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- PDB-5mq7: Structure of AaLS-13 -

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基本情報

登録情報
データベース: PDB / ID: 5mq7
タイトルStructure of AaLS-13
要素6,7-dimethyl-8-ribityllumazine synthase
キーワードTRANSFERASE / cryo-EM / porous protein cage / icosahedral symmetry / engineered lumazine synthase
機能・相同性
機能・相同性情報


6,7-dimethyl-8-ribityllumazine synthase / 6,7-dimethyl-8-ribityllumazine synthase activity / riboflavin synthase complex / riboflavin biosynthetic process / cytosol
類似検索 - 分子機能
Lumazine synthase / Lumazine/riboflavin synthase / Lumazine/riboflavin synthase superfamily / 6,7-dimethyl-8-ribityllumazine synthase
類似検索 - ドメイン・相同性
6,7-dimethyl-8-ribityllumazine synthase
類似検索 - 構成要素
生物種Aquifex aeolicus (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: 5.2 Å
データ登録者Sasaki, E. / Boehringer, D. / Leibundgut, M. / Ban, N. / Hilvert, D.
資金援助1件
組織認可番号国
European Research CouncilERC-dG-2012-321295
引用ジャーナル: Nat Commun / 年: 2017
タイトル: Structure and assembly of scalable porous protein cages.
著者: Eita Sasaki / Daniel Böhringer / Michiel van de Waterbeemd / Marc Leibundgut / Reinhard Zschoche / Albert J R Heck / Nenad Ban / Donald Hilvert /
要旨: Proteins that self-assemble into regular shell-like polyhedra are useful, both in nature and in the laboratory, as molecular containers. Here we describe cryo-electron microscopy (EM) structures of ...Proteins that self-assemble into regular shell-like polyhedra are useful, both in nature and in the laboratory, as molecular containers. Here we describe cryo-electron microscopy (EM) structures of two versatile encapsulation systems that exploit engineered electrostatic interactions for cargo loading. We show that increasing the number of negative charges on the lumenal surface of lumazine synthase, a protein that naturally assembles into a ∼1-MDa dodecahedron composed of 12 pentamers, induces stepwise expansion of the native protein shell, giving rise to thermostable ∼3-MDa and ∼6-MDa assemblies containing 180 and 360 subunits, respectively. Remarkably, these expanded particles assume unprecedented tetrahedrally and icosahedrally symmetric structures constructed entirely from pentameric units. Large keyhole-shaped pores in the shell, not present in the wild-type capsid, enable diffusion-limited encapsulation of complementarily charged guests. The structures of these supercharged assemblies demonstrate how programmed electrostatic effects can be effectively harnessed to tailor the architecture and properties of protein cages.
履歴
登録2016年12月20日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02017年3月22日Provider: repository / タイプ: Initial release
改定 1.12024年5月15日Group: Data collection / Database references
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_image_scans
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-3544
  • 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
