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- PDB-6tba: Virion of native gene transfer agent (GTA) particle -

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基本情報

登録情報
データベース: PDB / ID: 6tba
タイトルVirion of native gene transfer agent (GTA) particle
要素
  • (Uncharacterized ...) x 8
  • Phage major capsid protein, HK97 family
  • Phage major tail protein, TP901-1 family
  • Portal protein Rcc01684
キーワードVIRUS (ウイルス) / "virion" / "horizontal gene transfer" / "gene delivery" / "HK97"
機能・相同性
機能・相同性情報


Bacteriophage phiJL001, Gp84 / Bacteriophage phiJL001, Gp84, C-terminal / Bacteriophage phiJL001, Gp84, N-terminal / GTA TIM-barrel-like domain / Phage conserved hypothetical protein BR0599 / Uncharacterized conserved protein (DUF2163) / GTA TIM-barrel-like domain / Protein of unknown function DUF2460 / Conserved hypothetical protein 2217 (DUF2460) / Phage conserved hypothetical protein ...Bacteriophage phiJL001, Gp84 / Bacteriophage phiJL001, Gp84, C-terminal / Bacteriophage phiJL001, Gp84, N-terminal / GTA TIM-barrel-like domain / Phage conserved hypothetical protein BR0599 / Uncharacterized conserved protein (DUF2163) / GTA TIM-barrel-like domain / Protein of unknown function DUF2460 / Conserved hypothetical protein 2217 (DUF2460) / Phage conserved hypothetical protein / Tail completion protein / Protein of unknown function (DUF3168) / Gene transfer agent, major tail protein / Phage portal protein, HK97 / Bacteriophage SPP1, head-tail adaptor / Phage head-tail joining protein / Bacteriophage SPP1, head-tail adaptor superfamily / Bacteriophage/Gene transfer agent portal protein / Phage portal protein / Phage major tail protein TP901-1 / Tip attachment protein J / Phage tail tube protein / Putative phage tail protein / Phage capsid / Phage capsid family / Glycoside hydrolase superfamily
類似検索 - ドメイン・相同性
鉄・硫黄クラスター / Uncharacterized protein / Uncharacterized protein / Phage portal protein, HK97 family / Phage major capsid protein, HK97 family / Gene transfer agent protein / Head-tail adaptor protein / DUF3168 domain-containing protein / Phage major tail protein, TP901-1 family / TIGR02217 family protein ...鉄・硫黄クラスター / Uncharacterized protein / Uncharacterized protein / Phage portal protein, HK97 family / Phage major capsid protein, HK97 family / Gene transfer agent protein / Head-tail adaptor protein / DUF3168 domain-containing protein / Phage major tail protein, TP901-1 family / TIGR02217 family protein / Uncharacterized protein / Uncharacterized protein
類似検索 - 構成要素
生物種Rhodobacter capsulatus SB 1003 (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: 4.54 Å
データ登録者Bardy, P. / Fuzik, T. / Hrebik, D. / Pantucek, R. / Beatty, J.T. / Plevka, P.
資金援助 チェコ, 7件
組織認可番号国
Ministry of Education (MoE, Czech Republic)LQ1601 チェコ
European Regional Development FundCZ.1.05/1.1.00/02.0070 チェコ
Ministry of Education (MoE, Czech Republic)LM2011033 チェコ
Czech Science Foundation15-21631Y チェコ
Czech Science Foundation18-17810S チェコ
European Molecular Biology Organization (EMBO)3041 チェコ
Grant Agency of the Czech Republic18-13064S チェコ
引用ジャーナル: Nat Commun / 年: 2020
タイトル: Structure and mechanism of DNA delivery of a gene transfer agent.
著者: Pavol Bárdy / Tibor Füzik / Dominik Hrebík / Roman Pantůček / J Thomas Beatty / Pavel Plevka /
要旨: Alphaproteobacteria, which are the most abundant microorganisms of temperate oceans, produce phage-like particles called gene transfer agents (GTAs) that mediate lateral gene exchange. However, the ...Alphaproteobacteria, which are the most abundant microorganisms of temperate oceans, produce phage-like particles called gene transfer agents (GTAs) that mediate lateral gene exchange. However, the mechanism by which GTAs deliver DNA into cells is unknown. Here we present the structure of the GTA of Rhodobacter capsulatus (RcGTA) and describe the conformational changes required for its DNA ejection. The structure of RcGTA resembles that of a tailed phage, but it has an oblate head shortened in the direction of the tail axis, which limits its packaging capacity to less than 4,500 base pairs of linear double-stranded DNA. The tail channel of RcGTA contains a trimer of proteins that possess features of both tape measure proteins of long-tailed phages from the family Siphoviridae and tail needle proteins of short-tailed phages from the family Podoviridae. The opening of a constriction within the RcGTA baseplate enables the ejection of DNA into bacterial periplasm.
履歴
登録2019年11月1日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02020年7月22日Provider: repository / タイプ: Initial release
改定 1.12021年7月7日Group: Other / カテゴリ: pdbx_database_status / Item: _pdbx_database_status.process_site
改定 1.22021年7月14日Group: Derived calculations
カテゴリ: pdbx_struct_sheet_hbond / struct_sheet ...pdbx_struct_sheet_hbond / struct_sheet / struct_sheet_order / struct_sheet_range
改定 1.32024年5月22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

