[English] 日本語
Yorodumi
- PDB-3j7p: Structure of the 80S mammalian ribosome bound to eEF2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3j7p
TitleStructure of the 80S mammalian ribosome bound to eEF2
Components
  • (Ribosomal protein ...) x 77
  • 18S ribosomal RNA
  • 28S ribosomal RNA
  • 5.8S ribosomal RNA
  • 5S ribosomal RNA
  • Eukaryotic elongation factor 2EEF2
KeywordsRIBOSOME / mammalian / Sec61 / translocation / translation / eEF2
Function / homology
Function and homology information


TNFR1-mediated ceramide production / Translation initiation complex formation / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / SCF-beta-TrCP mediated degradation of Emi1 / Assembly of the pre-replicative complex / VLDLR internalisation and degradation / Interferon alpha/beta signaling / Negative regulators of DDX58/IFIH1 signaling / RAS processing ...TNFR1-mediated ceramide production / Translation initiation complex formation / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / SCF-beta-TrCP mediated degradation of Emi1 / Assembly of the pre-replicative complex / VLDLR internalisation and degradation / Interferon alpha/beta signaling / Negative regulators of DDX58/IFIH1 signaling / RAS processing / Inactivation of CSF3 (G-CSF) signaling / Regulation of BACH1 activity / KEAP1-NFE2L2 pathway / Regulation of NF-kappa B signaling / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Translesion synthesis by REV1 / Recognition of DNA damage by PCNA-containing replication complex / Translesion Synthesis by POLH / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Downregulation of ERBB4 signaling / 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 / 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 / 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) / Stimuli-sensing channels / FCERI mediated NF-kB activation / Regulation of innate immune responses to cytosolic DNA / Autodegradation of the E3 ubiquitin ligase COP1 / Deactivation of the beta-catenin transactivating complex / ABC-family proteins mediated transport / 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 / Asymmetric localization of PCP proteins / 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 / Regulation of RAS by GAPs / 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) / MAPK6/MAPK4 signaling / UCH proteinases / Josephin domain DUBs / Ub-specific processing proteases / Ovarian tumor domain proteases / Metalloprotease DUBs / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / DNA Damage Recognition in GG-NER / Formation of Incision Complex in GG-NER / Gap-filling DNA repair synthesis and ligation in GG-NER / Dual Incision in GG-NER / Fanconi Anemia Pathway / Regulation of TP53 Activity through Phosphorylation / Regulation of TP53 Degradation / Regulation of TP53 Activity through Methylation / Negative regulation of MET activity / Orc1 removal from chromatin / CDK-mediated phosphorylation and removal of Cdc6 / Cyclin D associated events in G1 / G2/M Checkpoints / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Ubiquitin-dependent degradation of Cyclin D / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Cargo recognition for clathrin-mediated endocytosis / Downregulation of ERBB2 signaling / Synthesis of active ubiquitin: roles of E1 and E2 enzymes
Similarity search - Function
: / 40S ribosomal protein SA / Ribosomal protein L2, archaeal-type / 40S ribosomal protein SA, C-terminal domain / 40S ribosomal protein SA C-terminus / : / Ribosomal protein S26e signature. / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e ...: / 40S ribosomal protein SA / Ribosomal protein L2, archaeal-type / 40S ribosomal protein SA, C-terminal domain / 40S ribosomal protein SA C-terminus / : / Ribosomal protein S26e signature. / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Ribosomal protein S21e, conserved site / Ribosomal protein S21e signature. / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / Ribosomal protein S2, eukaryotic / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein L29e / Ribosomal L29e protein family / Ribosomal protein S10, eukaryotic/archaeal / 40S Ribosomal protein S10 / S27a-like superfamily / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Ribosomal protein L38e / Plectin/S10, N-terminal / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / Plectin/S10 domain / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S17e, conserved site / Ribosomal protein S17e signature. / Ribosomal protein S8e subdomain, eukaryotes / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal L40e family / Ribosomal protein L44e signature. / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein L40e superfamily / Ribosomal protein L27e, conserved site / Ribosomal protein L27e signature. / Ribosomal protein L13e / Ribosomal protein L13e / Ribosomal protein L19, eukaryotic / Ribosomal protein S19e / Ribosomal protein S19e / Ribosomal_S19e / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein S19A/S15e / Ribosomal protein S8e, conserved site / Ribosomal protein S8e signature. / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S4e signature. / Ribosomal protein L44e / Ribosomal protein L44 / Ribosomal protein S17e / Ribosomal protein S17e-like superfamily / Ribosomal S17 / Ribosomal protein L34e, conserved site / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / