[English] 日本語
Yorodumi
- PDB-9spi: CRYO-EM STRUCTURE OF HUMAN 80S RIBOSOME WITH A/P/E-SITE TRNA AND ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9spi
TitleCRYO-EM STRUCTURE OF HUMAN 80S RIBOSOME WITH A/P/E-SITE TRNA AND MRNA CONTAINING URIDINE
Components
  • (40S ribosomal protein ...) x 29
  • (60S ribosomal protein ...) x 32
  • (Large ribosomal subunit protein ...) x 9
  • 18S rRNA
  • 28S rRNA
  • 5.8S rRNA
  • 5S rRNA
  • E site tRNA
  • P site tRNA Arg-ACG
  • Receptor of activated protein C kinase 1
  • Small ribosomal subunit protein eS4, X isoform
  • Synthetic mRNA
  • Ubiquitin
  • Ubiquitin-like FUBI-ribosomal protein eS30 fusion protein
  • Ubiquitin-ribosomal protein eL40 fusion protein
  • tRNA-Ile-AAT-9-1
KeywordsRIBOSOME / CRYO-EM STRUCTURE / HUMAN / 80S / N1-METHYLPSEUDOURIDINE
Function / homology
Function and homology information


embryonic brain development / translation at presynapse / exit from mitosis / optic nerve development / response to insecticide / eukaryotic 80S initiation complex / negative regulation of protein neddylation / regulation of translation involved in cellular response to UV / axial mesoderm development / negative regulation of formation of translation preinitiation complex ...embryonic brain development / translation at presynapse / exit from mitosis / optic nerve development / response to insecticide / eukaryotic 80S initiation complex / negative regulation of protein neddylation / regulation of translation involved in cellular response to UV / axial mesoderm development / negative regulation of formation of translation preinitiation complex / regulation of G1 to G0 transition / retinal ganglion cell axon guidance / oxidized pyrimidine DNA binding / response to TNF agonist / negative regulation of endoplasmic reticulum unfolded protein response / positive regulation of base-excision repair / ribosomal protein import into nucleus / protein-DNA complex disassembly / positive regulation of respiratory burst involved in inflammatory response / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of gastrulation / 90S preribosome assembly / protein tyrosine kinase inhibitor activity / positive regulation of endodeoxyribonuclease activity / nucleolus organization / IRE1-RACK1-PP2A complex / positive regulation of Golgi to plasma membrane protein transport / TNFR1-mediated ceramide production / alpha-beta T cell differentiation / negative regulation of DNA repair / negative regulation of RNA splicing / GAIT complex / positive regulation of DNA damage response, signal transduction by p53 class mediator / TORC2 complex binding / G1 to G0 transition / supercoiled DNA binding / NF-kappaB complex / neural crest cell differentiation / oxidized purine DNA binding / cysteine-type endopeptidase activator activity involved in apoptotic process / middle ear morphogenesis / positive regulation of ubiquitin-protein transferase activity / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / negative regulation of bicellular tight junction assembly / regulation of establishment of cell polarity / ubiquitin-like protein conjugating enzyme binding / rRNA modification in the nucleus and cytosol / negative regulation of phagocytosis / erythrocyte homeostasis / Formation of the ternary complex, and subsequently, the 43S complex / cytoplasmic side of rough endoplasmic reticulum membrane / negative regulation of ubiquitin protein ligase activity / protein kinase A binding / laminin receptor activity / homeostatic process / ion channel inhibitor activity / Ribosomal scanning and start codon recognition / pigmentation / Translation initiation complex formation / positive regulation of mitochondrial depolarization / macrophage chemotaxis / lung morphogenesis / positive regulation of T cell receptor signaling pathway / fibroblast growth factor binding / negative regulation of Wnt signaling pathway / positive regulation of natural killer cell proliferation / monocyte chemotaxis / TOR signaling / negative regulation of translational frameshifting / BH3 domain binding / positive regulation of activated T cell proliferation / Protein hydroxylation / SARS-CoV-1 modulates host translation machinery / iron-sulfur cluster binding / regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / regulation of cell division / cellular response to ethanol / mTORC1-mediated signalling / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / cellular response to actinomycin D / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Eukaryotic Translation Termination / blastocyst development / positive regulation of GTPase activity / negative regulation of ubiquitin-dependent protein catabolic process / protein serine/threonine kinase inhibitor activity / SRP-dependent cotranslational protein targeting to membrane / Response of EIF2AK4 (GCN2) to amino acid deficiency / ubiquitin ligase inhibitor activity / Viral mRNA Translation / negative regulation of respiratory burst involved in inflammatory response / positive regulation of signal transduction by p53 class mediator / protein localization to nucleus / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression
Similarity search - Function
