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- PDB-5ndw: Crystal structure of aminoglycoside TC007 bound to the yeast 80S ... -

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基本情報

登録情報
データベース: PDB / ID: 5ndw
タイトルCrystal structure of aminoglycoside TC007 bound to the yeast 80S ribosome
要素
  • (40S ribosomal protein ...) x 31
  • (60S ribosomal protein ...) x 40
  • 18S ribosomal RNA
  • 25S ribosomal RNA
  • 5.8S ribosomal RNA
  • 5S ribosomal RNA
  • Guanine nucleotide-binding protein subunit beta-like protein
  • Suppressor protein STM1
  • Ubiquitin-40S ribosomal protein S31
  • Ubiquitin-60S ribosomal protein L40
キーワードRIBOSOME / translation / 40S / 60S / 80S / eukaryote / RNA-protein complex / inhibitor / antibiotic / aminoglycoside
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 regulation of glucose mediated signaling pathway / negative regulation of translational frameshifting / Negative regulators of DDX58/IFIH1 signaling / RMTs methylate histone arginines ...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 regulation of glucose mediated signaling pathway / negative regulation of translational frameshifting / Negative regulators of DDX58/IFIH1 signaling / RMTs methylate histone arginines / positive regulation of translational fidelity / Protein methylation / mTORC1-mediated signalling / Protein hydroxylation / ribosome-associated ubiquitin-dependent protein catabolic process / GDP-dissociation inhibitor activity / nonfunctional rRNA decay / hexon binding / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / pre-mRNA 5'-splice site binding / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / preribosome, small subunit precursor / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Ribosomal scanning and start codon recognition / response to cycloheximide / telomeric DNA binding / Major pathway of rRNA processing in the nucleolus and cytosol / mRNA destabilization / 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) / Formation of a pool of free 40S subunits / negative regulation of mRNA splicing, via spliceosome / preribosome, large subunit precursor / regulation of amino acid metabolic process / L13a-mediated translational silencing of Ceruloplasmin expression / translational elongation / ribosomal large subunit export from nucleus / 90S preribosome / G-protein alpha-subunit binding / positive regulation of protein kinase activity / TOR signaling / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / regulation of translational fidelity / Ub-specific processing proteases / protein-RNA complex assembly / ribosomal subunit export from nucleus / ribosomal small subunit export from nucleus / translation regulator activity / translational termination / translation repressor activity / 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) / DNA-(apurinic or apyrimidinic site) endonuclease activity / maturation of LSU-rRNA / telomere maintenance / cellular response to amino acid starvation / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rescue of stalled ribosome / ribosome assembly / ribosomal large subunit biogenesis / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / small-subunit processome / translational initiation / macroautophagy / protein kinase C binding / maintenance of translational fidelity / modification-dependent protein catabolic process / cytoplasmic stress granule / protein tag activity / rRNA processing / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / ribosome biogenesis / viral capsid / ribosome binding / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / ribosomal large subunit assembly / cytoplasmic translation / cytosolic large ribosomal subunit / negative regulation of translation / rRNA binding / ribosome / protein ubiquitination / structural constituent of ribosome / positive regulation of protein phosphorylation / G protein-coupled receptor signaling pathway / translation / negative regulation of gene expression / response to antibiotic / mRNA binding / ubiquitin protein ligase binding / negative regulation of apoptotic process / host cell nucleus
類似検索 - 分子機能
