[English] 日本語
Yorodumi
- PDB-8q87: Structure of the G. gallus 80S rotated ribosome in complex with e... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8q87
TitleStructure of the G. gallus 80S rotated ribosome in complex with eEF2 and SERBP1
Components
  • (40S ribosomal protein ...) x 14
  • (60S ribosomal protein ...) x 15
  • (Large ribosomal subunit protein ...) x 12
  • (Ribosomal protein ...) x 24
  • (Small ribosomal subunit protein ...) x 8
  • 18S rRNA
  • 28S rRNA
  • 5.8S rRNA
  • 5S rRNA
  • DNA-(apurinic or apyrimidinic site) lyase
  • Elongation factor 2
  • Phe tRNA
  • Ribosomal protei uL14
  • Ribosomal protein
  • SERPINE1 mRNA binding protein 1
  • Ubiquitin
  • Ubiquitin-60S ribosomal protein L40
KeywordsRIBOSOME / translation / complex / eEF2 / SERBP1
Function / homology
Function and homology information


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) / Regulation of PLK1 Activity at G2/M Transition / 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)
Similarity search - Function
: / Glycerate/sugar phosphate transporter, conserved site / glpT family of transporters signature. / Hyaluronan / mRNA binding family / RNA binding protein HABP4/SERBP1 / Hyaluronan/mRNA-binding protein / Hyaluronan / mRNA binding family / 60s Acidic ribosomal protein / 60S acidic ribosomal protein P0 / Major facilitator superfamily ...: / Glycerate/sugar phosphate transporter, conserved site / glpT family of transporters signature. / Hyaluronan / mRNA binding family / RNA binding protein HABP4/SERBP1 / Hyaluronan/mRNA-binding protein / Hyaluronan / mRNA binding family / 60s Acidic ribosomal protein / 60S acidic ribosomal protein P0 / 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 / Elongation Factor G, domain II / Elongation Factor G, domain III / Ribosomal protein L2, archaeal-type / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / Ribosomal protein L30e / Ribosomal protein L28e / Translation elongation factor EFG/EF2, domain IV / Elongation factor G, domain IV / Elongation factor G, domain IV / Elongation factor G C-terminus / Elongation factor EFG, domain V-like / Elongation factor G C-terminus / 50S ribosomal protein L10, insertion domain superfamily / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / 60S ribosomal protein L10P, insertion domain / Insertion domain in 60S ribosomal protein L10P / EF-G domain III/V-like / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / : / Ribosomal protein S26e signature. / MFS transporter superfamily / Ribosomal protein L41 / Ribosomal protein L41 / metallochaperone-like domain / TRASH domain / : / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Ribosomal protein S12e signature. / Ribosomal protein S12e / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein L29e / Ribosomal L29e protein family / Ribosomal protein L14e domain / Ribosomal protein L1, conserved site / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein L1 signature. / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / Ribosomal protein S2, eukaryotic / Ribosomal protein L1 / Ribosomal protein L14 / Ribosomal protein L14, KOW motif / Ribosomal protein L14 / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / S27a-like superfamily / 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 S25 / S25 ribosomal protein / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / Ribosomal protein L10e / Ribosomal protein L13e / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein L13e / Ribosomal protein L19, eukaryotic / Ribosomal protein S27a / Ribosomal protein S8e subdomain, eukaryotes / Ribosomal protein S27a / Ribosomal protein S27a / : / Ribosomal protein S17e, conserved site / Ribosomal protein S17e signature. / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein S7e signature. / Ribosomal protein L24e, conserved site / Ribosomal protein L24e signature.
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein eS32 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL5 ...GUANOSINE-5'-DIPHOSPHATE / : / : / 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 / Large ribosomal subunit protein eL42 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein uS14 / SERPINE1 mRNA binding protein 1 / Small ribosomal subunit protein eS25 / Small ribosomal subunit protein uS4 / Large ribosomal subunit protein uL11 / 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 / Ribosomal protein L15 / Large ribosomal subunit protein uL24 / Ribosomal protein / 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 / Large ribosomal subunit protein uL10 / 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 / Small ribosomal subunit protein uS15 / 60S ribosomal protein L6 / Elongation factor 2 / 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
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.4 Å
AuthorsNurullina, L. / Jenner, L. / Yusupov, M.
Funding support France, 1items
OrganizationGrant numberCountry
Fondation pour la Recherche Medicale (FRM) France
CitationJournal: To Be Published
Title: Structural insights into inactive ribosome complexes derived from cold-treated chick embryo cells
Authors: Nurullina, L. / Terrosu, S. / Jenner, L. / Myasnikov, A. / Yusupov, M.
History
DepositionAug 18, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 28, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
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
BR: Ribosomal protein L19
BS: Ribosomal protein eL20
BT: 60S ribosomal protein L21
BU: Large ribosomal subunit protein eL22
BV: 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: Ribosomal protein eL33
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: Ribosomal protein eS1
AA: 40S ribosomal protein S27
AB: 40S ribosomal protein S28
Ab: 40S ribosomal protein S2
AC: Ubiquitin
Ac: DNA-(apurinic or apyrimidinic site) lyase
Ad: Small ribosomal subunit protein eS4
AD: Ribosomal protein eS30
AE: 40S ribosomal protein S26
Ae: Ribosomal protein S5
Af: Small ribosomal subunit protein eS6
AF: Small ribosomal subunit protein RACK1
Ag: 40S ribosomal protein S7
AG: 40S ribosomal protein S29
Ah: 40S ribosomal protein S8
Ai: 40S ribosomal protein S9
Aj: Ribosomal protein S10
Ak: 40S ribosomal protein S11
Al: Small ribosomal subunit protein eS12
Am: Small ribosomal subunit protein uS15
An: Ribosomal protein S14
Ao: Small ribosomal subunit protein uS19
Aq: Small ribosomal subunit protein eS17
Ar: 40S ribosomal protein S18
As: Ribosomal protein eS19
At: 40S ribosomal protein S20
Au: Ribosomal protein eS21
Av: 40S ribosomal protein S15a
Aw: Ribosomal protein uS12
Ax: 40S ribosomal protein S24
Ay: 40S ribosomal protein S25
AZ: Small ribosomal subunit protein uS2
Ap: Ribosomal protein S16
V: Phe tRNA
S: SERPINE1 mRNA binding protein 1
A: Elongation factor 2
Bs: Large ribosomal subunit protein uL10
Bt: 60S ribosomal protein L12
Bv: Ribosomal protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,822,411586
Polymers3,809,48785
Non-polymers12,925501
Water70,1683895
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