40S ribosomal protein SA / Ribosomal protein L6, N-terminal / Ribosomal protein L6, N-terminal domain / 40S ribosomal protein SA, C-terminal domain / 40S ribosomal protein SA C-terminus / Ubiquitin-like protein FUBI / Ribosomal protein L30e / Ribosomal protein L28e / Ribosomal L15/L27a, N-terminal / Ribosomal protein L23 ...40S ribosomal protein SA / Ribosomal protein L6, N-terminal / Ribosomal protein L6, N-terminal domain / 40S ribosomal protein SA, C-terminal domain / 40S ribosomal protein SA C-terminus / Ubiquitin-like protein FUBI / Ribosomal protein L30e / Ribosomal protein L28e / Ribosomal L15/L27a, N-terminal / Ribosomal protein L23 / Ribosomal protein L2, archaeal-type / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / metallochaperone-like domain / TRASH domain / : / Ribosomal protein S26e signature. / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein S21e, conserved site / Ribosomal protein S21e signature. / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / : / Ribosomal protein S12e signature. / Ribosomal protein L29e / Ribosomal L29e protein family / Ribosomal protein S12e / Ribosomal protein L27e, conserved site / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein L27e signature. / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / Ribosomal protein S2, eukaryotic / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / Ribosomal protein L13e / Ribosomal protein L13e / Ribosomal protein L19, eukaryotic / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / S27a-like superfamily / Ribosomal protein L44e signature. / Ribosomal protein L19/L19e conserved site / 40S Ribosomal protein S10 / Ribosomal protein L19e signature. / Ribosomal protein L24e, conserved site / : / Ribosomal protein L24e signature. / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein L10e / Ribosomal protein L6e signature. / Plectin/S10, N-terminal / Plectin/S10 domain / Ribosomal protein L18/L18-A/B/e, conserved site / Ribosomal protein L18e signature. / Ribosomal protein L34e, conserved site / Ribosomal protein L34e signature. / : / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal L40e family / Ribosomal protein L23/L25, N-terminal / Ribosomal protein L23, N-terminal domain / Ribosomal protein S30 / : / Ribosomal protein S30 / Ribosomal protein L44e / Ribosomal protein L44 / Ribosomal protein S7e signature. / Ribosomal protein S25 / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / S25 ribosomal protein / Ribosomal protein L30e signature 1. / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Ribosomal protein L36e signature. / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal protein S8e subdomain, eukaryotes / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / Ribosomal protein 60S L18 and 50S L18e / Ribosomal protein S27a / Ribosomal protein S17e, conserved site / Ribosomal protein S27a / Ribosomal protein S17e signature. / Ribosomal protein S27a / Ribosomal protein L35Ae, conserved site
Similarity search - Domain/homology
HYGROMYCIN B / : / 1,4-DIAMINOBUTANE / SPERMIDINE / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) ...HYGROMYCIN B / : / 1,4-DIAMINOBUTANE / SPERMIDINE / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein eS17 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS5 / Large ribosomal subunit protein eL33 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL22 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein eS12 / Large ribosomal subunit protein eL13 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein eL22 / Large ribosomal subunit protein uL4 / Small ribosomal subunit protein eS19 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL13 / Small ribosomal subunit protein eS27 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein eL21 / Large ribosomal subunit protein eL28 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein eS10 / Large ribosomal subunit protein eL29 / Large ribosomal subunit protein eL34 / Large ribosomal subunit protein eL14 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein eS1 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein eL15 / Large ribosomal subunit protein eL27 / Large ribosomal subunit protein eL43 / Large ribosomal subunit protein eL37 / Small ribosomal subunit protein eS7 / Small ribosomal subunit protein eS8 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein eL8 / Small ribosomal subunit protein eS4, X isoform / Large ribosomal subunit protein uL23 / Small ribosomal subunit protein eS6 / Large ribosomal subunit protein uL14 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein eS24 / Small ribosomal subunit protein eS25 / Small ribosomal subunit protein eS26 / Small ribosomal subunit protein eS28 / Ubiquitin-like FUBI-ribosomal protein eS30 fusion protein / Large ribosomal subunit protein eL30 / Large ribosomal subunit protein eL39 / Large ribosomal subunit protein eL31 / Large ribosomal subunit protein eL32 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein uL2 / Small ribosomal subunit protein eS32 / Ubiquitin-ribosomal protein eS31 fusion protein / Ubiquitin-ribosomal protein eL40 fusion protein / Large ribosomal subunit protein eL38 / Small ribosomal subunit protein eS21 / Small ribosomal subunit protein RACK1 / Large ribosomal subunit protein eL24 / Large ribosomal subunit protein eL42 / Large ribosomal subunit protein eL19 / Large ribosomal subunit protein eL20 / Large ribosomal subunit protein eL6 / Large ribosomal subunit protein eL18 / Large ribosomal subunit protein eL36