Ribosomal protein L34e signature. / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein S4e, N-terminal / RS4NT (NUC023) domain / Eukaryotic Ribosomal Protein L27, KOW domain / Ribosomal protein 60S L18 and 50S L18e / Ribosomal protein L30e signature 2. / Ribosomal protein L30e, conserved site / Ribosomal protein L27e / Ribosomal protein L27e superfamily / Ribosomal L27e protein family / Ribosomal protein S7e / Ribosomal protein S7e / 40S ribosomal protein S11, N-terminal / Ribosomal protein S4, KOW domain / Ribosomal_S17 N-terminal / Ribosomal protein S4e / Ribosomal protein S4e, central region / Ribosomal protein S4e, central domain superfamily / Ribosomal family S4e / Ribosomal protein L39e, conserved site / Ribosomal protein L39e signature. / 60S ribosomal protein L19 / Ribosomal protein S23, eukaryotic/archaeal / 60S ribosomal protein L35 / Ribosomal protein L34Ae / Ribosomal protein L34e / Ribosomal protein L35Ae, conserved site
Similarity search - Domain/homology
RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein eL14 / Large ribosomal subunit protein eL27 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein eS1 / Large ribosomal subunit protein uL15 / 40S ribosomal protein S19 ...RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein eL14 / Large ribosomal subunit protein eL27 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein eS1 / Large ribosomal subunit protein uL15 / 40S ribosomal protein S19 / Uncharacterized protein / 40S ribosomal protein S4 / Large ribosomal subunit protein eL21 / S10_plectin domain-containing protein / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein eL20 / 40S ribosomal protein S11 / Ribosomal protein L23/L25 N-terminal domain-containing protein / Large ribosomal subunit protein eL19 / Large ribosomal subunit protein eL30 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein eL38 / Large ribosomal subunit protein eL34 / Ribosomal protein S5 / 40S ribosomal protein S8 / : / Uncharacterized protein / 40S ribosomal protein S27a / 40S ribosomal protein S7 / Large ribosomal subunit protein eL18 / Large ribosomal subunit protein uL24 / Ribosomal protein L15 / Large ribosomal subunit protein uL6 / 60S ribosomal protein L13 / : / Large ribosomal subunit protein eL39 / Small ribosomal subunit protein eS26 / Large ribosomal subunit protein eL21 / Small ribosomal subunit protein uS13 / Large ribosomal subunit protein uL14 / Small ribosomal subunit protein uS19 / Large ribosomal subunit protein eL31 / Ubiquitin-ribosomal protein eL40 fusion protein / Small ribosomal subunit protein eS21 / Small ribosomal subunit protein RACK1 / Large ribosomal subunit protein eL22 / Large ribosomal subunit protein eL42 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS9 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein eL34 / Large ribosomal subunit protein uL29 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein eS17 / 60S ribosomal protein L12 / Large ribosomal subunit protein eL32 / Small ribosomal subunit protein eS28 / Small ribosomal subunit protein uS12 / Large ribosomal subunit protein eL29 / Large ribosomal subunit protein eL18
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsVoorhees, R.M. / Fernandez, I.S. / Scheres, S.H.W. / Hegde, R.S.
CitationJournal: Cell / Year: 2014
Title: Structure of the mammalian ribosome-Sec61 complex to 3.4 Å resolution.
Authors: Rebecca M Voorhees / Israel S Fernández / Sjors H W Scheres / Ramanujan S Hegde /
Abstract: Cotranslational protein translocation is a universally conserved process for secretory and membrane protein biosynthesis. Nascent polypeptides emerging from a translating ribosome are either ...Cotranslational protein translocation is a universally conserved process for secretory and membrane protein biosynthesis. Nascent polypeptides emerging from a translating ribosome are either transported across or inserted into the membrane via the ribosome-bound Sec61 channel. Here, we report structures of a mammalian ribosome-Sec61 complex in both idle and translating states, determined to 3.4 and 3.9 Å resolution. The data sets permit building of a near-complete atomic model of the mammalian ribosome, visualization of A/P and P/E hybrid-state tRNAs, and analysis of a nascent polypeptide in the exit tunnel. Unprecedented chemical detail is observed for both the ribosome-Sec61 interaction and the conformational state of Sec61 upon ribosome binding. Comparison of the maps from idle and translating complexes suggests how conformational changes to the Sec61 channel could facilitate translocation of a secreted polypeptide. The high-resolution structure of the mammalian ribosome-Sec61 complex provides a valuable reference for future functional and structural studies.
History
DepositionAug 1, 2014Deposition site: RCSB / Processing site: RCSB
SupersessionSep 3, 2014ID: 3J74, 4W21, 4W22, 4W23
Revision 1.0Sep 3, 2014Provider: repository / Type: Initial release
SupersessionDec 10, 2014ID: 4W21, 4W22, 4W23
Revision 1.1Dec 10, 2014Group: Other
Revision 1.2Dec 17, 2014Group: Other
Revision 1.3Apr 15, 2015Group: Non-polymer description
Revision 1.4Jul 18, 2018Group: Advisory / Data collection
Category: em_image_scans / em_software / pdbx_database_PDB_obs_spr
Item: _em_software.image_processing_id / _em_software.name / _pdbx_database_PDB_obs_spr.replace_pdb_id