ムービー
  • 登録構造単位
  • Jmolによる作画
  • ダウンロード
  • EMマップとの重ね合わせ
  • マップデータ: EMDB-10443
  • UCSF Chimeraによる作画
  • ダウンロード
ムービービューア
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
C5: Phage major capsid protein, HK97 family
X4: Phage major capsid protein, HK97 family
Y4: Phage major capsid protein, HK97 family
Z4: Phage major capsid protein, HK97 family
A5: Phage major capsid protein, HK97 family
B5: Phage major capsid protein, HK97 family
N4: Phage major capsid protein, HK97 family
R4: Phage major capsid protein, HK97 family
M4: Phage major capsid protein, HK97 family
Q4: Phage major capsid protein, HK97 family
O4: Phage major capsid protein, HK97 family
P4: Phage major capsid protein, HK97 family
W4: Phage major capsid protein, HK97 family
U4: Phage major capsid protein, HK97 family
T4: Phage major capsid protein, HK97 family
S4: Phage major capsid protein, HK97 family
K4: Phage major capsid protein, HK97 family
J4: Phage major capsid protein, HK97 family
V4: Phage major capsid protein, HK97 family
L4: Phage major capsid protein, HK97 family
H4: Phage major capsid protein, HK97 family
I4: Phage major capsid protein, HK97 family
A4: Phage major capsid protein, HK97 family
D4: Phage major capsid protein, HK97 family
E4: Phage major capsid protein, HK97 family
F4: Phage major capsid protein, HK97 family
G4: Phage major capsid protein, HK97 family
B4: Phage major capsid protein, HK97 family
C4: Phage major capsid protein, HK97 family
E3: Uncharacterized protein
D3: Uncharacterized protein
A3: Uncharacterized protein
C3: Uncharacterized protein
B3: Uncharacterized protein
F3: Uncharacterized protein
A1: Uncharacterized protein
E2: Uncharacterized protein
D2: Uncharacterized protein
A2: Uncharacterized protein
C2: Uncharacterized protein
B2: Uncharacterized protein
F2: Uncharacterized protein
CP: Phage major capsid protein, HK97 family
XO: Phage major capsid protein, HK97 family
YO: Phage major capsid protein, HK97 family
ZO: Phage major capsid protein, HK97 family
AP: Phage major capsid protein, HK97 family
BP: Phage major capsid protein, HK97 family
NO: Phage major capsid protein, HK97 family
RO: Phage major capsid protein, HK97 family
MO: Phage major capsid protein, HK97 family
QO: Phage major capsid protein, HK97 family
OO: Phage major capsid protein, HK97 family
PO: Phage major capsid protein, HK97 family
WO: Phage major capsid protein, HK97 family
UO: Phage major capsid protein, HK97 family
TO: Phage major capsid protein, HK97 family
SO: Phage major capsid protein, HK97 family
KO: Phage major capsid protein, HK97 family
JO: Phage major capsid protein, HK97 family
VO: Phage major capsid protein, HK97 family
LO: Phage major capsid protein, HK97 family
HO: Phage major capsid protein, HK97 family
IO: Phage major capsid protein, HK97 family
AO: Phage major capsid protein, HK97 family
DO: Phage major capsid protein, HK97 family
EO: Phage major capsid protein, HK97 family
FO: Phage major capsid protein, HK97 family
GO: Phage major capsid protein, HK97 family
BO: Phage major capsid protein, HK97 family
CO: Phage major capsid protein, HK97 family
EN: Uncharacterized protein
DN: Uncharacterized protein
AN: Uncharacterized protein
CN: Uncharacterized protein
BN: Uncharacterized protein
FN: Uncharacterized protein
AL: Uncharacterized protein
EM: Uncharacterized protein
DM: Uncharacterized protein
AM: Uncharacterized protein
CM: Uncharacterized protein
BM: Uncharacterized protein
FM: Uncharacterized protein
CK: Phage major capsid protein, HK97 family
XJ: Phage major capsid protein, HK97 family
YJ: Phage major capsid protein, HK97 family
ZJ: Phage major capsid protein, HK97 family
AK: Phage major capsid protein, HK97 family
BK: Phage major capsid protein, HK97 family
