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- PDB-8q7z: Structure of the G. gallus 80S non-rotated ribosome -

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基本情報

登録情報
データベース: PDB / ID: 8q7z
タイトルStructure of the G. gallus 80S non-rotated ribosome
要素
  • (40S ribosomal protein ...) x 18
  • (60S ribosomal protein ...) x 16
  • (Large ribosomal subunit protein ...) x 11
  • (Ribosomal protein ...) x 19
  • (Small ribosomal subunit protein ...) x 8
  • 18S rRNA
  • 28S rRNA
  • 5.8S rRNA
  • 5S rRNA
  • DNA-(apurinic or apyrimidinic site) lyase
  • Phe tRNA
  • Ubiquitin
  • Ubiquitin-60S ribosomal protein L40
キーワードRIBOSOME / translation
機能・相同性
機能・相同性情報


TNFR1-mediated ceramide production / Major pathway of rRNA processing in the nucleolus and cytosol / Protein hydroxylation / Translesion synthesis by REV1 / Recognition of DNA damage by PCNA-containing replication complex / Translesion Synthesis by POLH / Activation of NF-kappaB in B cells / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Spry regulation of FGF signaling / Downregulation of ERBB2:ERBB3 signaling ...TNFR1-mediated ceramide production / Major pathway of rRNA processing in the nucleolus and cytosol / Protein hydroxylation / Translesion synthesis by REV1 / Recognition of DNA damage by PCNA-containing replication complex / Translesion Synthesis by POLH / Activation of NF-kappaB in B cells / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Spry regulation of FGF signaling / Downregulation of ERBB2:ERBB3 signaling / APC/C:Cdc20 mediated degradation of Cyclin B / Autodegradation of Cdh1 by Cdh1:APC/C / SCF-beta-TrCP mediated degradation of Emi1 / APC/C:Cdc20 mediated degradation of Securin / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / APC-Cdc20 mediated degradation of Nek2A / EGFR downregulation / SCF(Skp2)-mediated degradation of p27/p21 / Degradation of beta-catenin by the destruction complex / TCF dependent signaling in response to WNT / Downstream TCR signaling / NRIF signals cell death from the nucleus / p75NTR recruits signalling complexes / NF-kB is activated and signals survival / Activated NOTCH1 Transmits Signal to the Nucleus / Downregulation of SMAD2/3:SMAD4 transcriptional activity / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / Senescence-Associated Secretory Phenotype (SASP) / FCERI mediated NF-kB activation / Regulation of innate immune responses to cytosolic DNA / Autodegradation of the E3 ubiquitin ligase COP1 / RAD18 and ubiquitinated PCNA-mediated recruitment of translesion polymerases / Nucleotide Excision Repair / Deactivation of the beta-catenin transactivating complex / TRAF6 mediated induction of proinflammatory cytokines / TAK1 activates NFkB by phosphorylation and activation of IKKs complex / NFkB activation mediated by RIP1 complexed with activated TLR3 / Activated TAK1 mediates p38 MAP kinase phosphorylation / Activated TAK1 mediates Jun kinases (JNK) phosphorylation and activation / activated TAK1 mediates p38 MAPK activation / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / AUF1 (hnRNP D0) binds and destabilizes mRNA / Degradation of AXIN / Degradation of DVL / Regulation of FZD by ubiquitination / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Regulation of TNFR1 signaling / TNFR1-induced NF-kappa-B signaling pathway / Hedgehog ligand biogenesis / CLEC7A (Dectin-1) signaling / Degradation of GLI1 by the proteasome / GLI3 is processed to GLI3R by the proteasome / Hedgehog 'on' state / Negative regulation of FGFR1 signaling / Negative regulation of FGFR2 signaling / Negative regulation of FGFR3 signaling / Negative regulation of FGFR4 signaling / Translesion synthesis by POLK / Translesion synthesis by POLI / Termination of translesion DNA synthesis / TNFR2 non-canonical NF-kB pathway / Negative regulation of MAPK pathway / Regulation of necroptotic cell death / MAP3K8 (TPL2)-dependent MAPK1/3 activation / HDR through Homologous Recombination (HRR) / Josephin domain DUBs / Ovarian tumor domain proteases / Formation of Incision Complex in GG-NER / Gap-filling DNA repair synthesis and ligation in GG-NER / Dual Incision in GG-NER / NFkB and MAPK activation mediated by TRAF6 upon TLR7 or TLR21 stimulation / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / Regulation of TP53 Activity through Phosphorylation / Regulation of TP53 Degradation / Regulation of TP53 Activity through Methylation / Negative regulation of MET activity / Assembly of the pre-replicative complex / CDK-mediated phosphorylation and removal of Cdc6 / Translation initiation complex formation / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Downregulation of ERBB2 signaling / VLDLR internalisation and degradation / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / E3 ubiquitin ligases ubiquitinate target proteins / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Regulation of RUNX2 expression and activity / Regulation of PTEN localization / Regulation of PTEN stability and activity / Neddylation / ER Quality Control Compartment (ERQC) / NOTCH3 Activation and Transmission of Signal to the Nucleus / Peroxisomal protein import / Endosomal Sorting Complex Required For Transport (ESCRT) / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE)
類似検索 - 分子機能
Glycerate/sugar phosphate transporter, conserved site / : / glpT family of transporters signature. / Major facilitator superfamily / Major Facilitator Superfamily / 40S ribosomal protein SA / 40S ribosomal protein SA, C-terminal domain / 40S ribosomal protein SA C-terminus / Ribosomal protein L6, N-terminal / Ribosomal protein L6, N-terminal domain ...Glycerate/sugar phosphate transporter, conserved site / : / glpT family of transporters signature. / Major facilitator superfamily / Major Facilitator Superfamily / 40S ribosomal protein SA / 40S ribosomal protein SA, C-terminal domain / 40S ribosomal protein SA C-terminus / Ribosomal protein L6, N-terminal / Ribosomal protein L6, N-terminal domain / Ribosomal protein L30e / Ribosomal protein L2, archaeal-type / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / Ribosomal protein L28e / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / : / Ribosomal protein S26e signature. / MFS transporter superfamily / metallochaperone-like domain / Ribosomal protein L41 / Ribosomal protein L41 / TRASH domain / 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 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 / Ribosomal protein L22e / Ribosomal protein L22e superfamily / S27a-like 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 / Ribosomal protein L10e, conserved site / Plectin/S10 domain / Ribosomal protein L10e signature. / Ribosomal protein S25 / S25 ribosomal protein / Ribosomal protein L10e / Ribosomal protein L13e / Ribosomal protein L13e / Ribosomal protein L19, eukaryotic / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S27a / 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 / : / 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 L44e / Ribosomal protein L44 / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein L34e, conserved site / Ribosomal protein L34e signature. / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / : / Ribosomal protein L30e signature 1. / Ribosomal protein L6e signature. / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal protein S3Ae, conserved site / Ribosomal protein S3Ae signature. / 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. / Ribosomal_L40e
