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- PDB-8wiw: Cryo-EM structure of the flagellar C ring in the CW state -

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基本情報

登録情報
データベース: PDB / ID: 8wiw
タイトルCryo-EM structure of the flagellar C ring in the CW state
要素
  • Chemotaxis protein CheY
  • Flagellar M-ring protein
  • Flagellar motor switch protein FliG
  • Flagellar motor switch protein FliM
  • Flagellar motor switch protein FliN
キーワードMOTOR PROTEIN / Flagellum / Flagellar motor / C ring / Switch complex
機能・相同性
機能・相同性情報


archaeal or bacterial-type flagellum-dependent cell motility / bacterial-type flagellum basal body, MS ring / bacterial-type flagellum basal body / bacterial-type flagellum-dependent swarming motility / positive chemotaxis / cytoskeletal motor activity / bacterial-type flagellum-dependent cell motility / phosphorelay signal transduction system / chemotaxis / metal ion binding ...archaeal or bacterial-type flagellum-dependent cell motility / bacterial-type flagellum basal body, MS ring / bacterial-type flagellum basal body / bacterial-type flagellum-dependent swarming motility / positive chemotaxis / cytoskeletal motor activity / bacterial-type flagellum-dependent cell motility / phosphorelay signal transduction system / chemotaxis / metal ion binding / plasma membrane / cytoplasm
類似検索 - 分子機能
Flagellar motor switch protein FliN, N-terminal / Flagellar motor switch protein FliN N-terminal / : / Flagellar motor switch FliN / Flagellar motor switch FliN/Type III secretion HrcQb / Flagellar motor switch protein FliM / Flagellar motor switch protein FliM / Flagellar motor switch protein FliG / Flagellar motor switch protein FliG, alpha-helical / Flagellar motor switch protein FliG, C-terminal ...Flagellar motor switch protein FliN, N-terminal / Flagellar motor switch protein FliN N-terminal / : / Flagellar motor switch FliN / Flagellar motor switch FliN/Type III secretion HrcQb / Flagellar motor switch protein FliM / Flagellar motor switch protein FliM / Flagellar motor switch protein FliG / Flagellar motor switch protein FliG, alpha-helical / Flagellar motor switch protein FliG, C-terminal / Flagellar motor switch protein FliG, N-terminal domain / Flagellar motor switch protein FliG, middle domain / FliG C-terminal domain / FliG middle domain / FliG N-terminal domain / CheC-like superfamily / Flagellar motor switch protein FliN-like, C-terminal domain / SpoA-like superfamily / Type III flagellar switch regulator (C-ring) FliN C-term / : / 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 / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily
類似検索 - ドメイン・相同性
Flagellar motor switch protein FliG / Chemotaxis protein CheY / Flagellar M-ring protein / Flagellar motor switch protein FliM / Flagellar motor switch protein FliN
類似検索 - 構成要素
生物種Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (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: 5.6 Å
データ登録者Tan, J.X. / Zhang, L. / Zhou, Y. / Zhu, Y.Q.
資金援助 中国, 3件
組織認可番号国
National Natural Science Foundation of China (NSFC)81925024 中国
National Natural Science Foundation of China (NSFC)U23A20163 中国
Ministry of Science and Technology (MoST, China)2017YFA0503900 中国
引用ジャーナル: Cell Res / 年: 2024
タイトル: Structural basis of the bacterial flagellar motor rotational switching.
著者: Jiaxing Tan / Ling Zhang / Xingtong Zhou / Siyu Han / Yan Zhou / Yongqun Zhu /
要旨: The bacterial flagellar motor is a huge bidirectional rotary nanomachine that drives rotation of the flagellum for bacterial motility. The cytoplasmic C ring of the flagellar motor functions as the ...The bacterial flagellar motor is a huge bidirectional rotary nanomachine that drives rotation of the flagellum for bacterial motility. The cytoplasmic C ring of the flagellar motor functions as the switch complex for the rotational direction switching from counterclockwise to clockwise. However, the structural basis of the rotational switching and how the C ring is assembled have long remained elusive. Here, we present two high-resolution cryo-electron microscopy structures of the C ring-containing flagellar basal body-hook complex from Salmonella Typhimurium, which are in the default counterclockwise state and in a constitutively active CheY mutant-induced clockwise state, respectively. In both complexes, the C ring consists of four subrings, but is in two different conformations. The CheY proteins are bound into an open groove between two adjacent protomers on the surface of the middle subring of the C ring and interact with the FliG and FliM subunits. The binding of the CheY protein induces a significant upward shift of the C ring towards the MS ring and inward movements of its protomers towards the motor center, which eventually remodels the structures of the FliG subunits and reverses the orientations and surface electrostatic potential of the α helices to trigger the counterclockwise-to-clockwise rotational switching. The conformational changes of the FliG subunits reveal that the stator units on the motor require a relocation process in the inner membrane during the rotational switching. This study provides unprecedented molecular insights into the rotational switching mechanism and a detailed overall structural view of the bacterial flagellar motors.
履歴
登録2023年9月25日登録サイト: PDBJ / 処理サイト: PDBJ
改定 1.02024年9月4日Provider: repository / タイプ: Initial release
改定 1.12025年3月26日Group: Data collection / Database references / Structure summary
カテゴリ: citation / citation_author ...citation / citation_author / em_admin / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

