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- PDB-6owg: Structure of a synthetic beta-carboxysome shell, T=4 -

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基本情報

登録情報
データベース: PDB / ID: 6owg
タイトルStructure of a synthetic beta-carboxysome shell, T=4
要素
  • Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
  • Microcompartments proteinBacterial microcompartment
キーワードSTRUCTURAL PROTEIN (タンパク質) / BACTERIAL MICROCOMPARTMENTS / CARBOXYSOME (カルボキシソーム)
機能・相同性
機能・相同性情報


structural constituent of carboxysome shell / カルボキシソーム / 炭素固定 / 光合成
類似検索 - 分子機能
Carboxysome shell vertex protein CcmL / Carboxysome shell protein CcmK / Bacterial microcompartment vertex (BMV) domain profile. / Ethanolamine utilization protein EutN/carboxysome shell vertex protein CcmL / EutN/Ccml superfamily / Ethanolamine utilisation protein EutN/carboxysome / CcmK/CsoS1, bacterial microcompartment domain / Bacterial microcompartment (BMC) domain profile. / BMC domain / Bacterial microcompartment domain ...Carboxysome shell vertex protein CcmL / Carboxysome shell protein CcmK / Bacterial microcompartment vertex (BMV) domain profile. / Ethanolamine utilization protein EutN/carboxysome shell vertex protein CcmL / EutN/Ccml superfamily / Ethanolamine utilisation protein EutN/carboxysome / CcmK/CsoS1, bacterial microcompartment domain / Bacterial microcompartment (BMC) domain profile. / BMC domain / Bacterial microcompartment domain / CcmK-like superfamily / BMC
類似検索 - ドメイン・相同性
Carboxysome shell vertex protein CcmL / Carboxysome shell protein CcmK
類似検索 - 構成要素
生物種Halothece sp.
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: 2.6 Å
データ登録者Sutter, M. / Laughlin, T.G. / Davies, K.M. / Kerfeld, C.A.
引用ジャーナル: Plant Physiol / 年: 2019
タイトル: Structure of a Synthetic -Carboxysome Shell.
著者: Markus Sutter / Thomas G Laughlin / Nancy B Sloan / Daniel Serwas / Karen M Davies / Cheryl A Kerfeld /
要旨: Carboxysomes are capsid-like, CO-fixing organelles that are present in all cyanobacteria and some chemoautotrophs and that substantially contribute to global primary production. They are composed of ...Carboxysomes are capsid-like, CO-fixing organelles that are present in all cyanobacteria and some chemoautotrophs and that substantially contribute to global primary production. They are composed of a selectively permeable protein shell that encapsulates Rubisco, the principal CO-fixing enzyme, and carbonic anhydrase. As the centerpiece of the carbon-concentrating mechanism, by packaging enzymes that collectively enhance catalysis, the carboxysome shell enables the generation of a locally elevated concentration of substrate CO and the prevention of CO escape. A functional carboxysome consisting of an intact shell and cargo is essential for cyanobacterial growth under ambient CO concentrations. Using cryo-electron microscopy, we have determined the structure of a recombinantly produced simplified β-carboxysome shell. The structure reveals the sidedness and the specific interactions between the carboxysome shell proteins. The model provides insight into the structural basis of selective permeability of the carboxysome shell and can be used to design modifications to investigate the mechanisms of cargo encapsulation and other physiochemical properties such as permeability. Notably, the permeability properties are of great interest for modeling and evaluating this carbon-concentrating mechanism in metabolic engineering. Moreover, we find striking similarity between the carboxysome shell and the structurally characterized, evolutionarily distant metabolosome shell, implying universal architectural principles for bacterial microcompartment shells.
履歴
登録2019年5月9日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02019年9月25日Provider: repository / タイプ: Initial release
改定 1.12019年11月20日Group: Database references / カテゴリ: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
改定 1.22019年12月18日Group: Other / カテゴリ: atom_sites / cell
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.Z_PDB
改定 1.32024年3月13日Group: Data collection / Database references / カテゴリ: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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構造の表示

