L-ring protein
O: Flagellar L-ring protein
P: Flagellar L-ring protein
Q: Flagellar L-ring protein
R: Flagellar L-ring protein
S: Flagellar L-ring protein
T: Flagellar L-ring protein
U: Flagellar L-ring protein
V: Flagellar L-ring protein
W: Flagellar L-ring protein
X: Flagellar L-ring protein
Y: Flagellar L-ring protein
Z: Flagellar L-ring protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,011,744130
Polymers1,953,01178
Non-polymers58,73352
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "6"
d_2ens_1chain "2"
d_3ens_1chain "3"
d_4ens_1chain "4"
d_5ens_1chain "5"
d_6ens_1chain "1"
d_7ens_1chain "7"
d_8ens_1chain "8"
d_9ens_1chain "9"
d_10ens_1chain "10"
d_11ens_1chain "11"
d_12ens_1chain "12"
d_13ens_1chain "13"
d_14ens_1chain "14"
d_15ens_1chain "15"
d_16ens_1chain "16"
d_17ens_1chain "17"
d_18ens_1chain "18"
d_19ens_1chain "19"
d_20ens_1chain "20"
d_21ens_1chain "21"
d_22ens_1chain "22"
d_23ens_1chain "23"
d_24ens_1chain "24"
d_25ens_1chain "25"
d_26ens_1chain "26"
d_1ens_2chain "B"
d_2ens_2chain "A"
d_3ens_2chain "C"
d_4ens_2chain "D"
d_5ens_2chain "E"
d_6ens_2chain "F"
d_7ens_2chain "G"
d_8ens_2chain "H"
d_9ens_2chain "I"
d_10ens_2chain "J"
d_11ens_2chain "K"
d_12ens_2chain "L"
d_13ens_2chain "M"
d_14ens_2chain "N"
d_15ens_2chain "O"
d_16ens_2chain "P"
d_17ens_2chain "Q"
d_18ens_2chain "R"
d_19ens_2chain "S"
d_20ens_2chain "T"
d_21ens_2chain "U"
d_22ens_2chain "V"
d_23ens_2chain "W"
d_24ens_2chain "X"
d_25ens_2chain "Y"
d_26ens_2chain "Z"
d_1ens_3chain "v"
d_2ens_3chain "b"
d_3ens_3chain "c"
d_4ens_3chain "d"
d_5ens_3chain "e"
d_6ens_3chain "f"
d_7ens_3chain "g"
d_8ens_3chain "h"
d_9ens_3chain "i"
d_10ens_3chain "j"
d_11ens_3chain "k"
d_12ens_3chain "l"
d_13ens_3chain "m"
d_14ens_3chain "n"
d_15ens_3chain "o"
d_16ens_3chain "p"
d_17ens_3chain "q"
d_18ens_3chain "r"
d_19ens_3chain "s"
d_20ens_3chain "t"
d_21ens_3chain "u"
d_22ens_3chain "a"
d_23ens_3chain "w"
d_24ens_3chain "x"
d_25ens_3chain "y"
d_26ens_3chain "z"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1CYSARGHA1 - 84
d_21ens_1CYSARGCA1 - 84
d_31ens_1CYSARGDA1 - 84
d_41ens_1CYSARGEA1 - 84
d_51ens_1CYSARGFA1 - 84
d_61ens_1CYSARGGA1 - 84
d_71ens_1CYSARGMA1 - 84
d_81ens_1CYSARGIA1 - 84
d_91ens_1CYSARGJA1 - 84
d_101ens_1CYSARGKA1 - 84
d_111ens_1CYSARGLA1 - 84
d_121ens_1CYSARGC1 - 84
d_131ens_1CYSARGNA1 - 84
d_141ens_1CYSARGOA1 - 84
d_151ens_1CYSARGPA1 - 84
d_161ens_1CYSARGQA1 - 84
d_171ens_1CYSARGRA1 - 84
d_181ens_1CYSARGSA1 - 84
d_191ens_1CYSARGTA1 - 84
d_201ens_1CYSARGUA1 - 84
d_211ens_1CYSARGVA1 - 84
d_221ens_1CYSARGWA1 - 84
d_231ens_1CYSARGXA1 - 84
d_241ens_1CYSARGYA1 - 84
d_251ens_1CYSARGZA1 - 84
d_261ens_1CYSARGAB1 - 84
d_11ens_2CYSMETG1 - 211
d_12ens_2SELSELG1
d_13ens_2AKDAKDG
d_21ens_2CYSMETB1 - 211
d_22ens_2SELSELB1