-
Components

-
RNA chain , 5 types, 5 molecules B5B8B7A2V

#1: RNA chain 28S rRNA


Mass: 1439489.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: GenBank: KT445934.2
#2: RNA chain 5.8S rRNA


Mass: 50446.855 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: GenBank: KT445934.2
#3: RNA chain 5S rRNA


Mass: 38322.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: GenBank: 63782
#46: RNA chain 18S rRNA


Mass: 588288.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: GenBank: KT445934.2
#80: RNA chain Phe tRNA


Mass: 24593.699 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo

-
60S ribosomal protein ... , 15 types, 15 molecules AzBABCBEBHBJBMBPBTBbBdBgBkBrBt

#4: Protein/peptide 60S ribosomal protein L41


Mass: 3473.451 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: The protein was modelled according to the O. cuniculus A0A087WNH4 sequence because we corresponding G. gallus sequence has not been published.
Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: A0A087WNH4
#5: Protein 60S ribosomal protein L8


Mass: 28086.889 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: F1NIX0
#7: Protein 60S ribosomal protein L4 C-terminal domain-containing protein


Mass: 46853.301 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: Q5ZII1
#9: Protein 60S ribosomal protein L6


Mass: 34014.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: Q8UWG7
#12: Protein 60S ribosomal protein L9


Mass: 21871.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: A0A1D5NVI1
#14: Protein 60S ribosomal protein L11


Mass: 20269.396 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: A0A1D5P3B1
#16: Protein 60S ribosomal protein L14


Mass: 15514.575 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: Q98TF9
#19: Protein 60S ribosomal protein L17


Mass: 21444.221 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: A0A1D5PR40
#23: Protein 60S ribosomal protein L21


Mass: 18622.045 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: R4GIQ2
#31: Protein 60S ribosomal protein L29


Mass: 8433.918 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: A0A1L1RNZ2
#33: Protein 60S ribosomal protein L31


Mass: 19836.283 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: A0A1L1RT94
#36: Protein 60S ribosomal protein L34


Mass: 13340.059 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: A0A1L1S0X5
#40: Protein 60S ribosomal protein L38


Mass: 8238.948 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embtyo / References: UniProt: E1BU66
#45: Protein 60S ribosomal protein L28


Mass: 15920.725 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: Q5F346
#84: Protein 60S ribosomal protein L12


Mass: 17766.545 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: E1BTG1

+
Ribosomal protein ... , 24 types, 24 molecules BBBIBNBOBQBRBSBWBXBYBaBeBfBjBoAaADAeAjAnAsAuAwAp

#6: Protein Ribosomal protein uL3


Mass: 46201.055 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: Q5ZJZ2
#13: Protein 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


