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- PDB-8p85: 80S yeast ribosome in complex with Fluorolissoclimide -

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基本情報

登録情報
データベース: PDB / ID: 8p85
タイトル80S yeast ribosome in complex with Fluorolissoclimide
要素
  • (40S ribosomal protein ...) x 25
  • (60S ribosomal protein ...) x 38
  • (Large ribosomal subunit protein ...) x 2
  • (Small ribosomal subunit protein ...) x 5
  • 16S ribosomal RNA
  • 25S ribosomal RNA
  • 5.8S ribosomal RNA
  • 5S ribosomal RNA
  • 60S acidic ribosomal protein P0
  • Guanine nucleotide-binding protein subunit beta-like protein
  • Suppressor protein STM1
  • Ubiquitin
  • Ubiquitin-60S ribosomal protein L40
キーワードRIBOSOME / eL42 / Translation inhibitors
機能・相同性
機能・相同性情報


triplex DNA binding / ribosome hibernation / translation elongation factor binding / Platelet degranulation / regulation of translational initiation in response to stress / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) / Negative regulators of DDX58/IFIH1 signaling / regulation of amino acid metabolic process / negative regulation of glucose mediated signaling pathway / positive regulation of translational fidelity ...triplex DNA binding / ribosome hibernation / translation elongation factor binding / Platelet degranulation / regulation of translational initiation in response to stress / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) / Negative regulators of DDX58/IFIH1 signaling / regulation of amino acid metabolic process / negative regulation of glucose mediated signaling pathway / positive regulation of translational fidelity / RMTs methylate histone arginines / Protein methylation / mTORC1-mediated signalling / Protein hydroxylation / ribosome-associated ubiquitin-dependent protein catabolic process / GDP-dissociation inhibitor activity / regulation of polysaccharide biosynthetic process / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / Ribosomal scanning and start codon recognition / preribosome, small subunit precursor / nonfunctional rRNA decay / transporter complex / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / response to cycloheximide / telomeric DNA binding / Major pathway of rRNA processing in the nucleolus and cytosol / mRNA destabilization / lipopolysaccharide transport / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / negative regulation of translational frameshifting / TOR signaling / Formation of a pool of free 40S subunits / positive regulation of protein kinase activity / preribosome, large subunit precursor / L13a-mediated translational silencing of Ceruloplasmin expression / Gram-negative-bacterium-type cell outer membrane assembly / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / translational elongation / ribosomal large subunit export from nucleus / G-protein alpha-subunit binding / 90S preribosome / Ub-specific processing proteases / ribosomal subunit export from nucleus / regulation of translational fidelity / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / protein-RNA complex assembly / translational termination / maturation of LSU-rRNA / ribosomal small subunit export from nucleus / translation regulator activity / translation repressor activity / DNA-(apurinic or apyrimidinic site) endonuclease activity / rescue of stalled ribosome / telomere maintenance / protein kinase C binding / cellular response to amino acid starvation / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / ribosome assembly / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / macroautophagy / small-subunit processome / translational initiation / modification-dependent protein catabolic process / protein tag activity / maintenance of translational fidelity / cell outer membrane / cytoplasmic stress granule / rRNA processing / ribosome biogenesis / ribosome binding / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / small ribosomal subunit rRNA binding / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / protein ubiquitination / negative regulation of translation / rRNA binding / structural constituent of ribosome / ribosome / translation / G protein-coupled receptor signaling pathway / negative regulation of gene expression / response to antibiotic / mRNA binding / ubiquitin protein ligase binding / negative regulation of apoptotic process / nucleolus
類似検索 - 分子機能
Stm1-like, N-terminal / Stm1 / Hyaluronan/mRNA-binding protein / Hyaluronan / mRNA binding family / 60s Acidic ribosomal protein / 60S acidic ribosomal protein P0 / : / LptD, C-terminal / LPS-assembly protein LptD / : ...Stm1-like, N-terminal / Stm1 / Hyaluronan/mRNA-binding protein / Hyaluronan / mRNA binding family / 60s Acidic ribosomal protein / 60S acidic ribosomal protein P0 / : / LptD, C-terminal / LPS-assembly protein LptD / : / LPS transport system D / Organic solvent tolerance-like, N-terminal / LptA/(LptD N-terminal domain) LPS transport protein / Group II dsDNA virus coat/capsid protein / 50S ribosomal protein L10, insertion domain superfamily / : / 60S ribosomal protein L10P, insertion domain / Insertion domain in 60S ribosomal protein L10P / : / Ribosomal protein S26e signature. / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein S21e, conserved site / Ribosomal protein S21e signature. / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Ribosomal protein L29e / Ribosomal L29e protein family / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / Ribosomal protein S5, eukaryotic/archaeal / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein S2, eukaryotic / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Ribosomal protein L27e, conserved site / Ribosomal protein L27e signature. / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / S27a-like superfamily / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / Ribosomal protein L10e / 40S Ribosomal protein S10 / : / Ribosomal protein L44e signature. / Ribosomal protein S7e signature. / Ribosomal protein L24e, conserved site / Ribosomal protein L24e signature. / Ribosomal protein L19/L19e conserved site / Ribosomal protein L19, eukaryotic / Ribosomal protein L19e signature. / Plectin/S10, N-terminal / Plectin/S10 domain / : / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein L6e signature. / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein S8e subdomain, eukaryotes / : / Ribosomal protein S17e, conserved site / Ribosomal protein S17e signature. / Ribosomal protein S25 / S25 ribosomal protein / Ribosomal protein L44e / Ribosomal protein S3Ae, conserved site / Ribosomal protein L44 / Ribosomal protein S3Ae signature. / Ribosomal protein S30 / Ribosomal protein S30 / Ribosomal protein S27a / Ribosomal protein L34e, conserved site / Ribosomal protein S27a / Ribosomal protein L34e signature. / Ribosomal protein S27a / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein L5 eukaryotic, C-terminal / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal L18 C-terminal region / Ribosomal L40e family / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / Ribosomal protein 60S L18 and 50S L18e / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Ribosomal protein L18/L18-A/B/e, conserved site / Ribosomal protein L18e signature. / Ribosomal protein L23/L25, N-terminal / : / Ribosomal protein L23, N-terminal domain / Ribosomal protein S27e signature. / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein S4e, N-terminal, conserved site
類似検索 - ドメイン・相同性
(2~{S})-2-azanylpropanal / : / osmium (III) hexammine / SPERMIDINE / : / : / : / : / : / RNA ...(2~{S})-2-azanylpropanal / : / osmium (III) hexammine / SPERMIDINE / : / : / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS4A / Large ribosomal subunit protein uL15 / Small ribosomal subunit protein eS17A / Large ribosomal subunit protein eL24A / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein eL39 / Large ribosomal subunit protein uL10 / Large ribosomal subunit protein uL30A / Large ribosomal subunit protein uL6A / Large ribosomal subunit protein uL22A / Large ribosomal subunit protein uL24A / Large ribosomal subunit protein eL33A / Large ribosomal subunit protein eL36A / Large ribosomal subunit protein eL29 / Large ribosomal subunit protein eL15A / Large ribosomal subunit protein eL22A / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS15 / Ubiquitin-ribosomal protein eS31 fusion protein / Small ribosomal subunit protein eS19A / Small ribosomal subunit protein eS21A / Small ribosomal subunit protein uS8A / Large ribosomal subunit protein eL27A / Large ribosomal subunit protein eL31A / Ubiquitin-ribosomal protein eL40A fusion protein / Large ribosomal subunit protein eL20A / Large ribosomal subunit protein eL43A / Large ribosomal subunit protein eL42A / Small ribosomal subunit protein uS12A / Small ribosomal subunit protein eS24A / Small ribosomal subunit protein eS30A / Small ribosomal subunit protein eS4A / Small ribosomal subunit protein eS6A / Small ribosomal subunit protein eS8A / Large ribosomal subunit protein uL14A / Large ribosomal subunit protein uL2A / Small ribosomal subunit protein uS17A / Large ribosomal subunit protein eL18A / Small ribosomal subunit protein uS9A / Small ribosomal subunit protein uS13A / Large ribosomal subunit protein eL19A / Large ribosomal subunit protein uL29A / Small ribosomal subunit protein eS32B / Large ribosomal subunit protein uL4A / Putative major capsid protein p72 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein eL8A / Small ribosomal subunit protein uS5 / Large ribosomal subunit protein uL18 / Small ribosomal subunit protein uS7 / Large ribosomal subunit protein uL13A / Small ribosomal subunit protein eS7A / Small ribosomal subunit protein uS2A / Small ribosomal subunit protein eS1A / Small ribosomal subunit protein eS27A / Large ribosomal subunit protein eL14A / Small ribosomal subunit protein RACK1 / Large ribosomal subunit protein eL32 / Small ribosomal subunit protein uS10 / Suppressor protein STM1 / Small ribosomal subunit protein uS11B / Small ribosomal subunit protein eS26B / Small ribosomal subunit protein uS14A / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein eL37A / Large ribosomal subunit protein eL38 / Large ribosomal subunit protein eL34A / Small ribosomal subunit protein uS19 / Large ribosomal subunit protein eL6A / Large ribosomal subunit protein eL21A / Small ribosomal subunit protein eS10A / LPS-assembly protein LptD / Large ribosomal subunit protein uL5B / Small ribosomal subunit protein eS25A / Small ribosomal subunit protein eS28A
類似検索 - 構成要素
生物種Saccharomyces cerevisiae (パン酵母)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.9 Å
データ登録者Terrosu, S. / Yusupov, M.
資金援助 米国, 1件
組織認可番号国
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM129264 米国
引用ジャーナル: To Be Published
タイトル: Role of Protein eL42 in the Ribosome Binding of Synthetic Analogues of Natural Lissoclimides
著者: Terrosu, S. / Yusupov, M.
履歴
登録2023年8月31日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02025年6月25日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