類似検索 - ドメイン・相同性
: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein eS32 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein uL22 ...: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein eS32 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein uL22 / 60S ribosomal protein L29 / Large ribosomal subunit protein eL31 / Large ribosomal subunit protein eL34 / 40S ribosomal protein S27 / Small ribosomal subunit protein eS28 / Small ribosomal subunit protein uS8 / Large ribosomal subunit protein eL24 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein eS1 / Large ribosomal subunit protein eL33 / Large ribosomal subunit protein eL42 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein uS14 / Large ribosomal subunit protein uL14 / Small ribosomal subunit protein eS21 / Small ribosomal subunit protein eS25 / Small ribosomal subunit protein uS4 / Large ribosomal subunit protein eL38 / 60S ribosomal protein L32 / Ribosomal protein S10 / Ribosomal protein L37 / 40S ribosomal protein S8 / 40S ribosomal protein S24 / Small ribosomal subunit protein uS10 / Large ribosomal subunit protein uL2 / 40S ribosomal protein S7 / DNA-(apurinic or apyrimidinic site) lyase / 60S ribosomal protein L18a / Ribosomal protein L15 / Large ribosomal subunit protein uL24 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS13 / Ubiquitin-ribosomal protein eL40 fusion protein / Small ribosomal subunit protein eS17 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein eL43 / Large ribosomal subunit protein eL8 / Large ribosomal subunit protein eL13 / Small ribosomal subunit protein eS4 / Small ribosomal subunit protein eS6 / Small ribosomal subunit protein uS2 / Large ribosomal subunit protein eL27 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein RACK1 / Large ribosomal subunit protein eL30 / Ubiquitin-ribosomal protein eS31 fusion protein / Small ribosomal subunit protein eS12 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein eL28 / Small ribosomal subunit protein uS11 / Large ribosomal subunit protein uL4 C-terminal domain-containing protein / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL3 / Ribosomal protein L19 / 40S ribosomal protein S26 / Ribosomal protein L18 / Small ribosomal subunit protein uS15 / 60S ribosomal protein L6 / Large ribosomal subunit protein eL39 / Large ribosomal subunit protein eL36 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein eL22 / Large ribosomal subunit protein eL14 / Small ribosomal subunit protein uS17 / 40S ribosomal protein S16 / 60S ribosomal protein L21
類似検索 - 構成要素
生物種Gallus gallus (ニワトリ)
手法電子顕微鏡法 / 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 2.5 Å
データ登録者Nurullina, L. / Jenner, L. / Yusupov, M.
資金援助 フランス, 1件
組織認可番号国
Fondation pour la Recherche Medicale (FRM) フランス
引用ジャーナル: To Be Published
タイトル: Structural insights into inactive ribosome complexes derived from cold-treated chick embryo cells
著者: Nurullina, L. / Terrosu, S. / Jenner, L. / Myasnikov, A. / Yusupov, M.
履歴
登録2023年8月17日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02024年8月28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
B5: 28S rRNA
B8: 5.8S rRNA
B7: 5S rRNA
Az: 60S ribosomal protein L41
BA: 60S ribosomal protein L8
BB: Ribosomal protein uL3
BC: 60S ribosomal protein L4 C-terminal domain-containing protein
BD: Large ribosomal subunit protein uL18
BE: 60S ribosomal protein L6
BF: Large ribosomal subunit protein uL30
BG: Large ribosomal subunit protein eL8
BH: 60S ribosomal protein L9
BI: Ribosomal protein uL16,Large ribosomal subunit protein uL16,Large ribosomal subunit protein uL16
BJ: 60S ribosomal protein L11
BL: Large ribosomal subunit protein eL13
BM: 60S ribosomal protein L14
BN: Ribosomal protein L15
BO: Ribosomal protein uL13
BP: 60S ribosomal protein L17
BQ: Ribosomal protein eL18,Ribosomal protein L18,Ribosomal protein L18
BR: Ribosomal protein L19
BS: Ribosomal protein eL20,60S ribosomal protein L18a,60S ribosomal protein L18a
BT: 60S ribosomal protein L21
BU: Large ribosomal subunit protein eL22
BV: 60S ribosomal protein L23,60S ribosomal protein L23,Ribosomal protei uL14
BW: Ribosomal protein L24
BX: Ribosomal protein uL23
BY: Ribosomal protein L26 like 1
BZ: Large ribosomal subunit protein eL27
Ba: Ribosomal protein uL15
Bb: 60S ribosomal protein L29
Bc: Large ribosomal subunit protein eL30
Bd: 60S ribosomal protein L31
Be: Ribosomal protein L32
Bf: 60S ribosomal protein L35a
Bg: 60S ribosomal protein L34
Bh: Large ribosomal subunit protein uL29
Bi: Large ribosomal subunit protein eL36
Bj: Ribosomal protein L37
Bk: 60S ribosomal protein L38
Bl: Large ribosomal subunit protein eL39
Bm: Ubiquitin-60S ribosomal protein L40
Bo: Ribosomal protein L36a like
Bp: Large ribosomal subunit protein eL43
Br: 60S ribosomal protein L28
A2: 18S rRNA
Aa: 40S ribosomal protein S3a,40S ribosomal protein S3a,Ribosomal protein eS1
AA: 40S ribosomal protein S27
AB: 40S ribosomal protein S28
Ab: 40S ribosomal protein S2
Ad: Small ribosomal subunit protein eS4
AD: Ribosomal protein eS30
AE: 40S ribosomal protein S26
Af: Small ribosomal subunit protein eS6
Ag: 40S ribosomal protein S7
Ah: 40S ribosomal protein S8
Ai: 40S ribosomal protein S9
Ak: 40S ribosomal protein S11
Am: Small ribosomal subunit protein uS15
An: Ribosomal protein S14
At: 40S ribosomal protein S20
Au: 40S ribosomal protein S21
Av: 40S ribosomal protein S15a
Aw: 40S ribosomal protein S23,40S ribosomal protein S23,Ribosomal protein uS12
Ax: 40S ribosomal protein S24
AZ: Small ribosomal subunit protein uS2
Ap: Ribosomal protein S16
AC: Ubiquitin
Ae: Ribosomal protein S5
AF: Small ribosomal subunit protein RACK1
AG: 40S ribosomal protein S29
Aj: Ribosomal protein S10
Al: Small ribosomal subunit protein eS12
Ao: Small ribosomal subunit protein uS19
Ar: 40S ribosomal protein S18
As: 40S ribosomal protein S19
Ay: 40S ribosomal protein S25
Ac: DNA-(apurinic or apyrimidinic site) lyase
V: Phe tRNA
Aq: Small ribosomal subunit protein eS17
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)3,606,019581
ポリマ－3,593,55480
非ポリマー12,465501
水106,3975906
1