d_23ens_2AKDAKDB
d_31ens_2CYSMETC1 - 211
d_32ens_2SELSELC1
d_33ens_2AKDAKDC
d_41ens_2CYSMETD1 - 211
d_42ens_2SELSELD1
d_43ens_2AKDAKDD
d_51ens_2CYSMETE1 - 211
d_52ens_2SELSELE1
d_53ens_2AKDAKDE
d_61ens_2CYSMETF1 - 211
d_62ens_2SELSELF1
d_63ens_2AKDAKDF
d_71ens_2CYSMETK1 - 211
d_72ens_2SELSELK1
d_73ens_2AKDAKDK
d_81ens_2CYSMETH1 - 211
d_82ens_2SELSELH1
d_83ens_2AKDAKDH
d_91ens_2CYSMETI1 - 211
d_92ens_2SELSELI1
d_93ens_2AKDAKDI
d_101ens_2CYSMETJ1 - 211
d_102ens_2SELSELJ1
d_103ens_2AKDAKDJ
d_111ens_2CYSMETA1 - 211
d_112ens_2SELSELA1
d_113ens_2AKDAKDA
d_121ens_2CYSMETL1 - 211
d_122ens_2SELSELL1
d_123ens_2AKDAKDL
d_131ens_2CYSMETM1 - 211
d_132ens_2SELSELM1
d_133ens_2AKDAKDM
d_141ens_2CYSMETN1 - 211
d_142ens_2SELSELN1
d_143ens_2AKDAKDN
d_151ens_2CYSMETO1 - 211
d_152ens_2SELSELO1
d_153ens_2AKDAKDO
d_161ens_2CYSMETP1 - 211
d_162ens_2SELSELP1
d_163ens_2AKDAKDP
d_171ens_2CYSMETQ1 - 211
d_172ens_2SELSELQ1
d_173ens_2AKDAKDQ
d_181ens_2CYSMETR1 - 211
d_182ens_2SELSELR1
d_183ens_2AKDAKDR
d_191ens_2CYSMETS1 - 211
d_192ens_2SELSELS1
d_193ens_2AKDAKDS
d_201ens_2CYSMETT1 - 211
d_202ens_2SELSELT1
d_203ens_2AKDAKDT
d_211ens_2CYSMETU1 - 211
d_212ens_2SELSELU1
d_213ens_2AKDAKDU
d_221ens_2CYSMETV1 - 211
d_222ens_2SELSELV1
d_223ens_2AKDAKDV
d_231ens_2CYSMETW1 - 211
d_232ens_2SELSELW1
d_233ens_2AKDAKDW
d_241ens_2CYSMETX1 - 211
d_242ens_2SELSELX1
d_243ens_2AKDAKDX
d_251ens_2CYSMETY1 - 211
d_252ens_2SELSELY1
d_253ens_2AKDAKDY
d_261ens_2CYSMETZ1 - 211
d_262ens_2SELSELZ1
d_263ens_2AKDAKDZ
d_11ens_3GLUILED1 - 306
d_21ens_3GLUILEB1 - 306
d_31ens_3GLUILEE1 - 306
d_41ens_3GLUILEF1 - 306
d_51ens_3GLUILEG1 - 306
d_61ens_3GLUILEH1 - 306
d_71ens_3GLUILEI1 - 306
d_81ens_3GLUILEJ1 - 306
d_91ens_3GLUILEK1 - 306
d_101ens_3GLUILEL1 - 306
d_111ens_3GLUILEM1 - 306
d_121ens_3GLUILEN1 - 306
d_131ens_3GLUILEO1 - 306
d_141ens_3GLUILEP1 - 306
d_151ens_3GLUILEQ1 - 306
d_161ens_3GLUILER1 - 306
d_171ens_3GLUILES1 - 306
d_181ens_3GLUILET1 - 306
d_191ens_3GLUILEU1 - 306
d_201ens_3GLUILEV1 - 306
d_211ens_3GLUILEW1 - 306
d_221ens_3GLUILEX1 - 306
d_231ens_3GLUILEY1 - 306
d_241ens_3GLUILEZ1 - 306
d_251ens_3GLUILEAA1 - 306
d_261ens_3GLUILEBA1 - 306

NCS ensembles:
ID
ens_1
ens_2
ens_3

NCS oper:
IDCodeMatrixVector
1given(0.748637067432, 0.662980041855, -7.32744832574E-5), (-0.662980027069, 0.748637067936, 0.000155626910531), (0.000158033529958, -6.79285550197E-5, 0.999999985206)-54.1142207097, 120.176062073, -0.0296923168644
2given(0.885449832365, 0.464734956271, -0.000121594720468), (-0.464734964114, 0.885449835434, -4.53821184085E-5), (8.6575368414E-5, 9.66929071903E-5, 0.999999991578)-46.0206479186, 76.1531252468, -0.0321564901268
3given(0.970953266891, 0.239269140066, -0.000179237435595), (-0.239269129507, 0.970953282862, 7.85198367711E-5), (0.000192818550325, -3.33531068388E-5, 0.999999980854)-27.6138953842, 35.2646736159, -0.0379275600371
