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- PDB-9n4z: CCW Flagellar Switch Complex - FliF, FliG, FliM, and FliN forming... -

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基本情報

登録情報
データベース: PDB / ID: 9n4z
タイトルCCW Flagellar Switch Complex - FliF, FliG, FliM, and FliN forming 34-mer C-ring from Salmonella
要素
  • 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 / C-ring / Bacterial / Chemotaxis / C ring / Flagellar Motor complex / switch complex / FliG / FliM / FliN / FliF
機能・相同性
機能・相同性情報


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 / chemotaxis / plasma membrane
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
類似検索 - ドメイン・相同性
Flagellar motor switch protein FliG / 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 (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: 3 Å
データ登録者Singh, P.K. / Iverson, T.M.
資金援助 米国, 1件
組織認可番号国
National Institutes of Health/John E. Fogarty International Center (NIH/FIC)GM61606 米国
引用
ジャーナル: J Struct Biol / 年: 2025
タイトル: Improving CryoEM maps of symmetry-mismatched macromolecular assemblies: A case study on the flagellar motor.
著者: Prashant K Singh / T M Iverson /
要旨: Advances in cryo-electron microscopy instrumentation and sample preparation have significantly improved the ability to collect quality data for biomolecular structures. However, achieving resolutions ...Advances in cryo-electron microscopy instrumentation and sample preparation have significantly improved the ability to collect quality data for biomolecular structures. However, achieving resolutions consistent with data quality remains challenging in structures with symmetry mismatches. As a case study, the bacterial flagellar motor is a large complex essential for bacterial chemotaxis and virulence. This motor contains a smaller membrane-supramembrane ring (MS-ring) and a larger cytoplasmic ring (C-ring). These two features have a 33:34 symmetry mismatch when expressed in E. coli. Because close symmetry mismatches are the most difficult to deconvolute, this makes the flagellar motor an excellent model system to evaluate refinement strategies for symmetry mismatch. We compared the performance of masked refinement, local refinement, and particle subtracted refinement on the same data. We found that particle subtraction prior to refinement was critical for approaching the smaller MS-ring. Additional processing resulted in final resolutions of 3.1 Å for the MS-ring and 3.0 Å for the C-ring, which improves the resolution of the MS-ring by 0.3 Å and the resolution of the C-ring by 1.0 Å as compared to past work. Although particle subtraction is fairly well-established, it is rarely applied to problems of symmetry mismatch, making this case study a valuable demonstration of its utility in this context.
#1: ジャーナル: Nat Microbiol / 年: 2024
タイトル: CryoEM structures reveal how the bacterial flagellum rotates and switches direction.
著者: Prashant K Singh / Pankaj Sharma / Oshri Afanzar / Margo H Goldfarb / Elena Maklashina / Michael Eisenbach / Gary Cecchini / T M Iverson /
要旨: Bacterial chemotaxis requires bidirectional flagellar rotation at different rates. Rotation is driven by a flagellar motor, which is a supercomplex containing multiple rings. Architectural ...Bacterial chemotaxis requires bidirectional flagellar rotation at different rates. Rotation is driven by a flagellar motor, which is a supercomplex containing multiple rings. Architectural uncertainty regarding the cytoplasmic C-ring, or 'switch', limits our understanding of how the motor transmits torque and direction to the flagellar rod. Here we report cryogenic electron microscopy structures for Salmonella enterica serovar typhimurium inner membrane MS-ring and C-ring in a counterclockwise pose (4.0 Å) and isolated C-ring in a clockwise pose alone (4.6 Å) and bound to a regulator (5.9 Å). Conformational differences between rotational poses include a 180° shift in FliF/FliG domains that rotates the outward-facing MotA/B binding site to inward facing. The regulator has specificity for the clockwise pose by bridging elements unique to this conformation. We used these structures to propose how the switch reverses rotation and transmits torque to the flagellum, which advances the understanding of bacterial chemotaxis and bidirectional motor rotation.
履歴
登録2025年2月3日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02025年3月19日Provider: repository / タイプ: Initial release