  • 登録構造と同一
  • 登録者が定義した集合体
  • 根拠: 電子顕微鏡法, not applicable
タイプ名称対称操作数
identity operation1_5551

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要素

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RNA鎖 , 5種, 5分子 B5B8B7A2V

#1: RNA鎖 28S rRNA


分子量: 1439503.375 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Gallus gallus (ニワトリ) / Plasmid details: embryo / 参照: GenBank: KT445934.2
#2: RNA鎖 5.8S rRNA


分子量: 50446.855 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Gallus gallus (ニワトリ) / Plasmid details: embryo / 参照: GenBank: KT445934.2
#3: RNA鎖 5S rRNA


分子量: 38322.688 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Gallus gallus (ニワトリ) / Plasmid details: embryo / 参照: GenBank: 63782
#46: RNA鎖 18S rRNA


分子量: 588302.312 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Gallus gallus (ニワトリ) / Plasmid details: embryo / 参照: GenBank: KT445934.2
#79: RNA鎖 Phe tRNA


分子量: 24593.699 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Gallus gallus (ニワトリ) / Plasmid details: embryo

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60S ribosomal protein ... , 16種, 16分子 AzBABCBEBHBJBMBPBTBVBbBdBfBgBkBr

#4: タンパク質・ペプチド 60S ribosomal protein L41


分子量: 3473.451 Da / 分子数: 1 / 由来タイプ: 天然
詳細: The protein was modelled according to the O. cuniculus sequence because we corresponding G. gallus sequence has not been published.
由来: (天然) Gallus gallus (ニワトリ) / Plasmid details: embryo / 参照: UniProt: A0A087WNH4
#5: タンパク質 60S ribosomal protein L8


分子量: 28086.889 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Gallus gallus (ニワトリ) / Plasmid details: embryo / 参照: UniProt: F1NIX0
#7: タンパク質 60S ribosomal protein L4 C-terminal domain-containing protein


分子量: 46853.301 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Gallus gallus (ニワトリ) / Plasmid details: embryo / 参照: UniProt: Q5ZII1
#9: タンパク質 60S ribosomal protein L6


分子量: 34014.535 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Gallus gallus (ニワトリ) / Plasmid details: embryo / 参照: UniProt: Q8UWG7
#12: タンパク質 60S ribosomal protein L9


