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- PDB-6rvw: Structure of right-handed protein cage consisting of 24 eleven-me... -

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基本情報

登録情報
データベース: PDB / ID: 6rvw
タイトルStructure of right-handed protein cage consisting of 24 eleven-membered ring proteins held together by gold (I) bridges.
要素Transcription attenuation protein MtrB
キーワードRNA BINDING PROTEIN / TRAP / protein cage / gold binding / snub cube
機能・相同性
機能・相同性情報


DNA-templated transcription termination / regulation of DNA-templated transcription / RNA binding / identical protein binding
類似検索 - 分子機能
Transcription attenuation protein MtrB / Tryptophan RNA-binding attenuator protein domain / Tryptophan RNA-binding attenuator protein / Tryptophan RNA-binding attenuator protein-like domain superfamily
類似検索 - ドメイン・相同性
: / Transcription attenuation protein MtrB
類似検索 - 構成要素
生物種Geobacillus stearothermophilus (バクテリア)
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: 3.7 Å
データ登録者Malay, A.D. / Miyazaki, N. / Biela, A.P. / Iwasaki, K. / Heddle, J.G.
資金援助 ポーランド, 日本, 5件
組織認可番号国
Polish National Science CentreNCN 2016/20/W/NZ1/00095 ポーランド
Other governmentFNP Homing/2016-2/20 ポーランド
Japan Society for the Promotion of ScienceNo. 2556023 日本
Other governmentMRPO.05.01.00-12-013/15 ポーランド
Japan Agency for Medical Research and Development (AMED) 日本
引用ジャーナル: Nature / 年: 2019
タイトル: An ultra-stable gold-coordinated protein cage displaying reversible assembly.
著者: Ali D Malay / Naoyuki Miyazaki / Artur Biela / Soumyananda Chakraborti / Karolina Majsterkiewicz / Izabela Stupka / Craig S Kaplan / Agnieszka Kowalczyk / Bernard M A G Piette / Georg K A ...著者: Ali D Malay / Naoyuki Miyazaki / Artur Biela / Soumyananda Chakraborti / Karolina Majsterkiewicz / Izabela Stupka / Craig S Kaplan / Agnieszka Kowalczyk / Bernard M A G Piette / Georg K A Hochberg / Di Wu / Tomasz P Wrobel / Adam Fineberg / Manish S Kushwah / Mitja Kelemen / Primož Vavpetič / Primož Pelicon / Philipp Kukura / Justin L P Benesch / Kenji Iwasaki / Jonathan G Heddle /
要旨: Symmetrical protein cages have evolved to fulfil diverse roles in nature, including compartmentalization and cargo delivery, and have inspired synthetic biologists to create novel protein assemblies ...Symmetrical protein cages have evolved to fulfil diverse roles in nature, including compartmentalization and cargo delivery, and have inspired synthetic biologists to create novel protein assemblies via the precise manipulation of protein-protein interfaces. Despite the impressive array of protein cages produced in the laboratory, the design of inducible assemblies remains challenging. Here we demonstrate an ultra-stable artificial protein cage, the assembly and disassembly of which can be controlled by metal coordination at the protein-protein interfaces. The addition of a gold (I)-triphenylphosphine compound to a cysteine-substituted, 11-mer protein ring triggers supramolecular self-assembly, which generates monodisperse cage structures with masses greater than 2 MDa. The geometry of these structures is based on the Archimedean snub cube and is, to our knowledge, unprecedented. Cryo-electron microscopy confirms that the assemblies are held together by 120 S-Au-S staples between the protein oligomers, and exist in two chiral forms. The cage shows extreme chemical and thermal stability, yet it readily disassembles upon exposure to reducing agents. As well as gold, mercury(II) is also found to enable formation of the protein cage. This work establishes an approach for linking protein components into robust, higher-order structures, and expands the design space available for supramolecular assemblies to include previously unexplored geometries.
履歴
登録2019年6月3日登録サイト: PDBE / 処理サイト: PDBE
置き換え2019年6月12日ID: 6IB4
改定 1.02019年6月12日Provider: repository / タイプ: Initial release
改定 1.12024年5月15日Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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構造の表示

ムービー
  • 登録構造単位
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  • マップデータ: EMDB-4444
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ムービービューア
構造ビューア分子:
MolmilJmol/JSmol