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.4 Å
AuthorsRajan, K.S. / Yonath, A.
Funding support Israel, 1items
OrganizationGrant numberCountry
The Helen and Milton A. Kimmelman Center for Biomolecular Structure and Assembly Israel
CitationJournal: Nature / Year: 2026
Title: N-Methylpseudouridine directly modulates translation dynamics.
Authors: Batsheva Rozman / Karin Broennimann / K Shanmugha Rajan / Aharon Nachshon / Chiranjeet Saha / Tamar Arazi / Vishnu Mohan / Tamar Geiger / Clayton J Wollner / Justin M Richner / Eric Westhof ...Authors: Batsheva Rozman / Karin Broennimann / K Shanmugha Rajan / Aharon Nachshon / Chiranjeet Saha / Tamar Arazi / Vishnu Mohan / Tamar Geiger / Clayton J Wollner / Justin M Richner / Eric Westhof / Ada Yonath / Anat Bashan / Noam Stern-Ginossar /
Abstract: The considerable success of mRNA vaccines against SARS-CoV-2 has underscored the potential of synthetic mRNA as a transformative biomedical technology. A critical feature of this approach is the ...The considerable success of mRNA vaccines against SARS-CoV-2 has underscored the potential of synthetic mRNA as a transformative biomedical technology. A critical feature of this approach is the incorporation of the modified nucleoside N-methylpseudouridine (mΨ), which enhances antigen expression while reducing immunogenicity. However, a comprehensive understanding of how mΨ influences translation remains incomplete. Here we use ribosome profiling at the subcodon resolution to show that mΨ increases ribosome density on synthetic mRNAs, leading to higher protein production independent of innate immune activation or eIF2α phosphorylation. We find that mΨ directly slows ribosome movement in defined sequence contexts while simultaneously promoting translation initiation. Structural studies using cryo-electron microscopy reveal that mΨ alters interactions within the ribosomal decoding centre, providing a mechanistic basis for slowed elongation. Furthermore, by introducing synonymous recoding that disrupts the modification-mediated changes in elongation, we show that the mΨ-dependent enhancement of protein output is modulated by codon composition, and that mΨ impact is strongest in mRNAs containing non-optimal codons with uridines at the wobble position. Together, these findings demonstrate that mΨ directly modulates translation dynamics, thereby increasing protein yield from synthetic mRNAs in specific sequence contexts.
History
DepositionSep 17, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 21, 2026Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
At: tRNA-Ile-AAT-9-1
Et: E site tRNA
L5: 28S rRNA
L7: 5S rRNA
L8: 5.8S rRNA
LA: Large ribosomal subunit protein uL2
LB: Large ribosomal subunit protein uL3
LC: 60S ribosomal protein L4
LD: 60S ribosomal protein L5
LE: Large ribosomal subunit protein eL6
LF: Large ribosomal subunit protein uL30
LG: 60S ribosomal protein L7a
LH: 60S ribosomal protein L9
LI: 60S ribosomal protein L10
LJ: 60S ribosomal protein L11
LL: Large ribosomal subunit protein eL13
LM: 60S ribosomal protein L14
LN: 60S ribosomal protein L15
LO: 60S ribosomal protein L13a
LP: 60S ribosomal protein L17
LQ: 60S ribosomal protein L18
LR: 60S ribosomal protein L19
LS: 60S ribosomal protein L18a
LT: 60S ribosomal protein L21
LU: 60S ribosomal protein L22
LV: 60S ribosomal protein L23
LW: 60S ribosomal protein L24
LX: 60S ribosomal protein L23a
LY: 60S ribosomal protein L26
LZ: 60S ribosomal protein L27
La: Large ribosomal subunit protein uL15
Lb: Large ribosomal subunit protein eL29
Lc: 60S ribosomal protein L30
Ld: 60S ribosomal protein L31
Le: 60S ribosomal protein L32
Lf: 60S ribosomal protein L35a
Lg: 60S ribosomal protein L34
Lh: 60S ribosomal protein L35
Li: 60S ribosomal protein L36
Lj: Large ribosomal subunit protein eL37
Lk: 60S ribosomal protein L38
Ll: 60S ribosomal protein L39
Lm: Ubiquitin-ribosomal protein eL40 fusion protein
Ln: 60S ribosomal protein L41
Lo: Large ribosomal subunit protein eL42
Lp: 60S ribosomal protein L37a
Lr: 60S ribosomal protein L28
Mr: Synthetic mRNA
Pt: P site tRNA Arg-ACG
S2: 18S rRNA
SA: 40S ribosomal protein SA
SB: 40S ribosomal protein S3a
SC: 40S ribosomal protein S2
SD: 40S ribosomal protein S3
SE: Small ribosomal subunit protein eS4, X isoform
SF: 40S ribosomal protein S5
SG: 40S ribosomal protein S6
SH: 40S ribosomal protein S7
SI: 40S ribosomal protein S8
SJ: 40S ribosomal protein S9
SK: 40S ribosomal protein S10
SL: 40S ribosomal protein S11
SM: 40S ribosomal protein S12
SN: 40S ribosomal protein S13
SO: 40S ribosomal protein S14
SP: 40S ribosomal protein S15
SQ: 40S ribosomal protein S16
SR: 40S ribosomal protein S17
SS: 40S ribosomal protein S18
ST: 40S ribosomal protein S19
SU: 40S ribosomal protein S20
SV: 40S ribosomal protein S21
SW: 40S ribosomal protein S15a
SX: 40S ribosomal protein S23
SY: 40S ribosomal protein S24
SZ: 40S ribosomal protein S25
Sa: 40S ribosomal protein S26
Sb: 40S ribosomal protein S27
Sc: 40S ribosomal protein S28
Sd: 40S ribosomal protein S29
Se: Ubiquitin-like FUBI-ribosomal protein eS30 fusion protein
Sf: Ubiquitin
Sg: Receptor of activated protein C kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,876,757387
Polymers3,864,78083
Non-polymers11,977304
Water179,1779946
1