0A: 6,7-dimethyl-8-ribityllumazine synthase
0B: 6,7-dimethyl-8-ribityllumazine synthase
0C: 6,7-dimethyl-8-ribityllumazine synthase
0D: 6,7-dimethyl-8-ribityllumazine synthase
0E: 6,7-dimethyl-8-ribityllumazine synthase
0X: 6,7-dimethyl-8-ribityllumazine synthase
1A: 6,7-dimethyl-8-ribityllumazine synthase
1B: 6,7-dimethyl-8-ribityllumazine synthase
1C: 6,7-dimethyl-8-ribityllumazine synthase
1D: 6,7-dimethyl-8-ribityllumazine synthase
1E: 6,7-dimethyl-8-ribityllumazine synthase
1X: 6,7-dimethyl-8-ribityllumazine synthase
2A: 6,7-dimethyl-8-ribityllumazine synthase
2B: 6,7-dimethyl-8-ribityllumazine synthase
2C: 6,7-dimethyl-8-ribityllumazine synthase
2D: 6,7-dimethyl-8-ribityllumazine synthase
2E: 6,7-dimethyl-8-ribityllumazine synthase
2X: 6,7-dimethyl-8-ribityllumazine synthase
3A: 6,7-dimethyl-8-ribityllumazine synthase
3B: 6,7-dimethyl-8-ribityllumazine synthase
3C: 6,7-dimethyl-8-ribityllumazine synthase
3D: 6,7-dimethyl-8-ribityllumazine synthase
3E: 6,7-dimethyl-8-ribityllumazine synthase
3X: 6,7-dimethyl-8-ribityllumazine synthase
4A: 6,7-dimethyl-8-ribityllumazine synthase
4B: 6,7-dimethyl-8-ribityllumazine synthase
4C: 6,7-dimethyl-8-ribityllumazine synthase
4D: 6,7-dimethyl-8-ribityllumazine synthase
4E: 6,7-dimethyl-8-ribityllumazine synthase
4X: 6,7-dimethyl-8-ribityllumazine synthase
5A: 6,7-dimethyl-8-ribityllumazine synthase
5B: 6,7-dimethyl-8-ribityllumazine synthase
5C: 6,7-dimethyl-8-ribityllumazine synthase
5D: 6,7-dimethyl-8-ribityllumazine synthase
5E: 6,7-dimethyl-8-ribityllumazine synthase
5X: 6,7-dimethyl-8-ribityllumazine synthase
6A: 6,7-dimethyl-8-ribityllumazine synthase
6B: 6,7-dimethyl-8-ribityllumazine synthase
6C: 6,7-dimethyl-8-ribityllumazine synthase
6D: 6,7-dimethyl-8-ribityllumazine synthase
6E: 6,7-dimethyl-8-ribityllumazine synthase
6X: 6,7-dimethyl-8-ribityllumazine synthase
7A: 6,7-dimethyl-8-ribityllumazine synthase
7B: 6,7-dimethyl-8-ribityllumazine synthase
7C: 6,7-dimethyl-8-ribityllumazine synthase
7D: 6,7-dimethyl-8-ribityllumazine synthase
7E: 6,7-dimethyl-8-ribityllumazine synthase
7X: 6,7-dimethyl-8-ribityllumazine synthase
8A: 6,7-dimethyl-8-ribityllumazine synthase
8B: 6,7-dimethyl-8-ribityllumazine synthase
8C: 6,7-dimethyl-8-ribityllumazine synthase
8D: 6,7-dimethyl-8-ribityllumazine synthase
8E: 6,7-dimethyl-8-ribityllumazine synthase
8X: 6,7-dimethyl-8-ribityllumazine synthase
9A: 6,7-dimethyl-8-ribityllumazine synthase
9B: 6,7-dimethyl-8-ribityllumazine synthase
9C: 6,7-dimethyl-8-ribityllumazine synthase
9D: 6,7-dimethyl-8-ribityllumazine synthase
9E: 6,7-dimethyl-8-ribityllumazine synthase
9X: 6,7-dimethyl-8-ribityllumazine synthase
AA: 6,7-dimethyl-8-ribityllumazine synthase
AB: 6,7-dimethyl-8-ribityllumazine synthase
AC: 6,7-dimethyl-8-ribityllumazine synthase
AD: 6,7-dimethyl-8-ribityllumazine synthase
AE: 6,7-dimethyl-8-ribityllumazine synthase
AX: 6,7-dimethyl-8-ribityllumazine synthase