分子量: 21871.422 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Gallus gallus (ニワトリ) / Plasmid details: embryo / 参照: UniProt: A0A1D5NVI1
#14: タンパク質 60S ribosomal protein L11


分子量: 20269.396 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Gallus gallus (ニワトリ) / Plasmid details: embryo / 参照: UniProt: A0A1D5P3B1
#16: タンパク質 60S ribosomal protein L14


分子量: 15514.575 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Gallus gallus (ニワトリ) / 参照: UniProt: Q98TF9
#19: タンパク質 60S ribosomal protein L17


分子量: 21444.221 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Gallus gallus (ニワトリ) / 参照: UniProt: A0A1D5PR40
#23: タンパク質 60S ribosomal protein L21


分子量: 18622.045 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Gallus gallus (ニワトリ) / Plasmid details: embryo / 参照: UniProt: R4GIQ2
#25: タンパク質 60S ribosomal protein L23,60S ribosomal protein L23,Ribosomal protei uL14


分子量: 14892.505 Da / 分子数: 1 / 由来タイプ: 天然
詳細: We modelled the protein according to the E1BY89 entry although it is an obsoleted entry, because the sequence fits the electron density contrary to the A0A8V0ZNU5 sequence.,We modelled the ...詳細: We modelled the protein according to the E1BY89 entry although it is an obsoleted entry, because the sequence fits the electron density contrary to the A0A8V0ZNU5 sequence.,We modelled the protein according to the E1BY89 entry although it is an obsoleted entry, because the sequence fits the electron density contrary to the A0A8V0ZNU5 sequence.,We modelled the protein according to the E1BY89 entry although it is an obsoleted entry, because the sequence fits the electron density contrary to the A0A8V0ZNU5 sequence.,We modelled the protein according to the E1BY89 entry although it is an obsoleted entry, because the sequence fits the electron density contrary to the A0A8V0ZNU5 sequence.
由来: (天然) Gallus gallus (ニワトリ) / Plasmid details: embryo / 参照: UniProt: A0A8V0ZNU5
#31: タンパク質 60S ribosomal protein L29


分子量: 8433.918 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Gallus gallus (ニワトリ) / Plasmid details: embryo / 参照: UniProt: A0A1L1RNZ2
#33: タンパク質 60S ribosomal protein L31


分子量: 19836.283 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Gallus gallus (ニワトリ) / Plasmid details: embryo / 参照: UniProt: A0A1L1RT94
#35: タンパク質 60S ribosomal protein L35a


分子量: 12609.809 Da / 分子数: 1 / 由来タイプ: 天然
詳細: We modelled the protein according to the F1NQ35 entry although it is an obsoleted entry, because the sequence fits the electron density contrary to the A0A8V0YS49 sequence.
由来: (天然) Gallus gallus (ニワトリ) / Plasmid details: embryo / 参照: UniProt: A0A8V0YS49
#36: タンパク質 60S ribosomal protein L34


分子量: 13340.059 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Gallus gallus (ニワトリ) / Plasmid details: embryo / 参照: UniProt: A0A1L1S0X5
#40: タンパク質 60S ribosomal protein L38


分子量: 8238.948 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Gallus gallus (ニワトリ) / Plasmid details: embryo / 参照: UniProt: E1BU66
#45: タンパク質 60S ribosomal protein L28


分子量: 15920.725 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Gallus gallus (ニワトリ) / Plasmid details: embryo / 参照: UniProt: Q5F346

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Ribosomal protein ... , 19種, 19分子 BBBIBNBOBQBRBSBWBXBYBaBeBjBoADAnApAeAj

#6: タンパク質 Ribosomal protein uL3


分子量: 46201.055 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Gallus gallus (ニワトリ) / Plasmid details: embryo / 参照: UniProt: Q5ZJZ2
#13: タンパク質 Ribosomal protein uL16,Large ribosomal subunit protein uL16,Large ribosomal subunit protein uL16 / 60S ribosomal protein L10 / Jun-binding protein JIF-1 / Ribosomal protein L10


分子量: 24506.912 Da / 分子数: 1 / 由来タイプ: 天然
詳細: The N terminal of the protein have been modelled in the density according to the O. cuniculus sequence, as the G. gallus sequence in the database was incomplete.,The N terminal of the protein ...詳細: The N terminal of the protein have been modelled in the density according to the O. cuniculus sequence, as the G. gallus sequence in the database was incomplete.,The N terminal of the protein have been modelled in the density according to the O. cuniculus sequence, as the G. gallus sequence in the database was incomplete.,The N terminal of the protein have been modelled in the density according to the O. cuniculus sequence, as the G. gallus sequence in the database was incomplete.,The N terminal of the protein have been modelled in the density according to the O. cuniculus sequence, as the G. gallus sequence in the database was incomplete.
由来: (天然) Gallus gallus (ニワトリ) / Plasmid details: embryo / 参照: UniProt: Q08200
#17: タンパク質 Ribosomal protein L15


分子量: 24193.258 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Gallus gallus (ニワトリ) / Plasmid details: embryo / 参照: UniProt: F1NQG5
#18: タンパク質 Ribosomal protein uL13


