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

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基本情報

登録情報
データベース: PDB / ID: 7bgl
タイトルSalmonella LP ring 26 mer refined in C26 map
要素
  • Flagellar L-ring protein
  • Flagellar P-ring protein
  • YecR
キーワードMEMBRANE PROTEIN / bacterial flagellum LP ring salmonella
機能・相同性
機能・相同性情報


bacterial-type flagellum basal body, distal rod, L ring / bacterial-type flagellum basal body, distal rod, P ring / cytoskeletal motor activity / bacterial-type flagellum-dependent cell motility / cell outer membrane / outer membrane-bounded periplasmic space / structural molecule activity
類似検索 - 分子機能
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.
類似検索 - ドメイン・相同性
Chem-TLW / Chem-TQN / Outer membrane lipoprotein / Flagellar L-ring protein / Flagellar P-ring protein
類似検索 - 構成要素
生物種Salmonella typhimurium (サルモネラ菌)
手法電子顕微鏡法 / 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 2.2 Å
データ登録者Johnson, S. / Furlong, E. / Lea, S.M.
資金援助 英国, 4件
組織認可番号国
Wellcome Trust219477 英国
Wellcome Trust209194 英国
Wellcome Trust201536 英国
Medical Research Council (MRC, United Kingdom)S021264 英国
引用ジャーナル: Nat Microbiol / 年: 2021
タイトル: Molecular structure of the intact bacterial flagellar basal body.
著者: 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 /
要旨: 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.
履歴
登録2021年1月7日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02021年5月5日Provider: repository / タイプ: Initial release
改定 2.02021年5月19日Group: Database references / Non-polymer description / カテゴリ: 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
改定 2.12021年6月9日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
改定 2.22021年7月14日Group: Derived calculations
カテゴリ: pdbx_struct_sheet_hbond / struct_sheet ...pdbx_struct_sheet_hbond / struct_sheet / struct_sheet_order / struct_sheet_range
改定 2.32024年10月9日Group: Data collection / Database references / Structure summary
カテゴリ: 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 ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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構造の表示

ムービー
  • 登録構造単位
  • Jmolによる作画
  • ダウンロード
  • 単純化した表面モデル + あてはめた原子モデル
  • マップデータ: EMDB-12183
  • Jmolによる作画
  • ダウンロード
  • EMマップとの重ね合わせ
  • マップデータ: EMDB-12183
  • UCSF Chimeraによる作画
  • ダウンロード
ムービービューア
構造ビューア分子:
MolmilJmol/JSmol

ダウンロードとリンク

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集合体

登録構造単位
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
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)2,011,744130
ポリマ－1,953,01178
非ポリマー58,73352
水00
1


  • 登録構造と同一
  • 登録者が定義した集合体
タイプ名称対称操作数
identity operation1_5551
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
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ドメイン領域:
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アンサンブル:
ID
ens_1
ens_2
ens_3

NCS oper:
IDCodeMatrixベクター
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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要素

#1: タンパク質 ...
Flagellar L-ring protein / Basal body L-ring protein


分子量: 24726.666 Da / 分子数: 26 / 由来タイプ: 天然
由来: (天然) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (サルモネラ菌)
参照: UniProt: P0A1N8
#2: タンパク質 ...
Flagellar P-ring protein / Basal body P-ring protein


分子量: 38194.176 Da / 分子数: 26 / 由来タイプ: 天然
由来: (天然) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (サルモネラ菌)
参照: UniProt: P15930
#3: タンパク質 ...
YecR


分子量: 12194.968 Da / 分子数: 26 / 由来タイプ: 天然
由来: (天然) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (サルモネラ菌)
参照: UniProt: A0A745A2I3
#4: 化合物...
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


分子量: 222.193 Da / 分子数: 26 / 由来タイプ: 合成 / 式: C8H14O7
#5: 化合物...
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 / 6-O-[3-O-[(3R)-1-オキソ-3-(ミリストイルオキシ)テトラデシル]-4-O-ホスホノ-2-[[(3R)(以下略)


分子量: 2036.774 Da / 分子数: 26 / 由来タイプ: 合成 / 式: C110H208N2O26P2
研究の焦点であるリガンドがあるかN
Has protein modificationY

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実験情報

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実験

実験手法: 電子顕微鏡法
EM実験試料の集合状態: PARTICLE / ３次元再構成法: 単粒子再構成法

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試料調製

構成要素名称: Flagellar LP ring / タイプ: COMPLEX / Entity ID: #1-#3 / 由来: NATURAL
分子量実験値: NO
由来(天然)生物種: Salmonella enterica subsp. enterica serovar Typhi (サルモネラ菌)
緩衝液pH: 8
試料包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES
急速凍結凍結剤: ETHANE

