[English] 日本語
Yorodumi
- PDB-7zjw: Rabbit 80S ribosome as it decodes the Sec-UGA codon -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7zjw
TitleRabbit 80S ribosome as it decodes the Sec-UGA codon
Components
  • (40S ribosomal protein ...) x 30
  • (60S ribosomal Protein ...) x 43
  • (Ribosomal protein ...) x 2
  • 18S rRNA18S ribosomal RNA
  • 28S rRNA28S ribosomal RNA
  • 5.8S rRNA5.8S ribosomal RNA
  • 5S rRNA5S ribosomal RNA
  • CrPV IRESCripavirus internal ribosome entry site
  • GPX4 SECIS element
  • RACK1Receptor for activated C kinase 1
  • Ribosomal_L18_c domain-containing protein
  • SECIS Binding Protein 2
  • eEFSec
  • human Ser-tRNA-Sec
KeywordsRIBOSOME / Selenocysteine / recoding / 80S
Function / homology
Function and homology information


forebrain neuron development / Translation initiation complex formation / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / selenocysteine incorporation / Major pathway of rRNA processing in the nucleolus and cytosol / GTP hydrolysis and joining of the 60S ribosomal subunit / selenocysteine insertion sequence binding / L13a-mediated translational silencing of Ceruloplasmin expression ...forebrain neuron development / Translation initiation complex formation / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / selenocysteine incorporation / Major pathway of rRNA processing in the nucleolus and cytosol / GTP hydrolysis and joining of the 60S ribosomal subunit / selenocysteine insertion sequence binding / L13a-mediated translational silencing of Ceruloplasmin expression / SRP-dependent cotranslational protein targeting to membrane / Formation of a pool of free 40S subunits / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / striatum development / ribosomal subunit / rRNA modification in the nucleus and cytosol / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / Translation initiation complex formation / SARS-CoV-1 modulates host translation machinery / Protein hydroxylation / TOR signaling / mTORC1-mediated signalling / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / organelle membrane / Response of EIF2AK4 (GCN2) to amino acid deficiency / translation regulator activity / SRP-dependent cotranslational protein targeting to membrane / Viral mRNA Translation / 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 / Major pathway of rRNA processing in the nucleolus and cytosol / gastrulation / rough endoplasmic reticulum / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / ribonucleoprotein complex binding / translation elongation factor activity / Nuclear events stimulated by ALK signaling in cancer / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / DNA-(apurinic or apyrimidinic site) lyase / small-subunit processome / cytosolic ribosome / mRNA 3'-UTR binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / ribosomal small subunit biogenesis / cytoplasmic ribonucleoprotein granule / rRNA processing / Regulation of expression of SLITs and ROBOs / cytosolic small ribosomal subunit / ribosome binding / large ribosomal subunit / glucose homeostasis / regulation of translation / heparin binding / cell body / cytoplasmic translation / small ribosomal subunit / 5S rRNA binding / cytosolic large ribosomal subunit / SARS-CoV-2 modulates host translation machinery / tRNA binding / postsynaptic density / rRNA binding / ribosome / structural constituent of ribosome / cadherin binding / ribonucleoprotein complex / translation / positive regulation of apoptotic process / focal adhesion / intracellular membrane-bounded organelle / GTPase activity / dendrite / synapse / positive regulation of cell population proliferation / GTP binding / nucleolus / protein kinase binding / endoplasmic reticulum / mitochondrion / DNA binding / RNA binding / nucleoplasm / membrane / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Selenocysteine insertion sequence-binding protein 2 / : / : / eEFSec C-terminal RIFT domain / Selenocysteine-specific elongation factor, eukaryotes, 3rd domain / Ribosomal protein L28e / Ribosomal protein L2, archaeal-type / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / : ...Selenocysteine insertion sequence-binding protein 2 / : / : / eEFSec C-terminal RIFT domain / Selenocysteine-specific elongation factor, eukaryotes, 3rd domain / Ribosomal protein L28e / Ribosomal protein L2, archaeal-type / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / : / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein S21e, conserved site / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S19e, conserved site / S27a-like superfamily / Ribosomal protein S26e / Ribosomal protein S25 / Ribosomal protein S26e signature. / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein S8e subdomain, eukaryotes / S25 ribosomal protein / Ribosomal protein L27e, conserved site / Ribosomal protein S21e signature. / Ribosomal protein S12e signature. / Ribosomal protein S27a / Ribosomal protein S19e / Ribosomal_S19e / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S8e, conserved site / Ribosomal protein S6, eukaryotic / 40S ribosomal protein S4, C-terminal domain / Eukaryotic Ribosomal Protein L27, KOW domain / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S19e signature. / Ribosomal protein L44e / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal protein L27e / Ribosomal protein L27e superfamily / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal protein S19e / Ribosomal protein S27, zinc-binding domain superfamily / Ribosomal L38e protein family / Ribosomal L22e protein family / 40S Ribosomal protein S10 / Ribosomal protein S27 / Ribosomal protein S28e conserved site / Ribosomal protein S6/S6e/A/B/2, conserved site / Ribosomal protein S28e / 40S ribosomal protein S4 C-terminus / Ribosomal protein S4e, N-terminal / Plectin/S10, N-terminal / Ribosomal protein L44 / Plectin/S10 domain / Ribosomal protein S8e / Ribosomal L27e protein family / Ribosomal protein S4, KOW domain / Ribosomal protein S5/S7, eukaryotic/archaeal / Ribosomal protein S4e / Ribosomal protein S4e, central region / Ribosomal protein S4e, central domain superfamily / Ribosomal protein S6e / Ribosomal protein S13/S15, N-terminal / Ribosomal protein S15P / Ribosomal S13/S15 N-terminal domain / Ribosomal protein S6e / RS4NT (NUC023) domain / Ribosomal protein L1 signature. / Ribosomal protein L37ae / Ribosomal protein S27 / Ribosomal protein L19, eukaryotic / Ribosomal protein S17e signature. / Ribosomal protein L36e / Ribosomal protein L36e domain superfamily / Ribosomal L40e family / Ribosomal protein L36e / Ribosomal protein S28e / Ribosomal protein L44e signature. / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Ribosomal family S4e / Ribosomal protein L7A/L8 / Ribosomal S13/S15 N-terminal domain / Ribosomal protein L27e signature. / Ribosomal protein L10e signature. / Ribosomal protein S7e signature. / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein L7, eukaryotic / Ribosomal protein L30, N-terminal / Ribosomal L30 N-terminal domain / Ribosomal protein L19/L19e conserved site / Ribosomal protein S6e / Ribosomal L37ae protein family
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / : / SERINE / : / : / : / : / : / RNA / RNA (> 10) ...GUANOSINE-5'-TRIPHOSPHATE / : / SERINE / : / : / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein eS32 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein eL38 / 60S ribosomal protein L36 / Small ribosomal subunit protein eS21 / Large ribosomal subunit protein eL20 / Ribosomal protein L19 / 40S ribosomal protein S26 / Small ribosomal subunit protein RACK1 / 40S ribosomal protein S25 / Small ribosomal subunit protein eS19 / Small ribosomal subunit protein eS28 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein eL28 / Ribosomal protein S5 / Large ribosomal subunit protein uL24 / Small ribosomal subunit protein uS15 / 60S ribosomal protein L37a / 40S ribosomal protein S24 / Large ribosomal subunit protein eL42 / 40S ribosomal protein S27 / Large ribosomal subunit protein uL30 / Small ribosomal subunit protein uS11 / 60S ribosomal protein L27 / Large ribosomal subunit protein uL2 / Ubiquitin-ribosomal protein eS31 fusion protein / Ubiquitin-ribosomal protein eL40 fusion protein / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL16 / Small ribosomal subunit protein uS4 / Large ribosomal subunit protein uL15/eL18 domain-containing protein / Large ribosomal subunit protein eL24 