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- PDB-9kmg: Cryo-EM Structure of Bacteriophage FCWL1 Capsid -

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基本情報

登録情報
データベース: PDB / ID: 9kmg
タイトルCryo-EM Structure of Bacteriophage FCWL1 Capsid
要素
  • Decoration protein
  • Major capsid protein
キーワードVIRUS / T1-like phage / capsid / icosahedrally averaged
機能・相同性Protein of unknown function DUF2184 / Major capsid protein / : / Structural cement protein (E217 gp24/Pam3 gp6) / Major capsid protein / Decoration protein
機能・相同性情報
生物種Escherichia phage FCWL1 (ファージ)
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: 3.1 Å
データ登録者Cai, C. / Wang, Y. / Liu, Y. / Shao, Q. / Wang, A. / Fang, Q.
資金援助 中国, 2件
組織認可番号国
Other governmentD2301008
National Natural Science Foundation of China (NSFC)32371285 中国
引用ジャーナル: Structure / 年: 2025
タイトル: Structures of a T1-like siphophage reveal capsid stabilization mechanisms and high structural similarities with a myophage.
著者: Can Cai / Yueting Wang / Yunshu Liu / Qianqian Shao / Aohan Wang / Lin Li / Yaqi Zheng / Tianyi Zhang / Ziwen Luo / Chongguang Yang / Qianglin Fang /
要旨: Bacteriophage T1, a member of Siphoviruses, infects Escherichia coli with high efficiency, making it a promising candidate for phage therapy. Here, we report the near-atomic structures of FCWL1, a T1- ...Bacteriophage T1, a member of Siphoviruses, infects Escherichia coli with high efficiency, making it a promising candidate for phage therapy. Here, we report the near-atomic structures of FCWL1, a T1-like phage that belongs to the T1 phage family. We focus on the head, the head-to-tail interface, and its surrounding components. The hexameric capsomer displays unique gaps between neighboring A domains of the major capsid proteins. These gaps are partially filled by the N-loop of the decoration protein, which adopts a unique conformation. These structural features suggest that the phage might employ a novel strategy for stabilizing its head. Furthermore, despite being a siphophage, the head and head-to-tail connector of the phage show high structural similarity to those of a myophage. These findings enhance our understanding of the structure, capsid stabilization mechanism, and evolution of phages in the T1 family.
履歴
登録2024年11月16日登録サイト: PDBJ / 処理サイト: PDBC
改定 1.02025年1月22日Provider: repository / タイプ: Initial release
改定 1.12025年7月2日Group: Data collection / Database references / カテゴリ: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 / _citation_author.identifier_ORCID / _em_admin.last_update

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構造の表示

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: Major capsid protein
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein
E: Major capsid protein
F: Major capsid protein
G: Major capsid protein
a: Decoration protein
b: Decoration protein
c: Decoration protein
d: Decoration protein
e: Decoration protein
f: Decoration protein
g: Decoration protein


分子量 (理論値)分子数
合計 (水以外)366,26514
ポリマ－366,26514
非ポリマー00
水00
1
A: Major capsid protein
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein
E: Major capsid protein
F: Major capsid protein
G: Major capsid protein
a: Decoration protein
b: Decoration protein
c: Decoration protein
d: Decoration protein
e: Decoration protein
f: Decoration protein
g: Decoration protein

A: Major capsid protein
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein
E: Major capsid protein
F: Major capsid protein
G: Major capsid protein
a: Decoration protein
b: Decoration protein
c: Decoration protein
d: Decoration protein
e: Decoration protein
f: Decoration protein
g: Decoration protein

A: Major capsid protein
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein
E: Major capsid protein
F: Major capsid protein
G: Major capsid protein
a: Decoration protein
b: Decoration protein
c: Decoration protein
d: Decoration protein
e: Decoration protein
f: Decoration protein
g: Decoration protein

A: Major capsid protein
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein
E: Major capsid protein
F: Major capsid protein
G: Major capsid protein
a: Decoration protein
b: Decoration protein
c: Decoration protein
d: Decoration protein
e: Decoration protein
f: Decoration protein
g: Decoration protein