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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
A: Microcompartments protein
B: Microcompartments protein
C: Microcompartments protein
D: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
E: Microcompartments protein
F: Microcompartments protein
G: Microcompartments protein
H: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
I: Microcompartments protein
J: Microcompartments protein
K: Microcompartments protein
L: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
M: Microcompartments protein
N: Microcompartments protein
O: Microcompartments protein
P: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
Q: Microcompartments protein
R: Microcompartments protein
S: Microcompartments protein
T: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
U: Microcompartments protein
V: Microcompartments protein
W: Microcompartments protein
X: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
Y: Microcompartments protein
Z: Microcompartments protein
0: Microcompartments protein
1: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
2: Microcompartments protein
3: Microcompartments protein
4: Microcompartments protein
5: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
6: Microcompartments protein
7: Microcompartments protein
8: Microcompartments protein
9: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
a: Microcompartments protein
b: Microcompartments protein
c: Microcompartments protein
d: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
e: Microcompartments protein
f: Microcompartments protein
g: Microcompartments protein
h: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
i: Microcompartments protein
j: Microcompartments protein
k: Microcompartments protein
l: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
m: Microcompartments protein
n: Microcompartments protein
o: Microcompartments protein
p: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
q: Microcompartments protein
r: Microcompartments protein
s: Microcompartments protein
t: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
u: Microcompartments protein
v: Microcompartments protein
w: Microcompartments protein
x: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
y: Microcompartments protein
z: Microcompartments protein
AA: Microcompartments protein
AB: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
AC: Microcompartments protein
AD: Microcompartments protein
AE: Microcompartments protein
AF: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
AG: Microcompartments protein
AH: Microcompartments protein
AI: Microcompartments protein
AJ: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
AK: Microcompartments protein
AL: Microcompartments protein
AM: Microcompartments protein
AN: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
AO: Microcompartments protein
AP: Microcompartments protein
AQ: Microcompartments protein
AR: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
AS: Microcompartments protein
AT: Microcompartments protein
AU: Microcompartments protein
AV: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
AW: Microcompartments protein
AX: Microcompartments protein
AY: Microcompartments protein
AZ: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
A0: Microcompartments protein
A1: Microcompartments protein
A2: Microcompartments protein
A3: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
A4: Microcompartments protein
A5: Microcompartments protein
A6: Microcompartments protein
A7: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
A8: Microcompartments protein
A9: Microcompartments protein
BA: Microcompartments protein
BB: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
BC: Microcompartments protein
BD: Microcompartments protein
BE: Microcompartments protein
BF: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
BG: Microcompartments protein
BH: Microcompartments protein
BI: Microcompartments protein
BJ: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
BK: Microcompartments protein
BL: Microcompartments protein
BM: Microcompartments protein
BN: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
BO: Microcompartments protein
BP: Microcompartments protein
BQ: Microcompartments protein
BR: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
BS: Microcompartments protein
BT: Microcompartments protein
BU: Microcompartments protein
BV: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
BW: Microcompartments protein
BX: Microcompartments protein
BY: Microcompartments protein
BZ: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
B0: Microcompartments protein
B1: Microcompartments protein
B2: Microcompartments protein
B3: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
B4: Microcompartments protein
B5: Microcompartments protein
B6: Microcompartments protein
B7: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
B8: Microcompartments protein
B9: Microcompartments protein
CA: Microcompartments protein
CB: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
CC: Microcompartments protein
CD: Microcompartments protein
CE: Microcompartments protein
CF: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
CG: Microcompartments protein
CH: Microcompartments protein
CI: Microcompartments protein
CJ: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
CK: Microcompartments protein
CL: Microcompartments protein
CM: Microcompartments protein
CN: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
CO: Microcompartments protein
CP: Microcompartments protein
CQ: Microcompartments protein
CR: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
CS: Microcompartments protein
CT: Microcompartments protein
CU: Microcompartments protein
CV: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
CW: Microcompartments protein
CX: Microcompartments protein
CY: Microcompartments protein
CZ: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
C0: Microcompartments protein
C1: Microcompartments protein
C2: Microcompartments protein
C3: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
C4: Microcompartments protein
C5: Microcompartments protein
C6: Microcompartments protein
C7: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
C8: Microcompartments protein
C9: Microcompartments protein
DA: Microcompartments protein
DB: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
DC: Microcompartments protein
DD: Microcompartments protein
DE: Microcompartments protein
DF: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
DG: Microcompartments protein
DH: Microcompartments protein
DI: Microcompartments protein
DJ: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
DK: Microcompartments protein
DL: Microcompartments protein
DM: Microcompartments protein
DN: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
DO: Microcompartments protein
DP: Microcompartments protein
DQ: Microcompartments protein
DR: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
DS: Microcompartments protein
DT: Microcompartments protein
DU: Microcompartments protein
DV: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
DW: Microcompartments protein
DX: Microcompartments protein
DY: Microcompartments protein
DZ: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
D0: Microcompartments protein
D1: Microcompartments protein
D2: Microcompartments protein
D3: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
D4: Microcompartments protein
D5: Microcompartments protein
D6: Microcompartments protein
D7: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
D8: Microcompartments protein
D9: Microcompartments protein
EA: Microcompartments protein
EB: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
EC: Microcompartments protein
ED: Microcompartments protein
EE: Microcompartments protein
EF: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
EG: Microcompartments protein
EH: Microcompartments protein
EI: Microcompartments protein
EJ: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
EK: Microcompartments protein
EL: Microcompartments protein
EM: Microcompartments protein
EN: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
EO: Microcompartments protein
EP: Microcompartments protein
EQ: Microcompartments protein
ER: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
ES: Microcompartments protein
ET: Microcompartments protein
EU: Microcompartments protein
EV: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
EW: Microcompartments protein
EX: Microcompartments protein
EY: Microcompartments protein
EZ: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
E0: Microcompartments protein
E1: Microcompartments protein
E2: Microcompartments protein
E3: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
E4: Microcompartments protein
E5: Microcompartments protein
E6: Microcompartments protein
E7: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml