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein eL33 / Small ribosomal subunit protein eS12 / Large ribosomal subunit protein eL29 / Small ribosomal subunit protein uS9 / Large ribosomal subunit protein eL31 / Large ribosomal subunit protein eL21 / Large ribosomal subunit protein uL29 / Small ribosomal subunit protein uS10 / Large ribosomal subunit protein eL6 / Large ribosomal subunit protein uL1 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL10 / Small ribosomal subunit protein eS1 / Small ribosomal subunit protein eS7 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein eL14 / Small ribosomal subunit protein uS12 / Large ribosomal subunit protein eL15 / Ubiquitin-like FUBI-ribosomal protein eS30 fusion protein / Large ribosomal subunit protein eL30 / Small ribosomal subunit protein uS8 / Large ribosomal subunit protein eL13 / Large ribosomal subunit protein uL3 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS3 / Plectin/eS10 N-terminal domain-containing protein / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein eL39 / Small ribosomal subunit protein eS17 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein eL34 / Small ribosomal subunit protein uS19 / Large ribosomal subunit protein eL32 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein uS5 / Selenocysteine-specific elongation factor / Large ribosomal subunit protein eL8 / Small ribosomal subunit protein eS6 / Large ribosomal subunit protein eL22 / Small ribosomal subunit protein eS8 / Small ribosomal subunit protein eS4 / Selenocysteine insertion sequence-binding protein 2 / Large ribosomal subunit protein eL37
Similarity search - Component
Biological speciesHomo sapiens (human)
Oryctolagus cuniculus (rabbit)
Cricket paralysis virus
Rattus norvegicus (Norway rat)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsHilal, T. / Simonovic, M. / Spahn, C.M.T.
Funding support Germany, United States, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG)SFB740, FOR1805 Germany
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM097042, GM077073 United States
CitationJournal: Science / Year: 2022
Title: Structure of the mammalian ribosome as it decodes the selenocysteine UGA codon.
Authors: Tarek Hilal / Benjamin Y Killam / Milica Grozdanović / Malgorzata Dobosz-Bartoszek / Justus Loerke / Jörg Bürger / Thorsten Mielke / Paul R Copeland / Miljan Simonović / Christian M T Spahn /
Abstract: The elongation of eukaryotic selenoproteins relies on a poorly understood process of interpreting in-frame UGA stop codons as selenocysteine (Sec). We used cryo-electron microscopy to visualize Sec ...The elongation of eukaryotic selenoproteins relies on a poorly understood process of interpreting in-frame UGA stop codons as selenocysteine (Sec). We used cryo-electron microscopy to visualize Sec UGA recoding in mammals. A complex between the noncoding Sec-insertion sequence (SECIS), SECIS-binding protein 2 (SBP2), and 40 ribosomal subunit enables Sec-specific elongation factor eEFSec to deliver Sec. eEFSec and SBP2 do not interact directly but rather deploy their carboxyl-terminal domains to engage with the opposite ends of the SECIS. By using its Lys-rich and carboxyl-terminal segments, the ribosomal protein eS31 simultaneously interacts with Sec-specific transfer RNA (tRNA) and SBP2, which further stabilizes the assembly. eEFSec is indiscriminate toward l-serine and facilitates its misincorporation at Sec UGA codons. Our results support a fundamentally distinct mechanism of Sec UGA recoding in eukaryotes from that in bacteria.
History
DepositionApr 12, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 19, 2022Provider: repository / Type: Initial release
Revision 2.0Nov 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / em_3d_fitting_list / pdbx_initial_refinement_model / pdbx_validate_main_chain_plane / pdbx_validate_polymer_linkage / pdbx_validate_rmsd_angle / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _pdbx_validate_polymer_linkage.auth_atom_id_2 / _struct_conn.ptnr1_label_atom_id
Revision 2.1Apr 24, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 ..._chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _chem_comp_bond.pdbx_aromatic_flag / _chem_comp_bond.value_order