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電子顕微鏡撮影

実験機器
モデル: Titan Krios / 画像提供: FEI Company
顕微鏡モデル: FEI TITAN KRIOS
電子銃電子線源: FIELD EMISSION GUN / 加速電圧: 300 kV / 照射モード: FLOOD BEAM
電子レンズモード: BRIGHT FIELD
撮影電子線照射量: 59 e/Å2
フィルム・検出器のモデル: GATAN K3 BIOQUANTUM (6k x 4k)

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解析

ソフトウェア
名称バージョン分類
phenix.real_space_refine1.19rc5_4047精密化
PHENIX1.19rc5_4047精密化
EMソフトウェア
ID名称バージョンカテゴリ
1SIMPLE3粒子像選択
4SIMPLE3CTF補正
10RELION3.1初期オイラー角割当
11RELION3.1最終オイラー角割当
12RELION3.1分類
13RELION3.1３次元再構成
CTF補正タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION
対称性点対称性: C26 (26回回転対称)
3次元再構成解像度: 2.2 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 31643 / 対称性のタイプ: POINT
精密化交差検証法: NONE
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
原子変位パラメータBiso mean: 64.42 Å2
拘束条件
Refine-IDタイプDev ideal数
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-IDRefine-IDタイプRms 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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万見について

-
お知らせ

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2022年2月9日: EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

  • EMDBのヘッダファイルのバージョン3が、公式のフォーマットとなりました。
  • これまでは公式だったバージョン1.9は、アーカイブから削除されます。

関連情報:EMDBヘッダ

外部リンク:wwPDBはEMDBデータモデルのバージョン3へ移行します

-
2020年8月12日: 新型コロナ情報

新型コロナ情報

URL: https://pdbj.org/emnavi/covid19.php

新ページ: EM Navigatorに新型コロナウイルスの特設ページを開設しました。

関連情報:Covid-19情報 / 2020年3月5日: 新型コロナウイルスの構造データ

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2020年3月5日: 新型コロナウイルスの構造データ

新型コロナウイルスの構造データ

関連情報:万見生物種 / 2020年8月12日: 新型コロナ情報

外部リンク:COVID-19特集ページ - PDBj / 今月の分子2020年2月：コロナウイルスプロテーアーゼ

+
2019年1月31日: EMDBのIDの桁数の変更

EMDBのIDの桁数の変更

  • EMDBエントリに付与されているアクセスコード(EMDB-ID)は4桁の数字(例、EMD-1234)でしたが、間もなく枯渇します。これまでの4桁のID番号は4桁のまま変更されませんが、4桁の数字を使い切った後に発行されるIDは5桁以上の数字(例、EMD-12345)になります。5桁のIDは2019年の春頃から発行される見通しです。
  • EM Navigator/万見では、接頭語「EMD-」は省略されています。

関連情報:Q: 「EMD」とは何ですか？ / 万見/EM NavigatorにおけるID/アクセスコードの表記

外部リンク:EMDB Accession Codes are Changing Soon! / PDBjへお問い合わせ

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2017年7月12日: PDB大規模アップデート

PDB大規模アップデート

  • 新バージョンのPDBx/mmCIF辞書形式に基づくデータがリリースされました。
  • 今回の更新はバージョン番号が4から5になる大規模なもので、全エントリデータの書き換えが行われる「Remediation」というアップデートに該当します。
  • このバージョンアップで、電子顕微鏡の実験手法に関する多くの項目の書式が改定されました(例：em_softwareなど)。
  • EM NavigatorとYorodumiでも、この改定に基づいた表示内容になります。

外部リンク:wwPDB Remediation / OneDepデータ基準に準拠した、より強化された内容のモデル構造ファイルが、PDBアーカイブで公開されました。

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万見 (Yorodumi)

幾万の構造データを、幾万の視点から

  • 万見(Yorodumi)は、EMDB/PDB/SASBDBなどの構造データを閲覧するためのページです。
  • EM Navigatorの詳細ページの後継、Omokage検索のフロントエンドも兼ねています。

関連情報:EMDB / PDB / SASBDB / 3つのデータバンクの比較 / 万見検索 / 2016年8月31日: 新しいEM Navigatorと万見 / 万見文献 / Jmol/JSmol / 機能・相同性情報 / 新しいEM Navigatorと万見の変更点

他の情報も見る