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集合体

登録構造単位
0: Flagellar motor switch protein FliN
C: Flagellar M-ring protein
S: Flagellar motor switch protein FliM
Z: Flagellar motor switch protein FliG
h: Chemotaxis protein CheY
o: Flagellar motor switch protein FliN
u: Flagellar motor switch protein FliN
AA: Flagellar motor switch protein FliN
D: Flagellar M-ring protein
T: Flagellar motor switch protein FliM
a: Flagellar motor switch protein FliG
i: Chemotaxis protein CheY
p: Flagellar motor switch protein FliN
v: Flagellar motor switch protein FliN
AB: Flagellar motor switch protein FliN
E: Flagellar M-ring protein
U: Flagellar motor switch protein FliM
b: Flagellar motor switch protein FliG
j: Chemotaxis protein CheY
q: Flagellar motor switch protein FliN
w: Flagellar motor switch protein FliN
AC: Flagellar motor switch protein FliN
F: Flagellar M-ring protein
V: Flagellar motor switch protein FliM
c: Flagellar motor switch protein FliG
k: Chemotaxis protein CheY
r: Flagellar motor switch protein FliN
x: Flagellar motor switch protein FliN
AD: Flagellar motor switch protein FliN
G: Flagellar M-ring protein
W: Flagellar motor switch protein FliM
d: Flagellar motor switch protein FliG
l: Chemotaxis protein CheY
s: Flagellar motor switch protein FliN
y: Flagellar motor switch protein FliN
AE: Flagellar motor switch protein FliN
H: Flagellar M-ring protein
X: Flagellar motor switch protein FliM
e: Flagellar motor switch protein FliG
m: Chemotaxis protein CheY
t: Flagellar motor switch protein FliN
z: Flagellar motor switch protein FliN
AF: Flagellar motor switch protein FliN
I: Flagellar M-ring protein
Y: Flagellar motor switch protein FliM
f: Flagellar motor switch protein FliG
n: Chemotaxis protein CheY
1: Flagellar motor switch protein FliN
2: Flagellar motor switch protein FliN
AG: Flagellar motor switch protein FliN
J: Flagellar M-ring protein
g: Flagellar motor switch protein FliM
3: Flagellar motor switch protein FliG
4: Chemotaxis protein CheY
5: Flagellar motor switch protein FliN
6: Flagellar motor switch protein FliN
AH: Flagellar motor switch protein FliN
K: Flagellar M-ring protein
7: Flagellar motor switch protein FliM
8: Flagellar motor switch protein FliG
9: Chemotaxis protein CheY
AI: Flagellar motor switch protein FliN
AJ: Flagellar motor switch protein FliN
AK: Flagellar motor switch protein FliN
L: Flagellar M-ring protein
AL: Flagellar motor switch protein FliM
AM: Flagellar motor switch protein FliG
AN: Chemotaxis protein CheY
AO: Flagellar motor switch protein FliN
AP: Flagellar motor switch protein FliN
AQ: Flagellar motor switch protein FliN
M: Flagellar M-ring protein
AR: Flagellar motor switch protein FliM
AS: Flagellar motor switch protein FliG
AT: Chemotaxis protein CheY
AU: Flagellar motor switch protein FliN
AV: Flagellar motor switch protein FliN
AW: Flagellar motor switch protein FliN
N: Flagellar M-ring protein