4given(0.568129509858, 0.822939139175, -0.00018232388218), (-0.822939158677, 0.568129486329, -0.000166969663881), (-3.38222979339E-5, 0.00024490185551, 0.99999996944)-51.4049485932, 164.973357346, -0.0157771741369
5given(0.970943052826, -0.239310622835, 0.000118180334942), (0.239310639116, 0.97094304424, -0.000151154654709), (-7.85734596153E-5, 0.000175044373378, 0.999999981593)35.2613063445, -27.6208804479, -0.00737959873183
6given(0.885440591894, -0.464752575685, 4.02620688789E-5), (0.464752577361, 0.885440589924, -5.95864646074E-5), (-7.95670711746E-6, 7.14721747722E-5, 0.999999997414)76.1472000406, -46.0280083016, -0.00154578636595
7given(0.748431730688, -0.663211827861, -0.00012603301518), (0.663211834949, 0.748431734729, 2.08270572353E-5), (8.05143574866E-5, -9.91742177536E-5, 0.999999991841)120.267420678, -54.1185240267, -0.00691815076848
8given(0.568085255233, -0.822969708261, 4.5518826388E-5), (0.822969708952, 0.568085251919, -6.85517102756E-5), (3.05574070506E-5, 7.6403831133E-5, 0.999999996614)164.959691488, -51.3951087762, -0.0158786373649
9given(0.354569632985, -0.935029608437, -8.19183344096E-5), (0.935029603117, 0.35456964034, -0.000106974790057), (0.000129070350428, -3.8666055662E-5, 0.999999990923)207.768931721, -38.0520521987, -0.022312045543
10given(0.120554139804, -0.992706753483, 3.1056277958E-5), (0.992706751008, 0.120554141802, 7.34632172929E-5), (-7.66713948761E-5, 2.19734818221E-5, 0.999999996819)246.10249333, -14.8924057054, 0.0146488162853
11given(-0.120517942039, -0.992711130636, 0.000191724695341), (0.992711138855, -0.120517910727, 0.00016729271601), (-0.00014296708154, 0.000210489014511, 0.999999967627)277.773548238, 16.7828617255, 0.00383818099742
12given(-0.354623221053, -0.935009276669, 0.000153732544651), (0.935009286889, -0.354623203518, 0.000130221306075), (-6.72410017306E-5, 0.000189920855955, 0.999999979704)300.966660573, 55.1457831702, -0.00688551838169
13given(-0.568128017683, -0.822940180756, 0.000120085933963), (0.822940182636, -0.568128025755, -4.64171961624E-5), (0.000106422760383, 7.24526307854E-5, 0.999999991712)314.307513769, 97.9659802698, -0.0320329952041
14given(-0.74846853774, -0.663170260789, 0.000230690545537), (0.663170293379, -0.748468536388, 0.000109620848478), (9.99673283036E-5, 0.00023503487293, 0.999999967383)316.993184528, 142.661394096, -0.045012574647
15given(-0.885455747746, -0.464723630609, 0.000256782281105), (0.464723640443, -0.885455779505, -2.35699612107E-5), (0.000238322872826, 9.8462638848E-5, 0.999999966754)308.908781184, 186.767339163, -0.0541530572308