分子量: 23533.299 Da / 分子数: 1 / 由来タイプ: 天然
詳細: The protein was modelled according to the O. cuniculus sequence from PDB entry 7O7Z (XP_002723961.2 ) because we corresponding G. gallus sequence has not been published.
由来: (天然) Gallus gallus (ニワトリ) / Plasmid details: embryo
#20: タンパク質 Ribosomal protein eL18,Ribosomal protein L18,Ribosomal protein L18


分子量: 21411.389 Da / 分子数: 1 / 由来タイプ: 天然
詳細: The N and C terminals have been modelled in the density according to the O. cuniculus sequence, as the G. gallus sequence in the database was incomplete.,The N and C terminals have been ...詳細: The N and C terminals have been modelled in the density according to the O. cuniculus sequence, as the G. gallus sequence in the database was incomplete.,The N and C terminals have been modelled in the density according to the O. cuniculus sequence, as the G. gallus sequence in the database was incomplete.,The N and C terminals have been modelled in the density according to the O. cuniculus sequence, as the G. gallus sequence in the database was incomplete.,The N and C terminals have been modelled in the density according to the O. cuniculus sequence, as the G. gallus sequence in the database was incomplete.,The N and C terminals have been modelled in the density according to the O. cuniculus sequence, as the G. gallus sequence in the database was incomplete.,The N and C terminals have been modelled in the density according to the O. cuniculus sequence, as the G. gallus sequence in the database was incomplete.,The N and C terminals have been modelled in the density according to the O. cuniculus sequence, as the G. gallus sequence in the database was incomplete.,The N and C terminals have been modelled in the density according to the O. cuniculus sequence, as the G. gallus sequence in the database was incomplete.,The N and C terminals have been modelled in the density according to the O. cuniculus sequence, as the G. gallus sequence in the database was incomplete.
由来: (天然) Gallus gallus (ニワトリ) / Plasmid details: embryo / 参照: UniProt: Q6EE60
#21: タンパク質 Ribosomal protein L19


分子量: 23481.229 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Gallus gallus (ニワトリ) / 参照: UniProt: Q5ZKK8
#22: タンパク質 Ribosomal protein eL20,60S ribosomal protein L18a,60S ribosomal protein L18a


分子量: 20856.602 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Gallus gallus (ニワトリ) / Plasmid details: embryo / 参照: UniProt: F1NPD3
#26: タンパク質 Ribosomal protein L24


分子量: 17837.100 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Gallus gallus (ニワトリ) / Plasmid details: embryo / 参照: UniProt: A0A8V0XRE7
#27: タンパク質 Ribosomal protein uL23


分子量: 17701.158 Da / 分子数: 1 / 由来タイプ: 天然
詳細: We modelled the protein according to the E1BS06 entry although it is an obsoleted entry, because the sequence fits the electron density contrary to the A0A8V1AGP8 and two more sequences.
由来: (天然) Gallus gallus (ニワトリ) / Plasmid details: embryo
#28: タンパク質 Ribosomal protein L26 like 1


分子量: 17303.363 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Gallus gallus (ニワトリ) / Plasmid details: embryo / 参照: UniProt: F2Z4K6
#30: タンパク質 Ribosomal protein uL15


分子量: 16851.850 Da / 分子数: 1 / 由来タイプ: 天然
詳細: We modelled the protein according to the F1NBX4 entry although it is an obsoleted entry, because the sequence fits the electron density contrary to the A0A8V0ZL98 sequence.
由来: (天然) Gallus gallus (ニワトリ) / Plasmid details: embryo
#34: タンパク質 Ribosomal protein L32


分子量: 15955.035 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Gallus gallus (ニワトリ) / Plasmid details: embryo / 参照: UniProt: E1BVB1
#39: タンパク質 Ribosomal protein L37


分子量: 11103.011 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Gallus gallus (ニワトリ) / 参照: UniProt: E1C810
#43: タンパク質 Ribosomal protein L36a like


分子量: 12335.784 Da / 分子数: 1 / 由来タイプ: 天然
詳細: We modelled the protein according to the F1NIK4 entry although it is an obsoleted entry, because the sequence fits the electron density contrary to the A0A8V0YUB1 sequence.
由来: (天然) Gallus gallus (ニワトリ) / Plasmid details: embryo / 参照: UniProt: A0A8V0YUB1
#52: タンパク質 Ribosomal protein eS30


分子量: 14536.841 Da / 分子数: 1 / 由来タイプ: 天然
詳細: We modelled the protein according to the A0A1D5PQV entry although it is an obsoleted entry, because no more entry in database.
由来: (天然) Gallus gallus (ニワトリ) / Plasmid details: embryo
#60: タンパク質 Ribosomal protein S14


分子量: 16302.772 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Gallus gallus (ニワトリ) / Plasmid details: embryo / 参照: UniProt: Q5ZHW8
#67: タンパク質 Ribosomal protein S16


分子量: 16445.377 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Gallus gallus (ニワトリ) / Plasmid details: embryo / 参照: UniProt: R4GGJ0
#69: タンパク質 Ribosomal protein S5


分子量: 22913.453 Da / 分子数: 1 / 由来タイプ: 天然
詳細: The protein was modelled according to the O. cuniculus sequence because we corresponding G. gallus sequence has not been published.
由来: (天然) Gallus gallus (ニワトリ) / Plasmid details: embryo / 参照: UniProt: G1TFM5
#72: タンパク質 Ribosomal protein S10


分子量: 18945.898 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Gallus gallus (ニワトリ) / Plasmid details: embryo / 参照: UniProt: E1C4N0