AX: Flagellar motor switch protein FliM
AY: Flagellar motor switch protein FliG
AZ: Chemotaxis protein CheY
Aa: Flagellar motor switch protein FliN
Ab: Flagellar motor switch protein FliN
Ac: Flagellar motor switch protein FliN
O: Flagellar M-ring protein
Ad: Flagellar motor switch protein FliM
Ae: Flagellar motor switch protein FliG
Af: Chemotaxis protein CheY
Ag: Flagellar motor switch protein FliN
Ah: Flagellar motor switch protein FliN
Ai: Flagellar motor switch protein FliN
P: Flagellar M-ring protein
Aj: Flagellar motor switch protein FliM
Ak: Flagellar motor switch protein FliG
Al: Chemotaxis protein CheY
Am: Flagellar motor switch protein FliN
An: Flagellar motor switch protein FliN
Ao: Flagellar motor switch protein FliN
Q: Flagellar M-ring protein
Ap: Flagellar motor switch protein FliM
Aq: Flagellar motor switch protein FliG
Ar: Chemotaxis protein CheY
As: Flagellar motor switch protein FliN
At: Flagellar motor switch protein FliN
Au: Flagellar motor switch protein FliN
R: Flagellar M-ring protein
Av: Flagellar motor switch protein FliM
Aw: Flagellar motor switch protein FliG
Ax: Chemotaxis protein CheY
Ay: Flagellar motor switch protein FliN
Az: Flagellar motor switch protein FliN
A1: Flagellar motor switch protein FliN
A2: Flagellar M-ring protein
A3: Flagellar motor switch protein FliM
A4: Flagellar motor switch protein FliG
A5: Chemotaxis protein CheY
A6: Flagellar motor switch protein FliN
A7: Flagellar motor switch protein FliN
A8: Flagellar motor switch protein FliN
A9: Flagellar M-ring protein
A0: Flagellar motor switch protein FliM
BA: Flagellar motor switch protein FliG
BB: Chemotaxis protein CheY
BC: Flagellar motor switch protein FliN
BD: Flagellar motor switch protein FliN
BE: Flagellar motor switch protein FliN
BF: Flagellar M-ring protein
BG: Flagellar motor switch protein FliM
BH: Flagellar motor switch protein FliG
BI: Chemotaxis protein CheY
BJ: Flagellar motor switch protein FliN
BK: Flagellar motor switch protein FliN
BL: Flagellar motor switch protein FliN
BM: Flagellar M-ring protein
BN: Flagellar motor switch protein FliM
BO: Flagellar motor switch protein FliG
BP: Chemotaxis protein CheY
BQ: Flagellar motor switch protein FliN
BR: Flagellar motor switch protein FliN
BS: Flagellar motor switch protein FliN
BT: Flagellar M-ring protein
BU: Flagellar motor switch protein FliM
BV: Flagellar motor switch protein FliG
BW: Chemotaxis protein CheY
BX: Flagellar motor switch protein FliN
BY: Flagellar motor switch protein FliN
BZ: Flagellar motor switch protein FliN
Ba: Flagellar M-ring protein
Bb: Flagellar motor switch protein FliM
Bc: Flagellar motor switch protein FliG
Bd: Chemotaxis protein CheY
Be: Flagellar motor switch protein FliN
Bf: Flagellar motor switch protein FliN
Bg: Flagellar motor switch protein FliN
Bh: Flagellar M-ring protein
Bi: Flagellar motor switch protein FliM
Bj: Flagellar motor switch protein FliG
Bk: Chemotaxis protein CheY