BA: 6,7-dimethyl-8-ribityllumazine synthase
BB: 6,7-dimethyl-8-ribityllumazine synthase
BC: 6,7-dimethyl-8-ribityllumazine synthase
BD: 6,7-dimethyl-8-ribityllumazine synthase
BE: 6,7-dimethyl-8-ribityllumazine synthase
BX: 6,7-dimethyl-8-ribityllumazine synthase
CA: 6,7-dimethyl-8-ribityllumazine synthase
CB: 6,7-dimethyl-8-ribityllumazine synthase
CC: 6,7-dimethyl-8-ribityllumazine synthase
CD: 6,7-dimethyl-8-ribityllumazine synthase
CE: 6,7-dimethyl-8-ribityllumazine synthase
CX: 6,7-dimethyl-8-ribityllumazine synthase
DA: 6,7-dimethyl-8-ribityllumazine synthase
DB: 6,7-dimethyl-8-ribityllumazine synthase
DC: 6,7-dimethyl-8-ribityllumazine synthase
DD: 6,7-dimethyl-8-ribityllumazine synthase
DE: 6,7-dimethyl-8-ribityllumazine synthase
DX: 6,7-dimethyl-8-ribityllumazine synthase
EA: 6,7-dimethyl-8-ribityllumazine synthase
EB: 6,7-dimethyl-8-ribityllumazine synthase
EC: 6,7-dimethyl-8-ribityllumazine synthase
ED: 6,7-dimethyl-8-ribityllumazine synthase
EE: 6,7-dimethyl-8-ribityllumazine synthase
EX: 6,7-dimethyl-8-ribityllumazine synthase
FA: 6,7-dimethyl-8-ribityllumazine synthase
FB: 6,7-dimethyl-8-ribityllumazine synthase
FC: 6,7-dimethyl-8-ribityllumazine synthase
FD: 6,7-dimethyl-8-ribityllumazine synthase
FE: 6,7-dimethyl-8-ribityllumazine synthase
FX: 6,7-dimethyl-8-ribityllumazine synthase
GA: 6,7-dimethyl-8-ribityllumazine synthase
GB: 6,7-dimethyl-8-ribityllumazine synthase
GC: 6,7-dimethyl-8-ribityllumazine synthase
GD: 6,7-dimethyl-8-ribityllumazine synthase
GE: 6,7-dimethyl-8-ribityllumazine synthase
GX: 6,7-dimethyl-8-ribityllumazine synthase
HA: 6,7-dimethyl-8-ribityllumazine synthase
HB: 6,7-dimethyl-8-ribityllumazine synthase
HC: 6,7-dimethyl-8-ribityllumazine synthase
HD: 6,7-dimethyl-8-ribityllumazine synthase
HE: 6,7-dimethyl-8-ribityllumazine synthase
HX: 6,7-dimethyl-8-ribityllumazine synthase
IA: 6,7-dimethyl-8-ribityllumazine synthase
IB: 6,7-dimethyl-8-ribityllumazine synthase
IC: 6,7-dimethyl-8-ribityllumazine synthase
ID: 6,7-dimethyl-8-ribityllumazine synthase
IE: 6,7-dimethyl-8-ribityllumazine synthase
IX: 6,7-dimethyl-8-ribityllumazine synthase
JA: 6,7-dimethyl-8-ribityllumazine synthase
JB: 6,7-dimethyl-8-ribityllumazine synthase
JC: 6,7-dimethyl-8-ribityllumazine synthase
JD: 6,7-dimethyl-8-ribityllumazine synthase
JE: 6,7-dimethyl-8-ribityllumazine synthase
JX: 6,7-dimethyl-8-ribityllumazine synthase
KA: 6,7-dimethyl-8-ribityllumazine synthase
KB: 6,7-dimethyl-8-ribityllumazine synthase
KC: 6,7-dimethyl-8-ribityllumazine synthase
KD: 6,7-dimethyl-8-ribityllumazine synthase
KE: 6,7-dimethyl-8-ribityllumazine synthase
KX: 6,7-dimethyl-8-ribityllumazine synthase
LA: 6,7-dimethyl-8-ribityllumazine synthase
LB: 6,7-dimethyl-8-ribityllumazine synthase
LC: 6,7-dimethyl-8-ribityllumazine synthase
LD: 6,7-dimethyl-8-ribityllumazine synthase
LE: 6,7-dimethyl-8-ribityllumazine synthase
LX: 6,7-dimethyl-8-ribityllumazine synthase