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集合体

登録構造単位
AA: Transcription attenuation protein MtrB
AB: Transcription attenuation protein MtrB
AC: Transcription attenuation protein MtrB
AD: Transcription attenuation protein MtrB
AE: Transcription attenuation protein MtrB
AF: Transcription attenuation protein MtrB
AG: Transcription attenuation protein MtrB
AH: Transcription attenuation protein MtrB
AI: Transcription attenuation protein MtrB
AJ: Transcription attenuation protein MtrB
AK: Transcription attenuation protein MtrB
BA: Transcription attenuation protein MtrB
BB: Transcription attenuation protein MtrB
BC: Transcription attenuation protein MtrB
BD: Transcription attenuation protein MtrB
BE: Transcription attenuation protein MtrB
BF: Transcription attenuation protein MtrB
BG: Transcription attenuation protein MtrB
BH: Transcription attenuation protein MtrB
BI: Transcription attenuation protein MtrB
BJ: Transcription attenuation protein MtrB
BK: Transcription attenuation protein MtrB
CA: Transcription attenuation protein MtrB
CB: Transcription attenuation protein MtrB
CC: Transcription attenuation protein MtrB
CD: Transcription attenuation protein MtrB
CE: Transcription attenuation protein MtrB
CF: Transcription attenuation protein MtrB
CG: Transcription attenuation protein MtrB
CH: Transcription attenuation protein MtrB
CI: Transcription attenuation protein MtrB
CJ: Transcription attenuation protein MtrB
CK: Transcription attenuation protein MtrB
DA: Transcription attenuation protein MtrB
DB: Transcription attenuation protein MtrB
DC: Transcription attenuation protein MtrB
DD: Transcription attenuation protein MtrB
DE: Transcription attenuation protein MtrB
DF: Transcription attenuation protein MtrB
DG: Transcription attenuation protein MtrB
DH: Transcription attenuation protein MtrB
DI: Transcription attenuation protein MtrB
DJ: Transcription attenuation protein MtrB
DK: Transcription attenuation protein MtrB
EA: Transcription attenuation protein MtrB
EB: Transcription attenuation protein MtrB
EC: Transcription attenuation protein MtrB
ED: Transcription attenuation protein MtrB
EE: Transcription attenuation protein MtrB
EF: Transcription attenuation protein MtrB
EG: Transcription attenuation protein MtrB
EH: Transcription attenuation protein MtrB
EI: Transcription attenuation protein MtrB
EJ: Transcription attenuation protein MtrB
EK: Transcription attenuation protein MtrB
FA: Transcription attenuation protein MtrB
FB: Transcription attenuation protein MtrB
FC: Transcription attenuation protein MtrB
FD: Transcription attenuation protein MtrB
FE: Transcription attenuation protein MtrB
FF: Transcription attenuation protein MtrB
FG: Transcription attenuation protein MtrB
FH: Transcription attenuation protein MtrB
FI: Transcription attenuation protein MtrB
FJ: Transcription attenuation protein MtrB
FK: Transcription attenuation protein MtrB
GA: Transcription attenuation protein MtrB
GB: Transcription attenuation protein MtrB
GC: Transcription attenuation protein MtrB
GD: Transcription attenuation protein MtrB
GE: Transcription attenuation protein MtrB
GF: Transcription attenuation protein MtrB
GG: Transcription attenuation protein MtrB
GH: Transcription attenuation protein MtrB
GI: Transcription attenuation protein MtrB
GJ: Transcription attenuation protein MtrB
GK: Transcription attenuation protein MtrB
HA: Transcription attenuation protein MtrB
HB: Transcription attenuation protein MtrB
HC: Transcription attenuation protein MtrB
HD: Transcription attenuation protein MtrB
HE: Transcription attenuation protein MtrB
HF: Transcription attenuation protein MtrB
HG: Transcription attenuation protein MtrB
HH: Transcription attenuation protein MtrB
HI: Transcription attenuation protein MtrB
HJ: Transcription attenuation protein MtrB
HK: Transcription attenuation protein MtrB
IA: Transcription attenuation protein MtrB
IB: Transcription attenuation protein MtrB
IC: Transcription attenuation protein MtrB
ID: Transcription attenuation protein MtrB
IE: Transcription attenuation protein MtrB
IF: Transcription attenuation protein MtrB
IG: Transcription attenuation protein MtrB
IH: Transcription attenuation protein MtrB
II: Transcription attenuation protein MtrB
IJ: Transcription attenuation protein MtrB
IK: Transcription attenuation protein MtrB
JA: Transcription attenuation protein MtrB
JB: Transcription attenuation protein MtrB
JC: Transcription attenuation protein MtrB
JD: Transcription attenuation protein MtrB
JE: Transcription attenuation protein MtrB
JF: Transcription attenuation protein MtrB
JG: Transcription attenuation protein MtrB
JH: Transcription attenuation protein MtrB
JI: Transcription attenuation protein MtrB
JJ: Transcription attenuation protein MtrB
JK: Transcription attenuation protein MtrB
KA: Transcription attenuation protein MtrB
KB: Transcription attenuation protein MtrB
KC: Transcription attenuation protein MtrB
KD: Transcription attenuation protein MtrB
KE: Transcription attenuation protein MtrB
KF: Transcription attenuation protein MtrB
KG: Transcription attenuation protein MtrB
KH: Transcription attenuation protein MtrB
KI: Transcription attenuation protein MtrB
KJ: Transcription attenuation protein MtrB
KK: Transcription attenuation protein MtrB
LA: Transcription attenuation protein MtrB
LB: Transcription attenuation protein MtrB
LC: Transcription attenuation protein MtrB
LD: Transcription attenuation protein MtrB
LE: Transcription attenuation protein MtrB
LF: Transcription attenuation protein MtrB
LG: Transcription attenuation protein MtrB
LH: Transcription attenuation protein MtrB
LI: Transcription attenuation protein MtrB
LJ: Transcription attenuation protein MtrB
LK: Transcription attenuation protein MtrB
MA: Transcription attenuation protein MtrB
MB: Transcription attenuation protein MtrB