Stm1-like, N-terminal / Stm1 / Hyaluronan/mRNA-binding protein / Hyaluronan / mRNA binding family / Pre-hexon-linking protein VIII / Adenovirus hexon associated protein, protein VIII / : / Ribosomal protein 60S L18 and 50S L18e / : / Ribosomal protein S26e signature. ...Stm1-like, N-terminal / Stm1 / Hyaluronan/mRNA-binding protein / Hyaluronan / mRNA binding family / Pre-hexon-linking protein VIII / Adenovirus hexon associated protein, protein VIII / : / Ribosomal protein 60S L18 and 50S L18e / : / Ribosomal protein S26e signature. / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein S26e / Ribosomal protein S21e, conserved site / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Ribosomal protein S21e signature. / : / Ribosomal protein S12e signature. / Ribosomal protein S12e / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / Ribosomal protein L29e / Ribosomal L29e protein family / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein S2, eukaryotic / Small (40S) ribosomal subunit Asc1/RACK1 / S27a-like superfamily / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / 40S Ribosomal protein S10 / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein L27e, conserved site / Ribosomal protein L27e signature. / Ribosomal protein L44e signature. / Plectin/S10, N-terminal / Plectin/S10 domain / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / Ribosomal protein S25 / S25 ribosomal protein / Ribosomal protein L10e / Ribosomal protein L13e / Ribosomal protein S27a / Ribosomal protein L13e / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein L19, eukaryotic / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein S8e subdomain, eukaryotes / Ribosomal protein S17e, conserved site / Ribosomal protein S17e signature. / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein S30 / : / Ribosomal protein S30 / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein S7e signature. / : / Ribosomal protein L24e, conserved site / Ribosomal protein L19/L19e conserved site / Ribosomal protein L19e signature. / Ribosomal protein L24e signature. / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein L44e / Ribosomal protein L44 / Ribosomal protein L34e, conserved site / Ribosomal protein L34e signature. / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / : / Ribosomal protein S19e / Ribosomal protein S3Ae, conserved site / Ribosomal protein S19e / Ribosomal protein L30e signature 1. / Ribosomal protein L6e signature. / Ribosomal protein S3Ae signature. / Ribosomal_S19e / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal protein S27e signature. / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal L40e family / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S4e signature. / 40S ribosomal protein S4, C-terminal domain / 40S ribosomal protein S4 C-terminus / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Ribosomal protein L23/L25, N-terminal
類似検索 - ドメイン・相同性
TC007 / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / : / Small ribosomal subunit protein uS4A / Large ribosomal subunit protein uL15 ...TC007 / : / : / 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 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 / Pre-hexon-linking protein VIII / Small ribosomal subunit protein uS9A / Small ribosomal subunit protein uS13A / Large ribosomal subunit protein eL19A / Large ribosomal subunit protein uL29A / Small ribosomal subunit protein eS32A / Large ribosomal subunit protein uL4A / Large ribosomal subunit protein eL30 / 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 / Small ribosomal subunit protein eS12 / 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 / Large ribosomal subunit protein eL13A / 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 S288c (パン酵母)
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: 3.7 Å
データ登録者Prokhorova, I. / Djumagulov, M. / Urzhumtsev, A. / Yusupov, M. / Yusupova, G.
引用ジャーナル: Proc. Natl. Acad. Sci. U.S.A. / 年: 2017
タイトル: Aminoglycoside interactions and impacts on the eukaryotic ribosome.
著者: Prokhorova, I. / Altman, R.B. / Djumagulov, M. / Shrestha, J.P. / Urzhumtsev, A. / Ferguson, A. / Chang, C.T. / Yusupov, M. / Blanchard, S.C. / Yusupova, G.
履歴
登録2017年3月9日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02017年12月13日Provider: repository / タイプ: Initial release
改定 1.12017年12月20日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
改定 1.22017年12月27日Group: Database references / カテゴリ: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
改定 1.32024年5月8日Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_residues / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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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
1: 25S ribosomal RNA
2: 18S ribosomal RNA
3: 5S ribosomal RNA
4: 5.8S ribosomal RNA
5: 25S ribosomal RNA
6: 18S ribosomal RNA
7: 5S ribosomal RNA
8: 5.8S ribosomal RNA
C0: 40S ribosomal protein S10-A
c0: 40S ribosomal protein S10-A
C1: 40S ribosomal protein S11-A
c1: 40S ribosomal protein S11-A
C2: 40S ribosomal protein S12