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

-
Components

-
RNA chain , 8 types, 8 molecules AtEtL5L7L8MrPtS2

#1: RNA chain tRNA-Ile-AAT-9-1


Mass: 24794.680 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#2: RNA chain E site tRNA


Mass: 24231.510 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: 174924
#3: RNA chain 28S rRNA


Mass: 1640884.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#4: RNA chain 5S rRNA


Mass: 38691.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: 23898
#5: RNA chain 5.8S rRNA


Mass: 50171.703 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#48: RNA chain Synthetic mRNA


Mass: 2157.331 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#49: RNA chain P site tRNA Arg-ACG


Mass: 24579.697 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#50: RNA chain 18S rRNA


Mass: 603580.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)

-
Large ribosomal subunit protein ... , 9 types, 9 molecules LALBLELFLLLaLbLjLo

#6: Protein Large ribosomal subunit protein uL2 / 60S ribosomal protein L8


Mass: 28103.855 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62917
#7: Protein Large ribosomal subunit protein uL3 / 60S ribosomal protein L3 / HIV-1 TAR RNA-binding protein B / TARBP-B


Mass: 46224.133 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P39023
#10: Protein Large ribosomal subunit protein eL6 / 60S ribosomal protein L6 / Neoplasm-related protein C140 / Tax-responsive enhancer element-binding ...60S ribosomal protein L6 / Neoplasm-related protein C140 / Tax-responsive enhancer element-binding protein 107 / TaxREB107


Mass: 32810.176 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q02878
#11: Protein Large ribosomal subunit protein uL30 / 60S ribosomal protein L7


Mass: 29290.973 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P18124
#16: Protein Large ribosomal subunit protein eL13 / 60S ribosomal protein L13 / Breast basic conserved protein 1


Mass: 24321.682 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P26373
#31: Protein Large ribosomal subunit protein uL15