16given(-0.970929939358, -0.239363832186, 9.32689367045E-5), (0.239363840629, -0.970929937282, 9.32165530614E-5), (6.82449315009E-5, 0.000112831953112, 0.999999991306)290.539667092, 227.616709949, -0.0169099666513
17given(-0.999999998338, -5.62869737416E-5, 1.25053630795E-5), (5.62902995194E-5, -0.999999963009, 0.000266107134377), (1.24903842516E-5, 0.000266107837866, 0.999999964515)262.914922835, 262.874888281, -0.0244684272996
18given(-0.970932024055, 0.239355393782, -1.15042384808E-5), (-0.239355393687, -0.970932018748, 0.000102389231371), (1.33375813015E-5, 0.000102166585187, 0.999999994692)227.628404465, 290.550387734, -0.0176695753886
19given(-0.885388411177, 0.464851942273, 0.000181986540522), (-0.464851942404, -0.88538842871, 4.41508279363E-5), (0.000181652375279, -4.55061654545E-5, 0.999999982466)186.718257812, 308.960902292, -0.040210510196
20given(-0.748512612611, 0.6631205528, 3.48647261319E-5), (-0.663120537734, -0.748512605079, 0.000180205918668), (0.000145594935387, 0.00011176688705, 0.999999983155)142.673759363, 317.010153023, -0.0483795616637
21given(-0.568010477643, 0.823021302922, 0.000179513116003), (-0.823021280811, -0.568010504783, 0.000194392341119), (0.000261954373502, -3.73262281258E-5, 0.999999964993)97.9129353601, 314.298215474, -0.0534800235598
22given(-0.354589187352, 0.935022195779, 4.01630425007E-5), (-0.935022194866, -0.354589188999, 4.64059015211E-5), (5.76319286054E-5, -2.10983052428E-5, 0.999999998117)55.1486962241, 300.983922255, -0.0120108586331
23given(-0.12053399477, 0.992709188309, -0.000153467013895), (-0.992709199609, -0.120533998466, -1.50305526776E-5), (-3.34189605658E-5, 0.000150536423972, 0.999999988111)16.8218098786, 277.808759746, -0.0165153695847
24given(0.119712037157, 0.992808541994, -0.000476553788116), (-0.992808650882, 0.119711972245, -0.000162586890602), (-0.00010436845995, 0.000492590331341, 0.999999873231)-14.6713969757, 246.185675808, -0.0102298053893
25given(0.354477777676, 0.93506440763, -0.000242315116395), (-0.935064372823, 0.35447764316, -0.000468162922275), (-0.00035186719423, 0.000392533584615, 0.999999861053)-38.0449476446, 207.853039948, 0.0330768243622
26given(0.120575449381, 0.992704161464, -9.3911283771E-5), (-0.992704153992, 0.12057546205, 0.000143521159357), (0.000153797448584, 7.59209932211E-5, 0.999999985291)-14.8823263303, 246.084073919, -0.0310879779797
27given(-0.885506960404, 0.464626108216, 5.13917896219E-5), (-0.464626110175, -0.885506960123, -3.62993903187E-5), (2.86421429489E-5, -5.60213300926E-5, 0.999999998021)186.779218213, 308.943020779, 0.00708492572349
28given(-0.748539008638, 0.663090756535, 3.38381645053E-5), (-0.66309074465, -0.748539003279, 0.000157890652402), (0.000130025018083, 9.57495387227E-5, 0.999999986963)142.688621062, 317.010580826, -0.0334870992348