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
E: eEFSec
F: human Ser-tRNA-Sec
I: CrPV IRES
S: GPX4 SECIS element
B: SECIS Binding Protein 2
L5: 28S rRNA
L7: 5S rRNA
L8: 5.8S rRNA
LD: 60S ribosomal protein uL2
LE: 60S ribosomal protein L3
LF: 60S ribosomal protein L4
LG: Ribosomal_L18_c domain-containing protein
LH: 60S ribosomal protein L6
LI: 60S ribosomal Protein uL30
LJ: 60S ribosomal protein eL8
LK: 60S ribosomal protein L9
LL: 60S ribosomal protein L10
LM: 60S ribosomal protein L11
LO: 60S ribosomal protein eL13
LP: 60S ribosomal protein L14
LQ: 60S ribosomal protein L15
LR: 60S ribosomal protein uL13
LS: 60S ribosomal protein uL22
LT: 60S ribosomal Protein eL18
LU: 60S ribosomal protein L19
LV: 60S ribosomal protein eL20
LW: 60S ribosomal protein eL21
LX: 60S ribosomal protein eL22
LY: 60S ribosomal protein L23
LZ: 60S ribosomal protein eL24
La: 60S ribosomal protein uL23
Lb: 60S ribosomal protein L26
Lc: 60S ribosomal protein L27
Ld: 60S ribosomal protein L27a
Le: 60S ribosomal protein L29
Lf: 60S ribosomal protein eL30
Lg: 60S ribosomal protein eL31
Lh: 60S ribosomal protein eL32
Li: 60S ribosomal protein eL33
Lj: 60S ribosomal protein L34
Lk: 60S ribosomal protein uL29
Ll: 60S ribosomal protein L36
Lm: 60S ribosomal protein L37
Ln: 60S ribosomal protein eL38
Lo: 60S ribosomal protein eL39
Lp: 60S ribosomal protein L40
Lq: 60S ribosomal protein eL42
Lr: 60S ribosomal protein eL43
Ls: 60S ribosomal protein eL28
Lt: 60S ribosomal protein P0
Lx: 60S ribosomal protein uL1
S2: 18S rRNA
SB: 40S ribosomal protein S27
SC: 40S ribosomal protein S28
SD: 40S ribosomal protein S27a
SE: 40S ribosomal protein S30
SF: Ribosomal protein eS26
SG: RACK1
SH: 40S ribosomal protein uS14
SL: 40S ribosomal protein SA
SM: 40S ribosomal protein S3a
SN: 40S ribosomal protein uS5
SO: 40S ribosomal protein S3
SP: 40S ribosomal protein eS4
SQ: Ribosomal protein S5
SR: 40S ribosomal protein S6
SS: 40S ribosomal protein S7
ST: 40S ribosomal protein S8
SU: 40S ribosomal protein S9
SV: 40S ribosomal protein eS10
SW: 40S ribosomal protein S11
SX: 40S ribosomal protein S12
SY: 40S ribosomal protein uS15
SZ: 40S ribosomal protein uS11
Sa: 40S ribosomal protein uS19
Sb: 40S ribosomal protein uS9
Sc: 40S ribosomal protein eS17
Sd: 40S ribosomal protein S18
Se: 40S Ribosomal protein eS19
Sf: 40S ribosomal protein uS10
Sg: 40S ribosomal protein eS21
Sh: 40S ribosomal protein S15a
Si: 40S ribosomal protein S23
Sj: 40S ribosomal protein S24
Sk: 40S ribosomal protein S25
Sl: 60S ribosomal protein L41
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,626,612342
Polymers4,618,67686
Non-polymers7,936256
Water1,928107
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