c2: 40S ribosomal protein S12
C3: 40S ribosomal protein S13
c3: 40S ribosomal protein S13
C4: 40S ribosomal protein S14-B
c4: 40S ribosomal protein S14-B
C5: 40S ribosomal protein S15
c5: 40S ribosomal protein S15
C6: 40S ribosomal protein S16-A
c6: 40S ribosomal protein S16-A
C7: 40S ribosomal protein S17-A
c7: 40S ribosomal protein S17-A
C8: 40S ribosomal protein S18-A
c8: 40S ribosomal protein S18-A
C9: 40S ribosomal protein S19-A
c9: 40S ribosomal protein S19-A
d0: 40S ribosomal protein S20
D0: 40S ribosomal protein S20
d1: 40S ribosomal protein S21-A
D1: 40S ribosomal protein S21-A
d2: 40S ribosomal protein S22-A
D2: 40S ribosomal protein S22-A
d3: 40S ribosomal protein S23-A
D3: 40S ribosomal protein S23-A
d4: 40S ribosomal protein S24-A
D4: 40S ribosomal protein S24-A
d5: 40S ribosomal protein S25-A
D5: 40S ribosomal protein S25-A
d6: 40S ribosomal protein S26-B
D6: 40S ribosomal protein S26-B
d7: 40S ribosomal protein S27-A
D7: 40S ribosomal protein S27-A
d8: 40S ribosomal protein S28-A
D8: 40S ribosomal protein S28-A
d9: 40S ribosomal protein S29-A
D9: 40S ribosomal protein S29-A
e0: 40S ribosomal protein S30-A
E0: 40S ribosomal protein S30-A
e1: Ubiquitin-40S ribosomal protein S31
E1: Ubiquitin-40S ribosomal protein S31
l2: 60S ribosomal protein L2-A
L2: 60S ribosomal protein L2-A
l3: 60S ribosomal protein L3
L3: 60S ribosomal protein L3
l4: 60S ribosomal protein L4-A
L4: 60S ribosomal protein L4-A
l5: 60S ribosomal protein L5
L5: 60S ribosomal protein L5
l6: 60S ribosomal protein L6-A
L6: 60S ribosomal protein L6-A
l7: 60S ribosomal protein L7-A
L7: 60S ribosomal protein L7-A
l8: 60S ribosomal protein L8-A
L8: 60S ribosomal protein L8-A
l9: 60S ribosomal protein L9-A
L9: 60S ribosomal protein L9-A
m0: 60S ribosomal protein L10
M0: 60S ribosomal protein L10
m1: 60S ribosomal protein L11-B
M1: 60S ribosomal protein L11-B
m3: 60S ribosomal protein L13-A
M3: 60S ribosomal protein L13-A
m4: 60S ribosomal protein L14-A
M4: 60S ribosomal protein L14-A
m5: 60S ribosomal protein L15-A
M5: 60S ribosomal protein L15-A
m6: 60S ribosomal protein L16-A
M6: 60S ribosomal protein L16-A
m7: 60S ribosomal protein L17-A
M7: 60S ribosomal protein L17-A
m8: 60S ribosomal protein L18-A
M8: 60S ribosomal protein L18-A
m9: 60S ribosomal protein L19-A
M9: 60S ribosomal protein L19-A
n0: 60S ribosomal protein L20-A
N0: 60S ribosomal protein L20-A
n1: 60S ribosomal protein L21-A
N1: 60S ribosomal protein L21-A
n2: 60S ribosomal protein L22-A
N2: 60S ribosomal protein L22-A
n3: 60S ribosomal protein L23-A
N3: 60S ribosomal protein L23-A
n4: 60S ribosomal protein L24-A
N4: 60S ribosomal protein L24-A
n5: 60S ribosomal protein L25
N5: 60S ribosomal protein L25
n6: 60S ribosomal protein L26-A
N6: 60S ribosomal protein L26-A
n7: 60S ribosomal protein L27-A
N7: 60S ribosomal protein L27-A
n8: 60S ribosomal protein L28
N8: 60S ribosomal protein L28
n9: 60S ribosomal protein L29
N9: 60S ribosomal protein L29
o0: 60S ribosomal protein L30
O0: 60S ribosomal protein L30
o1: 60S ribosomal protein L31-A
O1: 60S ribosomal protein L31-A
o2: 60S ribosomal protein L32
O2: 60S ribosomal protein L32
o3: 60S ribosomal protein L33-A
O3: 60S ribosomal protein L33-A
o4: 60S ribosomal protein L34-A
O4: 60S ribosomal protein L34-A
o5: 60S ribosomal protein L35-A
O5: 60S ribosomal protein L35-A
o6: 60S ribosomal protein L36-A
O6: 60S ribosomal protein L36-A
o7: 60S ribosomal protein L37-A
O7: 60S ribosomal protein L37-A
o8: 60S ribosomal protein L38
O8: 60S ribosomal protein L38
o9: 60S ribosomal protein L39
O9: 60S ribosomal protein L39
q0: Ubiquitin-60S ribosomal protein L40
Q0: Ubiquitin-60S ribosomal protein L40
q1: 60S ribosomal protein L41-A
Q1: 60S ribosomal protein L41-A
q2: 60S ribosomal protein L42-A
Q2: 60S ribosomal protein L42-A
q3: 60S ribosomal protein L43-A
Q3: 60S ribosomal protein L43-A
S0: 40S ribosomal protein S0-A
s0: 40S ribosomal protein S0-A
S1: 40S ribosomal protein S1-A
s1: 40S ribosomal protein S1-A
S2: 40S ribosomal protein S2
s2: 40S ribosomal protein S2
S3: 40S ribosomal protein S3
s3: 40S ribosomal protein S3
S4: 40S ribosomal protein S4-A
s4: 40S ribosomal protein S4-A
S5: 40S ribosomal protein S5
s5: 40S ribosomal protein S5
S6: 40S ribosomal protein S6-A
s6: 40S ribosomal protein S6-A
s7: 40S ribosomal protein S7-A
S7: 40S ribosomal protein S7-A
s8: 40S ribosomal protein S8-A
S8: 40S ribosomal protein S8-A
S9: 40S ribosomal protein S9-A
s9: 40S ribosomal protein S9-A
sM: Suppressor protein STM1
SM: Suppressor protein STM1
sR: Guanine nucleotide-binding protein subunit beta-like protein