29given(-0.568111439381, 0.822951612487, 0.000189601438622), (-0.822951605477, -0.568111465393, 0.000133906775574), (0.000217913548017, -7.99588373007E-5, 0.99999997306)97.934339056, 314.305326795, -0.00441626720449
30given(-0.35471355069, 0.934975001565, 0.00020833910666), (-0.934975024775, -0.35471354232, -7.70799469786E-5), (1.83287898024E-6, -0.000222133163091, 0.999999975327)55.1493708932, 301.006570306, 0.0434137543579
31given(-0.120529248253, 0.992709762409, 0.000167130250419), (-0.992709745209, -0.120529285005, 0.000230699977339), (0.000249162209278, -0.00013810573347, 0.999999959422)16.782104786, 277.773029697, 0.00834700655741
32given(-0.970928659268, 0.23936903071, 7.58172782163E-5), (-0.239369020615, -0.970928657028, 0.000122195390948), (0.000102862960407, 0.00010049469947, 0.99999998966)227.608338146, 290.544033749, -0.0342798690207
33given(0.354499956895, 0.935056029114, 5.45796300351E-5), (-0.935056027411, 0.35449995014, 0.000104661857021), (7.85162242993E-5, -8.81376358404E-5, 0.999999993033)-38.0690987271, 207.767190166, 0.0107969720351
34given(0.568017295695, 0.823016605955, -0.000134585999741), (-0.823016599115, 0.568017309837, 0.000115350071547), (0.000171382201896, 4.52456760971E-5, 0.99999998429)-51.3930537576, 164.973412694, -0.0255858019
35given(0.748462702318, 0.663176882279, -7.77776284087E-5), (-0.663176843829, 0.748462690868, 0.00027237466647), (0.000238846235169, -0.00015228195678, 0.999999959881)-54.1041994553, 120.218244287, 0.00957956463829
36given(0.885397957369, 0.464833778054, 0.000125967806949), (-0.464833794897, 0.885397915987, 0.000271088216479), (1.44793260976E-5, -0.000298575046876, 0.999999955322)-46.05884814, 76.1405936017, 0.0594394790123
37given(0.970934529174, 0.239345224684, -5.89768605315E-5), (-0.239345201722, 0.970934500913, 0.000263342645069), (0.000120292473199, -0.000241572638521, 0.999999963586)-27.639397363, 35.2544386188, 0.0388963934529
38given(-0.999999985545, 0.000126376717619, 0.000113745769402), (-0.000126402339335, -0.999999966637, -0.000225275245355), (0.000113717296061, -0.00022528961983, 0.999999968156)262.862865357, 262.954143747, 0.0390077822618
39given(0.970978135717, -0.239168259743, 5.90925222637E-5), (0.23916824958, 0.9709781296, 0.000142235911048), (-9.13958620592E-5, -0.000123974904628, 0.999999988139)35.2412035824, -27.6376306788, 0.0388707382394
40given(0.885499116986, -0.464641058067, 3.12342351441E-5), (0.464641059095, 0.885499115597, -4.98007995158E-5), (-4.51839141684E-6, 5.86112720938E-5, 0.999999998272)76.1169863269, -46.0242085494, -0.00384977615108
41given(0.74858167298, -0.663042580536, -0.00012359436712), (0.663042586346, 0.74858167799, 8.31099007188E-6), (8.70099384249E-5, -8.81697836853E-5, 0.999999992328)120.218905552, -54.1097997927, 0.0207928915363
