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- PDB-9mkb: Structure of the bacteriophage T4 portal-neck-tail complex -

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基本情報

登録情報
データベース: PDB / ID: 9mkb
タイトルStructure of the bacteriophage T4 portal-neck-tail complex
要素
  • (unassigned peptide ...) x 5
  • Hoc, highly immunogenic outer capsid protein
  • Soc, small outer capsid protein
  • gp10, baseplate wedge protein
  • gp11, baseplate wedge protein
  • gp12, short tail fiber protein
  • gp13, neck protein
  • gp14, neck protein
  • gp15, tail terminator protein
  • gp18, tail sheath protein
  • gp19, tail tube protein
  • gp20, portal protein
  • gp23, major capsid protein
  • gp25, baseplate protein
  • gp27, baseplate hub protein
  • gp29, tape measure protein
  • gp3, tube terminator protein
  • gp48, baseplate protein
  • gp5, baseplate central spike protein
  • gp5.4, tip of the central spike
  • gp53, baseplate wedge protein
  • gp54, baseplate protein
  • gp6, baseplate wedge protein
  • gp7, baseplate wedge protein
  • gp8, baseplate wedge protein
  • gp9, baseplate wedge tail fiber connector
  • gpwac, fibritin
キーワードVIRAL PROTEIN / bacteriophage T4 / portal vertex / phage neck / phage tail / contractile sheath / tail tube / baseplate / VIRUS
機能・相同性
機能・相同性情報