NJ: Phage major capsid protein, HK97 family
RJ: Phage major capsid protein, HK97 family
MJ: Phage major capsid protein, HK97 family
QJ: Phage major capsid protein, HK97 family
OJ: Phage major capsid protein, HK97 family
PJ: Phage major capsid protein, HK97 family
WJ: Phage major capsid protein, HK97 family
UJ: Phage major capsid protein, HK97 family
TJ: Phage major capsid protein, HK97 family
SJ: Phage major capsid protein, HK97 family
KJ: Phage major capsid protein, HK97 family
JJ: Phage major capsid protein, HK97 family
VJ: Phage major capsid protein, HK97 family
LJ: Phage major capsid protein, HK97 family
HJ: Phage major capsid protein, HK97 family
IJ: Phage major capsid protein, HK97 family
AJ: Phage major capsid protein, HK97 family
DJ: Phage major capsid protein, HK97 family
EJ: Phage major capsid protein, HK97 family
FJ: Phage major capsid protein, HK97 family
GJ: Phage major capsid protein, HK97 family
BJ: Phage major capsid protein, HK97 family
CJ: Phage major capsid protein, HK97 family
EI: Uncharacterized protein
DI: Uncharacterized protein
AI: Uncharacterized protein
CI: Uncharacterized protein
BI: Uncharacterized protein
FI: Uncharacterized protein
AG: Uncharacterized protein
EH: Uncharacterized protein
DH: Uncharacterized protein
AH: Uncharacterized protein
CH: Uncharacterized protein
BH: Uncharacterized protein
FH: Uncharacterized protein
CF: Phage major capsid protein, HK97 family
XE: Phage major capsid protein, HK97 family
YE: Phage major capsid protein, HK97 family
ZE: Phage major capsid protein, HK97 family
AF: Phage major capsid protein, HK97 family
BF: Phage major capsid protein, HK97 family
NE: Phage major capsid protein, HK97 family
RE: Phage major capsid protein, HK97 family
ME: Phage major capsid protein, HK97 family
QE: Phage major capsid protein, HK97 family
OE: Phage major capsid protein, HK97 family
PE: Phage major capsid protein, HK97 family
WE: Phage major capsid protein, HK97 family
UE: Phage major capsid protein, HK97 family
TE: Phage major capsid protein, HK97 family
SE: Phage major capsid protein, HK97 family
KE: Phage major capsid protein, HK97 family
JE: Phage major capsid protein, HK97 family
VE: Phage major capsid protein, HK97 family
LE: Phage major capsid protein, HK97 family
HE: Phage major capsid protein, HK97 family
IE: Phage major capsid protein, HK97 family
AE: Phage major capsid protein, HK97 family
DE: Phage major capsid protein, HK97 family
EE: Phage major capsid protein, HK97 family
FE: Phage major capsid protein, HK97 family
GE: Phage major capsid protein, HK97 family
BE: Phage major capsid protein, HK97 family
CE: Phage major capsid protein, HK97 family
ED: Uncharacterized protein
DD: Uncharacterized protein
AD: Uncharacterized protein
CD: Uncharacterized protein
BD: Uncharacterized protein
FD: Uncharacterized protein
AB: Uncharacterized protein
EC: Uncharacterized protein
DC: Uncharacterized protein
AC: Uncharacterized protein
CC: Uncharacterized protein
BC: Uncharacterized protein
FC: Uncharacterized protein
CA: Phage major capsid protein, HK97 family
X9: Phage major capsid protein, HK97 family
Y9: Phage major capsid protein, HK97 family
Z9: Phage major capsid protein, HK97 family
AA: Phage major capsid protein, HK97 family
BA: Phage major capsid protein, HK97 family
N9: Phage major capsid protein, HK97 family
R9: Phage major capsid protein, HK97 family
M9: Phage major capsid protein, HK97 family
Q9: Phage major capsid protein, HK97 family
O9: Phage major capsid protein, HK97 family
P9: Phage major capsid protein, HK97 family
W9: Phage major capsid protein, HK97 family
U9: Phage major capsid protein, HK97 family
T9: Phage major capsid protein, HK97 family
S9: Phage major capsid protein, HK97 family