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集合体

登録構造単位
A: 16S ribosomal RNA
B: 40S ribosomal protein S0-A
C: 40S ribosomal protein S1-A
D: 40S ribosomal protein S2
E: Small ribosomal subunit protein uS3
F: 40S ribosomal protein S4-A
G: 40S ribosomal protein S5
H: 40S ribosomal protein S6-A
I: 40S ribosomal protein S7-A
J: 40S ribosomal protein S8-A
K: 40S ribosomal protein S9-A
L: Small ribosomal subunit protein eS10A,Small ribosomal subunit protein eS10A,40S ribosomal protein S10-A
M: 40S ribosomal protein S11-A
O: 40S ribosomal protein S13
P: 40S ribosomal protein S14-B
Q: 40S ribosomal protein S15
R: 40S ribosomal protein S16-A
S: 40S ribosomal protein S17-A
T: 40S ribosomal protein S18-A
U: 40S ribosomal protein S19-A
V: Small ribosomal subunit protein uS10
W: 40S ribosomal protein S21-A
X: 40S ribosomal protein S22-A
Y: 40S ribosomal protein S23-A
Z: 40S ribosomal protein S24-A
AA: 60S ribosomal protein L27-A
DA: 60S ribosomal protein L26-A
AB: 60S ribosomal protein L28
DB: 60S ribosomal protein L27-A
AC: 60S ribosomal protein L29
DC: 60S ribosomal protein L28
AD: 60S ribosomal protein L30
CD: 60S ribosomal protein L2-A
DD: 60S ribosomal protein L29
AE: 60S ribosomal protein L31-A
CE: 60S ribosomal protein L3
DE: 60S ribosomal protein L30
AF: 60S ribosomal protein L32
1: 25S ribosomal RNA
3: 5S ribosomal RNA
4: 5.8S ribosomal RNA
j: 60S ribosomal protein L2-A
k: 60S ribosomal protein L3
l: 60S ribosomal protein L4-A
m: 60S ribosomal protein L5
n: 60S ribosomal protein L6-A
o: 60S ribosomal protein L7-A
p: 60S ribosomal protein L8-A
q: 60S ribosomal protein L9-A
r: 60S ribosomal protein L10
s: Large ribosomal subunit protein uL5B
t: 60S ribosomal protein L13-A
u: 60S ribosomal protein L14-A
v: 60S ribosomal protein L15-A
w: 60S ribosomal protein L16-A
x: 60S ribosomal protein L17-A
y: 60S ribosomal protein L18-A
z: 60S ribosomal protein L19-A
0: 60S ribosomal protein L20-A
2: 60S ribosomal protein L21-A
5: 60S ribosomal protein L22-A
6: 60S ribosomal protein L23-A
7: 60S ribosomal protein L24-A
8: 60S ribosomal protein L25
9: 60S ribosomal protein L26-A
AG: 60S ribosomal protein L33-A
AH: 60S ribosomal protein L34-A
AI: 60S ribosomal protein L35-A
AJ: 60S ribosomal protein L36-A
AK: 60S ribosomal protein L37-A
AL: 60S ribosomal protein L38
AM: 60S ribosomal protein L39
AN: Ubiquitin-60S ribosomal protein L40
AO: Large ribosomal subunit protein eL41B
AP: 60S ribosomal protein L42-A
AQ: 60S ribosomal protein L43-A
i: Suppressor protein STM1
AR: 25S ribosomal RNA
AS: 5S ribosomal RNA
AT: 5.8S ribosomal RNA
CF: 60S ribosomal protein L4-A
CG: 60S ribosomal protein L5
CH: 60S ribosomal protein L6-A
CI: 60S ribosomal protein L7-A
CJ: 60S ribosomal protein L8-A
CK: 60S ribosomal protein L9-A
CL: 60S ribosomal protein L10
CM: Large ribosomal subunit protein uL5B
CN: 60S ribosomal protein L13-A
CO: 60S ribosomal protein L14-A
CP: 60S ribosomal protein L15-A
CQ: 60S ribosomal protein L16-A
CR: 60S ribosomal protein L17-A
CS: 60S ribosomal protein L18-A
CT: 60S ribosomal protein L19-A
CU: 60S ribosomal protein L20-A
CV: 60S ribosomal protein L21-A
CW: 60S ribosomal protein L22-A
CX: 60S ribosomal protein L23-A
CY: 60S ribosomal protein L24-A
CZ: 60S ribosomal protein L25
DF: 60S ribosomal protein L31-A
DG: 60S ribosomal protein L32
DH: 60S ribosomal protein L33-A
DI: 60S ribosomal protein L34-A
DJ: 60S ribosomal protein L35-A
DK: 60S ribosomal protein L36-A
DL: 60S ribosomal protein L37-A
DM: 60S ribosomal protein L38
DN: 60S ribosomal protein L39
DO: Ubiquitin-60S ribosomal protein L40
DP: Large ribosomal subunit protein eL41B
DQ: 60S ribosomal protein L42-A
DR: 60S ribosomal protein L43-A
p0: 60S acidic ribosomal protein P0
sM: Suppressor protein STM1
a: 40S ribosomal protein S25-A
b: Small ribosomal subunit protein eS26B
c: 40S ribosomal protein S27-A
d: 40S ribosomal protein S28-A
e: Small ribosomal subunit protein uS14A
f: 40S ribosomal protein S30-A
g: Ubiquitin
h: Guanine nucleotide-binding protein subunit beta-like protein
sR: 16S ribosomal RNA
Rb: Guanine nucleotide-binding protein subunit beta-like protein
s0: 40S ribosomal protein S0-A
s1: 40S ribosomal protein S1-A
s2: 40S ribosomal protein S2
s3: Small ribosomal subunit protein uS3
s4: 40S ribosomal protein S4-A
s5: 40S ribosomal protein S5
s6: 40S ribosomal protein S6-A
s7: 40S ribosomal protein S7-A
s8: 40S ribosomal protein S8-A
s9: 40S ribosomal protein S9-A
c0: Small ribosomal subunit protein eS10A,Small ribosomal subunit protein eS10A,40S ribosomal protein S10-A
c1: 40S ribosomal protein S11-A
c3: 40S ribosomal protein S13
c4: 40S ribosomal protein S14-B
c5: 40S ribosomal protein S15
c6: 40S ribosomal protein S16-A
c7: 40S ribosomal protein S17-A
c8: 40S ribosomal protein S18-A
c9: 40S ribosomal protein S19-A
d0: Small ribosomal subunit protein uS10
d1: 40S ribosomal protein S21-A
d2: 40S ribosomal protein S22-A
d3: 40S ribosomal protein S23-A
d4: 40S ribosomal protein S24-A
d5: 40S ribosomal protein S25-A
d6: Small ribosomal subunit protein eS26B
d7: 40S ribosomal protein S27-A
d8: 40S ribosomal protein S28-A
d9: Small ribosomal subunit protein uS14A
e0: 40S ribosomal protein S30-A
e1: Ubiquitin
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)6,601,1192692
ポリマ－6,274,730157
非ポリマー326,3892535
水4,161231
1
A: 16S ribosomal RNA
B: 40S ribosomal protein S0-A
C: 40S ribosomal protein S1-A
D: 40S ribosomal protein S2