Mass: 24506.912 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: 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 ...Details: 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.
Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: Q08200
#17: Protein Ribosomal protein L15


Mass: 24193.258 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: F1NQG5
#18: Protein Ribosomal protein uL13


Mass: 23533.299 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: 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.
Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo
#20: Protein Ribosomal protein eL18


Mass: 21411.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: 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.
Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo
#21: Protein Ribosomal protein L19


Mass: 23481.229 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: Q5ZKK8
#22: Protein Ribosomal protein eL20


Mass: 20856.602 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo
#26: Protein Ribosomal protein L24


Mass: 17837.100 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: A0A8V0XRE7
#27: Protein Ribosomal protein uL23


Mass: 17701.158 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: 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
Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo
#28: Protein Ribosomal protein L26 like 1


Mass: 17303.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: F2Z4K6
#30: Protein Ribosomal protein uL15


Mass: 16851.850 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: 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.
Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo
#34: Protein Ribosomal protein L32


Mass: 15955.035 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: E1BVB1
#35: Protein Ribosomal protein eL33


Mass: 12609.809 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: 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.
Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo
#39: Protein Ribosomal protein L37


Mass: 11103.011 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: E1C810
#43: Protein Ribosomal protein L36a like


Mass: 12335.784 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: 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.
Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: A0A8V0YUB1
#47: Protein Ribosomal protein eS1


Mass: 29923.994 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: 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.
Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo
#54: Protein Ribosomal protein eS30


Mass: 14536.841 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: We modelled the protein according to the A0A1D5PQV entry although it is an obsoleted entry, because no more entry in database.
Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo
#56: Protein Ribosomal protein S5


Mass: 22913.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: The protein was modelled according to the O. cuniculus G1TFM5 sequence because we corresponding G. gallus sequence has not been published.
Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: G1TFM5
#63: Protein Ribosomal protein S10


Mass: 18945.898 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: E1C4N0
#67: Protein Ribosomal protein S14


Mass: 16302.772 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: Q5ZHW8
#71: Protein Ribosomal protein eS19


Mass: 16118.546 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: We modelled the protein according to the A0A1D5PDV6 entry although it is an obsoleted entry, because no more sequence in database.
Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo
#73: Protein Ribosomal protein eS21


Mass: 9173.397 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: 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.
Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo
#75: Protein Ribosomal protein uS12


Mass: 15844.666 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: 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.
Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo
#79: Protein Ribosomal protein S16


Mass: 16445.377 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: R4GGJ0

-
Large ribosomal subunit protein ... , 12 types, 12 molecules BDBFBGBLBUBZBcBhBiBlBpBs

#8: Protein Large ribosomal subunit protein uL18 / 60S ribosomal protein L5


Mass: 34156.391 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: P22451
#10: Protein Large ribosomal subunit protein uL30 / 60S ribosomal protein L7


Mass: 28844.486 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: Q5ZJ56
#11: Protein Large ribosomal subunit protein eL8 / 60S ribosomal protein L7a


Mass: 30064.742 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: P32429
#15: Protein Large ribosomal subunit protein eL13 / 60S ribosomal protein L13 / Breast basic conserved protein 1


Mass: 24455.928 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: P41125
#24: Protein Large ribosomal subunit protein eL22 / 60S ribosomal protein L22


Mass: 14754.892 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: Q98TF8
#29: Protein Large ribosomal subunit protein eL27 / 60S ribosomal protein L27


Mass: 15835.831 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: P61355
#32: Protein Large ribosomal subunit protein eL30 / 60S ribosomal protein L30


Mass: 12835.117 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: P67883
#37: Protein Large ribosomal subunit protein uL29 / 60S ribosomal protein L35


Mass: 14593.624 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: Q98TF7
#38: Protein Large ribosomal subunit protein eL36 / 60S ribosomal protein L36


Mass: 12331.951 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: Q98TF6
#41: Protein Large ribosomal subunit protein eL39 / 60S ribosomal protein L39


Mass: 6398.745 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: Q98TF5
#44: Protein Large ribosomal subunit protein eL43 / 60S ribosomal protein L37a


Mass: 10271.335 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: P32046
#83: Protein Large ribosomal subunit protein uL10 / 60S acidic ribosomal protein P0 / 60S ribosomal protein L10E


Mass: 34322.496 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: P47826

-
Protein , 7 types, 7 molecules BVBmACAcSABv

#25: Protein Ribosomal protei uL14


Mass: 14892.505 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: 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 other entries.
Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo
#42: Protein Ubiquitin-60S ribosomal protein L40


Mass: 14769.417 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: O42388
#51: Protein Ubiquitin


Mass: 18018.066 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: P79781
#52: Protein DNA-(apurinic or apyrimidinic site) lyase