K9: Phage major capsid protein, HK97 family
J9: Phage major capsid protein, HK97 family
V9: Phage major capsid protein, HK97 family
L9: Phage major capsid protein, HK97 family
H9: Phage major capsid protein, HK97 family
I9: Phage major capsid protein, HK97 family
A9: Phage major capsid protein, HK97 family
D9: Phage major capsid protein, HK97 family
E9: Phage major capsid protein, HK97 family
F9: Phage major capsid protein, HK97 family
G9: Phage major capsid protein, HK97 family
B9: Phage major capsid protein, HK97 family
C9: Phage major capsid protein, HK97 family
E8: Uncharacterized protein
D8: Uncharacterized protein
A8: Uncharacterized protein
C8: Uncharacterized protein
B8: Uncharacterized protein
F8: Uncharacterized protein
A6: Uncharacterized protein
E7: Uncharacterized protein
D7: Uncharacterized protein
A7: Uncharacterized protein
C7: Uncharacterized protein
B7: Uncharacterized protein
F7: Uncharacterized protein
2A: Uncharacterized protein
1A: Portal protein Rcc01684
1B: Portal protein Rcc01684
2B: Uncharacterized protein
4A: Uncharacterized protein
3A: Uncharacterized protein
5A: Phage major tail protein, TP901-1 family
5S: Phage major tail protein, TP901-1 family
5G: Phage major tail protein, TP901-1 family
5M: Phage major tail protein, TP901-1 family
2K: Uncharacterized protein
1K: Portal protein Rcc01684
1L: Portal protein Rcc01684
2L: Uncharacterized protein
4F: Uncharacterized protein
3F: Uncharacterized protein
5F: Phage major tail protein, TP901-1 family
5X: Phage major tail protein, TP901-1 family
5L: Phage major tail protein, TP901-1 family
5R: Phage major tail protein, TP901-1 family
2I: Uncharacterized protein
1I: Portal protein Rcc01684
1J: Portal protein Rcc01684
2J: Uncharacterized protein
4E: Uncharacterized protein
3E: Uncharacterized protein
5E: Phage major tail protein, TP901-1 family
5W: Phage major tail protein, TP901-1 family
5K: Phage major tail protein, TP901-1 family
5Q: Phage major tail protein, TP901-1 family
2G: Uncharacterized protein
1G: Portal protein Rcc01684
1H: Portal protein Rcc01684
2H: Uncharacterized protein
4D: Uncharacterized protein
3D: Uncharacterized protein
5D: Phage major tail protein, TP901-1 family
5V: Phage major tail protein, TP901-1 family
5J: Phage major tail protein, TP901-1 family
5P: Phage major tail protein, TP901-1 family
2E: Uncharacterized protein
1E: Portal protein Rcc01684
1F: Portal protein Rcc01684
2F: Uncharacterized protein
4C: Uncharacterized protein
3C: Uncharacterized protein
5C: Phage major tail protein, TP901-1 family
5U: Phage major tail protein, TP901-1 family
5I: Phage major tail protein, TP901-1 family
5O: Phage major tail protein, TP901-1 family
2C: Uncharacterized protein
1C: Portal protein Rcc01684
1D: Portal protein Rcc01684
2D: Uncharacterized protein
4B: Uncharacterized protein
3B: Uncharacterized protein
5B: Phage major tail protein, TP901-1 family
5T: Phage major tail protein, TP901-1 family
5H: Phage major tail protein, TP901-1 family
5N: Phage major tail protein, TP901-1 family
7A: Uncharacterized protein
8A: Uncharacterized protein
6B: Uncharacterized protein
6A: Uncharacterized protein
5Y: Phage major tail protein, TP901-1 family
5Z: Phage major tail protein, TP901-1 family
7C: Uncharacterized protein
8C: Uncharacterized protein
6F: Uncharacterized protein
6E: Uncharacterized protein
52: Phage major tail protein, TP901-1 family
53: Phage major tail protein, TP901-1 family
7B: Uncharacterized protein
8B: Uncharacterized protein
6D: Uncharacterized protein
6C: Uncharacterized protein
50: Phage major tail protein, TP901-1 family
51: Phage major tail protein, TP901-1 family
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)8,765,993291
ポリマ－8,764,939288
非ポリマー1,0553
水0
1