E: Small ribosomal subunit protein uS3
F: 40S ribosomal protein S4-A
G: 40S ribosomal protein S5
H: 40S ribosomal protein S6-A
I: 40S ribosomal protein S7-A
J: 40S ribosomal protein S8-A
K: 40S ribosomal protein S9-A
L: Small ribosomal subunit protein eS10A,Small ribosomal subunit protein eS10A,40S ribosomal protein S10-A
M: 40S ribosomal protein S11-A
O: 40S ribosomal protein S13
P: 40S ribosomal protein S14-B
Q: 40S ribosomal protein S15
R: 40S ribosomal protein S16-A
S: 40S ribosomal protein S17-A
T: 40S ribosomal protein S18-A
U: 40S ribosomal protein S19-A
V: Small ribosomal subunit protein uS10
W: 40S ribosomal protein S21-A
X: 40S ribosomal protein S22-A
Y: 40S ribosomal protein S23-A
Z: 40S ribosomal protein S24-A
AA: 60S ribosomal protein L27-A
AB: 60S ribosomal protein L28
AC: 60S ribosomal protein L29
AD: 60S ribosomal protein L30
AE: 60S ribosomal protein L31-A
AF: 60S ribosomal protein L32
1: 25S ribosomal RNA
3: 5S ribosomal RNA
4: 5.8S ribosomal RNA
j: 60S ribosomal protein L2-A
k: 60S ribosomal protein L3
l: 60S ribosomal protein L4-A
m: 60S ribosomal protein L5
n: 60S ribosomal protein L6-A
o: 60S ribosomal protein L7-A
p: 60S ribosomal protein L8-A
q: 60S ribosomal protein L9-A
r: 60S ribosomal protein L10
s: Large ribosomal subunit protein uL5B
t: 60S ribosomal protein L13-A
u: 60S ribosomal protein L14-A
v: 60S ribosomal protein L15-A
w: 60S ribosomal protein L16-A
x: 60S ribosomal protein L17-A
y: 60S ribosomal protein L18-A
z: 60S ribosomal protein L19-A
0: 60S ribosomal protein L20-A
2: 60S ribosomal protein L21-A
5: 60S ribosomal protein L22-A
6: 60S ribosomal protein L23-A
7: 60S ribosomal protein L24-A
8: 60S ribosomal protein L25
9: 60S ribosomal protein L26-A
AG: 60S ribosomal protein L33-A
AH: 60S ribosomal protein L34-A
AI: 60S ribosomal protein L35-A
AJ: 60S ribosomal protein L36-A
AK: 60S ribosomal protein L37-A
AL: 60S ribosomal protein L38
AM: 60S ribosomal protein L39
AN: Ubiquitin-60S ribosomal protein L40
AO: Large ribosomal subunit protein eL41B
AP: 60S ribosomal protein L42-A
AQ: 60S ribosomal protein L43-A
i: Suppressor protein STM1
a: 40S ribosomal protein S25-A
b: Small ribosomal subunit protein eS26B
c: 40S ribosomal protein S27-A
d: 40S ribosomal protein S28-A
e: Small ribosomal subunit protein uS14A
f: 40S ribosomal protein S30-A
g: Ubiquitin
h: Guanine nucleotide-binding protein subunit beta-like protein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)3,277,6321291
ポリマ－3,120,49078
非ポリマー157,1421213
水1267
タイプ名称対称操作数
identity operation1_555x,y,z1
2
DA: 60S ribosomal protein L26-A
DB: 60S ribosomal protein L27-A
DC: 60S ribosomal protein L28
CD: 60S ribosomal protein L2-A
DD: 60S ribosomal protein L29
CE: 60S ribosomal protein L3
DE: 60S ribosomal protein L30
AR: 25S ribosomal RNA
AS: 5S ribosomal RNA
AT: 5.8S ribosomal RNA
CF: 60S ribosomal protein L4-A
CG: 60S ribosomal protein L5
CH: 60S ribosomal protein L6-A
CI: 60S ribosomal protein L7-A
CJ: 60S ribosomal protein L8-A
CK: 60S ribosomal protein L9-A
CL: 60S ribosomal protein L10
CM: Large ribosomal subunit protein uL5B
CN: 60S ribosomal protein L13-A
CO: 60S ribosomal protein L14-A
CP: 60S ribosomal protein L15-A
CQ: 60S ribosomal protein L16-A
CR: 60S ribosomal protein L17-A
CS: 60S ribosomal protein L18-A
CT: 60S ribosomal protein L19-A
CU: 60S ribosomal protein L20-A
CV: 60S ribosomal protein L21-A
CW: 60S ribosomal protein L22-A
CX: 60S ribosomal protein L23-A
CY: 60S ribosomal protein L24-A
CZ: 60S ribosomal protein L25
DF: 60S ribosomal protein L31-A
DG: 60S ribosomal protein L32
DH: 60S ribosomal protein L33-A
DI: 60S ribosomal protein L34-A
DJ: 60S ribosomal protein L35-A
DK: 60S ribosomal protein L36-A
DL: 60S ribosomal protein L37-A
DM: 60S ribosomal protein L38
DN: 60S ribosomal protein L39
DO: Ubiquitin-60S ribosomal protein L40
DP: Large ribosomal subunit protein eL41B
DQ: 60S ribosomal protein L42-A
DR: 60S ribosomal protein L43-A
p0: 60S acidic ribosomal protein P0
sM: Suppressor protein STM1
sR: 16S ribosomal RNA
Rb: Guanine nucleotide-binding protein subunit beta-like protein
s0: 40S ribosomal protein S0-A
s1: 40S ribosomal protein S1-A
s2: 40S ribosomal protein S2
s3: Small ribosomal subunit protein uS3
s4: 40S ribosomal protein S4-A
s5: 40S ribosomal protein S5
s6: 40S ribosomal protein S6-A
s7: 40S ribosomal protein S7-A
s8: 40S ribosomal protein S8-A
s9: 40S ribosomal protein S9-A
c0: Small ribosomal subunit protein eS10A,Small ribosomal subunit protein eS10A,40S ribosomal protein S10-A
c1: 40S ribosomal protein S11-A
c3: 40S ribosomal protein S13
c4: 40S ribosomal protein S14-B
c5: 40S ribosomal protein S15
c6: 40S ribosomal protein S16-A
c7: 40S ribosomal protein S17-A
c8: 40S ribosomal protein S18-A
c9: 40S ribosomal protein S19-A
d0: Small ribosomal subunit protein uS10
d1: 40S ribosomal protein S21-A
d2: 40S ribosomal protein S22-A
d3: 40S ribosomal protein S23-A
d4: 40S ribosomal protein S24-A
d5: 40S ribosomal protein S25-A
d6: Small ribosomal subunit protein eS26B
d7: 40S ribosomal protein S27-A
d8: 40S ribosomal protein S28-A
d9: Small ribosomal subunit protein uS14A
e0: 40S ribosomal protein S30-A
e1: Ubiquitin
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)3,323,4871401
ポリマ－3,154,23979
非ポリマー169,2481322
水1267
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)303.680, 287.580, 435.090
Angle α, β, γ (deg.)90.00, 98.93, 90.00
Int Tables number4
Space group name H-MP1211