MA: 6,7-dimethyl-8-ribityllumazine synthase
MB: 6,7-dimethyl-8-ribityllumazine synthase
MC: 6,7-dimethyl-8-ribityllumazine synthase
MD: 6,7-dimethyl-8-ribityllumazine synthase
ME: 6,7-dimethyl-8-ribityllumazine synthase
MX: 6,7-dimethyl-8-ribityllumazine synthase
NA: 6,7-dimethyl-8-ribityllumazine synthase
NB: 6,7-dimethyl-8-ribityllumazine synthase
NC: 6,7-dimethyl-8-ribityllumazine synthase
ND: 6,7-dimethyl-8-ribityllumazine synthase
NE: 6,7-dimethyl-8-ribityllumazine synthase
NX: 6,7-dimethyl-8-ribityllumazine synthase
OA: 6,7-dimethyl-8-ribityllumazine synthase
OB: 6,7-dimethyl-8-ribityllumazine synthase
OC: 6,7-dimethyl-8-ribityllumazine synthase
OD: 6,7-dimethyl-8-ribityllumazine synthase
OE: 6,7-dimethyl-8-ribityllumazine synthase
OX: 6,7-dimethyl-8-ribityllumazine synthase
PA: 6,7-dimethyl-8-ribityllumazine synthase
PB: 6,7-dimethyl-8-ribityllumazine synthase
PC: 6,7-dimethyl-8-ribityllumazine synthase
PD: 6,7-dimethyl-8-ribityllumazine synthase
PE: 6,7-dimethyl-8-ribityllumazine synthase
PX: 6,7-dimethyl-8-ribityllumazine synthase
QA: 6,7-dimethyl-8-ribityllumazine synthase
QB: 6,7-dimethyl-8-ribityllumazine synthase
QC: 6,7-dimethyl-8-ribityllumazine synthase
QD: 6,7-dimethyl-8-ribityllumazine synthase
QE: 6,7-dimethyl-8-ribityllumazine synthase
QX: 6,7-dimethyl-8-ribityllumazine synthase
RA: 6,7-dimethyl-8-ribityllumazine synthase
RB: 6,7-dimethyl-8-ribityllumazine synthase
RC: 6,7-dimethyl-8-ribityllumazine synthase
RD: 6,7-dimethyl-8-ribityllumazine synthase
RE: 6,7-dimethyl-8-ribityllumazine synthase
RX: 6,7-dimethyl-8-ribityllumazine synthase
SA: 6,7-dimethyl-8-ribityllumazine synthase
SB: 6,7-dimethyl-8-ribityllumazine synthase
SC: 6,7-dimethyl-8-ribityllumazine synthase
SD: 6,7-dimethyl-8-ribityllumazine synthase
SE: 6,7-dimethyl-8-ribityllumazine synthase
SX: 6,7-dimethyl-8-ribityllumazine synthase
TA: 6,7-dimethyl-8-ribityllumazine synthase
TB: 6,7-dimethyl-8-ribityllumazine synthase
TC: 6,7-dimethyl-8-ribityllumazine synthase
TD: 6,7-dimethyl-8-ribityllumazine synthase
TE: 6,7-dimethyl-8-ribityllumazine synthase
TX: 6,7-dimethyl-8-ribityllumazine synthase
UA: 6,7-dimethyl-8-ribityllumazine synthase
UB: 6,7-dimethyl-8-ribityllumazine synthase
UC: 6,7-dimethyl-8-ribityllumazine synthase
UD: 6,7-dimethyl-8-ribityllumazine synthase
UE: 6,7-dimethyl-8-ribityllumazine synthase
UX: 6,7-dimethyl-8-ribityllumazine synthase
VA: 6,7-dimethyl-8-ribityllumazine synthase
VB: 6,7-dimethyl-8-ribityllumazine synthase
VC: 6,7-dimethyl-8-ribityllumazine synthase
VD: 6,7-dimethyl-8-ribityllumazine synthase
VE: 6,7-dimethyl-8-ribityllumazine synthase
VX: 6,7-dimethyl-8-ribityllumazine synthase
WA: 6,7-dimethyl-8-ribityllumazine synthase
WB: 6,7-dimethyl-8-ribityllumazine synthase
WC: 6,7-dimethyl-8-ribityllumazine synthase
WD: 6,7-dimethyl-8-ribityllumazine synthase
WE: 6,7-dimethyl-8-ribityllumazine synthase
WX: 6,7-dimethyl-8-ribityllumazine synthase
XA: 6,7-dimethyl-8-ribityllumazine synthase