A: Major capsid protein
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein
E: Major capsid protein
F: Major capsid protein
G: Major capsid protein
a: Decoration protein
b: Decoration protein
c: Decoration protein
d: Decoration protein
e: Decoration protein
f: Decoration protein
g: Decoration protein

A: Major capsid protein
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein
E: Major capsid protein
F: Major capsid protein
G: Major capsid protein
a: Decoration protein
b: Decoration protein
c: Decoration protein
d: Decoration protein
e: Decoration protein
f: Decoration protein
g: Decoration protein

A: Major capsid protein
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein
E: Major capsid protein
F: Major capsid protein
G: Major capsid protein
a: Decoration protein
b: Decoration protein
c: Decoration protein
d: Decoration protein
e: Decoration protein
f: Decoration protein
g: Decoration protein

A: Major capsid protein
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein
E: Major capsid protein
F: Major capsid protein
G: Major capsid protein
a: Decoration protein
b: Decoration protein
c: Decoration protein
d: Decoration protein
e: Decoration protein
f: Decoration protein
g: Decoration protein

A: Major capsid protein
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein
E: Major capsid protein
F: Major capsid protein
G: Major capsid protein
a: Decoration protein
b: Decoration protein
c: Decoration protein
d: Decoration protein
e: Decoration protein
f: Decoration protein
g: Decoration protein

A: Major capsid protein
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein
E: Major capsid protein
F: Major capsid protein
G: Major capsid protein
a: Decoration protein
b: Decoration protein
c: Decoration protein
d: Decoration protein
e: Decoration protein
f: Decoration protein
g: Decoration protein

A: Major capsid protein
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein
E: Major capsid protein
F: Major capsid protein
G: Major capsid protein
a: Decoration protein
b: Decoration protein
c: Decoration protein
d: Decoration protein
e: Decoration protein
f: Decoration protein
g: Decoration protein

A: Major capsid protein
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein
E: Major capsid protein
F: Major capsid protein
G: Major capsid protein
a: Decoration protein
b: Decoration protein
c: Decoration protein
d: Decoration protein
e: Decoration protein
f: Decoration protein
g: Decoration protein

A: Major capsid protein
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein
E: Major capsid protein
F: Major capsid protein
G: Major capsid protein
a: Decoration protein
b: Decoration protein
c: Decoration protein
d: Decoration protein
e: Decoration protein
f: Decoration protein
g: Decoration protein

A: Major capsid protein
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein
E: Major capsid protein
F: Major capsid protein
G: Major capsid protein
a: Decoration protein
b: Decoration protein
c: Decoration protein
d: Decoration protein
e: Decoration protein
f: Decoration protein
g: Decoration protein

A: Major capsid protein
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein
E: Major capsid protein
F: Major capsid protein
G: Major capsid protein
a: Decoration protein
b: Decoration protein
c: Decoration protein
d: Decoration protein
e: Decoration protein
f: Decoration protein
g: Decoration protein

A: Major capsid protein
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein
E: Major capsid protein
F: Major capsid protein
G: Major capsid protein
a: Decoration protein
b: Decoration protein
c: Decoration protein
d: Decoration protein
e: Decoration protein
f: Decoration protein
g: Decoration protein

A: Major capsid protein
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein
E: Major capsid protein
F: Major capsid protein
G: Major capsid protein
a: Decoration protein
b: Decoration protein
c: Decoration protein
d: Decoration protein
e: Decoration protein
f: Decoration protein
g: Decoration protein

A: Major capsid protein
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein
E: Major capsid protein
F: Major capsid protein
G: Major capsid protein
a: Decoration protein
b: Decoration protein
c: Decoration protein
d: Decoration protein
e: Decoration protein
f: Decoration protein
g: Decoration protein

A: Major capsid protein
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein
E: Major capsid protein
F: Major capsid protein
G: Major capsid protein
a: Decoration protein
b: Decoration protein
c: Decoration protein
d: Decoration protein
e: Decoration protein
f: Decoration protein
g: Decoration protein

A: Major capsid protein
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein
E: Major capsid protein
F: Major capsid protein
G: Major capsid protein
a: Decoration protein
b: Decoration protein
c: Decoration protein
d: Decoration protein
e: Decoration protein
f: Decoration protein
g: Decoration protein