改定 1.02025年3月19日Data content type: EM metadata / Data content type: EM metadata / Provider: repository / タイプ: Initial release
改定 1.02025年3月19日Data content type: Image / Data content type: Image / Provider: repository / タイプ: Initial release
改定 1.02025年3月19日Data content type: Primary map / Data content type: Primary map / Provider: repository / タイプ: Initial release
改定 1.02025年3月19日Data content type: Image / Data content type: Image / Provider: repository / タイプ: Initial release
改定 1.02025年3月19日Data content type: Primary map / Data content type: Primary map / Provider: repository / タイプ: Initial release
改定 1.12025年3月26日Group: Data collection / Database references / カテゴリ: citation / em_admin / Item: _citation.journal_volume / _em_admin.last_update
置き換え2025年4月2日ID: 8T8O
改定 1.22025年4月2日Group: Advisory / Data collection
カテゴリ: em_admin / em_obsolete / pdbx_database_PDB_obs_spr
Item: _em_admin.last_update
改定 1.12025年4月2日Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Advisory / Experimental summary / Data content type: EM metadata / EM metadata / EM metadata
カテゴリ: em_admin / em_obsolete / pdbx_database_PDB_obs_spr
Data content type: EM metadata / Item: _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
F: Flagellar M-ring protein
G: Flagellar motor switch protein FliG
M: Flagellar motor switch protein FliM
N: Flagellar motor switch protein FliN
P: Flagellar motor switch protein FliN
Q: Flagellar motor switch protein FliN
A: Flagellar M-ring protein
B: Flagellar motor switch protein FliG
C: Flagellar motor switch protein FliM
D: Flagellar motor switch protein FliN
E: Flagellar motor switch protein FliN
H: Flagellar motor switch protein FliN
I: Flagellar M-ring protein
J: Flagellar motor switch protein FliG
K: Flagellar motor switch protein FliM
L: Flagellar motor switch protein FliN
O: Flagellar motor switch protein FliN
R: Flagellar motor switch protein FliN
S: Flagellar M-ring protein
T: Flagellar motor switch protein FliG
V: Flagellar motor switch protein FliM
W: Flagellar motor switch protein FliN
X: Flagellar motor switch protein FliN
Y: Flagellar motor switch protein FliN
Z: Flagellar M-ring protein
AA: Flagellar motor switch protein FliG
BA: Flagellar motor switch protein FliM
CA: Flagellar motor switch protein FliN
DA: Flagellar motor switch protein FliN
EA: Flagellar motor switch protein FliN
FA: Flagellar M-ring protein
GA: Flagellar motor switch protein FliG
HA: Flagellar motor switch protein FliM
IA: Flagellar motor switch protein FliN
JA: Flagellar motor switch protein FliN
KA: Flagellar motor switch protein FliN
LA: Flagellar M-ring protein
MA: Flagellar motor switch protein FliG
NA: Flagellar motor switch protein FliM
OA: Flagellar motor switch protein FliN
PA: Flagellar motor switch protein FliN
QA: Flagellar motor switch protein FliN
RA: Flagellar M-ring protein
SA: Flagellar motor switch protein FliG
TA: Flagellar motor switch protein FliM
UA: Flagellar motor switch protein FliN
VA: Flagellar motor switch protein FliN
WA: Flagellar motor switch protein FliN
XA: Flagellar M-ring protein
YA: Flagellar motor switch protein FliG
ZA: Flagellar motor switch protein FliM
AB: Flagellar motor switch protein FliN
BB: Flagellar motor switch protein FliN
CB: Flagellar motor switch protein FliN
DB: Flagellar M-ring protein
EB: Flagellar motor switch protein FliG
FB: Flagellar motor switch protein FliM
GB: Flagellar motor switch protein FliN
HB: Flagellar motor switch protein FliN
IB: Flagellar motor switch protein FliN
JB: Flagellar M-ring protein
KB: Flagellar motor switch protein FliG
LB: Flagellar motor switch protein FliM
MB: Flagellar motor switch protein FliN
NB: Flagellar motor switch protein FliN
OB: Flagellar motor switch protein FliN
PB: Flagellar M-ring protein
QB: Flagellar motor switch protein FliG
RB: Flagellar motor switch protein FliM
SB: Flagellar motor switch protein FliN
TB: Flagellar motor switch protein FliN
UB: Flagellar motor switch protein FliN
VB: Flagellar M-ring protein
WB: Flagellar motor switch protein FliG
XB: Flagellar motor switch protein FliM
YB: Flagellar motor switch protein FliN
ZB: Flagellar motor switch protein FliN
AC: Flagellar motor switch protein FliN
BC: Flagellar M-ring protein
CC: Flagellar motor switch protein FliG
DC: Flagellar motor switch protein FliM
EC: Flagellar motor switch protein FliN
FC: Flagellar motor switch protein FliN
GC: Flagellar motor switch protein FliN
HC: Flagellar M-ring protein
IC: Flagellar motor switch protein FliG
JC: Flagellar motor switch protein FliM