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要素

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RNA鎖 , 4種, 8分子 AsR1AR3AS4AT

#1: RNA鎖 16S ribosomal RNA


分子量: 579761.938 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: GenBank: 874346701
#35: RNA鎖 25S ribosomal RNA


分子量: 1097493.875 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: GenBank: 834774822
#36: RNA鎖 5S ribosomal RNA


分子量: 38951.105 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: GenBank: 1329886537
#37: RNA鎖 5.8S ribosomal RNA


分子量: 50682.922 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: GenBank: 1331532632

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40S ribosomal protein ... , 25種, 50分子 Bs0Cs1Ds2Fs4Gs5Hs6Is7Js8Ks9Mc1Oc3Pc4Qc5Rc6Sc7...

#2: タンパク質 40S ribosomal protein S0-A / Nucleic acid-binding protein NAB1A / Small ribosomal subunit protein uS2-A


分子量: 28051.330 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: P32905
#3: タンパク質 40S ribosomal protein S1-A / RP10A / Small ribosomal subunit protein eS1-A


分子量: 28798.467 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: P33442
#4: タンパク質 40S ribosomal protein S2 / Omnipotent suppressor protein SUP44 / RP12 / S4 / Small ribosomal subunit protein uS5 / YS5


分子量: 27490.826 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: P25443
#6: タンパク質 40S ribosomal protein S4-A / RP5 / S7 / Small ribosomal subunit protein eS4-A / YS6


分子量: 29469.330 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: P0CX35
#7: タンパク質 40S ribosomal protein S5 / RP14 / S2 / Small ribosomal subunit protein uS7 / YS8


分子量: 25072.600 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: P26783
#8: タンパク質 40S ribosomal protein S6-A / RP9 / S10 / Small ribosomal subunit protein eS6-A / YS4


分子量: 27054.486 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: P0CX37
#9: タンパク質 40S ribosomal protein S7-A / RP30 / RP40 / Small ribosomal subunit protein eS7-A


分子量: 21658.209 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: P26786
#10: タンパク質 40S ribosomal protein S8-A / RP19 / S14 / Small ribosomal subunit protein eS8-A / YS9


分子量: 22537.803 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: P0CX39
#11: タンパク質 40S ribosomal protein S9-A / RP21 / S13 / Small ribosomal subunit protein uS4-A / YP28 / YS11


分子量: 22487.893 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: O13516
#13: タンパク質 40S ribosomal protein S11-A / RP41 / S18 / Small ribosomal subunit protein uS17-A / YS12


分子量: 17785.934 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: P0CX47
#14: タンパク質 40S ribosomal protein S13 / S27a / Small ribosomal subunit protein uS15 / YS15


分子量: 17059.945 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: P05756
#15: タンパク質 40S ribosomal protein S14-B / RP59B / Small ribosomal subunit protein uS11-B


分子量: 14675.771 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: P39516
#16: タンパク質 40S ribosomal protein S15 / RIG protein / RP52 / S21 / Small ribosomal subunit protein uS19 / YS21


分子量: 16031.907 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: Q01855
#17: タンパク質 40S ribosomal protein S16-A / RP61R / Small ribosomal subunit protein uS9-A


分子量: 15877.490 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: P0CX51
#18: タンパク質 40S ribosomal protein S17-A / RP51A / Small ribosomal subunit protein eS17-A


分子量: 15820.413 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: P02407
#19: タンパク質 40S ribosomal protein S18-A / Small ribosomal subunit protein uS13-A


分子量: 17071.641 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: P0CX55
#20: タンパク質 40S ribosomal protein S19-A / RP55A / S16a / Small ribosomal subunit protein eS19-A / YP45 / YS16A


分子量: 15942.125 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: P07280
#22: タンパク質 40S ribosomal protein S21-A / S26 / Small ribosomal subunit protein eS21-A / YS25


分子量: 9758.829 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: P0C0V8
#23: タンパク質 40S ribosomal protein S22-A / RP50 / S24 / Small ribosomal subunit protein uS8-A / YP58 / YS22


分子量: 14650.062 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: P0C0W1
#24: タンパク質 40S ribosomal protein S23-A / RP37 / S28 / Small ribosomal subunit protein uS12-A / YS14


分子量: 16073.896 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: P0CX29
#25: タンパク質 40S ribosomal protein S24-A / RP50 / Small ribosomal subunit protein eS24-A


分子量: 15362.848 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: P0CX31
#72: タンパク質 40S ribosomal protein S25-A / RP45 / S31 / Small ribosomal subunit protein eS25-A / YS23


分子量: 12067.272 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: Q3E792
#74: タンパク質 40S ribosomal protein S27-A / RP61 / Small ribosomal subunit protein eS27-A / YS20