A: Major capsid protein
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein
E: Major capsid protein
F: Major capsid protein
G: Major capsid protein
a: Decoration protein
b: Decoration protein
c: Decoration protein
d: Decoration protein
e: Decoration protein
f: Decoration protein
g: Decoration protein

A: Major capsid protein
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein
E: Major capsid protein
F: Major capsid protein
G: Major capsid protein
a: Decoration protein
b: Decoration protein
c: Decoration protein
d: Decoration protein
e: Decoration protein
f: Decoration protein
g: Decoration protein

A: Major capsid protein
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein
E: Major capsid protein
F: Major capsid protein
G: Major capsid protein
a: Decoration protein
b: Decoration protein
c: Decoration protein
d: Decoration protein
e: Decoration protein
f: Decoration protein
g: Decoration protein

A: Major capsid protein
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein
E: Major capsid protein
F: Major capsid protein
G: Major capsid protein
a: Decoration protein
b: Decoration protein
c: Decoration protein
d: Decoration protein
e: Decoration protein
f: Decoration protein
g: Decoration protein

A: Major capsid protein
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein
E: Major capsid protein
F: Major capsid protein
G: Major capsid protein
a: Decoration protein
b: Decoration protein
c: Decoration protein
d: Decoration protein
e: Decoration protein
f: Decoration protein
g: Decoration protein

A: Major capsid protein
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein
E: Major capsid protein
F: Major capsid protein
G: Major capsid protein
a: Decoration protein
b: Decoration protein
c: Decoration protein
d: Decoration protein
e: Decoration protein
f: Decoration protein
g: Decoration protein

A: Major capsid protein
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein
E: Major capsid protein
F: Major capsid protein
G: Major capsid protein
a: Decoration protein
b: Decoration protein
c: Decoration protein
d: Decoration protein
e: Decoration protein
f: Decoration protein
g: Decoration protein

A: Major capsid protein
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein
E: Major capsid protein
F: Major capsid protein
G: Major capsid protein
a: Decoration protein
b: Decoration protein
c: Decoration protein
d: Decoration protein
e: Decoration protein
f: Decoration protein
g: Decoration protein

A: Major capsid protein
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein
E: Major capsid protein
F: Major capsid protein
G: Major capsid protein
a: Decoration protein
b: Decoration protein
c: Decoration protein
d: Decoration protein
e: Decoration protein
f: Decoration protein
g: Decoration protein

A: Major capsid protein
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein
E: Major capsid protein
F: Major capsid protein
G: Major capsid protein
a: Decoration protein
b: Decoration protein
c: Decoration protein
d: Decoration protein
e: Decoration protein
f: Decoration protein
g: Decoration protein

A: Major capsid protein
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein
E: Major capsid protein
F: Major capsid protein
G: Major capsid protein
a: Decoration protein
b: Decoration protein
c: Decoration protein
d: Decoration protein
e: Decoration protein
f: Decoration protein
g: Decoration protein

A: Major capsid protein
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein
E: Major capsid protein
F: Major capsid protein
G: Major capsid protein
a: Decoration protein
b: Decoration protein
c: Decoration protein
d: Decoration protein
e: Decoration protein
f: Decoration protein
g: Decoration protein

A: Major capsid protein
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein
E: Major capsid protein
F: Major capsid protein
G: Major capsid protein
a: Decoration protein
b: Decoration protein
c: Decoration protein
d: Decoration protein
e: Decoration protein
f: Decoration protein
g: Decoration protein

A: Major capsid protein
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein
E: Major capsid protein
F: Major capsid protein
G: Major capsid protein
a: Decoration protein
b: Decoration protein
c: Decoration protein
d: Decoration protein
e: Decoration protein
f: Decoration protein
g: Decoration protein

A: Major capsid protein
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein
E: Major capsid protein
F: Major capsid protein
G: Major capsid protein
a: Decoration protein
b: Decoration protein
c: Decoration protein
d: Decoration protein
e: Decoration protein
f: Decoration protein
g: Decoration protein