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-2646
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
5: 28S ribosomal RNA
7: 5S ribosomal RNA
8: 5.8S ribosomal RNA
A: Ribosomal protein uL2
B: Ribosomal protein uL3
C: Ribosomal protein uL4
D: Ribosomal protein uL18
E: Ribosomal protein eL6
F: Ribosomal protein uL30
G: Ribosomal protein eL8
H: Ribosomal protein uL6
I: Ribosomal protein uL16
J: Ribosomal protein uL5
K: Ribosomal protein uL11
L: Ribosomal protein eL13
M: Ribosomal protein eL14
N: Ribosomal protein eL15
O: Ribosomal protein uL13
P: Ribosomal protein uL22
Q: Ribosomal protein eL18
R: Ribosomal protein eL19
S: Ribosomal protein eL20
T: Ribosomal protein eL21
U: Ribosomal protein eL22
V: Ribosomal protein uL14
W: Ribosomal protein eL24
X: Ribosomal protein uL23
Y: Ribosomal protein uL24
Z: Ribosomal protein eL27
a: Ribosomal protein uL15
b: Ribosomal protein eL29
c: Ribosomal protein eL30
d: Ribosomal protein eL31
e: Ribosomal protein eL32
f: Ribosomal protein eL33
g: Ribosomal protein eL34
h: Ribosomal protein uL29
i: Ribosomal protein eL36
j: Ribosomal protein eL37
k: Ribosomal protein eL38
l: Ribosomal protein eL39
m: Ribosomal protein eL40
n: Ribosomal protein eL41
o: Ribosomal protein eL42
p: Ribosomal protein eL43
q: Ribosomal protein uL10
r: Ribosomal protein eL28
4: Eukaryotic elongation factor 2
S2: 18S ribosomal RNA
SA: Ribosomal protein uS2
SB: Ribosomal protein eS1
SC: Ribosomal protein uS5
SD: Ribosomal protein uS3
SE: Ribosomal protein eS4
SF: Ribosomal protein uS7
SG: Ribosomal protein eS6
SH: Ribosomal protein eS7
SI: Ribosomal protein eS8
SJ: Ribosomal protein uS4
SK: Ribosomal protein eS10
SL: Ribosomal protein uS17
SM: Ribosomal protein eS12
SN: Ribosomal protein uS15
SO: Ribosomal protein uS11
SP: Ribosomal protein uS19
SQ: Ribosomal protein uS9
SR: Ribosomal protein eS17
SS: Ribosomal protein uS13
ST: Ribosomal protein eS19
SU: Ribosomal protein uS10
SV: Ribosomal protein eS21
SW: Ribosomal protein uS8
SX: Ribosomal protein uS12
SY: Ribosomal protein eS24
SZ: Ribosomal protein es25
Sa: Ribosomal protein eS26
Sb: Ribosomal protein eS27
Sc: Ribosomal protein eS28
Sd: Ribosomal protein uS14
Se: Ribosomal protein eS30
Sf: Ribosomal protein eS31
Sg: Ribosomal protein RACK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,407,321252
Polymers3,403,02582
Non-polymers4,296170
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

-
Components

-
RNA chain , 4 types, 4 molecules 578S2

#1: RNA chain 28S ribosomal RNA /


Mass: 1187230.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas
#2: RNA chain 5S ribosomal RNA /


Mass: 38691.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas
#3: RNA chain 5.8S ribosomal RNA /


Mass: 50143.648 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas
#49: RNA chain 18S ribosomal RNA /


Mass: 561958.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas

+
Ribosomal protein ... , 77 types, 77 molecules ABCDEFGHIJKLMNOPQRSTUVWXYZabcd...