KC: Flagellar motor switch protein FliN
LC: Flagellar motor switch protein FliN
MC: Flagellar motor switch protein FliN
NC: Flagellar M-ring protein
OC: Flagellar motor switch protein FliG
PC: Flagellar motor switch protein FliM
QC: Flagellar motor switch protein FliN
RC: Flagellar motor switch protein FliN
SC: Flagellar motor switch protein FliN
TC: Flagellar M-ring protein
UC: Flagellar motor switch protein FliG
VC: Flagellar motor switch protein FliM
WC: Flagellar motor switch protein FliN
XC: Flagellar motor switch protein FliN
YC: Flagellar motor switch protein FliN
ZC: Flagellar M-ring protein
AD: Flagellar motor switch protein FliG
BD: Flagellar motor switch protein FliM
CD: Flagellar motor switch protein FliN
DD: Flagellar motor switch protein FliN
ED: Flagellar motor switch protein FliN
FD: Flagellar M-ring protein
GD: Flagellar motor switch protein FliG
HD: Flagellar motor switch protein FliM
ID: Flagellar motor switch protein FliN
JD: Flagellar motor switch protein FliN
KD: Flagellar motor switch protein FliN
LD: Flagellar M-ring protein
MD: Flagellar motor switch protein FliG
ND: Flagellar motor switch protein FliM
OD: Flagellar motor switch protein FliN
PD: Flagellar motor switch protein FliN
QD: Flagellar motor switch protein FliN
RD: Flagellar M-ring protein
SD: Flagellar motor switch protein FliG
TD: Flagellar motor switch protein FliM
UD: Flagellar motor switch protein FliN
VD: Flagellar motor switch protein FliN
WD: Flagellar motor switch protein FliN
XD: Flagellar M-ring protein
YD: Flagellar motor switch protein FliG
ZD: Flagellar motor switch protein FliM
AE: Flagellar motor switch protein FliN
BE: Flagellar motor switch protein FliN
CE: Flagellar motor switch protein FliN
DE: Flagellar M-ring protein
EE: Flagellar motor switch protein FliG
FE: Flagellar motor switch protein FliM
GE: Flagellar motor switch protein FliN
HE: Flagellar motor switch protein FliN
IE: Flagellar motor switch protein FliN
JE: Flagellar M-ring protein
KE: Flagellar motor switch protein FliG
LE: Flagellar motor switch protein FliM
ME: Flagellar motor switch protein FliN
NE: Flagellar motor switch protein FliN
OE: Flagellar motor switch protein FliN
PE: Flagellar M-ring protein
QE: Flagellar motor switch protein FliG
RE: Flagellar motor switch protein FliM
SE: Flagellar motor switch protein FliN
TE: Flagellar motor switch protein FliN
UE: Flagellar motor switch protein FliN
VE: Flagellar M-ring protein
WE: Flagellar motor switch protein FliG
XE: Flagellar motor switch protein FliM
YE: Flagellar motor switch protein FliN
ZE: Flagellar motor switch protein FliN
AF: Flagellar motor switch protein FliN
BF: Flagellar M-ring protein
CF: Flagellar motor switch protein FliG
DF: Flagellar motor switch protein FliM
EF: Flagellar motor switch protein FliN
FF: Flagellar motor switch protein FliN
GF: Flagellar motor switch protein FliN
HF: Flagellar M-ring protein
IF: Flagellar motor switch protein FliG
JF: Flagellar motor switch protein FliM
KF: Flagellar motor switch protein FliN
LF: Flagellar motor switch protein FliN
MF: Flagellar motor switch protein FliN
NF: Flagellar M-ring protein
OF: Flagellar motor switch protein FliG
PF: Flagellar motor switch protein FliM
QF: Flagellar motor switch protein FliN
RF: Flagellar motor switch protein FliN
SF: Flagellar motor switch protein FliN
TF: Flagellar M-ring protein
UF: Flagellar motor switch protein FliG
VF: Flagellar motor switch protein FliM
WF: Flagellar motor switch protein FliN
XF: Flagellar motor switch protein FliN
YF: Flagellar motor switch protein FliN
ZF: Flagellar M-ring protein
AG: Flagellar motor switch protein FliG
BG: Flagellar motor switch protein FliM
CG: Flagellar motor switch protein FliN
DG: Flagellar motor switch protein FliN
EG: Flagellar motor switch protein FliN
FG: Flagellar M-ring protein
GG: Flagellar motor switch protein FliG
HG: Flagellar motor switch protein FliM
IG: Flagellar motor switch protein FliN
JG: Flagellar motor switch protein FliN
KG: Flagellar motor switch protein FliN
LG: Flagellar M-ring protein
MG: Flagellar motor switch protein FliG
NG: Flagellar motor switch protein FliM
OG: Flagellar motor switch protein FliN
PG: Flagellar motor switch protein FliN
QG: Flagellar motor switch protein FliN
RG: Flagellar M-ring protein
SG: Flagellar motor switch protein FliG
TG: Flagellar motor switch protein FliM
UG: Flagellar motor switch protein FliN
VG: Flagellar motor switch protein FliN
WG: Flagellar motor switch protein FliN