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Large ribosomal subunit protein ... , 11種, 11分子 BDBFBGBLBUBZBcBhBiBlBp

#8: タンパク質 Large ribosomal subunit protein uL18 / 60S ribosomal protein L5


分子量: 34156.391 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Gallus gallus (ニワトリ) / Plasmid details: embryo / 参照: UniProt: P22451
#10: タンパク質 Large ribosomal subunit protein uL30 / 60S ribosomal protein L7


分子量: 28844.486 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Gallus gallus (ニワトリ) / Plasmid details: embryo / 参照: UniProt: Q5ZJ56
#11: タンパク質 Large ribosomal subunit protein eL8 / 60S ribosomal protein L7a


分子量: 30064.742 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Gallus gallus (ニワトリ) / Plasmid details: embryo / 参照: UniProt: P32429
#15: タンパク質 Large ribosomal subunit protein eL13 / 60S ribosomal protein L13 / Breast basic conserved protein 1


分子量: 24455.928 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Gallus gallus (ニワトリ) / Plasmid details: embryo / 参照: UniProt: P41125
#24: タンパク質 Large ribosomal subunit protein eL22 / 60S ribosomal protein L22


分子量: 14754.892 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Gallus gallus (ニワトリ) / Plasmid details: embryo / 参照: UniProt: Q98TF8
#29: タンパク質 Large ribosomal subunit protein eL27 / 60S ribosomal protein L27


分子量: 15835.831 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Gallus gallus (ニワトリ) / Plasmid details: embryo / 参照: UniProt: P61355
#32: タンパク質 Large ribosomal subunit protein eL30 / 60S ribosomal protein L30


分子量: 12835.117 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Gallus gallus (ニワトリ) / 参照: UniProt: P67883
#37: タンパク質 Large ribosomal subunit protein uL29 / 60S ribosomal protein L35


分子量: 14593.624 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Gallus gallus (ニワトリ) / Plasmid details: embryo / 参照: UniProt: Q98TF7
#38: タンパク質 Large ribosomal subunit protein eL36 / 60S ribosomal protein L36


分子量: 12331.951 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Gallus gallus (ニワトリ) / Plasmid details: embryo / 参照: UniProt: Q98TF6
#41: タンパク質 Large ribosomal subunit protein eL39 / 60S ribosomal protein L39


分子量: 6398.745 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Gallus gallus (ニワトリ) / 参照: UniProt: Q98TF5
#44: タンパク質 Large ribosomal subunit protein eL43 / 60S ribosomal protein L37a


分子量: 10271.335 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Gallus gallus (ニワトリ) / Plasmid details: embryo / 参照: UniProt: P32046

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タンパク質 , 3種, 3分子 BmACAc

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


分子量: 14769.417 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Gallus gallus (ニワトリ) / Plasmid details: embryo / 参照: UniProt: O42388
#68: タンパク質 Ubiquitin


分子量: 18018.066 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Gallus gallus (ニワトリ) / 参照: UniProt: P79781
#78: タンパク質 DNA-(apurinic or apyrimidinic site) lyase


分子量: 26760.383 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Gallus gallus (ニワトリ) / Plasmid details: embryo
参照: UniProt: F1NPA9, DNA-(apurinic or apyrimidinic site) lyase

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40S ribosomal protein ... , 18種, 18分子 AaAAABAbAEAgAhAiAkAtAuAvAwAxAGArAsAy

#47: タンパク質 40S ribosomal protein S3a,40S ribosomal protein S3a,Ribosomal protein eS1


分子量: 29923.994 Da / 分子数: 1 / 由来タイプ: 天然
詳細: We modelled the protein according to the F2Z4K7 entry although it is an obsoleted entry, because the sequence fits the electron density contrary to the A0A8V0XXX0 sequence.,We modelled the ...詳細: We modelled the protein according to the F2Z4K7 entry although it is an obsoleted entry, because the sequence fits the electron density contrary to the A0A8V0XXX0 sequence.,We modelled the protein according to the F2Z4K7 entry although it is an obsoleted entry, because the sequence fits the electron density contrary to the A0A8V0XXX0 sequence.,We modelled the protein according to the F2Z4K7 entry although it is an obsoleted entry, because the sequence fits the electron density contrary to the A0A8V0XXX0 sequence.,We modelled the protein according to the F2Z4K7 entry although it is an obsoleted entry, because the sequence fits the electron density contrary to the A0A8V0XXX0 sequence.
由来: (天然) Gallus gallus (ニワトリ) / Plasmid details: embryo / 参照: UniProt: A0A8V0XXX0
#48: タンパク質 40S ribosomal protein S27


分子量: 9566.283 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Gallus gallus (ニワトリ) / Plasmid details: embryo / 参照: UniProt: A0A3Q2TV39
#49: タンパク質 40S ribosomal protein S28


分子量: 7855.052 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Gallus gallus (ニワトリ) / Plasmid details: embryo / 参照: UniProt: A0A3Q2U825
#50: タンパク質 40S ribosomal protein S2


分子量: 28875.881 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Gallus gallus (ニワトリ) / Plasmid details: embryo / 参照: UniProt: A0A8V0Z891
#53: タンパク質 40S ribosomal protein S26


分子量: 13063.532 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Gallus gallus (ニワトリ) / Plasmid details: embryo / 参照: UniProt: Q5ZM66
#55: タンパク質 40S ribosomal protein S7