#4: Protein Ribosomal protein uL2 /


Mass: 28088.863 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: F2Z567
#5: Protein Ribosomal protein uL3 /


Mass: 44759.359 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas
#6: Protein Ribosomal protein uL4 /


Mass: 41635.141 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas
#7: Protein Ribosomal protein uL18 /


Mass: 34417.738 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: F1S530
#8: Protein Ribosomal protein eL6 /


Mass: 27052.178 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas
#9: Protein Ribosomal protein uL30 /


Mass: 26590.725 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas
#10: Protein Ribosomal protein eL8 /


Mass: 30166.918 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: I3LVI8
#11: Protein Ribosomal protein uL6 /


Mass: 21899.471 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: I3LP78
#12: Protein Ribosomal protein uL16 /


Mass: 24465.791 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas
#13: Protein Ribosomal protein uL5 /


Mass: 20248.359 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: Q29205
#14: Protein Ribosomal protein uL11 /


Mass: 17689.461 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: Q6QAS5
#15: Protein Ribosomal protein eL13 /


Mass: 24365.762 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: I3LSD3
#16: Protein Ribosomal protein eL14 /


Mass: 23383.051 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: A1XQU3
#17: Protein Ribosomal protein eL15 /


Mass: 24207.285 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: I3LK33
#18: Protein Ribosomal protein uL13 /


Mass: 23765.492 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: F1RI01
#19: Protein Ribosomal protein uL22 /


Mass: 17757.627 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas
#20: Protein Ribosomal protein eL18 /


Mass: 21588.586 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: I3L6F1, UniProt: Q95342*PLUS
#21: Protein Ribosomal protein eL19 /


Mass: 23567.260 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: F2Z546
#22: Protein Ribosomal protein eL20 /


Mass: 26103.418 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: F1S935
#23: Protein Ribosomal protein eL21 /


Mass: 18609.988 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: F1RTJ9, UniProt: P49666*PLUS
#24: Protein Ribosomal protein eL22 /


Mass: 14784.962 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: P67985
#25: Protein Ribosomal protein uL14 /


Mass: 14892.505 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: P62831
#26: Protein Ribosomal protein eL24 /


Mass: 17825.111 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas
#27: Protein Ribosomal protein uL23 /


Mass: 17740.193 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: F2Z522
#28: Protein Ribosomal protein uL24 /


Mass: 17303.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: I3L7Y1
#29: Protein Ribosomal protein eL27 /


Mass: 15835.831 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: A1XQU5
#30: Protein Ribosomal protein uL15 /


Mass: 16631.520 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: F1RGC0
#31: Protein Ribosomal protein eL29 /


Mass: 17545.836 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: Q95281
#32: Protein Ribosomal protein eL30 /


Mass: 12805.092 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: F2Z554
#33: Protein Ribosomal protein eL31 /


Mass: 14494.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: P62901
#34: Protein Ribosomal protein eL32 /


Mass: 15898.932 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: Q6QAT0
#35: Protein Ribosomal protein eL33 /


Mass: 12564.743 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: F2Z5Q8
#36: Protein Ribosomal protein eL34 /


Mass: 13326.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: F2Z5B9, UniProt: Q29223*PLUS
#37: Protein Ribosomal protein uL29 /


Mass: 14591.649 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: Q29361
#38: Protein Ribosomal protein eL36 /


Mass: 12290.859 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: F2Z5K6
#39: Protein Ribosomal protein eL37 /


Mass: 10102.944 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas
#40: Protein Ribosomal protein eL38 /


Mass: 8238.948 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: F2Z568
#41: Protein Ribosomal protein eL39 /


Mass: 6426.759 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: K7GP63
#42: Protein Ribosomal protein eL40 /


Mass: 14758.394 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: P63053
#43: Protein/peptide Ribosomal protein eL41 /


Mass: 3473.451 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas
#44: Protein Ribosomal protein eL42 /


Mass: 12476.973 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: P83884
#45: Protein Ribosomal protein eL43 /


Mass: 10168.153 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas
#46: Protein Ribosomal protein uL10 /


Mass: 22217.840 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas
#47: Protein Ribosomal protein eL28 /


Mass: 14301.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas
#50: Protein Ribosomal protein uS2 /


Mass: 32958.012 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: Q4GWZ2
#51: Protein Ribosomal protein eS1 /


Mass: 29931.912 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: B6V8C8
#52: Protein Ribosomal protein uS5 /


Mass: 24091.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas
#53: Protein Ribosomal protein uS3 /


Mass: 26729.369 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: Q0Z8U2
#54: Protein Ribosomal protein eS4 /


Mass: 29654.869 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: F1RQ91
#55: Protein Ribosomal protein uS7 /


Mass: 22913.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: F2Z5E6
#56: Protein Ribosomal protein eS6 /