  • 登録構造と同一
  • 登録者が定義した集合体
タイプ名称対称操作数
identity operation1_5551

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要素

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タンパク質 , 3種, 187分子 C5X4Y4Z4A5B5N4R4M4Q4O4P4W4U4T4S4K4J4V4L4H4I4A4D4E4F4G4B4C4CP...

#1: タンパク質 ...
Phage major capsid protein, HK97 family


分子量: 40894.988 Da / 分子数: 145 / 由来タイプ: 天然
由来: (天然) Rhodobacter capsulatus SB 1003 (バクテリア)
参照: UniProt: D5ATZ3
#5: タンパク質
Portal protein Rcc01684


分子量: 42846.910 Da / 分子数: 12 / 由来タイプ: 天然
由来: (天然) Rhodobacter capsulatus SB 1003 (バクテリア)
参照: UniProt: D5ATZ0
#8: タンパク質 ...
Phage major tail protein, TP901-1 family


分子量: 14420.007 Da / 分子数: 30 / 由来タイプ: 天然
由来: (天然) Rhodobacter capsulatus SB 1003 (バクテリア)
参照: UniProt: D5ATZ7

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Uncharacterized ... , 8種, 101分子 E3D3A3C3B3A1E2D2A2C2B2ENDNANCNBNALEMDMAMCMBMEIDIAICIBIAGEHDH...

#2: タンパク質 ...
Uncharacterized protein


分子量: 9104.348 Da / 分子数: 55 / 由来タイプ: 天然
由来: (天然) Rhodobacter capsulatus SB 1003 (バクテリア)
参照: UniProt: D5AR33
#3: タンパク質
Uncharacterized protein


分子量: 32996.828 Da / 分子数: 10 / 由来タイプ: 天然
由来: (天然) Rhodobacter capsulatus SB 1003 (バクテリア)
参照: UniProt: D5AR34
#4: タンパク質
Uncharacterized protein


分子量: 20956.354 Da / 分子数: 12 / 由来タイプ: 天然
由来: (天然) Rhodobacter capsulatus SB 1003 (バクテリア)
参照: UniProt: D5ATZ4
#6: タンパク質
Uncharacterized protein


分子量: 13871.859 Da / 分子数: 6 / 由来タイプ: 天然
由来: (天然) Rhodobacter capsulatus SB 1003 (バクテリア)
参照: UniProt: D5ATZ6
#7: タンパク質
Uncharacterized protein


分子量: 12403.123 Da / 分子数: 6 / 由来タイプ: 天然
由来: (天然) Rhodobacter capsulatus SB 1003 (バクテリア)
参照: UniProt: D5ATZ5
#9: タンパク質 Uncharacterized protein


分子量: 31690.734 Da / 分子数: 3 / 由来タイプ: 天然
由来: (天然) Rhodobacter capsulatus SB 1003 (バクテリア)
参照: UniProt: D5AU02
#10: タンパク質 Uncharacterized protein


分子量: 138527.359 Da / 分子数: 3 / 由来タイプ: 天然
由来: (天然) Rhodobacter capsulatus SB 1003 (バクテリア)
参照: UniProt: D5AU04
#11: タンパク質
Uncharacterized protein