42given(0.568199683589, -0.822890704266, -9.16562970933E-5), (0.822890699883, 0.568199656599, 0.000215145432912), (-0.000124962100275, -0.00019766868137, 0.999999972656)164.943883574, -51.4383864055, 0.0636629087842
43given(0.354573481637, -0.935028140278, -0.000151681225941), (0.935028141929, 0.354573497419, -9.34260186744E-5), (0.00014113809927, -0.000108699826141, 0.999999984132)207.778695052, -38.0510729231, 0.00538208927615
44given(0.120470438424, -0.992716907648, 0.000121389486881), (0.99271691361, 0.120470430715, -6.8962559738E-5), (5.38364552778E-5, 0.000128813346568, 0.999999990254)246.106263195, -14.8598068383, -0.0378182847019
45given(-0.12043616066, -0.992721074117, -1.44743900329E-5), (0.992721074027, -0.120436160913, 1.81098680659E-5), (-1.97212876456E-5, -1.21879490394E-5, 0.999999999731)277.786668642, 16.7905681315, 0.00085576029565
46given(-0.354583592594, -0.935024301193, 0.000178999646619), (0.935024313564, -0.354583603613, -3.3053948824E-5), (9.43765851446E-5, 0.000155648633785, 0.999999983433)300.96451628, 55.1581922868, -0.0436829572308
47given(-0.568027727704, -0.823009411138, 9.86797739126E-5), (0.823009393013, -0.568027736009, -0.000173598858649), (0.000198926342997, -1.739458438E-5, 0.999999980063)314.304938813, 97.9623142407, -0.0175816135655
48given(-0.748442180173, -0.663200037266, -0.000116226045278), (0.663200047431, -0.748442170008, -0.000123455435265), (-5.11282427063E-6, -0.000169480373865, 0.999999985625)317.042152805, 142.68372021, 0.0309209932692
49given(-0.884872165136, -0.46583383688, -0.000296287045594), (0.46583393092, -0.884872003717, -0.000534641507826), (-1.31220067642E-5, -0.000611109947731, 0.999999813186)309.146380341, 186.524274501, 0.150937075549
50given(-0.970956669604, -0.239255322629, -0.000190644945758), (0.239255381861, -0.970956591415, -0.000399797283685), (-8.94543386095E-5, -0.00043379866838, 0.999999901908)290.530476379, 227.717897438, 0.106128393195

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Components

#1: 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 typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
References: UniProt: P0A1N8
#2: 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 typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
References: UniProt: P15930
#3: Protein ...
YecR


Mass: 12194.968 Da / Num. of mol.: 26 / Source method: isolated from a natural source
Source: (natural) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
References: UniProt: A0A745A2I3
#4: Chemical...
ChemComp-TLW / (2~{R},4~{R},5~{R},6~{R})-6-[(1~{R})-1,2-bis(oxidanyl)ethyl]-4,5-bis(oxidanyl)oxane-2-carboxylic acid


Mass: 222.193 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: C8H14O7
#5: Chemical...