SR: 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)6,188,1071565
ポリマ－6,141,731158
非ポリマー46,3761407
水30,7161705
1
5: 25S ribosomal RNA
6: 18S ribosomal RNA
7: 5S ribosomal RNA
8: 5.8S ribosomal RNA
c0: 40S ribosomal protein S10-A
c1: 40S ribosomal protein S11-A
c2: 40S ribosomal protein S12
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: 40S ribosomal protein S20
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: 40S ribosomal protein S26-B
d7: 40S ribosomal protein S27-A
d8: 40S ribosomal protein S28-A
d9: 40S ribosomal protein S29-A
e0: 40S ribosomal protein S30-A
e1: Ubiquitin-40S ribosomal protein S31
l2: 60S ribosomal protein L2-A
l3: 60S ribosomal protein L3
l4: 60S ribosomal protein L4-A
l5: 60S ribosomal protein L5
l6: 60S ribosomal protein L6-A
l7: 60S ribosomal protein L7-A
l8: 60S ribosomal protein L8-A
l9: 60S ribosomal protein L9-A
m0: 60S ribosomal protein L10
m1: 60S ribosomal protein L11-B
m3: 60S ribosomal protein L13-A
m4: 60S ribosomal protein L14-A
m5: 60S ribosomal protein L15-A
m6: 60S ribosomal protein L16-A
m7: 60S ribosomal protein L17-A
m8: 60S ribosomal protein L18-A
m9: 60S ribosomal protein L19-A
n0: 60S ribosomal protein L20-A
n1: 60S ribosomal protein L21-A
n2: 60S ribosomal protein L22-A
n3: 60S ribosomal protein L23-A
n4: 60S ribosomal protein L24-A
n5: 60S ribosomal protein L25
n6: 60S ribosomal protein L26-A
n7: 60S ribosomal protein L27-A
n8: 60S ribosomal protein L28
n9: 60S ribosomal protein L29
o0: 60S ribosomal protein L30
o1: 60S ribosomal protein L31-A
o2: 60S ribosomal protein L32
o3: 60S ribosomal protein L33-A
o4: 60S ribosomal protein L34-A
o5: 60S ribosomal protein L35-A
o6: 60S ribosomal protein L36-A
o7: 60S ribosomal protein L37-A
o8: 60S ribosomal protein L38
o9: 60S ribosomal protein L39
q0: Ubiquitin-60S ribosomal protein L40
q1: 60S ribosomal protein L41-A
q2: 60S ribosomal protein L42-A
q3: 60S ribosomal protein L43-A
s0: 40S ribosomal protein S0-A
s1: 40S ribosomal protein S1-A
s2: 40S ribosomal protein S2
s3: 40S ribosomal protein S3
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
sM: Suppressor protein STM1
sR: 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)3,092,532768
ポリマ－3,070,86579
非ポリマー21,667689
水55831
タイプ名称対称操作数
identity operation1_555x,y,z1
手法PISA
2
1: 25S ribosomal RNA
2: 18S ribosomal RNA
3: 5S ribosomal RNA
4: 5.8S ribosomal RNA
C0: 40S ribosomal protein S10-A
C1: 40S ribosomal protein S11-A
C2: 40S ribosomal protein S12
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: 40S ribosomal protein S20
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: 40S ribosomal protein S26-B
D7: 40S ribosomal protein S27-A
D8: 40S ribosomal protein S28-A
D9: 40S ribosomal protein S29-A
E0: 40S ribosomal protein S30-A
E1: Ubiquitin-40S ribosomal protein S31
L2: 60S ribosomal protein L2-A
L3: 60S ribosomal protein L3
L4: 60S ribosomal protein L4-A
L5: 60S ribosomal protein L5
L6: 60S ribosomal protein L6-A
L7: 60S ribosomal protein L7-A
L8: 60S ribosomal protein L8-A
L9: 60S ribosomal protein L9-A
M0: 60S ribosomal protein L10
M1: 60S ribosomal protein L11-B
M3: 60S ribosomal protein L13-A
M4: 60S ribosomal protein L14-A
M5: 60S ribosomal protein L15-A
M6: 60S ribosomal protein L16-A
M7: 60S ribosomal protein L17-A
M8: 60S ribosomal protein L18-A
M9: 60S ribosomal protein L19-A
N0: 60S ribosomal protein L20-A
N1: 60S ribosomal protein L21-A
N2: 60S ribosomal protein L22-A
N3: 60S ribosomal protein L23-A
N4: 60S ribosomal protein L24-A
N5: 60S ribosomal protein L25
N6: 60S ribosomal protein L26-A
N7: 60S ribosomal protein L27-A
N8: 60S ribosomal protein L28
N9: 60S ribosomal protein L29
O0: 60S ribosomal protein L30
O1: 60S ribosomal protein L31-A
O2: 60S ribosomal protein L32
O3: 60S ribosomal protein L33-A
O4: 60S ribosomal protein L34-A
O5: 60S ribosomal protein L35-A
O6: 60S ribosomal protein L36-A
O7: 60S ribosomal protein L37-A
O8: 60S ribosomal protein L38
O9: 60S ribosomal protein L39
Q0: Ubiquitin-60S ribosomal protein L40
Q1: 60S ribosomal protein L41-A
Q2: 60S ribosomal protein L42-A
Q3: 60S ribosomal protein L43-A
S0: 40S ribosomal protein S0-A
S1: 40S ribosomal protein S1-A
S2: 40S ribosomal protein S2
S3: 40S ribosomal protein S3
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
SM: Suppressor protein STM1
SR: 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)3,095,574797
ポリマ－3,070,86579
非ポリマー24,709718
水66737
タイプ名称対称操作数
identity operation1_555x,y,z1
手法PISA
単位格子
Length a, b, c (Å)442.140, 298.760, 299.770
Angle α, β, γ (deg.)90.000, 99.490, 90.000
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 15263748