分子量: 22985.713 Da / 分子数: 6 / 由来タイプ: 天然
由来: (天然) Rhodobacter capsulatus SB 1003 (バクテリア)
参照: UniProt: D5AU01

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非ポリマー , 1種, 3分子

#12: 化合物 ChemComp-SF4 / IRON/SULFUR CLUSTER / 鉄・硫黄クラスター


分子量: 351.640 Da / 分子数: 3 / 由来タイプ: 合成 / 式: Fe4S4

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詳細

研究の焦点であるリガンドがあるかN

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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
ID名称タイプ詳細Entity IDParent-ID由来
1Rhodobacter capsulatus DE442VIRUSphage-like particle mediating high-frequency horisontal gene transfer in Rhodobacterales species#1-#110NATURAL
2CapsidカプシドCOMPLEXOblate T=3 capsid#1-#31NATURAL
3Head spikeCOMPLEXpenton protrusion of the capsid#2-#31NATURAL
4ConnectorCOMPLEXspecial 5-fold vertex of the capsid, interconnecting capsid to tail#4-#51NATURAL
5Tail尾COMPLEXtubular structure interconnecting capsid to baseplate (host-recognition device)#6-#8, #111NATURAL
6Baseplate三脚COMPLEXhost-recognition device present at the tip of the tail#9-#101NATURAL
分子量
IDEntity assembly-ID値 (°)実験値
118.03 MDaNO
215.42 MDaNO
310.08 MDaNO
410.76 MDaNO
510.73 MDaNO
610.88 MDaNO
由来(天然)
IDEntity assembly-ID生物種Ncbi tax-ID株
21Rhodobacter capsulatus SB 1003 (バクテリア)272942Gene transfer agent
32Rhodobacter capsulatus SB 1003 (バクテリア)272942Gene transfer agent
43Rhodobacter capsulatus SB 1003 (バクテリア)272942Gene transfer agent
54Rhodobacter capsulatus SB 1003 (バクテリア)272942Gene transfer agent
65Rhodobacter capsulatus SB 1003 (バクテリア)272942Gene transfer agent
76Rhodobacter capsulatus SB 1003 (バクテリア)272942Gene transfer agent
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: Rhodobacter capsulatus
ウイルス殻名称: HK97-like oblate capsid / 直径: 945 nm / 三角数 (T数): 3
緩衝液pH: 7.8 / 詳細: G-buffer, doi: 10.1016/0003-9861(77)90508-2
緩衝液成分
ID濃度名称式Buffer-ID
110 mMTrisトリスヒドロキシメチルアミノメタン1
21 mMNaCl塩化ナトリウム1
31 mMMgCl21
41 mMCaCl21
50.01 mg/mlBovine serum albuminウシ血清アルブミン1
試料濃度: 20 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: 100 % / 凍結前の試料温度: 293.15 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 FIELDBright-field microscopy / 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 / Cs: 2.7 mm / C2レンズ絞り径: 50 µm / アライメント法: ZEMLIN TABLEAU
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: 42.75 e/Å2 / 検出モード: INTEGRATING
フィルム・検出器のモデル: FEI FALCON III (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名称バージョンカテゴリ
1RELION2.1粒子像選択
2EPU2.1画像取得
4RELION2.1CTF補正
7Coot0.9モデルフィッティング
9PHENIX1.16モデル精密化
10RELION2.1初期オイラー角割当
11RELION3最終オイラー角割当
12RELION3分類
13RELION3３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: 53432
対称性点対称性: C1 (非対称)
3次元再構成解像度: 4.54 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 27724 / アルゴリズム: BACK PROJECTION
詳細: Map is generated from merged maps of GTA capsid (EMD-10442), neck (EMD-10477), tail tube (EMD-10478) and baseplate (EMD-10490). Internal map regions corresponds to the genome from asymmetric ...詳細: Map is generated from merged maps of GTA capsid (EMD-10442), neck (EMD-10477), tail tube (EMD-10478) and baseplate (EMD-10490). Internal map regions corresponds to the genome from asymmetric reconstruction (EMD-10568) and tape-measure protein density from C3 reconstruction of tail tube (EMD-10570). Shown resoluton value corresponds to the map with lowest resolution (C3 tail tube).
対称性のタイプ: POINT
原子モデル構築プロトコル: AB INITIO MODEL / 空間: REAL

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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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