分子量: 8893.391 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: P35997
#75: タンパク質 40S ribosomal protein S28-A / S33 / Small ribosomal subunit protein eS28-A / YS27


分子量: 7605.847 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: Q3E7X9
#77: タンパク質 40S ribosomal protein S30-A / Small ribosomal subunit protein eS30-A


分子量: 7137.541 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: P0CX33

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Small ribosomal subunit protein ... , 5種, 10分子 Es3Lc0Vd0bd6ed9

#5: タンパク質 Small ribosomal subunit protein uS3 / 40S ribosomal protein S3 / RP13 / YS3


分子量: 26542.789 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: P05750
#12: タンパク質 Small ribosomal subunit protein eS10A,Small ribosomal subunit protein eS10A,40S ribosomal protein S10-A / 40S ribosomal protein S10-A


分子量: 12757.445 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: Q08745
#21: タンパク質 Small ribosomal subunit protein uS10 / 40S ribosomal protein S20


分子量: 13929.044 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: P38701
#73: タンパク質 Small ribosomal subunit protein eS26B / 40S ribosomal protein S26-B


分子量: 13480.886 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: P39939
#76: タンパク質 Small ribosomal subunit protein uS14A / 40S ribosomal protein S29-A / S36 / YS29


分子量: 6675.723 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: P41057

+
60S ribosomal protein ... , 38種, 76分子 AADBDA9ABDCACDDADDECDjAEDFCEkAFDGlCFmCGnCHoCIpCJqCK...

#26: タンパク質 60S ribosomal protein L27-A / Large ribosomal subunit protein eL27-A


分子量: 15568.360 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: P0C2H6
#27: タンパク質 60S ribosomal protein L26-A / L33 / Large ribosomal subunit protein uL24-A / YL33


分子量: 14265.784 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: P05743
#28: タンパク質 60S ribosomal protein L28 / L27a / L29 / Large ribosomal subunit protein uL15 / RP44 / RP62 / YL24


分子量: 16761.666 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: P02406
#29: タンパク質 60S ribosomal protein L29 / Large ribosomal subunit protein eL29 / YL43


分子量: 6691.884 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: P05747
#30: タンパク質 60S ribosomal protein L30 / L32 / Large ribosomal subunit protein eL30 / RP73 / YL38


分子量: 11430.364 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: P14120
#31: タンパク質 60S ribosomal protein L2-A / L5 / Large ribosomal subunit protein uL2-A / RP8 / YL6


分子量: 27463.574 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: P0CX45
#32: タンパク質 60S ribosomal protein L31-A / L34 / Large ribosomal subunit protein eL31-A / YL28


分子量: 12980.158 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: P0C2H8
#33: タンパク質 60S ribosomal protein L3 / Large ribosomal subunit protein uL3 / Maintenance of killer protein 8 / RP1 / Trichodermin ...Large ribosomal subunit protein uL3 / Maintenance of killer protein 8 / RP1 / Trichodermin resistance protein / YL1


分子量: 43850.793 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: P14126
#34: タンパク質 60S ribosomal protein L32 / Large ribosomal subunit protein eL32


分子量: 14809.441 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: P38061
#38: タンパク質 60S ribosomal protein L4-A / L2 / Large ribosomal subunit protein uL4-A / RP2 / YL2


分子量: 39159.125 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: P10664
#39: タンパク質 60S ribosomal protein L5 / L1 / L1a / Large ribosomal subunit protein uL18 / Ribosomal 5S RNA-binding protein / YL3


分子量: 33764.828 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: P26321
#40: タンパク質 60S ribosomal protein L6-A / L17 / Large ribosomal subunit protein eL6-A / RP18 / YL16


分子量: 20000.564 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: Q02326
#41: タンパク質 60S ribosomal protein L7-A / L6 / Large ribosomal subunit protein uL30-A / RP11 / YL8


分子量: 27686.281 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: P05737
#42: タンパク質 60S ribosomal protein L8-A / L4 / L4-2 / L7a-1 / Large ribosomal subunit protein eL8-A / Maintenance of killer protein 7 / RP6 / YL5


分子量: 28175.820 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: P17076
#43: タンパク質 60S ribosomal protein L9-A / L8 / Large ribosomal subunit protein uL6-A / RP24 / YL11


分子量: 21605.061 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: P05738
#44: タンパク質 60S ribosomal protein L10 / L9 / Large ribosomal subunit protein uL16 / Ubiquinol-cytochrome C reductase complex subunit VI- ...L9 / Large ribosomal subunit protein uL16 / Ubiquinol-cytochrome C reductase complex subunit VI-requiring protein


分子量: 25410.465 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: P41805
#46: タンパク質 60S ribosomal protein L13-A / Large ribosomal subunit protein eL13-A


分子量: 22604.164 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: Q12690
#47: タンパク質 60S ribosomal protein L14-A / Large ribosomal subunit protein eL14-A


分子量: 15195.066 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: P36105
#48: タンパク質 60S ribosomal protein L15-A / L13 / Large ribosomal subunit protein eL15-A / RP15R / YL10 / YP18


分子量: 24482.357 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: P05748
#49: タンパク質 60S ribosomal protein L16-A / L13a / L21 / Large ribosomal subunit protein uL13-A / RP22 / YL15


分子量: 22247.227 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: P26784
#50: タンパク質 60S ribosomal protein L17-A / L20A / Large ribosomal subunit protein uL22-A / YL17


分子量: 20589.518 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: P05740
#51: タンパク質 60S ribosomal protein L18-A / Large ribosomal subunit protein eL18-A / RP28


分子量: 20609.252 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: P0CX49
#52: タンパク質 60S ribosomal protein L19-A / L23 / Large ribosomal subunit protein eL19-A / RP15L / RP33 / YL14