A: Major capsid protein
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein
E: Major capsid protein
F: Major capsid protein
G: Major capsid protein
a: Decoration protein
b: Decoration protein
c: Decoration protein
d: Decoration protein
e: Decoration protein
f: Decoration protein
g: Decoration protein

A: Major capsid protein
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein
E: Major capsid protein
F: Major capsid protein
G: Major capsid protein
a: Decoration protein
b: Decoration protein
c: Decoration protein
d: Decoration protein
e: Decoration protein
f: Decoration protein
g: Decoration protein

A: Major capsid protein
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein
E: Major capsid protein
F: Major capsid protein
G: Major capsid protein
a: Decoration protein
b: Decoration protein
c: Decoration protein
d: Decoration protein
e: Decoration protein
f: Decoration protein
g: Decoration protein

A: Major capsid protein
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein
E: Major capsid protein
F: Major capsid protein
G: Major capsid protein
a: Decoration protein
b: Decoration protein
c: Decoration protein
d: Decoration protein
e: Decoration protein
f: Decoration protein
g: Decoration protein

A: Major capsid protein
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein
E: Major capsid protein
F: Major capsid protein
G: Major capsid protein
a: Decoration protein
b: Decoration protein
c: Decoration protein
d: Decoration protein
e: Decoration protein
f: Decoration protein
g: Decoration protein

A: Major capsid protein
B: Major capsid protein
C: Major capsid protein
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E: Major capsid protein
F: Major capsid protein
G: Major capsid protein
a: Decoration protein
b: Decoration protein
c: Decoration protein
d: Decoration protein
e: Decoration protein
f: Decoration protein
g: Decoration protein

A: Major capsid protein
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein
E: Major capsid protein
F: Major capsid protein
G: Major capsid protein
a: Decoration protein
b: Decoration protein
c: Decoration protein
d: Decoration protein
e: Decoration protein
f: Decoration protein
g: Decoration protein

A: Major capsid protein
B: Major capsid protein
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D: Major capsid protein
E: Major capsid protein
F: Major capsid protein
G: Major capsid protein
a: Decoration protein
b: Decoration protein
c: Decoration protein
d: Decoration protein
e: Decoration protein
f: Decoration protein
g: Decoration protein

A: Major capsid protein
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein
E: Major capsid protein
F: Major capsid protein
G: Major capsid protein
a: Decoration protein
b: Decoration protein
c: Decoration protein
d: Decoration protein
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f: Decoration protein
g: Decoration protein

A: Major capsid protein
B: Major capsid protein
C: Major capsid protein
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E: Major capsid protein
F: Major capsid protein
G: Major capsid protein
a: Decoration protein
b: Decoration protein
c: Decoration protein
d: Decoration protein
e: Decoration protein
f: Decoration protein
g: Decoration protein

A: Major capsid protein
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein
E: Major capsid protein
F: Major capsid protein
G: Major capsid protein
a: Decoration protein
b: Decoration protein
c: Decoration protein
d: Decoration protein
e: Decoration protein
f: Decoration protein
g: Decoration protein

A: Major capsid protein
B: Major capsid protein
C: Major capsid protein
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E: Major capsid protein
F: Major capsid protein
G: Major capsid protein
a: Decoration protein
b: Decoration protein
c: Decoration protein
d: Decoration protein
e: Decoration protein
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g: Decoration protein

A: Major capsid protein
B: Major capsid protein
C: Major capsid protein
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E: Major capsid protein
F: Major capsid protein
G: Major capsid protein
a: Decoration protein
b: Decoration protein
c: Decoration protein
d: Decoration protein
e: Decoration protein
f: Decoration protein
g: Decoration protein

A: Major capsid protein
B: Major capsid protein
C: Major capsid protein
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E: Major capsid protein
F: Major capsid protein
G: Major capsid protein
a: Decoration protein
b: Decoration protein
c: Decoration protein
d: Decoration protein
e: Decoration protein
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g: Decoration protein

A: Major capsid protein
B: Major capsid protein
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D: Major capsid protein
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F: Major capsid protein
G: Major capsid protein
a: Decoration protein
b: Decoration protein
c: Decoration protein
d: Decoration protein
e: Decoration protein
f: Decoration protein
g: Decoration protein