Mass: 16619.527 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46776
#32: Protein Large ribosomal subunit protein eL29 / 60S ribosomal protein L29 / Cell surface heparin-binding protein HIP


Mass: 17817.295 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P47914
#40: Protein Large ribosomal subunit protein eL37 / 60S ribosomal protein L37 / G1.16


Mass: 11111.032 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61927
#45: Protein Large ribosomal subunit protein eL42 / 60S ribosomal protein L36a / 60S ribosomal protein L44 / Cell growth-inhibiting gene 15 protein / ...60S ribosomal protein L36a / 60S ribosomal protein L44 / Cell growth-inhibiting gene 15 protein / Cell migration-inducing gene 6 protein


Mass: 12489.991 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P83881

+
60S ribosomal protein ... , 32 types, 32 molecules LCLDLGLHLILJLMLNLOLPLQLRLSLTLULVLWLXLYLZLcLdLeLfLgLhLiLkLlLnLpLr

#8: Protein 60S ribosomal protein L4 / 60S ribosomal protein L1 / Large ribosomal subunit protein uL4


Mass: 47804.621 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P36578
#9: Protein 60S ribosomal protein L5 / Large ribosomal subunit protein uL18


Mass: 34426.789 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46777
#12: Protein 60S ribosomal protein L7a / Large ribosomal subunit protein eL8 / PLA-X polypeptide / Surfeit locus protein 3


Mass: 30061.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62424
#13: Protein 60S ribosomal protein L9 / Large ribosomal subunit protein uL6


Mass: 21899.471 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P32969
#14: Protein 60S ribosomal protein L10 / Laminin receptor homolog / Large ribosomal subunit protein uL16 / Protein QM / Ribosomal protein ...Laminin receptor homolog / Large ribosomal subunit protein uL16 / Protein QM / Ribosomal protein L10 / Tumor suppressor QM


Mass: 24630.061 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P27635
#15: Protein 60S ribosomal protein L11 / CLL-associated antigen KW-12 / Large ribosomal subunit protein uL5


Mass: 20288.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62913
#17: Protein 60S ribosomal protein L14 / CAG-ISL 7 / Large ribosomal subunit protein eL14


Mass: 23485.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P50914
#18: Protein 60S ribosomal protein L15 / Large ribosomal subunit protein eL15


Mass: 24207.285 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61313
#19: Protein 60S ribosomal protein L13a / 23 kDa highly basic protein / Large ribosomal subunit protein uL13


Mass: 23633.412 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P40429
#20: Protein 60S ribosomal protein L17 / 60S ribosomal protein L23 / Large ribosomal subunit protein uL22 / PD-1


Mass: 21443.170 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P18621
#21: Protein 60S ribosomal protein L18 / Large ribosomal subunit protein eL18


Mass: 21687.676 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q07020
#22: Protein 60S ribosomal protein L19 / Large ribosomal subunit protein eL19


Mass: 23535.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P84098
#23: Protein 60S ribosomal protein L18a / Large ribosomal subunit protein eL20


Mass: 20808.514 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q02543
#24: Protein 60S ribosomal protein L21 / Large ribosomal subunit protein eL21


Mass: 18609.988 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46778
#25: Protein 60S ribosomal protein L22 / EBER-associated protein / EAP / Epstein-Barr virus small RNA-associated protein / Heparin-binding ...EBER-associated protein / EAP / Epstein-Barr virus small RNA-associated protein / Heparin-binding protein HBp15 / Large ribosomal subunit protein eL22


Mass: 14813.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P35268
#26: Protein 60S ribosomal protein L23 / 60S ribosomal protein L17 / Large ribosomal subunit protein uL14


Mass: 14892.505 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62829
#27: Protein 60S ribosomal protein L24 / 60S ribosomal protein L30 / Large ribosomal subunit protein eL24


Mass: 17825.111 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P83731
#28: Protein 60S ribosomal protein L23a / Large ribosomal subunit protein uL23


Mass: 17740.193 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62750
#29: Protein 60S ribosomal protein L26 / Large ribosomal subunit protein uL24


Mass: 17303.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61254
#30: Protein 60S ribosomal protein L27 / Large ribosomal subunit protein eL27


Mass: 15835.831 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61353
#33: Protein 60S ribosomal protein L30 / Large ribosomal subunit protein eL30


Mass: 12805.092 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62888
#34: Protein 60S ribosomal protein L31 / Large ribosomal subunit protein eL31