virus tail, sheath / symbiont genome ejection through host cell envelope, contractile tail mechanism / viral capsid, decoration / symbiont entry into host cell via disruption of host cell wall peptidoglycan / T=13 icosahedral viral capsid / virus tail, baseplate / viral genome packaging / viral tail assembly / virus tail, fiber / symbiont entry into host cell via disruption of host cell envelope ...virus tail, sheath / symbiont genome ejection through host cell envelope, contractile tail mechanism / viral capsid, decoration / symbiont entry into host cell via disruption of host cell wall peptidoglycan / T=13 icosahedral viral capsid / virus tail, baseplate / viral genome packaging / viral tail assembly / virus tail, fiber / symbiont entry into host cell via disruption of host cell envelope / viral release from host cell / peptidoglycan catabolic process / virion component / cell wall macromolecule catabolic process / lysozyme / viral capsid / lysozyme activity / killing of cells of another organism / entry receptor-mediated virion attachment to host cell / defense response to bacterium / symbiont entry into host cell / structural molecule activity / metal ion binding / identical protein binding
類似検索 - 分子機能
Bacteriophage T4, Gp14, neck protein / Virus neck protein / Portal protein Gp20 / Bacteriophage T4-like portal protein (Gp20) / Highly immunogenic outer capsid protein / Bacteriophage T4, Gp12 / Baseplate tail-tube protein gp48, T4-like virus / Short tail fibre protein, C-terminal / Small outer capsid protein / Myoviridae tail sheath stabiliser ...Bacteriophage T4, Gp14, neck protein / Virus neck protein / Portal protein Gp20 / Bacteriophage T4-like portal protein (Gp20) / Highly immunogenic outer capsid protein / Bacteriophage T4, Gp12 / Baseplate tail-tube protein gp48, T4-like virus / Short tail fibre protein, C-terminal / Small outer capsid protein / Myoviridae tail sheath stabiliser / Small outer capsid protein superfamily / Myoviridae tail sheath stabiliser superfamily / Short tail fibre protein, C-terminal superfamily / Phage short tail fibre protein gp12, middle domain / Tail-tube assembly protein / Short tail fibre protein receptor-binding domain / T4-like virus Myoviridae tail sheath stabiliser / Small outer capsid protein / Baseplate wedge protein gp53, bacteriophage T4 / Baseplate wedge protein gp7 / : / : / : / Base plate wedge protein 53 / Baseplate wedge protein gp7, domain V / Baseplate wedge protein gp7, helical domain / Baseplate wedge protein gp7, domain VI / Bacteriophage T4, Gp27, baseplate hub, C-terminal / Bacteriophage T4, Gp27, baseplate hub, N-terminal / Gp27, baseplate hub, domain 3 / Gp27, baseplate hub, domain 4 / Gp27, baseplate hub, domain 2 / Baseplate structural protein, domain 2 / Baseplate structural protein, domain 1 / Baseplate structural protein Gp11 / Bacteriophage T4, Gp11, C-terminal finger domain / Baseplate structural protein Gp11, N-terminal domain superfamily / Baseplate structural protein Gp11 superfamily / Major capsid protein, Myoviridae / Baseplate structural protein Gp11, C-terminal domain / GP11 baseplate wedge protein / Major capsid protein Gp23 / Baseplate wedge protein gp10 / Baseplate wedge protein gp6 / Phage tail collar domain superfamily / : / : / : / : / : / : / Baseplate wedge protein gp6-like, helical domain / Baseplate structural protein gp6, C-terminal domain I / Baseplate structural protein gp6, C-terminal domain II / Baseplate wedge protein gp6, domain II / Baseplate structural protein gp6, C-terminal domain III / Baseplate wedge protein gp10 domain 3 / : / Tail sheath protein Gp18-like domain I / Capsid protein, T4-like bacteriophage-like / Phage tail collar domain / Baseplate structural protein Gp9 C-terminal domain superfamily / Phage Tail Collar Domain / Bacteriophage T4, Gp8 / Bacteriophage T4, Gp8 superfamily / Bacteriophage T4, Gp8 / Gp5, C-terminal / Gp5 C-terminal repeat (3 copies) / : / Baseplate structural protein Gp10, C-terminal domain / Baseplate structural protein Gp9/Gp10 / Baseplate structural protein Gp9/Gp10 middle domain superfamily / Gp9-like superfamily / : / Bacteriophage T4 gp9/10-like protein, N-terminal / Bacteriophage T4 gp9/10-like protein, C-terminal / Protein Gp5, N-terminal OB-fold domain / Pre-baseplate central spike protein Gp5 / Gp5 N-terminal OB domain / : / Tail sheath protein Gp18 domain III N-terminal region / IraD/Gp25-like / PAAR motif / Baseplate wedge protein gp25 / PAAR motif / Phage tail sheath protein, beta-sandwich domain / Phage tail sheath protein beta-sandwich domain / Bacteriophage T4, Gp19, tail tube / T4-like virus tail tube protein gp19 / PKD domain / : / Tail sheath protein, subtilisin-like domain / Phage tail sheath protein subtilisin-like domain / Tail sheath protein, C-terminal domain / Phage tail sheath C-terminal domain / PKD domain / PKD domain superfamily / PKD/Chitinase domain / Repeats in polycystic kidney disease 1 (PKD1) and other proteins / Fibritin C-terminal
類似検索 - ドメイン・相同性
Tail completion and sheath stabilizer protein / Pre-baseplate central spike protein Gp5 / Tail tube protein / Small outer capsid protein / Phospholipase / Baseplate tail tube cap / Tail sheath protein / Baseplate wedge subunit / Highly immunogenic outer capsid protein / Portal protein ...Tail completion and sheath stabilizer protein / Pre-baseplate central spike protein Gp5 / Tail tube protein / Small outer capsid protein / Phospholipase / Baseplate tail tube cap / Tail sheath protein / Baseplate wedge subunit / Highly immunogenic outer capsid protein / Portal protein / Baseplate wedge subunit and tail pin / Baseplate wedge subunit / Baseplate wedge tail fiber connector / Tail sheath stabilizer and completion protein / Baseplate hub subunit / Baseplate wedge subunit / Major capsid protein / Fibritin / Baseplate wedge protein gp10 / Short tail fiber protein gp12 / Neck protein gp13 / Neck protein gp14 / Tape measure protein / Baseplate tail-tube junction protein gp54 / Baseplate wedge protein gp6 / Baseplate wedge protein gp7
類似検索 - 構成要素
生物種Escherichia phage T4 (ファージ)
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: 3.8 Å
データ登録者Fokine, A. / Zhu, J. / Klose, T. / Vago, F. / Arnaud, C. / Wang, Z. / Khare, B. / Rossmann, M.G. / Chen, Z. / Sun, L. ...Fokine, A. / Zhu, J. / Klose, T. / Vago, F. / Arnaud, C. / Wang, Z. / Khare, B. / Rossmann, M.G. / Chen, Z. / Sun, L. / Fang, Q. / Kuhn, R. / Rao, V.B.
資金援助 米国, 1件
組織認可番号国
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI081726 米国
引用ジャーナル: To Be Published
タイトル: In situ Atomic Structure of Phage T4 Head-Tail Connector Complex Shows Molecular Gates Open for Genome Ejection and DNA Pushed into the Tail Tube
著者: Fokine, A. / Zhu, J. / Klose, T. / Vago, F. / Arnaud, C. / Wang, Z. / Khare, B. / Rossmann, M.G. / Chen, Z. / Sun, L. / Fang, Q. / Kuhn, R. / Rao, V.B.
履歴
登録2024年12月17日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02025年12月24日Provider: repository / タイプ: Initial release
改定 1.02025年12月24日Data content type: EM metadata / Data content type: EM metadata / Provider: repository / タイプ: Initial release
改定 1.02025年12月24日Data content type: Image / Data content type: Image / Provider: repository / タイプ: Initial release
改定 1.02025年12月24日Data content type: Primary map / Data content type: Primary map / Provider: repository / タイプ: Initial release