A: Major capsid protein
B: Major capsid protein
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G: Major capsid protein
a: Decoration protein
b: Decoration protein
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d: Decoration protein
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g: Decoration protein

A: Major capsid protein
B: Major capsid protein
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G: Major capsid protein
a: Decoration protein
b: Decoration protein
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A: Major capsid protein
B: Major capsid protein
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G: Major capsid protein
a: Decoration protein
b: Decoration protein
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A: Major capsid protein
B: Major capsid protein
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G: Major capsid protein
a: Decoration protein
b: Decoration protein
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A: Major capsid protein
B: Major capsid protein
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G: Major capsid protein
a: Decoration protein
b: Decoration protein
c: Decoration protein
d: Decoration protein
e: Decoration protein
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A: Major capsid protein
B: Major capsid protein
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G: Major capsid protein
a: Decoration protein
b: Decoration protein
c: Decoration protein
d: Decoration protein
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g: Decoration protein

A: Major capsid protein
B: Major capsid protein
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E: Major capsid protein
F: Major capsid protein
G: Major capsid protein
a: Decoration protein
b: Decoration protein
c: Decoration protein
d: Decoration protein
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A: Major capsid protein
B: Major capsid protein
C: Major capsid protein
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E: Major capsid protein
F: Major capsid protein
G: Major capsid protein
a: Decoration protein
b: Decoration protein
c: Decoration protein
d: Decoration protein
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A: Major capsid protein
B: Major capsid protein
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E: Major capsid protein
F: Major capsid protein
G: Major capsid protein
a: Decoration protein
b: Decoration protein
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A: Major capsid protein
B: Major capsid protein
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E: Major capsid protein
F: Major capsid protein
G: Major capsid protein
a: Decoration protein
b: Decoration protein
c: Decoration protein
d: Decoration protein
e: Decoration protein
f: Decoration protein
g: Decoration protein


分子量 (理論値)分子数
合計 (水以外)21,975,874840
ポリマ－21,975,874840
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
point symmetry operation59

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要素

#1: タンパク質
Major capsid protein


分子量: 35301.375 Da / 分子数: 7 / 由来タイプ: 天然 / 由来: (天然) Escherichia phage FCWL1 (ファージ) / 参照: UniProt: A0AAX4MTV7
#2: タンパク質
Decoration protein


分子量: 17022.135 Da / 分子数: 7 / 由来タイプ: 天然 / 由来: (天然) Escherichia phage FCWL1 (ファージ) / 参照: UniProt: A0AAX4MUC4
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: Escherichia phage FCWL1 / タイプ: VIRUS / Entity ID: all / 由来: NATURAL
由来(天然)生物種: Escherichia phage FCWL1 (ファージ)
ウイルスについての詳細中空か: NO / エンベロープを持つか: NO / 単離: STRAIN / タイプ: VIRION
天然宿主生物種: Escherichia coli
緩衝液pH: 7
試料包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES
試料支持グリッドの材料: COPPER / グリッドのタイプ: Quantifoil R2/1
急速凍結装置: FEI VITROBOT MARK IV / 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: FLOOD BEAM
電子レンズモード: BRIGHT FIELD / 倍率（公称値）: 75000 X / 最大 デフォーカス（公称値）: 3000 nm / 最小 デフォーカス（公称値）: 1000 nm
試料ホルダ試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER
撮影電子線照射量: 25.8 e/Å2
フィルム・検出器のモデル: FEI FALCON IV (4k 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
2EPU画像取得
12RELION4３次元再構成
13PHENIX1.19.2-4158-000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: 84600
対称性点対称性: I (正20面体型対称)
3次元再構成解像度: 3.1 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 74400 / 対称性のタイプ: POINT
拘束条件
Refine-IDタイプDev ideal数
ELECTRON MICROSCOPYf_bond_d0.00324388
ELECTRON MICROSCOPYf_angle_d0.48933141
ELECTRON MICROSCOPYf_dihedral_angle_d3.8843303
ELECTRON MICROSCOPYf_chiral_restr0.0443883
ELECTRON MICROSCOPYf_plane_restr0.0044229

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万見について

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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

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

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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

  • 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

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