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- PDB-8r59: Structure of the Co(II) triggered TRAP (S33HK35H) protein cage (l... -

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基本情報

登録情報
データベース: PDB / ID: 8r59
タイトルStructure of the Co(II) triggered TRAP (S33HK35H) protein cage (levo form)
要素Transcription attenuation protein MtrB
キーワードVIRUS LIKE PARTICLE / TRAP protein / protein cage
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: 2.86 Å
データ登録者Biela, A.P. / Heddle, J.G.
資金援助 ポーランド, 1件
組織認可番号国
Polish National Science Centre2019/34/A/NZ1/00196 ポーランド
引用ジャーナル: Macromol Rapid Commun / 年: 2025
タイトル: Designed, Programmable Protein Cages Utilizing Diverse Metal Coordination Geometries Show Reversible, pH-Dependent Assembly.
著者: Norbert Osiński / Karolina Majsterkiewicz / Zuzanna Pakosz-Stępień / Yusuke Azuma / Artur P Biela / Szymon Gaweł / Jonathan G Heddle /
要旨: The rational design and production of a novel series of engineered protein cages are presented, which have emerged as versatile and adaptable platforms with significant applications in biomedicine. ...The rational design and production of a novel series of engineered protein cages are presented, which have emerged as versatile and adaptable platforms with significant applications in biomedicine. These protein cages are assembled from multiple protein subunits, and precise control over their interactions is crucial for regulating assembly and disassembly, such as the on-demand release of encapsulated therapeutic agents. This approach employs a homo-undecameric, ring-shaped protein scaffold with strategically positioned metal binding sites. These engineered proteins can self-assemble into highly stable cages in the presence of cobalt or zinc ions. Furthermore, the cages can be disassembled on demand by employing external triggers such as chelating agents and changes in pH. Interestingly, for certain triggers, the disassembly process is reversible, allowing the cages to reassemble upon reversal or outcompeting of triggering conditions/agents. This work offers a promising platform for the development of advanced drug delivery systems and other biomedical applications.
履歴
登録2023年11月16日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02024年12月25日Provider: repository / タイプ: Initial release
改定 1.12025年4月2日Group: Data collection / Database references / カテゴリ: citation / em_admin
Item: _citation.journal_volume / _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
A: Transcription attenuation protein MtrB
L: Transcription attenuation protein MtrB
M: Transcription attenuation protein MtrB
N: Transcription attenuation protein MtrB
O: Transcription attenuation protein MtrB
P: Transcription attenuation protein MtrB
Q: Transcription attenuation protein MtrB
R: Transcription attenuation protein MtrB
S: Transcription attenuation protein MtrB
T: Transcription attenuation protein MtrB
U: Transcription attenuation protein MtrB
V: Transcription attenuation protein MtrB
W: Transcription attenuation protein MtrB
Y: Transcription attenuation protein MtrB
Z: Transcription attenuation protein MtrB
a: Transcription attenuation protein MtrB
b: Transcription attenuation protein MtrB
c: Transcription attenuation protein MtrB
d: Transcription attenuation protein MtrB
e: Transcription attenuation protein MtrB
f: Transcription attenuation protein MtrB
g: Transcription attenuation protein MtrB
h: Transcription attenuation protein MtrB
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l: Transcription attenuation protein MtrB
m: Transcription attenuation protein MtrB
n: Transcription attenuation protein MtrB
o: Transcription attenuation protein MtrB
p: Transcription attenuation protein MtrB
q: Transcription attenuation protein MtrB
r: Transcription attenuation protein MtrB
s: Transcription attenuation protein MtrB
t: Transcription attenuation protein MtrB
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0: Transcription attenuation protein MtrB
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AA: Transcription attenuation protein MtrB
BA: Transcription attenuation protein MtrB
CA: Transcription attenuation protein MtrB
DA: Transcription attenuation protein MtrB
EA: Transcription attenuation protein MtrB
FA: Transcription attenuation protein MtrB
GA: Transcription attenuation protein MtrB
HA: Transcription attenuation protein MtrB
IA: Transcription attenuation protein MtrB
JA: Transcription attenuation protein MtrB
KA: Transcription attenuation protein MtrB
LA: Transcription attenuation protein MtrB
MA: Transcription attenuation protein MtrB
NA: Transcription attenuation protein MtrB
OA: Transcription attenuation protein MtrB
PA: Transcription attenuation protein MtrB
QA: Transcription attenuation protein MtrB
RA: Transcription attenuation protein MtrB
SA: Transcription attenuation protein MtrB
D: Transcription attenuation protein MtrB
TA: Transcription attenuation protein MtrB
UA: Transcription attenuation protein MtrB
VA: Transcription attenuation protein MtrB
WA: Transcription attenuation protein MtrB
XA: Transcription attenuation protein MtrB
YA: Transcription attenuation protein MtrB
ZA: Transcription attenuation protein MtrB
aA: Transcription attenuation protein MtrB
bA: Transcription attenuation protein MtrB
cA: Transcription attenuation protein MtrB
dA: Transcription attenuation protein MtrB
eA: Transcription attenuation protein MtrB
fA: Transcription attenuation protein MtrB
gA: Transcription attenuation protein MtrB
hA: Transcription attenuation protein MtrB
iA: Transcription attenuation protein MtrB
jA: Transcription attenuation protein MtrB
kA: Transcription attenuation protein MtrB
lA: Transcription attenuation protein MtrB
mA: Transcription attenuation protein MtrB
nA: Transcription attenuation protein MtrB
oA: Transcription attenuation protein MtrB
pA: Transcription attenuation protein MtrB
E: Transcription attenuation protein MtrB
qA: Transcription attenuation protein MtrB
rA: Transcription attenuation protein MtrB
sA: Transcription attenuation protein MtrB
tA: Transcription attenuation protein MtrB
uA: Transcription attenuation protein MtrB
vA: Transcription attenuation protein MtrB
wA: Transcription attenuation protein MtrB
xA: Transcription attenuation protein MtrB
yA: Transcription attenuation protein MtrB
zA: Transcription attenuation protein MtrB
0A: Transcription attenuation protein MtrB
1A: Transcription attenuation protein MtrB
2A: Transcription attenuation protein MtrB
3A: Transcription attenuation protein MtrB
4A: Transcription attenuation protein MtrB
5A: Transcription attenuation protein MtrB
6A: Transcription attenuation protein MtrB
7A: Transcription attenuation protein MtrB