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構造の表示

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
0: gp14, neck protein
1: gp18, tail sheath protein
2: gp18, tail sheath protein
3: gp18, tail sheath protein
4: gp18, tail sheath protein
5: gp18, tail sheath protein
6: gp19, tail tube protein
7: gp19, tail tube protein
8: gp19, tail tube protein
9: gp19, tail tube protein
A: gpwac, fibritin
A0: gp20, portal protein
A1: gp20, portal protein
A2: gp20, portal protein
A3: gp20, portal protein
A4: gp23, major capsid protein
A5: gp23, major capsid protein
A6: gp13, neck protein
A7: gp23, major capsid protein
A8: gp23, major capsid protein
A9: gp23, major capsid protein
AA: gp19, tail tube protein
AB: gp15, tail terminator protein
AC: gp3, tube terminator protein
AD: gp18, tail sheath protein
AE: gp19, tail tube protein
AF: gp19, tail tube protein
AG: gp19, tail tube protein
AH: gp19, tail tube protein
AI: gp19, tail tube protein
AJ: gp19, tail tube protein
AK: gp18, tail sheath protein
AL: gp18, tail sheath protein
AM: gp18, tail sheath protein
AN: gp18, tail sheath protein
AO: gp18, tail sheath protein
AP: gp18, tail sheath protein
AQ: Hoc, highly immunogenic outer capsid protein
AR: Hoc, highly immunogenic outer capsid protein
AS: Hoc, highly immunogenic outer capsid protein
AT: Hoc, highly immunogenic outer capsid protein
AU: Hoc, highly immunogenic outer capsid protein
AV: gp23, major capsid protein
AW: gp23, major capsid protein
AX: gp23, major capsid protein
AY: gp13, neck protein
AZ: gp23, major capsid protein
Aa: gp13, neck protein
Ab: gp13, neck protein
Ac: gp23, major capsid protein
Ad: gp23, major capsid protein
Ae: gp23, major capsid protein
Af: gp23, major capsid protein
Ag: gp23, major capsid protein
Ah: gp23, major capsid protein
Ai: gp23, major capsid protein
Aj: gp23, major capsid protein
Ak: gp23, major capsid protein
Al: gp13, neck protein
Am: gp23, major capsid protein
An: gp23, major capsid protein
Ao: gp23, major capsid protein
Ap: gp23, major capsid protein
Aq: gp13, neck protein
Ar: gp13, neck protein
As: gp13, neck protein
At: gp13, neck protein
Au: gp23, major capsid protein
Av: gp20, portal protein
Aw: gp23, major capsid protein
Ax: gp20, portal protein
Ay: gp23, major capsid protein
Az: gp23, major capsid protein
B: gpwac, fibritin
B1: gp18, tail sheath protein
B2: gp18, tail sheath protein
B3: gp18, tail sheath protein
B4: gp18, tail sheath protein
B5: gp18, tail sheath protein
B6: gp18, tail sheath protein
B7: gp18, tail sheath protein
BA: gp20, portal protein
BB: gp20, portal protein
BC: gp13, neck protein
BD: gp20, portal protein
BE: gp13, neck protein
BF: gp20, portal protein
BG: gp20, portal protein
BH: gp20, portal protein
BI: gp23, major capsid protein
BJ: gp23, major capsid protein
BK: gp23, major capsid protein
BL: gp13, neck protein
BM: gp23, major capsid protein
BN: Soc, small outer capsid protein
BO: Soc, small outer capsid protein
BP: Soc, small outer capsid protein
BQ: Soc, small outer capsid protein
BR: Soc, small outer capsid protein
BS: Soc, small outer capsid protein
BT: Soc, small outer capsid protein
BU: Soc, small outer capsid protein
BV: Soc, small outer capsid protein
BW: Soc, small outer capsid protein
BX: gp19, tail tube protein
BY: gp19, tail tube protein
BZ: gp19, tail tube protein
Ba: gp19, tail tube protein
Bb: gp19, tail tube protein
Bc: gp19, tail tube protein
Bd: gp19, tail tube protein
Be: gp19, tail tube protein
Bf: gp19, tail tube protein
Bg: gp19, tail tube protein
Bh: gp19, tail tube protein
Bi: gp19, tail tube protein
Bj: gp19, tail tube protein
Bk: gp19, tail tube protein
Bl: gp19, tail tube protein
Bm: gp19, tail tube protein
Bn: gp19, tail tube protein
Bo: gp19, tail tube protein
Bp: gp18, tail sheath protein
Bq: gp18, tail sheath protein
Br: gp18, tail sheath protein
Bs: gp18, tail sheath protein
Bt: gp18, tail sheath protein
Bu: gp18, tail sheath protein
Bv: gp18, tail sheath protein
Bw: gp18, tail sheath protein
Bx: gp18, tail sheath protein
By: gp18, tail sheath protein
Bz: gp18, tail sheath protein
C: gpwac, fibritin
D: gpwac, fibritin
E: gpwac, fibritin