分子量: 21762.316 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: P0CX82
#53: タンパク質 60S ribosomal protein L20-A / L18a / Large ribosomal subunit protein eL20-A


分子量: 20478.852 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: P0CX23
#54: タンパク質 60S ribosomal protein L21-A / Large ribosomal subunit protein eL21-A


分子量: 18279.266 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: Q02753
#55: タンパク質 60S ribosomal protein L22-A / L1c / Large ribosomal subunit protein eL22-A / RP4 / YL31


分子量: 13711.359 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: P05749
#56: タンパク質 60S ribosomal protein L23-A / L17a / Large ribosomal subunit protein uL14-A / YL32


分子量: 14493.950 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: P0CX41
#57: タンパク質 60S ribosomal protein L24-A / L30 / Large ribosomal subunit protein eL24-A / RP29 / YL21


分子量: 17661.717 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: P04449
#58: タンパク質 60S ribosomal protein L25 / Large ribosomal subunit protein uL23 / RP16L / YL25 / YP42'


分子量: 15787.612 Da / 分子数: 2 / 由来タイプ: 天然
詳細: MAPSAKATAAKKAVVKGTNGKKALKVRTSATFRLPKTLKLARAPKYASKAVPHYNRLDSYKVIEQPITSETAMKKVEDGNILVFQVSMKANKYQIKKAVKELYEVDVLKVNTLVRPNGTKKAYVRLTADYDALDIANRIGYI
由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: P04456
#59: タンパク質 60S ribosomal protein L33-A / L37 / Large ribosomal subunit protein eL33-A / RP47 / YL37


分子量: 12177.130 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: P05744
#60: タンパク質 60S ribosomal protein L34-A / Large ribosomal subunit protein eL34-A


分子量: 13673.196 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: P87262
#61: タンパク質 60S ribosomal protein L35-A / Large ribosomal subunit protein uL29-A


分子量: 13942.640 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: P0CX84
#62: タンパク質 60S ribosomal protein L36-A / L39 / Large ribosomal subunit protein eL36-A / YL39


分子量: 11151.259 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: P05745
#63: タンパク質 60S ribosomal protein L37-A / L43 / Large ribosomal subunit protein eL37-A / YL35 / YP55


分子量: 9877.395 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: P49166
#64: タンパク質 60S ribosomal protein L38 / Large ribosomal subunit protein eL38


分子量: 8845.561 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: P49167
#65: タンパク質 60S ribosomal protein L39 / L46 / Large ribosomal subunit protein eL39 / YL40


分子量: 6358.640 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: P04650
#68: タンパク質 60S ribosomal protein L42-A / L41 / Large ribosomal subunit protein eL42-A / YL27 / YP44


分子量: 12246.658 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: P0CX27
#69: タンパク質 60S ribosomal protein L43-A / L37a / Large ribosomal subunit protein eL43-A / YL35


分子量: 10112.952 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: P0CX25

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Large ribosomal subunit protein ... , 2種, 4分子 sCMAODP

#45: タンパク質 Large ribosomal subunit protein uL5B / 60S ribosomal protein L11-B / L16 / RP39 / YL22


分子量: 19785.719 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: Q3E757
#67: タンパク質・ペプチド Large ribosomal subunit protein eL41B / 60S ribosomal protein L41-B / L47 / YL41


分子量: 3354.243 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: P0CX87

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タンパク質 , 5種, 9分子 ANDOisMp0ge1hRb

#66: タンパク質 Ubiquitin-60S ribosomal protein L40


分子量: 14583.077 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: P0CH08
#70: タンパク質 Suppressor protein STM1 / 3BP1 / GU4 nucleic-binding protein 2 / G4p2 protein / POP2 multicopy suppressor protein 4 / ...3BP1 / GU4 nucleic-binding protein 2 / G4p2 protein / POP2 multicopy suppressor protein 4 / Ribosomal subunits association factor / AF / TOM1 suppressor protein 1 / Triplex-binding protein 1


分子量: 30048.010 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: P39015
#71: タンパク質 60S acidic ribosomal protein P0 / A0 / L10e / Large ribosomal subunit protein uL10


分子量: 33749.121 Da / 分子数: 1 / 由来タイプ: 天然
詳細: There is something wrong in the extracted sequence, it does not match the one present in the pdb file. The first part actually matches, in the second part I modeled amminoacids from 189 till ...詳細: There is something wrong in the extracted sequence, it does not match the one present in the pdb file. The first part actually matches, in the second part I modeled amminoacids from 189 till the end. I do not understand what is going on with this particular chain.
由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: P05317
#78: タンパク質 Ubiquitin


分子量: 17254.227 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: P05759
#79: タンパク質 Guanine nucleotide-binding protein subunit beta-like protein / Receptor for activated C kinase / Receptor of activated protein kinase C 1 / RACK1 / Small ...Receptor for activated C kinase / Receptor of activated protein kinase C 1 / RACK1 / Small ribosomal subunit protein RACK1


分子量: 34841.219 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: P38011

-
非ポリマー , 8種, 2766分子

#80: 化合物...
ChemComp-OHX / osmium (III) hexammine / osmium(6+) hexaazanide


分子量: 286.365 Da / 分子数: 1003 / 由来タイプ: 合成 / 式: H12N6Os
#81: 化合物...
ChemComp-MG / MAGNESIUM ION / マグネシウムジカチオン


分子量: 24.305 Da / 分子数: 1502 / 由来タイプ: 合成 / 式: Mg
#82: 化合物
ChemComp-K / POTASSIUM ION / カリウムカチオン


分子量: 39.098 Da / 分子数: 4 / 由来タイプ: 合成 / 式: K
#83: 化合物 ChemComp-SPD / SPERMIDINE / N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE / PA(34) / スペルミジン