-
Protein , 4 types, 4 molecules EBLGSG

#1: Protein eEFSec / Elongation factor sec / Eukaryotic elongation factor / selenocysteine-tRNA-specific


Mass: 67564.945 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P57772
#5: Protein SECIS Binding Protein 2


Mass: 95640.016 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q96T21
#12: Protein Ribosomal_L18_c domain-containing protein


Mass: 34523.863 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SYJ6
#58: Protein RACK1 / Receptor for activated C kinase 1


Mass: 35115.652 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: A0A2K6K8B0

-
RNA chain , 7 types, 7 molecules FISL5L7L8S2

#2: RNA chain human Ser-tRNA-Sec


Mass: 28908.084 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: GenBank: 436409
#3: RNA chain CrPV IRES / Cripavirus internal ribosome entry site


Mass: 345547.031 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Cricket paralysis virus
#4: RNA chain GPX4 SECIS element


Mass: 275721.688 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Rattus norvegicus (Norway rat) / References: GenBank: 25123295
#6: RNA chain 28S rRNA / 28S ribosomal RNA


Mass: 1557505.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#7: RNA chain 5S rRNA / 5S ribosomal RNA


Mass: 38346.707 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: GenBank: 39
#8: RNA chain 5.8S rRNA / 5.8S ribosomal RNA


Mass: 50809.047 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: GenBank: 57148
#52: RNA chain 18S rRNA / 18S ribosomal RNA


Mass: 603814.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: GenBank: 37956930

+
60S ribosomal Protein ... , 43 types, 43 molecules LDLELFLHLILJLKLLLMLOLPLQLRLSLTLULVLWLXLYLZLaLbLcLdLeLfLgLhLi...

#9: Protein 60S ribosomal protein uL2 /


Mass: 28088.863 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: A0A8B8VPA8
#10: Protein 60S ribosomal protein L3 /


Mass: 46120.996 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TL06
#11: Protein 60S ribosomal protein L4 /


Mass: 46430.895 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SVW5
#13: Protein 60S ribosomal protein L6 /


Mass: 33028.336 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SKF7
#14: Protein 60S ribosomal Protein uL30 /


Mass: 29201.836 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: A0A7J8C453
#15: Protein 60S ribosomal protein eL8 /


Mass: 30061.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P62424
#16: Protein 60S ribosomal protein L9 /


Mass: 21871.418 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SWI6
#17: Protein 60S ribosomal protein L10 /


Mass: 24643.057 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: B7NZQ2
#18: Protein 60S ribosomal protein L11 /


Mass: 20288.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TUB8
#19: Protein 60S ribosomal protein eL13 /


Mass: 24331.723 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TKB3
#20: Protein 60S ribosomal protein L14 /


Mass: 23870.549 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SZ12
#21: Protein 60S ribosomal protein L15 /


Mass: 24207.285 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1T0C1
#22: Protein 60S ribosomal protein uL13 /


Mass: 23533.299 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: A0A0N8ETI8
#23: Protein 60S ribosomal protein uL22 /


Mass: 21444.221 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: A0A8J4KQ25
#24: Protein 60S ribosomal Protein eL18 /


Mass: 21699.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: F6QKI9
#25: Protein 60S ribosomal protein L19 /


Mass: 23535.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: A0A2J8KH59
#26: Protein 60S ribosomal protein eL20 /


Mass: 20749.391 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: A0A1Z5LHJ5
#27: Protein 60S ribosomal protein eL21 /


Mass: 18609.988 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SHQ2
#28: Protein 60S ribosomal protein eL22 /


Mass: 14756.909 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: Q4R5I3
#29: Protein 60S ribosomal protein L23 /


Mass: 14892.505 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: A0A3P9HH38
#30: Protein 60S ribosomal protein eL24 /


Mass: 17825.111 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SE28
#31: Protein 60S ribosomal protein uL23 /