#1: 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 S288c (パン酵母)
参照: REF: 831416132
#2: RNA鎖 18S 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 S288c (パン酵母)
参照: REF: 831416132
#3: 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: 1039024062
#4: 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: 1102645687

+
40S ribosomal protein ... , 31種, 62分子 C0c0C1c1C2c2C3c3C4c4C5c5C6c6C7c7C8c8C9c9d0D0d1D1d2D2d3D3d4D4...

#5: タンパク質 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 (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 参照: UniProt: Q08745
#6: タンパク質 40S ribosomal protein S11-A / RP41 / S18 / YS12


分子量: 17785.934 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 参照: UniProt: P0CX47
#7: タンパク質 40S ribosomal protein S12


分子量: 15488.631 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 参照: UniProt: P48589
#8: タンパク質 40S ribosomal protein S13 / S27a / YS15


分子量: 16928.748 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 参照: UniProt: P05756
#9: タンパク質 40S ribosomal protein S14-B / RP59B


分子量: 13560.528 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 参照: UniProt: P39516
#10: タンパク質 40S ribosomal protein S15 / RIG protein / RP52 / S21 / YS21


分子量: 15900.712 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 参照: UniProt: Q01855
#11: タンパク質 40S ribosomal protein S16-A / RP61R


分子量: 15659.216 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 参照: UniProt: P0CX51
#12: タンパク質 40S ribosomal protein S17-A / RP51A


分子量: 15820.413 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 参照: UniProt: P02407
#13: タンパク質 40S ribosomal protein S18-A


分子量: 16940.443 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 参照: UniProt: P0CX55
#14: タンパク質 40S ribosomal protein S19-A / RP55A / S16a / YP45 / YS16A


分子量: 15810.930 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 参照: UniProt: P07280
#15: タンパク質 40S ribosomal protein S20


分子量: 12190.175 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 参照: UniProt: P38701
#16: タンパク質 40S ribosomal protein S21-A / S26 / YS25


分子量: 9758.829 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 参照: UniProt: P0C0V8
#17: タンパク質 40S ribosomal protein S22-A / RP50 / S24 / YP58 / YS22


分子量: 14518.867 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 参照: UniProt: P0C0W1
#18: タンパク質 40S ribosomal protein S23-A / RP37 / S28 / YS14


分子量: 15942.699 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 参照: UniProt: P0CX29
#19: タンパク質 40S ribosomal protein S24-A / RP50


分子量: 15231.650 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 参照: UniProt: P0CX31
#20: タンパク質 40S ribosomal protein S25-A / RP45 / S31 / YS23


分子量: 8001.377 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 参照: UniProt: Q3E792
#21: タンパク質 40S ribosomal protein S26-B


分子量: 11022.989 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 参照: UniProt: P39939
#22: タンパク質 40S ribosomal protein S27-A / RP61 / YS20


分子量: 8762.195 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 参照: UniProt: P35997
#23: タンパク質 40S ribosomal protein S28-A / S33 / YS27


分子量: 7116.281 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 参照: UniProt: Q3E7X9
#24: タンパク質 40S ribosomal protein S29-A / S36 / YS29


分子量: 6335.303 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 参照: UniProt: P41057
#25: タンパク質 40S ribosomal protein S30-A


分子量: 6878.217 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 参照: UniProt: P0CX33
#68: タンパク質 40S ribosomal protein S0-A / Nucleic acid-binding protein NAB1A


分子量: 22811.074 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 参照: UniProt: P32905
#69: タンパク質 40S ribosomal protein S1-A / RP10A


分子量: 24498.365 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 参照: UniProt: P33442
#70: タンパク質 40S ribosomal protein S2 / Omnipotent suppressor protein SUP44 / RP12 / S4 / YS5


分子量: 23212.979 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 参照: UniProt: P25443
#71: タンパク質 40S ribosomal protein S3 / RP13 / YS3


分子量: 24702.791 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 参照: UniProt: P05750
#72: タンパク質 40S ribosomal protein S4-A / RP5 / S7 / YS6


分子量: 29338.133 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 参照: UniProt: P0CX35
#73: タンパク質 40S ribosomal protein S5 / RP14 / S2 / YS8


分子量: 22908.338 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 参照: UniProt: P26783
#74: タンパク質 40S ribosomal protein S6-A / RP9 / S10 / YS4


分子量: 27054.486 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 参照: UniProt: P0CX37
#75: タンパク質 40S ribosomal protein S7-A / RP30 / RP40


分子量: 21000.492 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 参照: UniProt: P26786
#76: タンパク質 40S ribosomal protein S8-A / RP19 / S14 / YS9


分子量: 22537.803 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 参照: UniProt: P0CX39
#77: タンパク質 40S ribosomal protein S9-A / RP21 / S13 / YP28 / YS11