Mass: 28751.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas
#57: Protein Ribosomal protein eS7 /


Mass: 22168.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: I3L5B2
#58: Protein Ribosomal protein eS8 /


Mass: 24263.387 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: F2Z5F5
#59: Protein Ribosomal protein uS4 /


Mass: 22641.564 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas
#60: Protein Ribosomal protein eS10 /


Mass: 18967.861 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: F1RZ28
#61: Protein Ribosomal protein uS17 /


Mass: 18468.826 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: F2Z4Y8
#62: Protein Ribosomal protein eS12 /


Mass: 13776.030 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas
#63: Protein Ribosomal protein uS15 /


Mass: 17259.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas
#64: Protein Ribosomal protein uS11 /


Mass: 16302.772 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas
#65: Protein Ribosomal protein uS19 /


Mass: 17076.207 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: P62844
#66: Protein Ribosomal protein uS9 /


Mass: 16477.377 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: Q29201
#67: Protein Ribosomal protein eS17 /


Mass: 15552.119 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: Q6QAP7
#68: Protein Ribosomal protein uS13 /


Mass: 17759.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: P62272
#69: Protein Ribosomal protein eS19 /


Mass: 16091.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: F1RGG1
#70: Protein Ribosomal protein uS10 /


Mass: 13357.730 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: A1XQU9
#71: Protein Ribosomal protein eS21 /


Mass: 9124.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: P63221
#72: Protein Ribosomal protein uS8 /


Mass: 14865.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas
#73: Protein Ribosomal protein uS12 /


Mass: 15854.684 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: Q6SA96
#74: Protein Ribosomal protein eS24 /


Mass: 15366.284 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas
#75: Protein Ribosomal protein es25 /


Mass: 13776.224 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas
#76: Protein Ribosomal protein eS26 /


Mass: 13047.532 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: P49171
#77: Protein Ribosomal protein eS27 /


Mass: 9480.186 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas
#78: Protein Ribosomal protein eS28 /


Mass: 7855.052 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: Q6QAT1
#79: Protein Ribosomal protein uS14 /


Mass: 6612.728 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: Q6QAP6
#80: Protein Ribosomal protein eS30 /


Mass: 14411.733 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas
#81: Protein Ribosomal protein eS31 /


Mass: 18004.041 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: F2Z5U0
#82: Protein Ribosomal protein RACK1 /


Mass: 35115.652 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: P63246

-
Protein , 1 types, 1 molecules 4

#48: Protein Eukaryotic elongation factor 2 / EEF2


Mass: 95232.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas

-
Non-polymers , 2 types, 170 molecules

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


Mass: 24.305 Da / Num. of mol.: 166 / Source method: obtained synthetically / Formula: Mg
#84: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: The 80S-eEF2 complex purified from porcine pancreas / Type: RIBOSOME
Buffer solutionName: 50 mM HEPES, 200 mM potassium acetate, 15 mM magnesium acetate, 1 mM DTT, 0.25% Digitonin
pH: 7.5
Details: 50 mM HEPES, 200 mM potassium acetate, 15 mM magnesium acetate, 1 mM DTT, 0.25% Digitonin
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: Quantifoil R2/2 400 mesh copper grids
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temp: 120 K
Details: 3 uL sample was incubated on the grid for 30 seconds and blotted for 9 seconds before being plunged into liquid ethane (FEI VITROBOT MARK IV).

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS / Date: Apr 7, 2014
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 59000 X / Calibrated magnification: 104478 X / Nominal defocus max: 3500 nm / Nominal defocus min: 2500 nm / Cs: 2.7 mm
Specimen holderSpecimen holder type: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature: 70 K / Tilt angle max: 0 ° / Tilt angle min: 0 °
Image recordingElectron dose: 27 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k) / Details: Back-thinned
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

-
Processing

EM software
IDNameCategory
1REFMACmodel fitting
2RELION3D reconstruction
CTF correctionDetails: Each particle
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionMethod: Single particleSingle particle analysis / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 36667 / Nominal pixel size: 1.34 Å / Symmetry type: POINT
Atomic model buildingB value: 37 / Protocol: OTHER / Space: RECIPROCAL / Target criteria: R-factor and FSC / Details: METHOD--Maximum likelihood
Atomic model building
IDPDB-ID 3D fitting-ID
13J3A

3j3a
PDB Unreleased entry

1
23J3B

3j3b
PDB Unreleased entry

1
33J3D

3j3d
PDB Unreleased entry

1
43J3F

3j3f
PDB Unreleased entry

1
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms100258 121258 170 0 221686

+
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://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