Mass: 17768.246 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SE76
#32: Protein 60S ribosomal protein L26 /


Mass: 17303.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: A0A5N3X333
#33: Protein 60S ribosomal protein L27 /


Mass: 15835.831 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: A0A851LWS6
#34: Protein 60S ribosomal protein L27a /


Mass: 16620.561 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SNY0
#35: Protein 60S ribosomal protein L29 /


Mass: 26721.727 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SGR6
#36: Protein 60S ribosomal protein eL30 /


Mass: 12807.065 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TDL2
#37: Protein 60S ribosomal protein eL31 /


Mass: 14494.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SHG0
#38: Protein 60S ribosomal protein eL32 /


Mass: 15898.932 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1U437
#39: Protein 60S ribosomal protein eL33 /


Mass: 12580.809 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SF08
#40: Protein 60S ribosomal protein L34 /


Mass: 13326.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TXG5
#41: Protein 60S ribosomal protein uL29 /


Mass: 14566.599 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SIT5
#42: Protein 60S ribosomal protein L36 /


Mass: 12263.834 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: A0A1S3FQR5
#43: Protein 60S ribosomal protein L37 /


Mass: 11111.032 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: U3KPD5
#44: Protein 60S ribosomal protein eL38 /


Mass: 8238.948 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: A0A1A7W9T9
#45: Protein 60S ribosomal protein eL39 /


Mass: 6455.775 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TTN1
#46: Protein 60S ribosomal protein L40 /


Mass: 14800.474 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: A0A8C8Y9V5
#47: Protein 60S ribosomal protein eL42 /


Mass: 12489.991 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: A0A7J7V6K8
#48: Protein 60S ribosomal protein eL43 /


Mass: 10299.350 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: A0A6I9ZMF9
#49: Protein 60S ribosomal protein eL28 /


Mass: 15844.696 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: A0A4U1EJN3
#50: Protein 60S ribosomal protein P0 /


Mass: 34364.480 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SPK4
#51: Protein 60S ribosomal protein uL1 /


Mass: 24875.410 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SKZ8
#86: Protein/peptide 60S ribosomal protein L41 /


Mass: 3473.451 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: A0A087WNH4

+
40S ribosomal protein ... , 30 types, 30 molecules SBSCSDSESHSLSMSNSOSPSRSSSTSUSVSWSXSYSZSaSbScSdSeSfSgShSiSjSk

#53: Protein 40S ribosomal protein S27 /


Mass: 9480.186 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: A0A7J8BG50
#54: Protein 40S ribosomal protein S28 /


Mass: 7855.052 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: A0A3M0JHZ8
#55: Protein 40S ribosomal protein S27a /


Mass: 18004.041 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: A0A8C0T835
#56: Protein 40S ribosomal protein S30 /


Mass: 14498.884 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1T8A2
#59: Protein 40S ribosomal protein uS14 /


Mass: 6690.821 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1U7M4
#60: 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 / Laminin receptor 1 / LamR / Laminin-binding protein precursor p40 / LBP/p40


Mass: 32970.023 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TLT8
#61: Protein 40S ribosomal protein S3a /


Mass: 30002.061 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SS70
#62: Protein 40S ribosomal protein uS5 /


Mass: 31285.426 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: O18789
#63: Protein 40S ribosomal protein S3 /


Mass: 31146.607 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
References: UniProt: G1TNM3, DNA-(apurinic or apyrimidinic site) lyase
#64: Protein 40S ribosomal protein eS4 /


Mass: 29654.869 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: Q76N24
#66: 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) Oryctolagus cuniculus (rabbit) / References: UniProt: P62753
#67: Protein 40S ribosomal protein S7 /


Mass: 47356.172 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SVB0
#68: Protein 40S ribosomal protein S8 /


Mass: 24263.387 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: Q5E958
#69: Protein 40S ribosomal protein S9 /