F: gpwac, fibritin
G: gpwac, fibritin
H: gpwac, fibritin
I: gpwac, fibritin
J: gpwac, fibritin
K: gpwac, fibritin
K0: gp18, tail sheath protein
K1: gp18, tail sheath protein
K2: gp18, tail sheath protein
K3: gp18, tail sheath protein
K4: gp18, tail sheath protein
K5: gp18, tail sheath protein
K6: gp18, tail sheath protein
K7: gp18, tail sheath protein
K8: gp18, tail sheath protein
K9: gp18, tail sheath protein
L: gpwac, fibritin
L0: gp18, tail sheath protein
L1: gp18, tail sheath protein
L2: gp18, tail sheath protein
L3: gp18, tail sheath protein
L4: gp18, tail sheath protein
L5: gp18, tail sheath protein
L6: gp18, tail sheath protein
L7: gp18, tail sheath protein
L8: gp18, tail sheath protein
L9: gp18, tail sheath protein
LS: gp18, tail sheath protein
LU: gp18, tail sheath protein
LV: gp18, tail sheath protein
LW: gp18, tail sheath protein
LX: gp18, tail sheath protein
LY: gp18, tail sheath protein
LZ: gp18, tail sheath protein
La: gp18, tail sheath protein
Lb: gp18, tail sheath protein
Lc: gp18, tail sheath protein
Ld: gp18, tail sheath protein
Le: gp18, tail sheath protein
Lx: gp18, tail sheath protein
Lz: gp18, tail sheath protein
M: gpwac, fibritin
M0: gp18, tail sheath protein
M1: gp18, tail sheath protein
M2: gp18, tail sheath protein
M3: gp18, tail sheath protein
M4: gp18, tail sheath protein
M5: gp18, tail sheath protein
M6: gp18, tail sheath protein
M7: gp18, tail sheath protein
M8: gp18, tail sheath protein
M9: gp18, tail sheath protein
MS: gp18, tail sheath protein
MU: gp18, tail sheath protein
MV: gp18, tail sheath protein
MW: gp18, tail sheath protein
MX: gp18, tail sheath protein
MY: gp18, tail sheath protein
MZ: gp18, tail sheath protein
Ma: gp18, tail sheath protein
Mb: gp18, tail sheath protein
Mc: gp18, tail sheath protein
Md: gp18, tail sheath protein
Me: gp18, tail sheath protein
Mx: gp18, tail sheath protein
Mz: gp18, tail sheath protein
N: gpwac, fibritin
NX: gp18, tail sheath protein
NZ: gp18, tail sheath protein
Na: gp18, tail sheath protein
Nb: gp18, tail sheath protein
Nc: gp18, tail sheath protein
Nd: gp18, tail sheath protein
Ne: gp18, tail sheath protein
Nf: gp18, tail sheath protein
Ng: gp18, tail sheath protein
Nh: gp18, tail sheath protein
Ni: gp18, tail sheath protein
Nj: gp18, tail sheath protein
Nx: gp18, tail sheath protein
Nz: gp18, tail sheath protein
O: gpwac, fibritin
OE: gp19, tail tube protein
OF: gp19, tail tube protein
OG: gp19, tail tube protein
OH: gp19, tail tube protein
OI: gp19, tail tube protein
OJ: gp19, tail tube protein
OK: gp19, tail tube protein
OL: gp19, tail tube protein
OM: gp19, tail tube protein
ON: gp19, tail tube protein
OO: gp19, tail tube protein
Oj: gp19, tail tube protein
Ok: gp19, tail tube protein
Ol: gp19, tail tube protein
Om: gp19, tail tube protein
On: gp19, tail tube protein
Oo: gp19, tail tube protein
Op: gp19, tail tube protein
Oq: gp19, tail tube protein
Or: gp19, tail tube protein
Os: gp19, tail tube protein
Ot: gp19, tail tube protein
P: gpwac, fibritin
PE: gp19, tail tube protein
PF: gp19, tail tube protein
PG: gp19, tail tube protein
PH: gp19, tail tube protein
PI: gp19, tail tube protein
PJ: gp19, tail tube protein
PK: gp19, tail tube protein
PL: gp19, tail tube protein
PM: gp19, tail tube protein
PN: gp19, tail tube protein
PO: gp19, tail tube protein
Pj: gp19, tail tube protein
Pk: gp19, tail tube protein
Pl: gp19, tail tube protein
Pm: gp19, tail tube protein
Pn: gp19, tail tube protein
Po: gp19, tail tube protein
Pp: gp19, tail tube protein
Pq: gp19, tail tube protein
Pr: gp19, tail tube protein
Ps: gp19, tail tube protein
Pt: gp19, tail tube protein
Q: gpwac, fibritin
R: gpwac, fibritin
RE: gp19, tail tube protein
RF: gp19, tail tube protein
RG: gp19, tail tube protein
RH: gp19, tail tube protein
RI: gp19, tail tube protein
RJ: gp19, tail tube protein
RK: gp19, tail tube protein
RL: gp19, tail tube protein
RM: gp19, tail tube protein
RN: gp19, tail tube protein
RO: gp19, tail tube protein
RT: gp19, tail tube protein
Rk: gp19, tail tube protein
Rl: gp19, tail tube protein
Rm: gp19, tail tube protein
Rn: gp19, tail tube protein