8A: Transcription attenuation protein MtrB
9A: Transcription attenuation protein MtrB
AB: Transcription attenuation protein MtrB
BB: Transcription attenuation protein MtrB
CB: Transcription attenuation protein MtrB
F: Transcription attenuation protein MtrB
DB: Transcription attenuation protein MtrB
EB: Transcription attenuation protein MtrB
FB: Transcription attenuation protein MtrB
GB: Transcription attenuation protein MtrB
HB: Transcription attenuation protein MtrB
IB: Transcription attenuation protein MtrB
JB: Transcription attenuation protein MtrB
KB: Transcription attenuation protein MtrB
LB: Transcription attenuation protein MtrB
MB: Transcription attenuation protein MtrB
NB: Transcription attenuation protein MtrB
OB: Transcription attenuation protein MtrB
PB: Transcription attenuation protein MtrB
QB: Transcription attenuation protein MtrB
RB: Transcription attenuation protein MtrB
SB: Transcription attenuation protein MtrB
TB: Transcription attenuation protein MtrB
UB: Transcription attenuation protein MtrB
VB: Transcription attenuation protein MtrB
WB: Transcription attenuation protein MtrB
XB: Transcription attenuation protein MtrB
YB: Transcription attenuation protein MtrB
ZB: Transcription attenuation protein MtrB
G: Transcription attenuation protein MtrB
aB: Transcription attenuation protein MtrB
bB: Transcription attenuation protein MtrB
cB: Transcription attenuation protein MtrB
dB: Transcription attenuation protein MtrB
eB: Transcription attenuation protein MtrB
fB: Transcription attenuation protein MtrB
gB: Transcription attenuation protein MtrB
hB: Transcription attenuation protein MtrB
iB: Transcription attenuation protein MtrB
jB: Transcription attenuation protein MtrB
kB: Transcription attenuation protein MtrB
lB: Transcription attenuation protein MtrB
mB: Transcription attenuation protein MtrB
nB: Transcription attenuation protein MtrB
oB: Transcription attenuation protein MtrB
pB: Transcription attenuation protein MtrB
qB: Transcription attenuation protein MtrB
rB: Transcription attenuation protein MtrB
sB: Transcription attenuation protein MtrB
tB: Transcription attenuation protein MtrB
uB: Transcription attenuation protein MtrB
vB: Transcription attenuation protein MtrB
wB: Transcription attenuation protein MtrB
H: Transcription attenuation protein MtrB
xB: Transcription attenuation protein MtrB
yB: Transcription attenuation protein MtrB
zB: Transcription attenuation protein MtrB
0B: Transcription attenuation protein MtrB
1B: Transcription attenuation protein MtrB
2B: Transcription attenuation protein MtrB
3B: Transcription attenuation protein MtrB
4B: Transcription attenuation protein MtrB
5B: Transcription attenuation protein MtrB
6B: Transcription attenuation protein MtrB
7B: Transcription attenuation protein MtrB
8B: Transcription attenuation protein MtrB
9B: Transcription attenuation protein MtrB
AC: Transcription attenuation protein MtrB
BC: Transcription attenuation protein MtrB
CC: Transcription attenuation protein MtrB
DC: Transcription attenuation protein MtrB
EC: Transcription attenuation protein MtrB
FC: Transcription attenuation protein MtrB
GC: Transcription attenuation protein MtrB
HC: Transcription attenuation protein MtrB
IC: Transcription attenuation protein MtrB
JC: Transcription attenuation protein MtrB
I: Transcription attenuation protein MtrB
KC: Transcription attenuation protein MtrB
LC: Transcription attenuation protein MtrB
MC: Transcription attenuation protein MtrB
NC: Transcription attenuation protein MtrB
OC: Transcription attenuation protein MtrB
PC: Transcription attenuation protein MtrB
QC: Transcription attenuation protein MtrB
RC: Transcription attenuation protein MtrB
SC: Transcription attenuation protein MtrB
TC: Transcription attenuation protein MtrB
UC: Transcription attenuation protein MtrB
VC: Transcription attenuation protein MtrB
WC: Transcription attenuation protein MtrB
XC: Transcription attenuation protein MtrB
YC: Transcription attenuation protein MtrB
ZC: Transcription attenuation protein MtrB
aC: Transcription attenuation protein MtrB
bC: Transcription attenuation protein MtrB
cC: Transcription attenuation protein MtrB
dC: Transcription attenuation protein MtrB
eC: Transcription attenuation protein MtrB
fC: Transcription attenuation protein MtrB
gC: Transcription attenuation protein MtrB
J: Transcription attenuation protein MtrB
hC: Transcription attenuation protein MtrB
iC: Transcription attenuation protein MtrB
jC: Transcription attenuation protein MtrB
kC: Transcription attenuation protein MtrB
lC: Transcription attenuation protein MtrB
mC: Transcription attenuation protein MtrB
nC: Transcription attenuation protein MtrB
oC: Transcription attenuation protein MtrB
pC: Transcription attenuation protein MtrB
qC: Transcription attenuation protein MtrB
rC: Transcription attenuation protein MtrB
sC: Transcription attenuation protein MtrB
tC: Transcription attenuation protein MtrB
uC: Transcription attenuation protein MtrB
vC: Transcription attenuation protein MtrB
wC: Transcription attenuation protein MtrB
xC: Transcription attenuation protein MtrB
yC: Transcription attenuation protein MtrB
zC: Transcription attenuation protein MtrB
0C: Transcription attenuation protein MtrB
1C: Transcription attenuation protein MtrB
2C: Transcription attenuation protein MtrB
3C: Transcription attenuation protein MtrB
K: Transcription attenuation protein MtrB
4C: Transcription attenuation protein MtrB
5C: Transcription attenuation protein MtrB
6C: Transcription attenuation protein MtrB
7C: Transcription attenuation protein MtrB
8C: Transcription attenuation protein MtrB
9C: Transcription attenuation protein MtrB
AD: Transcription attenuation protein MtrB
BD: Transcription attenuation protein MtrB
CD: Transcription attenuation protein MtrB
DD: Transcription attenuation protein MtrB
ED: Transcription attenuation protein MtrB
FD: Transcription attenuation protein MtrB
GD: Transcription attenuation protein MtrB
HD: Transcription attenuation protein MtrB
ID: Transcription attenuation protein MtrB
JD: Transcription attenuation protein MtrB
KD: Transcription attenuation protein MtrB
LD: Transcription attenuation protein MtrB
MD: Transcription attenuation protein MtrB
ND: Transcription attenuation protein MtrB
OD: Transcription attenuation protein MtrB
PD: Transcription attenuation protein MtrB
QD: Transcription attenuation protein MtrB
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)2,202,869384
ポリマ－2,195,797264
非ポリマー7,072120
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 ...
Transcription attenuation protein MtrB / Trp RNA-binding attenuation protein / TRAP / Tryptophan RNA-binding attenuator protein