XB: 6,7-dimethyl-8-ribityllumazine synthase
XC: 6,7-dimethyl-8-ribityllumazine synthase
XD: 6,7-dimethyl-8-ribityllumazine synthase
XE: 6,7-dimethyl-8-ribityllumazine synthase
XX: 6,7-dimethyl-8-ribityllumazine synthase
YA: 6,7-dimethyl-8-ribityllumazine synthase
YB: 6,7-dimethyl-8-ribityllumazine synthase
YC: 6,7-dimethyl-8-ribityllumazine synthase
YD: 6,7-dimethyl-8-ribityllumazine synthase
YE: 6,7-dimethyl-8-ribityllumazine synthase
YX: 6,7-dimethyl-8-ribityllumazine synthase
ZA: 6,7-dimethyl-8-ribityllumazine synthase
ZB: 6,7-dimethyl-8-ribityllumazine synthase
ZC: 6,7-dimethyl-8-ribityllumazine synthase
ZD: 6,7-dimethyl-8-ribityllumazine synthase
ZE: 6,7-dimethyl-8-ribityllumazine synthase
ZX: 6,7-dimethyl-8-ribityllumazine synthase
aA: 6,7-dimethyl-8-ribityllumazine synthase
aB: 6,7-dimethyl-8-ribityllumazine synthase
aC: 6,7-dimethyl-8-ribityllumazine synthase
aD: 6,7-dimethyl-8-ribityllumazine synthase
aE: 6,7-dimethyl-8-ribityllumazine synthase
aX: 6,7-dimethyl-8-ribityllumazine synthase
bA: 6,7-dimethyl-8-ribityllumazine synthase
bB: 6,7-dimethyl-8-ribityllumazine synthase
bC: 6,7-dimethyl-8-ribityllumazine synthase
bD: 6,7-dimethyl-8-ribityllumazine synthase
bE: 6,7-dimethyl-8-ribityllumazine synthase
bX: 6,7-dimethyl-8-ribityllumazine synthase
cA: 6,7-dimethyl-8-ribityllumazine synthase
cB: 6,7-dimethyl-8-ribityllumazine synthase
cC: 6,7-dimethyl-8-ribityllumazine synthase
cD: 6,7-dimethyl-8-ribityllumazine synthase
cE: 6,7-dimethyl-8-ribityllumazine synthase
cX: 6,7-dimethyl-8-ribityllumazine synthase
dA: 6,7-dimethyl-8-ribityllumazine synthase
dB: 6,7-dimethyl-8-ribityllumazine synthase
dC: 6,7-dimethyl-8-ribityllumazine synthase
dD: 6,7-dimethyl-8-ribityllumazine synthase
dE: 6,7-dimethyl-8-ribityllumazine synthase
dX: 6,7-dimethyl-8-ribityllumazine synthase
eA: 6,7-dimethyl-8-ribityllumazine synthase
eB: 6,7-dimethyl-8-ribityllumazine synthase
eC: 6,7-dimethyl-8-ribityllumazine synthase
eD: 6,7-dimethyl-8-ribityllumazine synthase
eE: 6,7-dimethyl-8-ribityllumazine synthase
eX: 6,7-dimethyl-8-ribityllumazine synthase
fA: 6,7-dimethyl-8-ribityllumazine synthase
fB: 6,7-dimethyl-8-ribityllumazine synthase
fC: 6,7-dimethyl-8-ribityllumazine synthase
fD: 6,7-dimethyl-8-ribityllumazine synthase
fE: 6,7-dimethyl-8-ribityllumazine synthase
fX: 6,7-dimethyl-8-ribityllumazine synthase
gA: 6,7-dimethyl-8-ribityllumazine synthase
gB: 6,7-dimethyl-8-ribityllumazine synthase
gC: 6,7-dimethyl-8-ribityllumazine synthase
gD: 6,7-dimethyl-8-ribityllumazine synthase
gE: 6,7-dimethyl-8-ribityllumazine synthase
gX: 6,7-dimethyl-8-ribityllumazine synthase
hA: 6,7-dimethyl-8-ribityllumazine synthase
hB: 6,7-dimethyl-8-ribityllumazine synthase
hC: 6,7-dimethyl-8-ribityllumazine synthase
hD: 6,7-dimethyl-8-ribityllumazine synthase
hE: 6,7-dimethyl-8-ribityllumazine synthase
hX: 6,7-dimethyl-8-ribityllumazine synthase
iA: 6,7-dimethyl-8-ribityllumazine synthase