Ro: gp19, tail tube protein
Rp: gp19, tail tube protein
Rq: gp19, tail tube protein
Rr: gp19, tail tube protein
Rs: gp19, tail tube protein
Rt: gp19, tail tube protein
S: gpwac, fibritin
S0: gp12, short tail fiber protein
S1: gp12, short tail fiber protein
S2: gp12, short tail fiber protein
S3: gp12, short tail fiber protein
S4: gp12, short tail fiber protein
S5: gp12, short tail fiber protein
S6: gp12, short tail fiber protein
S7: gp12, short tail fiber protein
S8: gp12, short tail fiber protein
SA: gp12, short tail fiber protein
SO: gp12, short tail fiber protein
SP: gp12, short tail fiber protein
SQ: gp12, short tail fiber protein
Sv: gp12, short tail fiber protein
Sw: gp12, short tail fiber protein
Sx: gp12, short tail fiber protein
Sy: gp12, short tail fiber protein
Sz: gp12, short tail fiber protein
T: gpwac, fibritin
T1: gp9, baseplate wedge tail fiber connector
T2: gp9, baseplate wedge tail fiber connector
T3: gp9, baseplate wedge tail fiber connector
T4: gp9, baseplate wedge tail fiber connector
T5: gp9, baseplate wedge tail fiber connector
T6: gp9, baseplate wedge tail fiber connector
T7: gp9, baseplate wedge tail fiber connector
T8: gp9, baseplate wedge tail fiber connector
T9: gp9, baseplate wedge tail fiber connector
TF: gp9, baseplate wedge tail fiber connector
TG: gp9, baseplate wedge tail fiber connector
TH: gp9, baseplate wedge tail fiber connector
Td: gp9, baseplate wedge tail fiber connector
Te: gp9, baseplate wedge tail fiber connector
Tf: gp9, baseplate wedge tail fiber connector
Tg: gp9, baseplate wedge tail fiber connector
Th: gp9, baseplate wedge tail fiber connector
Ti: gp9, baseplate wedge tail fiber connector
U: gpwac, fibritin
UL: gp11, baseplate wedge protein
UM: gp11, baseplate wedge protein
UN: gp11, baseplate wedge protein
Up: gp11, baseplate wedge protein
Uq: gp11, baseplate wedge protein
Ur: gp11, baseplate wedge protein
Us: gp11, baseplate wedge protein
Ut: gp11, baseplate wedge protein
Uu: gp11, baseplate wedge protein
V: gpwac, fibritin
VL: gp11, baseplate wedge protein
VM: gp11, baseplate wedge protein
VN: gp11, baseplate wedge protein
Vp: gp11, baseplate wedge protein
Vq: gp11, baseplate wedge protein
Vr: gp11, baseplate wedge protein
Vs: gp11, baseplate wedge protein
Vt: gp11, baseplate wedge protein
Vu: gp11, baseplate wedge protein
W: gpwac, fibritin
WI: gp10, baseplate wedge protein
WJ: gp10, baseplate wedge protein
WK: gp10, baseplate wedge protein
Wj: gp10, baseplate wedge protein
Wk: gp10, baseplate wedge protein
Wl: gp10, baseplate wedge protein
Wm: gp10, baseplate wedge protein
Wn: gp10, baseplate wedge protein
Wo: gp10, baseplate wedge protein
X: gpwac, fibritin
XI: gp10, baseplate wedge protein
XJ: gp10, baseplate wedge protein
XK: gp10, baseplate wedge protein
Xj: gp10, baseplate wedge protein
Xk: gp10, baseplate wedge protein
Xl: gp10, baseplate wedge protein
Xm: gp10, baseplate wedge protein
Xn: gp10, baseplate wedge protein
Xo: gp10, baseplate wedge protein
Y: gpwac, fibritin
YC: gp7, baseplate wedge protein
YX: gp7, baseplate wedge protein
YY: gp7, baseplate wedge protein
Yc: gp7, baseplate wedge protein
Yx: gp7, baseplate wedge protein
Yy: gp7, baseplate wedge protein
Z: gpwac, fibritin
ZD: gp8, baseplate wedge protein
ZE: gp8, baseplate wedge protein
ZZ: gp8, baseplate wedge protein
Za: gp8, baseplate wedge protein
Zb: gp8, baseplate wedge protein
Zc: gp8, baseplate wedge protein
a: gpwac, fibritin
aD: gp8, baseplate wedge protein
aE: gp8, baseplate wedge protein
aZ: gp8, baseplate wedge protein
aa: gp8, baseplate wedge protein
ab: gp8, baseplate wedge protein
ac: gp8, baseplate wedge protein
b: gpwac, fibritin
b0: gp18, tail sheath protein
b3: gp18, tail sheath protein
b4: gp18, tail sheath protein
b5: gp18, tail sheath protein
b6: gp18, tail sheath protein
b7: gp18, tail sheath protein
b8: gp18, tail sheath protein
b9: gp18, tail sheath protein
bN: gp18, tail sheath protein
bO: gp18, tail sheath protein
bP: gp18, tail sheath protein
bQ: gp18, tail sheath protein
bR: gp18, tail sheath protein
bY: gp18, tail sheath protein
c: gpwac, fibritin
cA: gp18, tail sheath protein