分子量: 22153.943 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Gallus gallus (ニワトリ) / Plasmid details: embryo / 参照: UniProt: F1NN16
#56: タンパク質 40S ribosomal protein S8


分子量: 24112.203 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Gallus gallus (ニワトリ) / Plasmid details: embryo / 参照: UniProt: F1NB02
#57: タンパク質 40S ribosomal protein S9


分子量: 22641.564 Da / 分子数: 1 / 由来タイプ: 天然
詳細: The protein was modelled according to the O. cuniculus sequence because we corresponding G. gallus sequence has not been published.
由来: (天然) Gallus gallus (ニワトリ) / Plasmid details: embryo / 参照: UniProt: B7NZS8
#58: タンパク質 40S ribosomal protein S11


分子量: 18384.668 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Gallus gallus (ニワトリ) / Plasmid details: embryo / 参照: UniProt: Q98TH5
#61: タンパク質 40S ribosomal protein S20


分子量: 13399.751 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Gallus gallus (ニワトリ) / Plasmid details: embryo / 参照: UniProt: F1NH93
#62: タンパク質 40S ribosomal protein S21


分子量: 9173.397 Da / 分子数: 1 / 由来タイプ: 天然
詳細: We modelled the protein according to the E1BSJ2 entry although it is an obsoleted entry, because the sequence fits the electron density contrary to the A0A8V0ZQ38 and A0A8V0ZC45 sequences.
由来: (天然) Gallus gallus (ニワトリ) / Plasmid details: embryo / 参照: UniProt: A0A8V0ZQ38
#63: タンパク質 40S ribosomal protein S15a


分子量: 14881.555 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Gallus gallus (ニワトリ) / Plasmid details: embryo / 参照: UniProt: A0A3Q3A7P6
#64: タンパク質 40S ribosomal protein S23,40S ribosomal protein S23,Ribosomal protein uS12


分子量: 15844.666 Da / 分子数: 1 / 由来タイプ: 天然
詳細: We modelled the protein according to the F1NDC2 entry although it is an obsoleted entry, because the sequence fits the electron density contrary to the A0A8V0XRS9 sequence.,We modelled the ...詳細: We modelled the protein according to the F1NDC2 entry although it is an obsoleted entry, because the sequence fits the electron density contrary to the A0A8V0XRS9 sequence.,We modelled the protein according to the F1NDC2 entry although it is an obsoleted entry, because the sequence fits the electron density contrary to the A0A8V0XRS9 sequence.,We modelled the protein according to the F1NDC2 entry although it is an obsoleted entry, because the sequence fits the electron density contrary to the A0A8V0XRS9 sequence.,We modelled the protein according to the F1NDC2 entry although it is an obsoleted entry, because the sequence fits the electron density contrary to the A0A8V0XRS9 sequence.
由来: (天然) Gallus gallus (ニワトリ) / Plasmid details: embryo / 参照: UniProt: A0A8V0XRS9
#65: タンパク質 40S ribosomal protein S24


分子量: 15237.104 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Gallus gallus (ニワトリ) / Plasmid details: embryo / 参照: UniProt: F1NF89
#71: タンパク質 40S ribosomal protein S29


分子量: 18662.643 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Gallus gallus (ニワトリ) / Plasmid details: embryo / 参照: UniProt: A0A8V0Z8V3
#75: タンパク質 40S ribosomal protein S18


分子量: 17759.777 Da / 分子数: 1 / 由来タイプ: 天然
詳細: The protein was modelled according to the O. cuniculus sequence because we corresponding G. gallus sequence has not been published.
由来: (天然) Gallus gallus (ニワトリ) / Plasmid details: embryo / 参照: UniProt: G1TPG3
#76: タンパク質 40S ribosomal protein S19


分子量: 16118.546 Da / 分子数: 1 / 由来タイプ: 天然
詳細: We modelled the protein according to the A0A1D5PDV6 entry although it is an obsoleted entry, because no more sequence in database.
由来: (天然) Gallus gallus (ニワトリ) / Plasmid details: embryo
#77: タンパク質 40S ribosomal protein S25


分子量: 13746.198 Da / 分子数: 1 / 由来タイプ: 天然
詳細: We modelled the protein according to the F1NU56 entry although it is an obsoleted entry, because no more sequence in database.
由来: (天然) Gallus gallus (ニワトリ) / Plasmid details: embryo / 参照: UniProt: A0A8V1A7V4

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Small ribosomal subunit protein ... , 8種, 8分子 AdAfAmAZAFAlAoAq

#51: タンパク質 Small ribosomal subunit protein eS4 / 40S ribosomal protein S4


分子量: 29652.877 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Gallus gallus (ニワトリ) / Plasmid details: embryo / 参照: UniProt: P47836
#54: タンパク質 Small ribosomal subunit protein eS6 / 40S ribosomal protein S6


分子量: 28723.727 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Gallus gallus (ニワトリ) / Plasmid details: embryo / 参照: UniProt: P47838
#59: タンパク質 Small ribosomal subunit protein uS15 / 40S ribosomal protein S13