iB: 6,7-dimethyl-8-ribityllumazine synthase
iC: 6,7-dimethyl-8-ribityllumazine synthase
iD: 6,7-dimethyl-8-ribityllumazine synthase
iE: 6,7-dimethyl-8-ribityllumazine synthase
iX: 6,7-dimethyl-8-ribityllumazine synthase
jA: 6,7-dimethyl-8-ribityllumazine synthase
jB: 6,7-dimethyl-8-ribityllumazine synthase
jC: 6,7-dimethyl-8-ribityllumazine synthase
jD: 6,7-dimethyl-8-ribityllumazine synthase
jE: 6,7-dimethyl-8-ribityllumazine synthase
jX: 6,7-dimethyl-8-ribityllumazine synthase
kA: 6,7-dimethyl-8-ribityllumazine synthase
kB: 6,7-dimethyl-8-ribityllumazine synthase
kC: 6,7-dimethyl-8-ribityllumazine synthase
kD: 6,7-dimethyl-8-ribityllumazine synthase
kE: 6,7-dimethyl-8-ribityllumazine synthase
kX: 6,7-dimethyl-8-ribityllumazine synthase
lA: 6,7-dimethyl-8-ribityllumazine synthase
lB: 6,7-dimethyl-8-ribityllumazine synthase
lC: 6,7-dimethyl-8-ribityllumazine synthase
lD: 6,7-dimethyl-8-ribityllumazine synthase
lE: 6,7-dimethyl-8-ribityllumazine synthase
lX: 6,7-dimethyl-8-ribityllumazine synthase
mA: 6,7-dimethyl-8-ribityllumazine synthase
mB: 6,7-dimethyl-8-ribityllumazine synthase
mC: 6,7-dimethyl-8-ribityllumazine synthase
mD: 6,7-dimethyl-8-ribityllumazine synthase
mE: 6,7-dimethyl-8-ribityllumazine synthase
mX: 6,7-dimethyl-8-ribityllumazine synthase
nA: 6,7-dimethyl-8-ribityllumazine synthase
nB: 6,7-dimethyl-8-ribityllumazine synthase
nC: 6,7-dimethyl-8-ribityllumazine synthase
nD: 6,7-dimethyl-8-ribityllumazine synthase
nE: 6,7-dimethyl-8-ribityllumazine synthase
nX: 6,7-dimethyl-8-ribityllumazine synthase
oA: 6,7-dimethyl-8-ribityllumazine synthase
oB: 6,7-dimethyl-8-ribityllumazine synthase
oC: 6,7-dimethyl-8-ribityllumazine synthase
oD: 6,7-dimethyl-8-ribityllumazine synthase
oE: 6,7-dimethyl-8-ribityllumazine synthase
oX: 6,7-dimethyl-8-ribityllumazine synthase
pA: 6,7-dimethyl-8-ribityllumazine synthase
pB: 6,7-dimethyl-8-ribityllumazine synthase
pC: 6,7-dimethyl-8-ribityllumazine synthase
pD: 6,7-dimethyl-8-ribityllumazine synthase
pE: 6,7-dimethyl-8-ribityllumazine synthase
pX: 6,7-dimethyl-8-ribityllumazine synthase
qA: 6,7-dimethyl-8-ribityllumazine synthase
qB: 6,7-dimethyl-8-ribityllumazine synthase
qC: 6,7-dimethyl-8-ribityllumazine synthase
qD: 6,7-dimethyl-8-ribityllumazine synthase
qE: 6,7-dimethyl-8-ribityllumazine synthase
qX: 6,7-dimethyl-8-ribityllumazine synthase
rA: 6,7-dimethyl-8-ribityllumazine synthase
rB: 6,7-dimethyl-8-ribityllumazine synthase
rC: 6,7-dimethyl-8-ribityllumazine synthase
rD: 6,7-dimethyl-8-ribityllumazine synthase
rE: 6,7-dimethyl-8-ribityllumazine synthase
rX: 6,7-dimethyl-8-ribityllumazine synthase
sA: 6,7-dimethyl-8-ribityllumazine synthase
sB: 6,7-dimethyl-8-ribityllumazine synthase
sC: 6,7-dimethyl-8-ribityllumazine synthase
sD: 6,7-dimethyl-8-ribityllumazine synthase
sE: 6,7-dimethyl-8-ribityllumazine synthase
sX: 6,7-dimethyl-8-ribityllumazine synthase
tA: 6,7-dimethyl-8-ribityllumazine synthase