Mass: 26760.383 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo
References: UniProt: F1NPA9, DNA-(apurinic or apyrimidinic site) lyase
#81: Protein SERPINE1 mRNA binding protein 1


Mass: 43470.684 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: A0A8V0ZUK5
#82: Protein Elongation factor 2 / EF-2


Mass: 95645.508 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo
References: UniProt: Q90705, Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement
#85: Protein Ribosomal protein


Mass: 24755.352 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: F6SU35

-
40S ribosomal protein ... , 14 types, 14 molecules AAABAbAEAgAGAhAiAkArAtAvAxAy

#48: Protein 40S ribosomal protein S27


Mass: 9566.283 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: A0A3Q2TV39
#49: Protein 40S ribosomal protein S28


Mass: 7855.052 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: A0A3Q2U825
#50: Protein 40S ribosomal protein S2


Mass: 28875.881 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: A0A8V0Z891
#55: Protein 40S ribosomal protein S26


Mass: 13063.532 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: Q5ZM66
#59: Protein 40S ribosomal protein S7


Mass: 22153.943 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: F1NN16
#60: Protein 40S ribosomal protein S29


Mass: 18662.643 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: A0A8V0Z8V3
#61: Protein 40S ribosomal protein S8


Mass: 24112.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: F1NB02
#62: Protein 40S ribosomal protein S9


Mass: 22641.564 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: The protein was modelled according to the O. cuniculus B7NZS8 sequence because we corresponding G. gallus sequence has not been published.
Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: B7NZS8
#64: Protein 40S ribosomal protein S11


Mass: 18384.668 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: Q98TH5
#70: Protein 40S ribosomal protein S18


Mass: 17759.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: The protein was modelled according to the O. cuniculus G1TPG3 sequence because we corresponding G. gallus sequence has not been published.
Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: G1TPG3
#72: Protein 40S ribosomal protein S20


Mass: 13399.751 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: F1NH93
#74: Protein 40S ribosomal protein S15a


Mass: 14881.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: A0A3Q3A7P6
#76: Protein 40S ribosomal protein S24


Mass: 15237.104 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: F1NF89
#77: Protein 40S ribosomal protein S25


Mass: 13746.198 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: We modelled the protein according to the F1NU56 entry although it is an obsoleted entry, because no more sequence in database.
Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: A0A8V1A7V4

-
Small ribosomal subunit protein ... , 8 types, 8 molecules AdAfAFAlAmAoAqAZ

#53: Protein Small ribosomal subunit protein eS4 / 40S ribosomal protein S4


Mass: 29652.877 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: P47836
#57: Protein Small ribosomal subunit protein eS6 / 40S ribosomal protein S6


Mass: 28723.727 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: P47838
#58: Protein 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


Mass: 35115.652 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: P63247
#65: Protein Small ribosomal subunit protein eS12 / 40S ribosomal protein S12


Mass: 14569.013 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: P84175
#66: Protein Small ribosomal subunit protein uS15 / 40S ribosomal protein S13


Mass: 17259.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: Q6ITC7
#68: Protein Small ribosomal subunit protein uS19 / 40S ribosomal protein S15 / RIG protein


Mass: 17076.207 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: P62846
#69: Protein Small ribosomal subunit protein eS17 / 40S ribosomal protein S17


Mass: 15566.146 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Plasmid details: embryo / References: UniProt: P08636
#78: Protein 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


Mass: 33093.180 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P50890

-
Non-polymers , 4 types, 4396 molecules

#86: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 492 / Source method: obtained synthetically / Formula: Mg
#87: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#88: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#89: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3895 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: 80S ribosome / Type: RIBOSOME / Details: Contains endogenous P/E tRNA, SERBP1 and eEF2 / Entity ID: #1-#85 / Source: NATURAL
Molecular weightValue: 4.2 MDa / Experimental value: NO
Source (natural)Organism: Gallus gallus (chicken)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE / Humidity: 95 %

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 96000 X / Nominal defocus max: 1500 nm / Nominal defocus min: 300 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

-
Processing

EM softwareName: PHENIX / Version: 1.19rc4_4035: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.4 Å / Resolution method: FSC 3 SIGMA CUT-OFF / Num. of particles: 100204 / Algorithm: FOURIER SPACE / Num. of class averages: 2 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Target criteria: Cross_correlation coefficient
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.003239958
ELECTRON MICROSCOPYf_angle_d0.545351384
ELECTRON MICROSCOPYf_dihedral_angle_d13.2383622
ELECTRON MICROSCOPYf_chiral_restr0.03643437
ELECTRON MICROSCOPYf_plane_restr0.00523929

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more