分子量: 17259.389 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Gallus gallus (ニワトリ) / Plasmid details: embryo / 参照: UniProt: Q6ITC7
#66: タンパク質 Small ribosomal subunit protein uS2 / 37 kDa laminin receptor precursor / 37LRP / 37/67 kDa laminin receptor / LRP/LR / 40S ribosomal ...37 kDa laminin receptor precursor / 37LRP / 37/67 kDa laminin receptor / LRP/LR / 40S ribosomal protein SA / 67 kDa laminin receptor / 67LR / Laminin receptor 1 / LamR / Laminin-binding protein precursor p40 / LBP/p40


分子量: 33093.180 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Gallus gallus (ニワトリ) / Plasmid details: embryo / 参照: UniProt: P50890
#70: タンパク質 Small ribosomal subunit protein RACK1 / Guanine nucleotide-binding protein subunit beta-like protein 12.3 / Receptor for activated C kinase ...Guanine nucleotide-binding protein subunit beta-like protein 12.3 / Receptor for activated C kinase / Receptor of activated protein C kinase 1 / Receptor of activated protein kinase C 1 / RACK1


分子量: 35115.652 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Gallus gallus (ニワトリ) / Plasmid details: embryo / 参照: UniProt: P63247
#73: タンパク質 Small ribosomal subunit protein eS12 / 40S ribosomal protein S12


分子量: 14569.013 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Gallus gallus (ニワトリ) / Plasmid details: embryo / 参照: UniProt: P84175
#74: タンパク質 Small ribosomal subunit protein uS19 / 40S ribosomal protein S15 / RIG protein


分子量: 17076.207 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Gallus gallus (ニワトリ) / Plasmid details: embryo / 参照: UniProt: P62846
#80: タンパク質 Small ribosomal subunit protein eS17 / 40S ribosomal protein S17


分子量: 15566.146 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Gallus gallus (ニワトリ) / Plasmid details: embryo / 参照: UniProt: P08636

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非ポリマー , 3種, 6407分子

#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: 494 / 由来タイプ: 合成 / 式: Mg
#82: 化合物
ChemComp-ZN / ZINC ION


分子量: 65.409 Da / 分子数: 7 / 由来タイプ: 合成 / 式: Zn
#83: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 5906 / 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N

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実験情報

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実験

実験手法: 電子顕微鏡法
EM実験試料の集合状態: PARTICLE / ３次元再構成法: 単粒子再構成法

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試料調製

構成要素名称: Gallus gallus 80S ribosome / タイプ: RIBOSOME / 詳細: Contains endogenous E-site tRNA / Entity ID: #1-#80 / 由来: NATURAL
分子量値: 4.2 MDa / 実験値: NO
由来(天然)生物種: Gallus gallus (ニワトリ)
緩衝液pH: 7.5
試料包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES
急速凍結凍結剤: ETHANE / 湿度: 95 %

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電子顕微鏡撮影

実験機器
モデル: Titan Krios / 画像提供: FEI Company
顕微鏡モデル: FEI TITAN KRIOS
電子銃電子線源: FIELD EMISSION GUN / 加速電圧: 300 kV / 照射モード: FLOOD BEAM
電子レンズモード: BRIGHT FIELD / 倍率（公称値）: 96000 X / 最大 デフォーカス（公称値）: 1500 nm / 最小 デフォーカス（公称値）: 300 nm
撮影電子線照射量: 40 e/Å2
フィルム・検出器のモデル: FEI FALCON IV (4k x 4k)

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解析

EMソフトウェア
ID名称バージョンカテゴリ
7PHENIXモデルフィッティング
9PHENIX1.19rc4_4035:モデル精密化
10cryoSPARC初期オイラー角割当
11cryoSPARC最終オイラー角割当
13cryoSPARC３次元再構成
CTF補正タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION
3次元再構成解像度: 2.5 Å / 解像度の算出法: FSC 3 SIGMA CUT-OFF / 粒子像の数: 122598 / アルゴリズム: FOURIER SPACE / クラス平均像の数: 1 / 対称性のタイプ: POINT
原子モデル構築プロトコル: RIGID BODY FIT / 空間: REAL / Target criteria: Cross-correlation coefficient
原子モデル構築PDB-ID: 7O7Z

7o7z


Accession code: 7O7Z / Source name: PDB / タイプ: experimental model
拘束条件
Refine-IDタイプDev ideal数
ELECTRON MICROSCOPYf_bond_d0.006228844
ELECTRON MICROSCOPYf_angle_d0.652336440
ELECTRON MICROSCOPYf_dihedral_angle_d14.53682314
ELECTRON MICROSCOPYf_chiral_restr0.04241721
ELECTRON MICROSCOPYf_plane_restr0.00622039

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万見について

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お知らせ

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2022年2月9日: EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

  • EMDBのヘッダファイルのバージョン3が、公式のフォーマットとなりました。
  • これまでは公式だったバージョン1.9は、アーカイブから削除されます。

関連情報:EMDBヘッダ

外部リンク:wwPDBはEMDBデータモデルのバージョン3へ移行します

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2020年8月12日: 新型コロナ情報

新型コロナ情報

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

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

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

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2020年3月5日: 新型コロナウイルスの構造データ

新型コロナウイルスの構造データ

関連情報:万見生物種 / 2020年8月12日: 新型コロナ情報

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

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2019年1月31日: EMDBのIDの桁数の変更

EMDBのIDの桁数の変更

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

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

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

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2017年7月12日: PDB大規模アップデート

PDB大規模アップデート

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

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

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万見 (Yorodumi)

幾万の構造データを、幾万の視点から

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

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

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