MC: Transcription attenuation protein MtrB
MD: Transcription attenuation protein MtrB
ME: Transcription attenuation protein MtrB
MF: Transcription attenuation protein MtrB
MG: Transcription attenuation protein MtrB
MH: Transcription attenuation protein MtrB
MI: Transcription attenuation protein MtrB
MJ: Transcription attenuation protein MtrB
MK: Transcription attenuation protein MtrB
NA: Transcription attenuation protein MtrB
NB: Transcription attenuation protein MtrB
NC: Transcription attenuation protein MtrB
ND: Transcription attenuation protein MtrB
NE: Transcription attenuation protein MtrB
NF: Transcription attenuation protein MtrB
NG: Transcription attenuation protein MtrB
NH: Transcription attenuation protein MtrB
NI: Transcription attenuation protein MtrB
NJ: Transcription attenuation protein MtrB
NK: Transcription attenuation protein MtrB
OA: Transcription attenuation protein MtrB
OB: Transcription attenuation protein MtrB
OC: Transcription attenuation protein MtrB
OD: Transcription attenuation protein MtrB
OE: Transcription attenuation protein MtrB
OF: Transcription attenuation protein MtrB
OG: Transcription attenuation protein MtrB
OH: Transcription attenuation protein MtrB
OI: Transcription attenuation protein MtrB
OJ: Transcription attenuation protein MtrB
OK: Transcription attenuation protein MtrB
PA: Transcription attenuation protein MtrB
PB: Transcription attenuation protein MtrB
PC: Transcription attenuation protein MtrB
PD: Transcription attenuation protein MtrB
PE: Transcription attenuation protein MtrB
PF: Transcription attenuation protein MtrB
PG: Transcription attenuation protein MtrB
PH: Transcription attenuation protein MtrB
PI: Transcription attenuation protein MtrB
PJ: Transcription attenuation protein MtrB
PK: Transcription attenuation protein MtrB
QA: Transcription attenuation protein MtrB
QB: Transcription attenuation protein MtrB
QC: Transcription attenuation protein MtrB
QD: Transcription attenuation protein MtrB
QE: Transcription attenuation protein MtrB
QF: Transcription attenuation protein MtrB
QG: Transcription attenuation protein MtrB
QH: Transcription attenuation protein MtrB
QI: Transcription attenuation protein MtrB
QJ: Transcription attenuation protein MtrB
QK: Transcription attenuation protein MtrB
RA: Transcription attenuation protein MtrB
RB: Transcription attenuation protein MtrB
RC: Transcription attenuation protein MtrB
RD: Transcription attenuation protein MtrB
RE: Transcription attenuation protein MtrB
RF: Transcription attenuation protein MtrB
RG: Transcription attenuation protein MtrB
RH: Transcription attenuation protein MtrB
RI: Transcription attenuation protein MtrB
RJ: Transcription attenuation protein MtrB
RK: Transcription attenuation protein MtrB
SA: Transcription attenuation protein MtrB
SB: Transcription attenuation protein MtrB
SC: Transcription attenuation protein MtrB
SD: Transcription attenuation protein MtrB
SE: Transcription attenuation protein MtrB
SF: Transcription attenuation protein MtrB
SG: Transcription attenuation protein MtrB
SH: Transcription attenuation protein MtrB
SI: Transcription attenuation protein MtrB
SJ: Transcription attenuation protein MtrB
SK: Transcription attenuation protein MtrB
TA: Transcription attenuation protein MtrB
TB: Transcription attenuation protein MtrB
TC: Transcription attenuation protein MtrB
TD: Transcription attenuation protein MtrB
TE: Transcription attenuation protein MtrB
TF: Transcription attenuation protein MtrB
TG: Transcription attenuation protein MtrB
TH: Transcription attenuation protein MtrB
TI: Transcription attenuation protein MtrB
TJ: Transcription attenuation protein MtrB
TK: Transcription attenuation protein MtrB
UA: Transcription attenuation protein MtrB
UB: Transcription attenuation protein MtrB
UC: Transcription attenuation protein MtrB
UD: Transcription attenuation protein MtrB
UE: Transcription attenuation protein MtrB
UF: Transcription attenuation protein MtrB
UG: Transcription attenuation protein MtrB
UH: Transcription attenuation protein MtrB
UI: Transcription attenuation protein MtrB
UJ: Transcription attenuation protein MtrB
UK: Transcription attenuation protein MtrB
VA: Transcription attenuation protein MtrB
VB: Transcription attenuation protein MtrB
VC: Transcription attenuation protein MtrB
VD: Transcription attenuation protein MtrB
VE: Transcription attenuation protein MtrB
VF: Transcription attenuation protein MtrB
VG: Transcription attenuation protein MtrB
VH: Transcription attenuation protein MtrB
VI: Transcription attenuation protein MtrB
VJ: Transcription attenuation protein MtrB
VK: Transcription attenuation protein MtrB
WA: Transcription attenuation protein MtrB
WB: Transcription attenuation protein MtrB
WC: Transcription attenuation protein MtrB
WD: Transcription attenuation protein MtrB
WE: Transcription attenuation protein MtrB
WF: Transcription attenuation protein MtrB
WG: Transcription attenuation protein MtrB
WH: Transcription attenuation protein MtrB
WI: Transcription attenuation protein MtrB
WJ: Transcription attenuation protein MtrB
WK: Transcription attenuation protein MtrB
XA: Transcription attenuation protein MtrB
XB: Transcription attenuation protein MtrB
XC: Transcription attenuation protein MtrB
XD: Transcription attenuation protein MtrB
XE: Transcription attenuation protein MtrB
XF: Transcription attenuation protein MtrB
XG: Transcription attenuation protein MtrB
XH: Transcription attenuation protein MtrB
XI: Transcription attenuation protein MtrB
XJ: Transcription attenuation protein MtrB
XK: Transcription attenuation protein MtrB
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)2,178,199384
ポリマ－2,154,563264
非ポリマー23,636120
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
  • 根拠: gel filtration
タイプ名称対称操作数
identity operation1_5551
手法PISA