Bl: Flagellar motor switch protein FliN
Bm: Flagellar motor switch protein FliN
Bn: Flagellar motor switch protein FliN
Bo: Flagellar M-ring protein
Bp: Flagellar motor switch protein FliM
Bq: Flagellar motor switch protein FliG
Br: Chemotaxis protein CheY
Bs: Flagellar motor switch protein FliN
Bt: Flagellar motor switch protein FliN
Bu: Flagellar motor switch protein FliN
Bv: Flagellar M-ring protein
Bw: Flagellar motor switch protein FliM
Bx: Flagellar motor switch protein FliG
By: Chemotaxis protein CheY
Bz: Flagellar motor switch protein FliN
B1: Flagellar motor switch protein FliN
B2: Flagellar motor switch protein FliN
B3: Flagellar M-ring protein
B4: Flagellar motor switch protein FliM
B5: Flagellar motor switch protein FliG
B6: Chemotaxis protein CheY
B7: Flagellar motor switch protein FliN
B8: Flagellar motor switch protein FliN
B9: Flagellar motor switch protein FliN
B0: Flagellar M-ring protein
CA: Flagellar motor switch protein FliM
CB: Flagellar motor switch protein FliG
CC: Chemotaxis protein CheY
CD: Flagellar motor switch protein FliN
CE: Flagellar motor switch protein FliN
CF: Flagellar motor switch protein FliN
CG: Flagellar M-ring protein
CH: Flagellar motor switch protein FliM
CI: Flagellar motor switch protein FliG
CJ: Chemotaxis protein CheY
CK: Flagellar motor switch protein FliN
CL: Flagellar motor switch protein FliN
CM: Flagellar motor switch protein FliN
CN: Flagellar M-ring protein
CO: Flagellar motor switch protein FliM
CP: Flagellar motor switch protein FliG
CQ: Chemotaxis protein CheY
CR: Flagellar motor switch protein FliN
CS: Flagellar motor switch protein FliN
CT: Flagellar motor switch protein FliN
CU: Flagellar M-ring protein
CV: Flagellar motor switch protein FliM
CW: Flagellar motor switch protein FliG
CX: Chemotaxis protein CheY
CY: Flagellar motor switch protein FliN
CZ: Flagellar motor switch protein FliN
Ca: Flagellar motor switch protein FliN
Cb: Flagellar M-ring protein
Cc: Flagellar motor switch protein FliM
Cd: Flagellar motor switch protein FliG
Ce: Chemotaxis protein CheY
Cf: Flagellar motor switch protein FliN
Cg: Flagellar motor switch protein FliN
Ch: Flagellar motor switch protein FliN
Ci: Flagellar M-ring protein
Cj: Flagellar motor switch protein FliM
Ck: Flagellar motor switch protein FliG
Cl: Chemotaxis protein CheY
Cm: Flagellar motor switch protein FliN
Cn: Flagellar motor switch protein FliN
Co: Flagellar motor switch protein FliN
Cp: Flagellar M-ring protein
Cq: Flagellar motor switch protein FliM
Cr: Flagellar motor switch protein FliG
Cs: Chemotaxis protein CheY
Ct: Flagellar motor switch protein FliN
Cu: Flagellar motor switch protein FliN
Cv: Flagellar motor switch protein FliN
Cw: Flagellar M-ring protein
Cx: Flagellar motor switch protein FliM
Cy: Flagellar motor switch protein FliG
Cz: Chemotaxis protein CheY
C1: Flagellar motor switch protein FliN
C2: Flagellar motor switch protein FliN