tB: 6,7-dimethyl-8-ribityllumazine synthase
tC: 6,7-dimethyl-8-ribityllumazine synthase
tD: 6,7-dimethyl-8-ribityllumazine synthase
tE: 6,7-dimethyl-8-ribityllumazine synthase
tX: 6,7-dimethyl-8-ribityllumazine synthase
uA: 6,7-dimethyl-8-ribityllumazine synthase
uB: 6,7-dimethyl-8-ribityllumazine synthase
uC: 6,7-dimethyl-8-ribityllumazine synthase
uD: 6,7-dimethyl-8-ribityllumazine synthase
uE: 6,7-dimethyl-8-ribityllumazine synthase
uX: 6,7-dimethyl-8-ribityllumazine synthase
vA: 6,7-dimethyl-8-ribityllumazine synthase
vB: 6,7-dimethyl-8-ribityllumazine synthase
vC: 6,7-dimethyl-8-ribityllumazine synthase
vD: 6,7-dimethyl-8-ribityllumazine synthase
vE: 6,7-dimethyl-8-ribityllumazine synthase
vX: 6,7-dimethyl-8-ribityllumazine synthase
wA: 6,7-dimethyl-8-ribityllumazine synthase
wB: 6,7-dimethyl-8-ribityllumazine synthase
wC: 6,7-dimethyl-8-ribityllumazine synthase
wD: 6,7-dimethyl-8-ribityllumazine synthase
wE: 6,7-dimethyl-8-ribityllumazine synthase
wX: 6,7-dimethyl-8-ribityllumazine synthase
xA: 6,7-dimethyl-8-ribityllumazine synthase
xB: 6,7-dimethyl-8-ribityllumazine synthase
xC: 6,7-dimethyl-8-ribityllumazine synthase
xD: 6,7-dimethyl-8-ribityllumazine synthase
xE: 6,7-dimethyl-8-ribityllumazine synthase
xX: 6,7-dimethyl-8-ribityllumazine synthase


分子量 (理論値)分子数
合計 (水以外)6,325,148360
ポリマ－6,325,148360
非ポリマー00
水00
1


  • 登録構造と同一
  • ソフトウェアが定義した集合体
タイプ名称対称操作数
identity operation1_555x,y,z1
手法PISA

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要素

#1: タンパク質 ...
6,7-dimethyl-8-ribityllumazine synthase / Lumazine synthase


分子量: 17569.855 Da / 分子数: 360 / 由来タイプ: 組換発現 / 由来: (組換発現) Aquifex aeolicus (バクテリア) / 株: VF5 / 遺伝子: ribH, aq_132 / 発現宿主: Escherichia coli (大腸菌)
参照: UniProt: O66529, 6,7-dimethyl-8-ribityllumazine synthase

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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: AaLS-13 / タイプ: COMPLEX / Entity ID: all / 由来: RECOMBINANT
分子量実験値: NO
由来(天然)生物種: Aquifex aeolicus (バクテリア)
由来(組換発現)生物種: Escherichia coli (大腸菌)
緩衝液pH: 7.8
試料包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES
急速凍結凍結剤: 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: 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
撮影電子線照射量: 4 e/Å2
フィルム・検出器のモデル: FEI FALCON II (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
4CTFFIND3CTF補正
5RELION1.4CTF補正
11RELION1.4初期オイラー角割当
12RELION1.4最終オイラー角割当
13RELION1.4分類
14RELION1.4３次元再構成
CTF補正タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION
対称性点対称性: I (正20面体型対称)
3次元再構成解像度: 5.2 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 9900 / 対称性のタイプ: POINT

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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://pdbjlvh1.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

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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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