分子量: 21210.662 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 参照: UniProt: O13516

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タンパク質 , 4種, 8分子 e1E1q0Q0sMSMsRSR

#26: タンパク質 Ubiquitin-40S ribosomal protein S31


分子量: 8388.049 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 参照: UniProt: P05759
#64: タンパク質 Ubiquitin-60S ribosomal protein L40


分子量: 6032.321 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 参照: UniProt: P0CH08
#78: 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: 29916.814 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 参照: UniProt: P39015
#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


分子量: 34710.023 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 参照: UniProt: P38011

+
60S ribosomal protein ... , 40種, 80分子 l2L2l3L3l4L4l5L5l6L6l7L7l8L8l9L9m0M0m1M1m3M3m4M4m5M5m6M6m7M7...

#27: タンパク質 60S ribosomal protein L2-A / L5 / RP8 / YL6


分子量: 27217.289 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 参照: UniProt: P0CX45
#28: タンパク質 60S ribosomal protein L3 / Maintenance of killer protein 8 / RP1 / Trichodermin resistance protein / YL1


分子量: 43719.602 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 参照: UniProt: P14126
#29: タンパク質 60S ribosomal protein L4-A / L2 / RP2 / YL2


分子量: 39027.926 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 参照: UniProt: P10664
#30: タンパク質 60S ribosomal protein L5 / L1 / L1a / Ribosomal 5S RNA-binding protein / YL3


分子量: 33633.633 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 参照: UniProt: P26321
#31: タンパク質 60S ribosomal protein L6-A / L17 / 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 (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 参照: UniProt: Q02326
#32: タンパク質 60S ribosomal protein L7-A / L6 / RP11 / YL8


分子量: 25341.480 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 参照: UniProt: P05737
#33: タンパク質 60S ribosomal protein L8-A / L4 / L4-2 / L7a-1 / Maintenance of killer protein 7 / RP6 / YL5


分子量: 25814.998 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 参照: UniProt: P17076
#34: タンパク質 60S ribosomal protein L9-A / L8 / 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 (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 参照: UniProt: P05738
#35: タンパク質 60S ribosomal protein L10 / L9 / 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 (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 参照: UniProt: P41805
#36: タンパク質 60S ribosomal protein L11-B / L16 / RP39 / YL22


分子量: 19266.082 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 参照: UniProt: Q3E757
#37: タンパク質 60S ribosomal protein L13-A


分子量: 21956.312 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 参照: UniProt: Q12690
#38: タンパク質 60S ribosomal protein L14-A


分子量: 15063.870 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 参照: UniProt: P36105
#39: タンパク質 60S ribosomal protein L15-A / L13 / RP15R / YL10 / YP18


分子量: 24351.162 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 参照: UniProt: P05748
#40: タンパク質 60S ribosomal protein L16-A / L13a / L21 / RP22 / YL15


分子量: 22028.951 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 参照: UniProt: P26784
#41: タンパク質 60S ribosomal protein L17-A / L20A / YL17


分子量: 20589.518 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 参照: UniProt: P05740
#42: タンパク質 60S ribosomal protein L18-A / RP28


分子量: 20478.059 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 参照: UniProt: P0CX49
#43: タンパク質 60S ribosomal protein L19-A / L23 / RP15L / RP33 / YL14


分子量: 21631.121 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 参照: UniProt: P0CX82
#44: タンパク質 60S ribosomal protein L20-A / L18a


分子量: 20478.852 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 参照: UniProt: P0CX23
#45: タンパク質 60S ribosomal protein L21-A


分子量: 18148.066 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 参照: UniProt: Q02753
#46: タンパク質 60S ribosomal protein L22-A / L1c / RP4 / YL31


分子量: 11263.863 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 参照: UniProt: P05749
#47: タンパク質 60S ribosomal protein L23-A / L17a / YL32


分子量: 14362.755 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 参照: UniProt: P0CX41
#48: タンパク質 60S ribosomal protein L24-A / L30 / 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 (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 参照: UniProt: P04449
#49: タンパク質 60S ribosomal protein L25 / RP16L / YL25 / YP42'


分子量: 13771.176 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 参照: UniProt: P04456
#50: タンパク質 60S ribosomal protein L26-A / L33 / YL33


分子量: 14134.588 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 参照: UniProt: P05743
#51: タンパク質 60S ribosomal protein L27-A


分子量: 15437.166 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 参照: UniProt: P0C2H6
#52: タンパク質 60S ribosomal protein L28 / L27a / L29 / RP44 / RP62 / YL24


分子量: 16630.471 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 参照: UniProt: P02406
#53: タンパク質 60S ribosomal protein L29 / YL43


分子量: 6560.688 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 参照: UniProt: P05747
#54: タンパク質 60S ribosomal protein L30 / L32 / RP73 / YL38


分子量: 10902.664 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 参照: UniProt: P14120
#55: タンパク質 60S ribosomal protein L31-A / L34 / YL28