分子量 (理論値)分子数
合計 (水以外)2,880,053240
ポリマ－2,880,053240
非ポリマー00
水0
1


  • 登録構造と同一
  • 登録者が定義した集合体
  • 根拠: microscopy
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 ...
Microcompartments protein / Bacterial microcompartment


分子量: 12163.887 Da / 分子数: 180 / 由来タイプ: 組換発現
由来: (組換発現) Halothece sp. (strain PCC 7418) (バクテリア)
株: PCC 7418 / 遺伝子: PCC7418_3532 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: K9YHS7
#2: タンパク質 ...
Ethanolamine utilization protein EutN/carboxysome structural protein Ccml


分子量: 11509.216 Da / 分子数: 60 / 由来タイプ: 組換発現
由来: (組換発現) Halothece sp. (strain PCC 7418) (バクテリア)
株: PCC 7418 / 遺伝子: PCC7418_3533 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: K9YFK1

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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: Synthetic beta-carboxysome shell (T=4) / タイプ: COMPLEX / 詳細: bacterial microcompartment shell / Entity ID: all / 由来: RECOMBINANT
由来(天然)生物種: Halothece sp. PCC 7418 (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: 0.6 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 R1.2/1.3
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: blot for 6 seconds before plunging

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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 FIELDBright-field microscopy / 倍率（補正後）: 56000 X / 最大 デフォーカス（公称値）: 2000 nm / 最小 デフォーカス（公称値）: 2.7 nm / Calibrated defocus min: 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
撮影平均露光時間: 6 sec. / 電子線照射量: 50 e/Å2 / 検出モード: SUPER-RESOLUTION
フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k)
撮影したグリッド数: 1 / 実像数: 1343
電子光学装置エネルギーフィルター名称: GIF Quantum LS / エネルギーフィルタースリット幅: 25 eV
画像スキャン動画フレーム数/画像: 25 / 利用したフレーム数/画像: 1-25

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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
1Gautomatch0.56粒子像選択
2SerialEM画像取得
4Gctf1.06CTF補正
5RELION3.0.b2CTF補正
11cryoSPARC2初期オイラー角割当
12RELION3.0.b2最終オイラー角割当
14RELION3.0b2３次元再構成
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: 47121
対称性点対称性: I (正20面体型対称)
3次元再構成解像度: 2.6 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 35384 / 対称性のタイプ: POINT

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