cB: gp18, tail sheath protein
cC: gp18, tail sheath protein
cD: gp18, tail sheath protein
cE: gp18, tail sheath protein
cF: gp18, tail sheath protein
cG: gp18, tail sheath protein
cH: gp18, tail sheath protein
cI: gp18, tail sheath protein
cJ: gp18, tail sheath protein
cK: gp18, tail sheath protein
cL: gp18, tail sheath protein
cM: gp18, tail sheath protein
cN: gp18, tail sheath protein
cO: gp18, tail sheath protein
cP: gp18, tail sheath protein
d: gpwac, fibritin
dS: gp18, tail sheath protein
dT: gp18, tail sheath protein
dU: gp18, tail sheath protein
dV: gp18, tail sheath protein
dW: gp18, tail sheath protein
dZ: gp18, tail sheath protein
e: gpwac, fibritin
eB: gp6, baseplate wedge protein
eU: gp6, baseplate wedge protein
eW: gp6, baseplate wedge protein
f: gpwac, fibritin
f9: gp6, baseplate wedge protein
fA: gp6, baseplate wedge protein
fB: gp6, baseplate wedge protein
fR: gp6, baseplate wedge protein
fS: gp6, baseplate wedge protein
fU: gp6, baseplate wedge protein
fW: gp6, baseplate wedge protein
fr: gp6, baseplate wedge protein
fs: gp6, baseplate wedge protein
g: gpwac, fibritin
gE: gp5, baseplate central spike protein
gG: gp5, baseplate central spike protein
gH: gp5, baseplate central spike protein
gd: gp5.4, tip of the central spike
h: gpwac, fibritin
h1: gp19, tail tube protein
h2: gp19, tail tube protein
hI: gp19, tail tube protein
hJ: gp19, tail tube protein
hK: gp19, tail tube protein
hL: gp19, tail tube protein
hM: gp19, tail tube protein
hX: gp19, tail tube protein
he: gp19, tail tube protein
hf: gp19, tail tube protein
hg: gp19, tail tube protein
hh: gp19, tail tube protein
hi: gp19, tail tube protein
hj: gp19, tail tube protein
hk: gp19, tail tube protein
hl: gp19, tail tube protein
hm: gp19, tail tube protein
hn: gp19, tail tube protein
ho: gp19, tail tube protein
hp: gp19, tail tube protein
hq: gp19, tail tube protein
hr: gp19, tail tube protein
hs: gp19, tail tube protein
ht: gp19, tail tube protein
hu: gp19, tail tube protein
hv: gp19, tail tube protein
hw: gp19, tail tube protein
hx: gp19, tail tube protein
hy: gp19, tail tube protein
hz: gp19, tail tube protein
i: gpwac, fibritin
iC: gp27, baseplate hub protein
iD: gp27, baseplate hub protein
iF: gp27, baseplate hub protein
j: gpwac, fibritin
ja: gp29, tape measure protein
jb: gp29, tape measure protein
jc: gp29, tape measure protein
k: gp14, neck protein
k3: gp53, baseplate wedge protein
k4: gp53, baseplate wedge protein
k7: gp53, baseplate wedge protein
k8: gp53, baseplate wedge protein
kV: gp53, baseplate wedge protein
l: gp14, neck protein
lV: gp53, baseplate wedge protein
m: gp14, neck protein
m1: gp25, baseplate protein
m2: gp25, baseplate protein
m5: gp25, baseplate protein
m6: gp25, baseplate protein
mT: gp25, baseplate protein
n: gp14, neck protein
nT: gp25, baseplate protein
o: gp19, tail tube protein
o0: gp48, baseplate protein
o1: gp48, baseplate protein
o2: gp48, baseplate protein
o6: gp48, baseplate protein
p: gp14, neck protein
pA: gp48, baseplate protein
pB: gp48, baseplate protein
q: gp15, tail terminator protein
q3: gp54, baseplate protein
q4: gp54, baseplate protein
q5: gp54, baseplate protein
q7: gp54, baseplate protein
q8: gp54, baseplate protein
q9: gp54, baseplate protein
r: gp15, tail terminator protein
rc: unassigned peptide A
rd: unassigned peptide A
re: unassigned peptide A
rf: unassigned peptide A
rg: unassigned peptide A
rh: unassigned peptide A
s: gp15, tail terminator protein
sQ: unassigned peptide B
sT: unassigned peptide B
sU: unassigned peptide B
t: gp15, tail terminator protein
tS: unassigned peptide C
tX: unassigned peptide C
tY: unassigned peptide C
u: gp15, tail terminator protein
uR: unassigned peptide D
uV: unassigned peptide D
uW: unassigned peptide D
v: gp3, tube terminator protein
vZ: unassigned peptide E
va: unassigned peptide E
vb: unassigned peptide E
w: gp3, tube terminator protein
x: gp3, tube terminator protein
y: gp3, tube terminator protein
z: gp3, tube terminator protein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)24,141,063547
ポリマ－24,140,671541
非ポリマー3926
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