ChemComp-TQN / [(3~{R})-1-[[(2~{R},3~{R},4~{R},5~{S},6~{R})-6-[[(2~{R},3~{R},4~{R},5~{S},6~{R})-3-[[(3~{R})-3-dodecanoyloxytetradecanoyl]amino]-6-(hydroxymethyl)-5-phosphonooxy-4-[(3~{R})-3-tetradecanoyloxytetradecanoyl]oxy-oxan-2-yl]oxymethyl]-5-oxidanyl-4-[(3~{R})-3-oxidanyltetradecanoyl]oxy-2-phosphonooxy-oxan-3-yl]amino]-1-oxidanylidene-tetradecan-3-yl] hexadecanoate


Mass: 2036.774 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: C110H208N2O26P2
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Flagellar LP ring / Type: COMPLEX / Entity ID: #1-#3 / 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

-
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 FIELDBright-field microscopy
Image recordingElectron dose: 59 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

-
Processing

Software
NameVersionClassification
phenix.real_space_refine1.19rc5_4047refinement
PHENIX1.19rc5_4047refinement
EM software
IDNameVersionCategory
1SIMPLE3particle selection
4SIMPLE3CTF correction
10RELION3.1initial Euler assignment
11RELION3.1final Euler assignment
12RELION3.1classification
13RELION3.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C26 (26回回転対称)
3D reconstructionResolution: 2.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 31643 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 64.42 Å2
Refine LS restraints
Refinement-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0018122096
ELECTRON MICROSCOPYf_angle_d0.526165256
ELECTRON MICROSCOPYf_chiral_restr0.040919292
ELECTRON MICROSCOPYf_plane_restr0.002421580
ELECTRON MICROSCOPYf_dihedral_angle_d11.263819006
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefinement-IDTypeRms dev position (Å)
ens_1d_27ELECTRON MICROSCOPYNCS constraints0.000699072060892
ens_1d_37ELECTRON MICROSCOPYNCS constraints0.000704889003819
ens_1d_47ELECTRON MICROSCOPYNCS constraints0.000712575597431
ens_1d_57ELECTRON MICROSCOPYNCS constraints0.000695728769964
ens_1d_67ELECTRON MICROSCOPYNCS constraints0.000706538478857
ens_1d_77ELECTRON MICROSCOPYNCS constraints0.000713300408835
ens_1d_87ELECTRON MICROSCOPYNCS constraints0.000702107452705
ens_1d_97ELECTRON MICROSCOPYNCS constraints0.000724332008709
ens_1d_107ELECTRON MICROSCOPYNCS constraints0.000720941108882
ens_1d_117ELECTRON MICROSCOPYNCS constraints0.000705045552057
ens_1d_127ELECTRON MICROSCOPYNCS constraints0.000707520434168
ens_1d_137ELECTRON MICROSCOPYNCS constraints0.000695496833096
ens_1d_147ELECTRON MICROSCOPYNCS constraints0.000705054203404
ens_1d_157ELECTRON MICROSCOPYNCS constraints0.000715289770284
ens_1d_167ELECTRON MICROSCOPYNCS constraints0.000703740544266
ens_1d_177ELECTRON MICROSCOPYNCS constraints0.000692651220983
ens_1d_187ELECTRON MICROSCOPYNCS constraints0.000718833272322
ens_1d_197ELECTRON MICROSCOPYNCS constraints0.000704914946907
ens_1d_207ELECTRON MICROSCOPYNCS constraints0.000697263883655
ens_1d_217ELECTRON MICROSCOPYNCS constraints0.000695876298861
ens_1d_227ELECTRON MICROSCOPYNCS constraints0.000709865347033
ens_1d_237ELECTRON MICROSCOPYNCS constraints0.0007181664835
ens_1d_247ELECTRON MICROSCOPYNCS constraints0.000703316946968
ens_1d_257ELECTRON MICROSCOPYNCS constraints0.000697307043486