分子量 (理論値)分子数
合計 (水以外)6,136,767204
ポリマ－6,136,767204
非ポリマー00
水00
1


  • 登録構造と同一
  • 登録者が定義した集合体
  • 根拠: 電子顕微鏡法, not applicable
タイプ名称対称操作数
identity operation1_5551

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要素

#1: タンパク質 ...
Flagellar M-ring protein / FliF


分子量: 61295.645 Da / 分子数: 34 / 由来タイプ: 組換発現
由来: (組換発現) Salmonella enterica subsp. enterica serovar Typhimurium (サルモネラ菌)
遺伝子: fliF, fla AII.1, fla BI, STM1969 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: P15928
#2: 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: 組換発現
由来: (組換発現) Salmonella enterica subsp. enterica serovar Typhimurium (サルモネラ菌)
遺伝子: fliG, fla AII.2, fla BII, STM1970 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: P0A1J9
#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: 組換発現
由来: (組換発現) Salmonella enterica subsp. enterica serovar Typhimurium (サルモネラ菌)
遺伝子: fliM, cheC2, fla AII, fla QII, STM1976 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: P26418
#4: 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: 組換発現
由来: (組換発現) Salmonella enterica subsp. enterica serovar Typhimurium (サルモネラ菌)
遺伝子: fliN, flaN, motD, STM1977 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: P26419
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: Bacterial flagellar motor switch complex / タイプ: COMPLEX / Entity ID: all / 由来: RECOMBINANT
分子量値: 4.103 MDa / 実験値: NO
由来(天然)生物種: Salmonella enterica subsp. enterica serovar Typhimurium (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: 7.4
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: TFS KRIOS
電子銃電子線源: FIELD EMISSION GUN / 加速電圧: 300 kV / 照射モード: OTHER
電子レンズモード: BRIGHT FIELD / 最大 デフォーカス（公称値）: 2000 nm / 最小 デフォーカス（公称値）: 1000 nm
撮影電子線照射量: 51.557 e/Å2 / フィルム・検出器のモデル: GATAN K3 (6k x 4k)

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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
7Coot0.9モデルフィッティング
9PHENIX1.20.1-4487-000モデル精密化
13cryoSPARC4.5.3３次元再構成
CTF補正タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION
3次元再構成解像度: 3 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 20863 / 対称性のタイプ: POINT

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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

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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

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2019年1月31日: EMDBのIDの桁数の変更

EMDBのIDの桁数の変更

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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

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  • 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。
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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)

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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

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