分子量: 12649.754 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 参照: UniProt: P0C2H8
#56: タンパク質 60S ribosomal protein L32


分子量: 14478.054 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 参照: UniProt: P38061
#57: タンパク質 60S ribosomal protein L33-A / L37 / RP47 / YL37


分子量: 12045.935 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 参照: UniProt: P05744
#58: タンパク質 60S ribosomal protein L34-A


分子量: 12608.831 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 参照: UniProt: P87262
#59: タンパク質 60S ribosomal protein L35-A


分子量: 13811.444 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 参照: UniProt: P0CX84
#60: タンパク質 60S ribosomal protein L36-A / L39 / YL39


分子量: 11020.063 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 参照: UniProt: P05745
#61: タンパク質 60S ribosomal protein L37-A / L43 / YL35 / YP55


分子量: 9746.199 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 参照: UniProt: P49166
#62: タンパク質 60S ribosomal protein L38


分子量: 8714.363 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 参照: UniProt: P49167
#63: タンパク質・ペプチド 60S ribosomal protein L39 / L46 / YL40


分子量: 6227.444 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 参照: UniProt: P04650
#65: タンパク質・ペプチド 60S ribosomal protein L41-A / 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) / 株: ATCC 204508 / S288c / 参照: UniProt: P0CX86
#66: タンパク質 60S ribosomal protein L42-A / L41 / YL27 / YP44


分子量: 12115.462 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 参照: UniProt: P0CX27
#67: タンパク質 60S ribosomal protein L43-A / L37a / YL35


分子量: 9981.756 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c / 参照: UniProt: P0CX25

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非ポリマー , 4種, 3112分子

#80: 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: 1365 / 由来タイプ: 天然 / 式: Mg
#81: 化合物...
ChemComp-8UZ / TC007 / 3α-[(2,6-ジアミノ-2,6-ジデオキシ-α-D-グルコピラノシル)オキシ]-2β-[(3-アミノ-3-デオキシ(以下略)


分子量: 483.514 Da / 分子数: 25 / 由来タイプ: 合成 / 式: C18H37N5O10
#82: 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
#83: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 1705 / 由来タイプ: 天然 / 式: H2O

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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: 3.18 Å3/Da / 溶媒含有率: 61.32 %
結晶化温度: 277 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 7
詳細: PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine

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データ収集

回折平均測定温度: 90 K
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: 2016年4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: 3.7→147.832 Å / Num. obs: 814535 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / 冗長度: 47.714 % / Biso Wilson estimate: 133.94 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.303 / Rrim(I) all: 0.306 / Χ2: 0.974 / Net I/σ(I): 13.97 / Num. measured all: 38865024 / Scaling rejects: 3776
反射 シェル

Diffraction-ID: 1

解像度 (Å)冗長度 (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
3.7-3.86.9241.7650.9843058462468621850.3611.90499.5
3.8-3.913.6161.8371.4876486156192561750.5841.907100
3.9-424.0091.8542.08121977250817508040.7261.894100
4-4.122.5881.5532.47103862445985459810.7731.589100
4.1-4.230.6551.7532.95127667041651416470.8341.782100
4.2-4.337.5021.6333.54141858337828378270.891.656100
4.3-4.454.1751.5944.4187308934587345750.9191.609100
4.4-4.559.5931.4575.1187896331527315300.9391.47100
4.5-562.7481.0957.0576933031226321226070.9671.103100
5-5.564.7240.74110.74530998782049820410.9850.747100
5.5-661.2770.52514.21349444357037570270.9920.529100
6-7.565.2050.29322.6609284593450934410.9970.295100
7.5-1065.9070.13444.32374655856856568460.9990.135100
10-2562.7210.06775.342455592391653915110.068100
25-5064.5780.045116.211548592404239810.04699.8
50-7557.5810.063115.241318625422910.06390.2
75-10047.750.073105.42101624410.07571
100-14541.3330.08195.6899231240.9960.08277.4
145-15040.00529.84124310.00675
147.832-15013