ens_1d_267ELECTRON MICROSCOPYNCS constraints0.000696750546119
ens_2d_2GELECTRON MICROSCOPYNCS constraints0.000702176291714
ens_2d_3GELECTRON MICROSCOPYNCS constraints0.000696227380278
ens_2d_4GELECTRON MICROSCOPYNCS constraints0.000705658256819
ens_2d_5GELECTRON MICROSCOPYNCS constraints0.000701635612453
ens_2d_6GELECTRON MICROSCOPYNCS constraints0.000710028479207
ens_2d_7GELECTRON MICROSCOPYNCS constraints0.000701293710833
ens_2d_8GELECTRON MICROSCOPYNCS constraints0.000709493630961
ens_2d_9GELECTRON MICROSCOPYNCS constraints0.00070876226633
ens_2d_10GELECTRON MICROSCOPYNCS constraints0.000719368871234
ens_2d_11GELECTRON MICROSCOPYNCS constraints0.000713373938199
ens_2d_12GELECTRON MICROSCOPYNCS constraints0.000704045359908
ens_2d_13GELECTRON MICROSCOPYNCS constraints0.00071203535857
ens_2d_14GELECTRON MICROSCOPYNCS constraints0.00071217313723
ens_2d_15GELECTRON MICROSCOPYNCS constraints0.000707045690255
ens_2d_16GELECTRON MICROSCOPYNCS constraints0.000702728263201
ens_2d_17GELECTRON MICROSCOPYNCS constraints0.000695860856254
ens_2d_18GELECTRON MICROSCOPYNCS constraints0.000697285161824
ens_2d_19GELECTRON MICROSCOPYNCS constraints0.000710862527402
ens_2d_20GELECTRON MICROSCOPYNCS constraints0.00071365173063
ens_2d_21GELECTRON MICROSCOPYNCS constraints0.000706111271219
ens_2d_22GELECTRON MICROSCOPYNCS constraints0.000711798425438
ens_2d_23GELECTRON MICROSCOPYNCS constraints0.000714424339594
ens_2d_24GELECTRON MICROSCOPYNCS constraints0.000704446666953
ens_2d_25GELECTRON MICROSCOPYNCS constraints0.000706876015151
ens_2d_26GELECTRON MICROSCOPYNCS constraints0.000701084072475
ens_3d_222ELECTRON MICROSCOPYNCS constraints0.000708626463705
ens_3d_322ELECTRON MICROSCOPYNCS constraints0.000700259770995
ens_3d_422ELECTRON MICROSCOPYNCS constraints0.000711323219219
ens_3d_522ELECTRON MICROSCOPYNCS constraints0.000704055382545
ens_3d_622ELECTRON MICROSCOPYNCS constraints0.000707030174205
ens_3d_722ELECTRON MICROSCOPYNCS constraints0.000705251790961
ens_3d_822ELECTRON MICROSCOPYNCS constraints0.000708429270699
ens_3d_922ELECTRON MICROSCOPYNCS constraints0.000702045439419
ens_3d_1022ELECTRON MICROSCOPYNCS constraints0.000703993361332
ens_3d_1122ELECTRON MICROSCOPYNCS constraints0.000709785112556
ens_3d_1222ELECTRON MICROSCOPYNCS constraints0.000697683328481
ens_3d_1322ELECTRON MICROSCOPYNCS constraints0.000700811729673
ens_3d_1422ELECTRON MICROSCOPYNCS constraints0.00071921953739
ens_3d_1522ELECTRON MICROSCOPYNCS constraints0.000708099109731
ens_3d_1622ELECTRON MICROSCOPYNCS constraints0.000706094143773
ens_3d_1722ELECTRON MICROSCOPYNCS constraints0.000706245681161
ens_3d_1822ELECTRON MICROSCOPYNCS constraints0.000711852955708
ens_3d_1922ELECTRON MICROSCOPYNCS constraints0.000698858424412
ens_3d_2022ELECTRON MICROSCOPYNCS constraints0.000705921624322
ens_3d_2122ELECTRON MICROSCOPYNCS constraints0.000714493127587
ens_3d_2222ELECTRON MICROSCOPYNCS constraints0.000704062920676
ens_3d_2322ELECTRON MICROSCOPYNCS constraints0.000706851093736
ens_3d_2422ELECTRON MICROSCOPYNCS constraints0.000712360051163
ens_3d_2522ELECTRON MICROSCOPYNCS constraints0.000707075113917
ens_3d_2622ELECTRON MICROSCOPYNCS constraints0.000711497380841

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