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タンパク質 , 26種, 523分子 0klmnp12345ADAKALAMANAOAPB1B2B3B4B5B6B7BpBqBrBsBt...

#1: タンパク質
gp14, neck protein / Gene product 14 / gp14


分子量: 29597.836 Da / 分子数: 6 / 由来タイプ: 天然 / 由来: (天然) Escherichia phage T4 (ファージ) / 参照: UniProt: P11111
#2: タンパク質 ...
gp18, tail sheath protein


分子量: 71348.625 Da / 分子数: 138 / 由来タイプ: 天然 / 由来: (天然) Escherichia phage T4 (ファージ) / 参照: UniProt: A0A7S9SVW9
#3: タンパク質 ...
gp19, tail tube protein


分子量: 18479.613 Da / 分子数: 126 / 由来タイプ: 天然 / 由来: (天然) Escherichia phage T4 (ファージ) / 参照: UniProt: A0A7S9SVI2
#4: タンパク質 ...
gpwac, fibritin / Collar protein / Whisker antigen control protein


分子量: 51909.164 Da / 分子数: 36 / 由来タイプ: 天然 / 由来: (天然) Escherichia phage T4 (ファージ) / 参照: UniProt: P10104
#5: タンパク質
gp20, portal protein / gp20


分子量: 61117.082 Da / 分子数: 12 / 由来タイプ: 天然 / 由来: (天然) Escherichia phage T4 (ファージ) / 参照: UniProt: A0A7S9SW10
#6: タンパク質 ...
gp23, major capsid protein / Gene product 23 / Major head protein / gp23


分子量: 56074.242 Da / 分子数: 30 / 由来タイプ: 天然 / 由来: (天然) Escherichia phage T4 (ファージ) / 参照: UniProt: P04535
#7: タンパク質
gp13, neck protein / Gene product 13 / gp13


分子量: 34772.211 Da / 分子数: 12 / 由来タイプ: 天然 / 由来: (天然) Escherichia phage T4 (ファージ) / 参照: UniProt: P11110
#8: タンパク質
gp15, tail terminator protein


分子量: 31587.486 Da / 分子数: 6 / 由来タイプ: 天然 / 由来: (天然) Escherichia phage T4 (ファージ) / 参照: UniProt: A0A7S9XHN5
#9: タンパク質
gp3, tube terminator protein


分子量: 19723.143 Da / 分子数: 6 / 由来タイプ: 天然 / 由来: (天然) Escherichia phage T4 (ファージ) / 参照: UniProt: A0A7S9SU76
#10: タンパク質
Hoc, highly immunogenic outer capsid protein


分子量: 40416.547 Da / 分子数: 5 / 由来タイプ: 天然 / 由来: (天然) Escherichia phage T4 (ファージ) / 参照: UniProt: A0A7S9SW08
#11: タンパク質
Soc, small outer capsid protein / Soc


分子量: 9129.147 Da / 分子数: 10 / 由来タイプ: 天然 / 由来: (天然) Escherichia phage T4 (ファージ) / 参照: UniProt: A0A7S9SVQ6
#12: タンパク質
gp12, short tail fiber protein / Gene product 12 / gp12


分子量: 56253.926 Da / 分子数: 18 / 由来タイプ: 天然 / 由来: (天然) Escherichia phage T4 (ファージ) / 参照: UniProt: P10930
#13: タンパク質
gp9, baseplate wedge tail fiber connector


分子量: 31024.725 Da / 分子数: 18 / 由来タイプ: 天然 / 由来: (天然) Escherichia phage T4 (ファージ) / 参照: UniProt: A0A7S9SWG4
#14: タンパク質
gp11, baseplate wedge protein


分子量: 23725.523 Da / 分子数: 18 / 由来タイプ: 天然 / 由来: (天然) Escherichia phage T4 (ファージ) / 参照: UniProt: A0A7S9SW18
#15: タンパク質
gp10, baseplate wedge protein / Gene product 10 / gp10


分子量: 66281.680 Da / 分子数: 18 / 由来タイプ: 天然 / 由来: (天然) Escherichia phage T4 (ファージ) / 参照: UniProt: P10928
#16: タンパク質
gp7, baseplate wedge protein / Gene product 7 / gp7


分子量: 119336.516 Da / 分子数: 6 / 由来タイプ: 天然 / 由来: (天然) Escherichia phage T4 (ファージ) / 参照: UniProt: P19061
#17: タンパク質
gp8, baseplate wedge protein


分子量: 38041.668 Da / 分子数: 12 / 由来タイプ: 天然 / 由来: (天然) Escherichia phage T4 (ファージ) / 参照: UniProt: A0A7S9SVZ9
#18: タンパク質
gp6, baseplate wedge protein / Gene product 6 / gp6


分子量: 74492.641 Da / 分子数: 12 / 由来タイプ: 天然 / 由来: (天然) Escherichia phage T4 (ファージ) / 参照: UniProt: P19060
#19: タンパク質 gp5, baseplate central spike protein / Pre-Gp5 / Peptidoglycan hydrolase gp5