分子量: 145.246 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C7H19N3
#84: 化合物 ChemComp-VDU / fluorolissoclimide / (3R)-3-[(1S)-2-[(1R,3S,4aS,7S,8aS)-7-fluoranyl-5,5,8a-trimethyl-2-methylidene-3-oxidanyl-3,4,4a,6,7,8-hexahydro-1H-naphthalen-1-yl]-1-oxidanyl-ethyl]pyrrolidine-2,5-dione


分子量: 367.455 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C20H30FNO4 / タイプ: SUBJECT OF INVESTIGATION
#85: 化合物
ChemComp-ZN / ZINC ION


分子量: 65.409 Da / 分子数: 17 / 由来タイプ: 合成 / 式: Zn
#86: 化合物
ChemComp-5XU / (2~{S})-2-azanylpropanal / Ala-aldehyde / (S)-2-アミノプロパナ-ル


タイプ: L-peptide linking / 分子量: 73.094 Da / 分子数: 5 / 由来タイプ: 合成 / 式: C3H7NO
#87: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 231 / 由来タイプ: 天然 / 式: H2O

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詳細

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

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実験情報

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実験

実験手法: X線回折 / 使用した結晶の数: 1

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試料調製

結晶マシュー密度: 3.21 Å3/Da / 溶媒含有率: 61.73 %
結晶化温度: 277.15 K / 手法: 蒸気拡散法, ハンギングドロップ法
詳細: ll lissoclimides/80S complexes were formed in 5.5 mM Tris-acetate at pH 7.0, 3 mM K(OAc) at pH 7.2, 5.5 mM NH4(OAc), 2 mM Mg(OAc)2, 1.3 mM DTT by incubation of 80S ribosomes (1.5 uM) with 30- ...詳細: ll lissoclimides/80S complexes were formed in 5.5 mM Tris-acetate at pH 7.0, 3 mM K(OAc) at pH 7.2, 5.5 mM NH4(OAc), 2 mM Mg(OAc)2, 1.3 mM DTT by incubation of 80S ribosomes (1.5 uM) with 30-fold molar excess of lissoclimide congeners for 15 min at 30 C. Crystals were grown at 4 C by hanging-drop vapor diffusion

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データ収集

回折平均測定温度: 100 K / Serial crystal experiment: N
放射光源由来: シンクロトロン / サイト: SLS / ビームライン: X06SA / 波長: 1 Å
検出器タイプ: DECTRIS EIGER X 16M / 検出器: PIXEL / 日付: 2021年6月10日
放射プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長波長: 1 Å / 相対比: 1
反射解像度: 2.9→207.6 Å / Num. obs: 3210225 / % possible obs: 99.69 % / 冗長度: 12 % / Biso Wilson estimate: 76.98 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.094 / Rrim(I) all: 0.13 / Net I/σ(I): 25.4
反射 シェル解像度: 2.9→3 Å / Mean I/σ(I) obs: 0.8 / Num. unique obs: 229131 / CC1/2: 0.12

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解析

ソフトウェア
名称バージョン分類
PHENIX1精密化
XDSデータ削減
XSCALEデータスケーリング
PHENIX位相決定
精密化構造決定の手法: 分子置換 / 解像度: 2.9→207.6 Å / 交差検証法: FREE R-VALUE
Rfactor反射数%反射
Rfree0.223 -1.55 %
Rwork0.2202 --
obs0.2203 3198596 99.53 %
精密化ステップサイクル: LAST / 解像度: 2.9→207.6 Å
タンパク質核酸リガンド溶媒全体
原子数174883 221181 8606 231 404901
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.007431875
X-RAY DIFFRACTIONf_angle_d1.305640725
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.940.453414700.429493269X-RAY DIFFRACTION88
2.94-2.970.403616530.4215104846X-RAY DIFFRACTION99
2.97-3.010.402816520.4104105097X-RAY DIFFRACTION100
3.01-3.040.384616570.3796105223X-RAY DIFFRACTION100
3.04-3.080.349116650.3632105529X-RAY DIFFRACTION100
3.08-3.130.344716560.3472105469X-RAY DIFFRACTION100
3.13-3.170.325816540.3295105334X-RAY DIFFRACTION100
3.17-3.220.316616630.3137105587X-RAY DIFFRACTION100
3.22-3.270.301316640.3031105349X-RAY DIFFRACTION100
3.27-3.320.299116550.2957105141X-RAY DIFFRACTION100
3.32-3.380.290216550.2864105205X-RAY DIFFRACTION100
3.38-3.440.292116540.2781105309X-RAY DIFFRACTION100
3.44-3.510.276116590.2708105603X-RAY DIFFRACTION100
3.51-3.580.254516560.2571105428X-RAY DIFFRACTION100
3.58-3.660.233316620.2312105450X-RAY DIFFRACTION100
3.66-3.740.217816660.2152105579X-RAY DIFFRACTION100
3.74-3.840.211316630.2045105577X-RAY DIFFRACTION100
3.84-3.940.20716550.1938105324X-RAY DIFFRACTION100
3.94-4.060.185216620.1887105455X-RAY DIFFRACTION100
4.06-4.190.188216570.1815105469X-RAY DIFFRACTION100
4.19-4.340.186316590.1827105411X-RAY DIFFRACTION100
4.34-4.510.171716600.173105479X-RAY DIFFRACTION100
4.51-4.720.173416630.1694105482X-RAY DIFFRACTION100
4.72-4.960.16716660.1671105350X-RAY DIFFRACTION100
4.96-5.270.169516530.171105368X-RAY DIFFRACTION100
5.27-5.680.170116550.169105530X-RAY DIFFRACTION100
5.68-6.250.179916570.1818105555X-RAY DIFFRACTION100
6.25-7.160.198716580.1894105365X-RAY DIFFRACTION100
7.16-9.020.200816610.2025105530X-RAY DIFFRACTION100
9.02-207.60.213516530.2041104720X-RAY DIFFRACTION99

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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)。
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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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