Mass: 14494.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62899
#35: Protein 60S ribosomal protein L32 / Large ribosomal subunit protein eL32


Mass: 15898.932 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62910
#36: Protein 60S ribosomal protein L35a / Cell growth-inhibiting gene 33 protein / Large ribosomal subunit protein eL33


Mass: 12564.743 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P18077
#37: Protein 60S ribosomal protein L34 / Large ribosomal subunit protein eL34


Mass: 13326.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P49207
#38: Protein 60S ribosomal protein L35 / Large ribosomal subunit protein uL29


Mass: 14593.624 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P42766
#39: Protein 60S ribosomal protein L36 / Large ribosomal subunit protein eL36


Mass: 12290.859 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y3U8
#41: Protein 60S ribosomal protein L38 / Large ribosomal subunit protein eL38


Mass: 8238.948 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P63173
#42: Protein 60S ribosomal protein L39 / Large ribosomal subunit protein eL39


Mass: 6426.759 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62891
#44: Protein/peptide 60S ribosomal protein L41 / HG12 / Large ribosomal subunit protein eL41


Mass: 3473.451 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62945
#46: Protein 60S ribosomal protein L37a / Large ribosomal subunit protein eL43


Mass: 10299.350 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61513
#47: Protein 60S ribosomal protein L28 / Large ribosomal subunit protein eL28


Mass: 15784.622 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46779

-
Protein , 5 types, 5 molecules LmSESeSfSg

#43: Protein Ubiquitin-ribosomal protein eL40 fusion protein / CEP52 / Ubiquitin A-52 residue ribosomal protein fusion product 1


Mass: 14800.474 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62987
#55: Protein Small ribosomal subunit protein eS4, X isoform / 40S ribosomal protein S4 / SCR10 / Single copy abundant mRNA protein


Mass: 29654.869 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62701
#81: Protein Ubiquitin-like FUBI-ribosomal protein eS30 fusion protein / FAU ubiquitin like and ribosomal protein S30 fusion


Mass: 14415.724 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62861
#82: Protein Ubiquitin


Mass: 18004.041 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62979
#83: Protein Receptor of activated protein C kinase 1 / Cell proliferation-inducing gene 21 protein / Guanine nucleotide-binding protein subunit beta-2- ...Cell proliferation-inducing gene 21 protein / Guanine nucleotide-binding protein subunit beta-2-like 1 / Guanine nucleotide-binding protein subunit beta-like protein 12.3 / Human lung cancer oncogene 7 protein / HLC-7 / Receptor for activated C kinase / Small ribosomal subunit protein RACK1


Mass: 35115.652 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P63244

+
40S ribosomal protein ... , 29 types, 29 molecules SASBSCSDSFSGSHSISJSKSLSMSNSOSPSQSRSSSTSUSVSWSXSYSZSaSbScSd

#51: Protein 40S ribosomal protein SA / 37 kDa laminin receptor precursor / 37LRP / 37/67 kDa laminin receptor / LRP/LR / 67 kDa laminin ...37 kDa laminin receptor precursor / 37LRP / 37/67 kDa laminin receptor / LRP/LR / 67 kDa laminin receptor / 67LR / Colon carcinoma laminin-binding protein / Laminin receptor 1 / LamR / Laminin-binding protein precursor p40 / LBP/p40 / Multidrug resistance-associated protein MGr1-Ag / NEM/1CHD4 / Small ribosomal subunit protein uS2


Mass: 32883.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P08865
#52: Protein 40S ribosomal protein S3a / Small ribosomal subunit protein eS1 / v-fos transformation effector protein / Fte-1


Mass: 30002.061 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61247
#53: Protein 40S ribosomal protein S2 / 40S ribosomal protein S4 / Protein LLRep3 / Small ribosomal subunit protein uS5


Mass: 31376.516 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P15880
#54: Protein 40S ribosomal protein S3 / Small ribosomal subunit protein uS3


Mass: 26729.369 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: P23396, DNA-(apurinic or apyrimidinic site) lyase
#56: Protein 40S ribosomal protein S5 / Small ribosomal subunit protein uS7


Mass: 22913.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46782
#57: Protein 40S ribosomal protein S6 / Phosphoprotein NP33 / Small ribosomal subunit protein eS6


Mass: 28751.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62753
#58: Protein 40S ribosomal protein S7 / Small ribosomal subunit protein eS7