Mass: 22641.564 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: B7NZS8
#70: Protein 40S ribosomal protein eS10 /


Mass: 18933.846 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TPV3
#71: Protein 40S ribosomal protein S11 /


Mass: 18468.826 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TRM4
#72: Protein 40S ribosomal protein S12 /


Mass: 14538.987 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SFR8
#73: Protein 40S ribosomal protein uS15 /


Mass: 17259.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: A0A663F1C0
#74: Protein 40S ribosomal protein uS11 /


Mass: 16302.772 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: A0A7L0BEC6
#75: Protein 40S ribosomal protein uS19 /


Mass: 17049.182 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1U0Q2
#76: Protein 40S ribosomal protein uS9 /


Mass: 19213.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SGX4
#77: Protein 40S ribosomal protein eS17 /


Mass: 15552.119 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TU13
#78: Protein 40S ribosomal protein S18 /


Mass: 17801.814 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: H0WTR0
#79: Protein 40S Ribosomal protein eS19 /


Mass: 16104.579 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: A0A2Y9E7Q1
#80: Protein 40S ribosomal protein uS10 /


Mass: 13398.763 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SIZ2
#81: Protein 40S ribosomal protein eS21 /


Mass: 9181.374 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: A0A1Z5KTU7
#82: Protein 40S ribosomal protein S15a /


Mass: 14865.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TG89
#83: Protein 40S ribosomal protein S23 /


Mass: 15860.666 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SZ47
#84: Protein 40S ribosomal protein S24 /


Mass: 15107.924 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: A0A6J1UT65
#85: Protein 40S ribosomal protein S25 /


Mass: 13645.028 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: A0A2U4BVW1

-
Ribosomal protein ... , 2 types, 2 molecules SFSQ

#57: Protein Ribosomal protein eS26 /


Mass: 13047.532 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: A0A2K5LQY6
#65: Protein Ribosomal protein S5 /


Mass: 22913.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: A0A5F9DBR8

-
Non-polymers , 7 types, 363 molecules

#87: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#88: Chemical ChemComp-SER / SERINE / Serine


Type: L-peptide linking / Mass: 105.093 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C3H7NO3
#89: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 225 / Source method: obtained synthetically / Formula: Mg
#90: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: K
#91: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Zn
#92: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#93: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 107 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
180S-SelenosomeCOMPLEX#1, #3-#860MULTIPLE SOURCES
2eEFSec and SECIS Binding Protein 2COMPLEX#1, #51RECOMBINANT
3Ser-tRNA-SecCOMPLEX#21RECOMBINANT
4CrPV IRESCripavirus internal ribosome entry siteCOMPLEX#31RECOMBINANT
5GPX4 SECIS elementCOMPLEX#41RECOMBINANT
680S RibosomeEukaryotic ribosomeRIBOSOME#6-#861NATURAL
Molecular weightValue: 3.5 MDa / Experimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Homo sapiens (human)9606
33Homo sapiens (human)9606
44Cricket paralysis virus12136
55Rattus norvegicus (Norway rat)10116
66Oryctolagus cuniculus (rabbit)9986
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
12Escherichia coli (E. coli)562
23synthetic construct (others)32630
34synthetic construct (others)32630
45synthetic construct (others)32630
Buffer solutionpH: 7.6
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER/RHODIUM / Grid type: Quantifoil R3/3
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Humidity: 100 %

-
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 FIELDBright-field microscopy / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm / Alignment procedure: ZEMLIN TABLEAU
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 30 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 13921
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

-
Processing

EM software
IDNameVersionCategory
2EPU2.8image acquisition
4cryoSPARCCTF correction
7PHENIX1.19.2model fitting
9PHENIX1.19.2model refinement
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
12cryoSPARCclassification
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1685923
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 77142 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingPDB-ID: 7O7Y

7o7y


Accession code: 7O7Y / Source name: PDB / Type: experimental model

+
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