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解析

ソフトウェア
名称バージョン分類
PHENIX精密化
XSCALEデータスケーリング
PDB_EXTRACT3.22データ抽出
XDSデータ削減
PHENIX位相決定
精密化構造決定の手法: 分子置換 / 解像度: 3.7→147.832 Å / SU ML: 0.46 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 23.77 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2347 16288 2 %
Rwork0.1919 798024 -
obs0.1927 814312 99.93 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL
原子変位パラメータBiso max: 457.07 Å2 / Biso mean: 150.1253 Å2 / Biso min: 63.95 Å2
精密化ステップサイクル: final / 解像度: 3.7→147.832 Å
タンパク質核酸リガンド溶媒全体
原子数177720 218488 3803 103 400114
Biso mean--110.87 101.75 -
残基数----32778
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.009427946
X-RAY DIFFRACTIONf_angle_d1.382627207
X-RAY DIFFRACTIONf_chiral_restr0.06178573
X-RAY DIFFRACTIONf_plane_restr0.00741232
X-RAY DIFFRACTIONf_dihedral_angle_d20.55192859
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.7-3.7420.3445370.3348262702680799
3.742-3.78610.33785410.30522653927080100
3.7861-3.83220.32425410.29322648027021100
3.8322-3.88080.31955420.28562656227104100
3.8808-3.93180.29725410.26562651727058100
3.9318-3.98570.29695430.24872661327156100
3.9857-4.04260.2975410.2442649927040100
4.0426-4.1030.28195420.23852656027102100
4.103-4.16710.27625400.22682653927079100
4.1671-4.23540.26245440.21762657427118100
4.2354-4.30850.24575410.21342651327054100
4.3085-4.38680.25455430.20852659727140100
4.3868-4.47120.24845430.2032661127154100
4.4712-4.56250.2415410.19812654727088100
4.5625-4.66170.2365420.19122651527057100
4.6617-4.77010.24125430.19262663127174100
4.7701-4.88940.24395420.1872657327115100
4.8894-5.02160.21615420.17122658227124100
5.0216-5.16940.22885440.17232663927183100
5.1694-5.33630.20455440.16152660727151100
5.3363-5.5270.22355430.16632665727200100
5.527-5.74830.2195430.17192657427117100
5.7483-6.00990.22935420.1692661027152100
6.0099-6.32680.21755460.1582668527231100
6.3268-6.72320.20815420.15992663127173100
6.7232-7.24220.21145450.15592669827243100
7.2422-7.9710.2075460.15622673627282100
7.971-9.12430.19435450.15972670927254100
9.1243-11.4950.19255480.16052679527343100
11.495-147.95050.24255510.2133269612751299
精密化 TLS

S33: -0 Å ° / 手法: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0960.03220.01540.03140.0150.00840.0882-0.0484-0.0083-0.0145-0.08380.0237-0.01130.00860.7746-0.0304-0.03290.7334-0.10690.8252-1.13150.996871.231
20.0819-0.0059-0.02090.0311-0.00790.00570.05230.0575-0.04070.0161-0.0706-0.0107-0.02670.00220.809-0.0060.00530.84790.00310.7022183.49467.3142225.9243
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth seq-ID
1X-RAY DIFFRACTION1segid *A0
2X-RAY DIFFRACTION2segid *B0

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万見について

-
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

-
2020年8月12日: 新型コロナ情報

新型コロナ情報

URL: https://pdbj.org/emnavi/covid19.php

新ページ: EM Navigatorに新型コロナウイルスの特設ページを開設しました。

関連情報:Covid-19情報 / 2020年3月5日: 新型コロナウイルスの構造データ

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2020年3月5日: 新型コロナウイルスの構造データ

新型コロナウイルスの構造データ

関連情報:万見生物種 / 2020年8月12日: 新型コロナ情報

外部リンク:COVID-19特集ページ - PDBj / 今月の分子2020年2月：コロナウイルスプロテーアーゼ

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2019年1月31日: EMDBのIDの桁数の変更

EMDBのIDの桁数の変更

  • EMDBエントリに付与されているアクセスコード(EMDB-ID)は4桁の数字(例、EMD-1234)でしたが、間もなく枯渇します。これまでの4桁のID番号は4桁のまま変更されませんが、4桁の数字を使い切った後に発行されるIDは5桁以上の数字(例、EMD-12345)になります。5桁のIDは2019年の春頃から発行される見通しです。
  • EM Navigator/万見では、接頭語「EMD-」は省略されています。

関連情報:Q: 「EMD」とは何ですか？ / 万見/EM NavigatorにおけるID/アクセスコードの表記

外部リンク:EMDB Accession Codes are Changing Soon! / PDBjへお問い合わせ

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2017年7月12日: PDB大規模アップデート

PDB大規模アップデート

  • 新バージョンのPDBx/mmCIF辞書形式に基づくデータがリリースされました。
  • 今回の更新はバージョン番号が4から5になる大規模なもので、全エントリデータの書き換えが行われる「Remediation」というアップデートに該当します。
  • このバージョンアップで、電子顕微鏡の実験手法に関する多くの項目の書式が改定されました(例：em_softwareなど)。
  • EM NavigatorとYorodumiでも、この改定に基づいた表示内容になります。

外部リンク:wwPDB Remediation / OneDepデータ基準に準拠した、より強化された内容のモデル構造ファイルが、PDBアーカイブで公開されました。

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万見 (Yorodumi)

幾万の構造データを、幾万の視点から

  • 万見(Yorodumi)は、EMDB/PDB/SASBDBなどの構造データを閲覧するためのページです。
  • EM Navigatorの詳細ページの後継、Omokage検索のフロントエンドも兼ねています。

関連情報:EMDB / PDB / SASBDB / 3つのデータバンクの比較 / 万見検索 / 2016年8月31日: 新しいEM Navigatorと万見 / 万見文献 / Jmol/JSmol / 機能・相同性情報 / 新しいEM Navigatorと万見の変更点

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