Mass: 22168.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62081
#59: Protein 40S ribosomal protein S8 / Small ribosomal subunit protein eS8


Mass: 24263.387 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62241
#60: Protein 40S ribosomal protein S9 / Small ribosomal subunit protein uS4


Mass: 22641.564 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46781
#61: Protein 40S ribosomal protein S10 / Small ribosomal subunit protein eS10


Mass: 18933.846 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46783
#62: Protein 40S ribosomal protein S11 / Small ribosomal subunit protein uS17


Mass: 18468.826 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62280
#63: Protein 40S ribosomal protein S12 / Small ribosomal subunit protein eS12


Mass: 14538.987 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P25398
#64: Protein 40S ribosomal protein S13 / Small ribosomal subunit protein uS15


Mass: 17259.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62277
#65: Protein 40S ribosomal protein S14 / Small ribosomal subunit protein uS11


Mass: 16302.772 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62263
#66: Protein 40S ribosomal protein S15 / RIG protein / Small ribosomal subunit protein uS19


Mass: 17076.207 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62841
#67: Protein 40S ribosomal protein S16 / Small ribosomal subunit protein uS9


Mass: 16477.377 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62249
#68: Protein 40S ribosomal protein S17 / Small ribosomal subunit protein eS17


Mass: 15578.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P08708
#69: Protein 40S ribosomal protein S18 / Ke-3 / Ke3 / Small ribosomal subunit protein uS13


Mass: 17759.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62269
#70: Protein 40S ribosomal protein S19 / Small ribosomal subunit protein eS19


Mass: 16091.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P39019
#71: Protein 40S ribosomal protein S20 / Small ribosomal subunit protein uS10


Mass: 13398.763 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P60866
#72: Protein 40S ribosomal protein S21 / Small ribosomal subunit protein eS21


Mass: 9124.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P63220
#73: Protein 40S ribosomal protein S15a / Small ribosomal subunit protein uS8


Mass: 14865.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62244
#74: Protein 40S ribosomal protein S23


Mass: 15860.666 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: A0A4W2DI10
#75: Protein 40S ribosomal protein S24 / Small ribosomal subunit protein eS24


Mass: 15463.333 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62847
#76: Protein 40S ribosomal protein S25 / Small ribosomal subunit protein eS25


Mass: 13776.224 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62851
#77: Protein 40S ribosomal protein S26 / Small ribosomal subunit protein eS26


Mass: 13047.532 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62854
#78: Protein 40S ribosomal protein S27 / Metallopan-stimulin 1 / MPS-1 / Small ribosomal subunit protein eS27


Mass: 9480.186 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P42677
#79: Protein 40S ribosomal protein S28 / Small ribosomal subunit protein eS28


Mass: 7855.052 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62857
#80: Protein 40S ribosomal protein S29 / Small ribosomal subunit protein uS14


Mass: 6690.821 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62273

-
Non-polymers , 7 types, 10250 molecules

#84: Chemical
ChemComp-PUT / 1,4-DIAMINOBUTANE / PUTRESCINE


Mass: 88.151 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C4H12N2
#85: Chemical
ChemComp-SPD / SPERMIDINE / N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE / PA(34)


Mass: 145.246 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C7H19N3
#86: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 195 / Source method: obtained synthetically / Formula: Mg
#87: Chemical...
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 75 / Source method: obtained synthetically / Formula: K
#88: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Zn
#89: Chemical ChemComp-HYG / HYGROMYCIN B / HYGROMIX / ANTIHELMYCIN / HYDROMYCIN B / DESTOMYSIN / ANTIBIOTIC A-396-II


Mass: 527.520 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H37N3O13 / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic*YM
#90: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9946 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: CRYO-EM STRUCTURE OF HUMAN 80S RIBOSOME WITH A/P/E-SITE TRNA AND MRNA CONTAINING N1-METHYLPSEUDOURIDINE
Type: RIBOSOME
Details: CRYO-EM STRUCTURE OF HUMAN 80S RIBOSOME WITH A/P/E-SITE TRNA AND MRNA CONTAINING N1-METHYLPSEUDOURIDINE
Entity ID: #1-#49, #51-#83, #50 / Source: NATURAL
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 7.6
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1700 nm / Nominal defocus min: 600 nm
Image recordingElectron dose: 1.077 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

-
Processing

EM software
IDNameCategory
1RELIONparticle selection
13RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 94974 / Symmetry type: POINT

+
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