分子量: 63183.723 Da / 分子数: 3 / 由来タイプ: 天然 / 由来: (天然) Escherichia phage T4 (ファージ) / 参照: UniProt: A0A7S9SVH6, lysozyme
#20: タンパク質 gp5.4, tip of the central spike


分子量: 10233.663 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Escherichia phage T4 (ファージ) / 参照: UniProt: A0A7S9SVS3
#21: タンパク質 gp27, baseplate hub protein


分子量: 44431.062 Da / 分子数: 3 / 由来タイプ: 天然 / 由来: (天然) Escherichia phage T4 (ファージ) / 参照: UniProt: A0A7S9XHP4
#22: タンパク質 gp29, tape measure protein / TMP / Gene product 29 / gp29 / Tail length regulator


分子量: 64485.539 Da / 分子数: 3 / 由来タイプ: 天然 / 由来: (天然) Escherichia phage T4 (ファージ) / 参照: UniProt: P13337
#23: タンパク質
gp53, baseplate wedge protein


分子量: 22990.885 Da / 分子数: 6 / 由来タイプ: 天然 / 由来: (天然) Escherichia phage T4 (ファージ) / 参照: UniProt: A0A7S9XI21
#24: タンパク質
gp25, baseplate protein


分子量: 15111.101 Da / 分子数: 6 / 由来タイプ: 天然 / 由来: (天然) Escherichia phage T4 (ファージ) / 参照: UniProt: A0A7S9SW44
#25: タンパク質
gp48, baseplate protein


分子量: 39770.332 Da / 分子数: 6 / 由来タイプ: 天然 / 由来: (天然) Escherichia phage T4 (ファージ) / 参照: UniProt: A0A7S9SVT9
#26: タンパク質
gp54, baseplate protein / Gene product 54 / gp54


分子量: 35001.188 Da / 分子数: 6 / 由来タイプ: 天然 / 由来: (天然) Escherichia phage T4 (ファージ) / 参照: UniProt: P13341

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Unassigned peptide ... , 5種, 18分子 rcrdrerfrgrhsQsTsUtStXtYuRuVuWvZvavb

#27: タンパク質・ペプチド
unassigned peptide A


分子量: 2145.636 Da / 分子数: 6 / 由来タイプ: 天然 / 由来: (天然) Escherichia phage T4 (ファージ)
#28: タンパク質・ペプチド unassigned peptide B


分子量: 1549.902 Da / 分子数: 3 / 由来タイプ: 天然 / 由来: (天然) Escherichia phage T4 (ファージ)
#29: タンパク質・ペプチド unassigned peptide C


分子量: 869.063 Da / 分子数: 3 / 由来タイプ: 天然 / 由来: (天然) Escherichia phage T4 (ファージ)
#30: タンパク質・ペプチド unassigned peptide D


分子量: 613.749 Da / 分子数: 3 / 由来タイプ: 天然 / 由来: (天然) Escherichia phage T4 (ファージ)
#31: タンパク質・ペプチド unassigned peptide E


分子量: 783.958 Da / 分子数: 3 / 由来タイプ: 天然 / 由来: (天然) Escherichia phage T4 (ファージ)

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非ポリマー , 1種, 6分子

#32: 化合物
ChemComp-ZN / ZINC ION


分子量: 65.409 Da / 分子数: 6 / 由来タイプ: 合成 / 式: Zn

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詳細

研究の焦点であるリガンドがあるかN
Has protein modificationY

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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: Escherichia phage T4 / タイプ: VIRUS / Entity ID: #1-#31 / 由来: NATURAL
由来(天然)生物種: Escherichia phage T4 (ファージ)
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: Escherichia coli / 株: B
緩衝液pH: 7.5
試料包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES
試料支持グリッドのタイプ: PELCO Ultrathin Carbon with Lacey Carbon
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: Ted Pella lacey carbon 400 mesh grids (catalog No: 01824) were used.

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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: TFS 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）: 2000 nm / 最小 デフォーカス（公称値）: 600 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: 38 e/Å2 / フィルム・検出器のモデル: GATAN K3 (6k x 4k)

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解析

CTF補正タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION
3次元再構成解像度: 3.8 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 69000
詳細: This is the composite map based on the asymmetric reconstruction focused on the phage neck, the 3-fold-symmetric reconstruction focused on the middle part of the tail, and the 3-fold- ...詳細: This is the composite map based on the asymmetric reconstruction focused on the phage neck, the 3-fold-symmetric reconstruction focused on the middle part of the tail, and the 3-fold-symmetric reconstruction focused on the baseplate. The resolutions of these reconstructions are 3.8A, 3.4A and 3.6A, respectively. (The number of particles is given for the asymmetric reconstruction focused on the phage neck.)
対称性のタイプ: POINT
原子モデル構築詳細: The structures were fitted into the composite map using ChimeraX.

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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

他の情報も見る