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要素

#1: タンパク質 ...
Transcription attenuation protein MtrB / Trp RNA-binding attenuation protein / TRAP / Tryptophan RNA-binding attenuator protein


分子量: 8161.224 Da / 分子数: 264 / 変異: K35C, R64S / 由来タイプ: 組換発現
由来: (組換発現) Geobacillus stearothermophilus (バクテリア)
遺伝子: mtrB / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q9X6J6
#2: 化合物...
ChemComp-AU / GOLD ION


分子量: 196.967 Da / 分子数: 120 / 由来タイプ: 合成 / 式: Au / タイプ: SUBJECT OF INVESTIGATION

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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: RH TRAP protein cage / タイプ: COMPLEX / Entity ID: #1 / 由来: RECOMBINANT
分子量値: 2.16 MDa / 実験値: YES
由来(天然)生物種: Geobacillus stearothermophilus (バクテリア)
由来(組換発現)生物種: Escherichia coli (大腸菌)
緩衝液pH: 8
試料濃度: 0.89 mg/ml / 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES
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 K / 詳細: 3.0 s blotting time

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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
試料ホルダ凍結剤: NITROGEN
試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER
撮影電子線照射量: 40 e/Å2 / 検出モード: INTEGRATING
フィルム・検出器のモデル: FEI FALCON II (4k x 4k)
画像スキャン横: 4096 / 縦: 4096

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解析

EMソフトウェア
ID名称カテゴリ
7PHENIXモデルフィッティング
11RELION分類
13PHENIXモデル精密化
CTF補正タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION
3次元再構成解像度: 3.7 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 94388 / 対称性のタイプ: POINT
原子モデル構築プロトコル: OTHER / 空間: REAL
Target criteria: gradient-driven minimization of combined map and restraints target
原子モデル構築

3D fitting-ID: 1 / Accession code: 4V4F / Initial refinement model-ID: 1 / PDB-ID: 4V4F

4v4f

/ Source name: PDB / タイプ: experimental model

IDPDB chain-ID
1AA
2AB
3AC
4AD
5AE
6AF
7AG
8AH
9AI
10AJ
11AK

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