分子量: 8317.413 Da / 分子数: 264 / 変異: S33H,K35H / 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-CO / COBALT (II) ION


分子量: 58.933 Da / 分子数: 120 / 由来タイプ: 合成 / 式: Co / タイプ: SUBJECT OF INVESTIGATION
研究の焦点であるリガンドがあるかY
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: TRAP(S33HK35C) protein cage / タイプ: COMPLEX / Entity ID: #1 / 由来: RECOMBINANT
分子量値: 2.2 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: 7.9
試料濃度: 1 mg/ml / 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 / グリッドのサイズ: 300 divisions/in. / 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 / 湿度: 95 % / 凍結前の試料温度: 277 K

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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 / 最大 デフォーカス（公称値）: 2500 nm / 最小 デフォーカス（公称値）: 500 nm
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 / 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名称カテゴリ
1cryoSPARC粒子像選択
2EPU画像取得
4cryoSPARCCTF補正
7UCSF ChimeraXモデルフィッティング
9cryoSPARC初期オイラー角割当
10cryoSPARC最終オイラー角割当
12cryoSPARC３次元再構成
13PHENIXモデル精密化
CTF補正タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION
対称性点対称性: O (正8面体型対称)
3次元再構成解像度: 2.86 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 157100 / アルゴリズム: FOURIER SPACE / クラス平均像の数: 1 / 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: 4v4f

4v4f


Accession code: 4v4f / Source name: PDB / タイプ: experimental model
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: 23.79 Å2
拘束条件
Refine-IDタイプDev ideal数
ELECTRON MICROSCOPYf_bond_d0.006144936
ELECTRON MICROSCOPYf_angle_d0.6904195360
ELECTRON MICROSCOPYf_chiral_restr0.054522440
ELECTRON MICROSCOPYf_plane_restr0.003125344
ELECTRON MICROSCOPYf_dihedral_angle_d5.772919272

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