分子量 (理論値)分子数
合計 (水以外)6,618,802238
ポリマ－6,618,802238
非ポリマー00
水00
1


  • 登録構造と同一
  • 登録者・ソフトウェアが定義した集合体
タイプ名称対称操作数
identity operation1_555x,y,z1

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要素

#1: タンパク質 ...
Flagellar motor switch protein FliN


分子量: 14801.823 Da / 分子数: 102 / 由来タイプ: 天然
由来: (天然) Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (サルモネラ菌)
参照: UniProt: P26419
#2: タンパク質 ...
Flagellar M-ring protein


分子量: 61295.645 Da / 分子数: 34 / 由来タイプ: 天然
由来: (天然) Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (サルモネラ菌)
参照: UniProt: P15928
#3: タンパク質 ...
Flagellar motor switch protein FliM


分子量: 37901.066 Da / 分子数: 34 / 由来タイプ: 天然
由来: (天然) Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (サルモネラ菌)
参照: UniProt: P26418
#4: タンパク質 ...
Flagellar motor switch protein FliG


分子量: 36890.957 Da / 分子数: 34 / 由来タイプ: 天然
由来: (天然) Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (サルモネラ菌)
参照: UniProt: P0A1J9
#5: タンパク質 ...
Chemotaxis protein CheY


分子量: 14177.512 Da / 分子数: 34 / Mutation: D13K, Y106W / 由来タイプ: 組換発現
由来: (組換発現) Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (サルモネラ菌)
遺伝子: cheY, STM1916 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: P0A2D5
Has protein modificationN

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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: C ring-containing flagellar motor-hook complex in the CW state
タイプ: COMPLEX / Entity ID: all / 由来: MULTIPLE SOURCES
分子量実験値: NO
由来(天然)生物種: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (サルモネラ菌)
由来(組換発現)生物種: Escherichia coli BL21(DE3) (大腸菌)
緩衝液pH: 8
緩衝液成分
ID濃度名称式Buffer-ID
111.7 mMtris(hydroxymethyl)aminomethane hydrochlorideTris-HCl1
24.17 mMethylenediaminetetraacetic acidEDTA1
30.083 % (v/v)octylphenol ethoxylateTX-1001
425 mMsodium chlorideNaCl1
試料包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES
詳細: This sample was prepared by incubating the C ring-containing flagellar motor-hook complex with the constitutively active mutant of CheY (CheY**)
試料支持グリッドの材料: GOLD / グリッドのサイズ: 200 divisions/in. / グリッドのタイプ: Quantifoil R0.6/1
急速凍結装置: FEI VITROBOT MARK IV / 凍結剤: ETHANE / 湿度: 100 % / 凍結前の試料温度: 277.15 K
詳細: Blot time: 4 Blot force: 10 Wait time: 30 Blot total: 1 Drain time: 2

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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 / 倍率（公称値）: 105000 X / 最大 デフォーカス（公称値）: 1800 nm / 最小 デフォーカス（公称値）: 1200 nm / Cs: 2.7 mm
撮影電子線照射量: 50 e/Å2
フィルム・検出器のモデル: FEI FALCON IV (4k x 4k)
電子光学装置エネルギーフィルター名称: TFS Selectris / エネルギーフィルタースリット幅: 10 eV

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解析

EMソフトウェア
ID名称バージョンカテゴリ
1cryoSPARC4.1.1粒子像選択
2EPU画像取得
4cryoSPARC4.1.1CTF補正
7UCSF Chimera1.17モデルフィッティング
8UCSF ChimeraX1.5モデルフィッティング
9Coot0.9.8.7モデルフィッティング
11cryoSPARC4.1.1初期オイラー角割当
12cryoSPARC4.1.1最終オイラー角割当
14cryoSPARC4.1.1３次元再構成
15PHENIX1.20.1_4487:モデル精密化
CTF補正タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION
粒子像の選択選択した粒子像数: 46058 / 詳細: Particles were manually picked using cryoSPARC
対称性点対称性: C34 (34回回転対称)
3次元再構成解像度: 5.6 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 28119 / 対称性のタイプ: POINT
原子モデル構築プロトコル: RIGID BODY FIT / 空間: REAL
原子モデル構築PDB-ID: 8XP1

8xp1


Accession code: 8XP1 / Source name: PDB / タイプ: experimental model

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