[English] 日本語
Yorodumi
- PDB-4v7r: Yeast 80S ribosome. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4v7r
TitleYeast 80S ribosome.
Components
  • (40S ribosomal protein ...) x 19
  • (60S ribosomal protein ...) x 32
  • (Unassigned secondary ...) x 16
  • 18S ribosomal RNA
  • 25S ribosomal RNA
  • 5.8S ribosomal RNA
  • 5S ribosomal RNA
  • 60S acidic ribosomal protein P0
  • Guanine nucleotide-binding protein subunit beta-like protein; RACK-1
KeywordsRIBOSOME / Ribosomal rRNA and proteins / Translating the genetic code to proteins / eukaryotic / yeast
Function / homology
Function and homology information


: / negative regulation of glucose mediated signaling pathway / negative regulation of translational frameshifting / RMTs methylate histone arginines / positive regulation of translational fidelity / Protein methylation / Protein hydroxylation / ribosome-associated ubiquitin-dependent protein catabolic process / GDP-dissociation inhibitor activity / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay ...: / negative regulation of glucose mediated signaling pathway / negative regulation of translational frameshifting / RMTs methylate histone arginines / positive regulation of translational fidelity / Protein methylation / Protein hydroxylation / ribosome-associated ubiquitin-dependent protein catabolic process / GDP-dissociation inhibitor activity / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / nonfunctional rRNA decay / pre-mRNA 5'-splice site binding / preribosome, small subunit precursor / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Ribosomal scanning and start codon recognition / response to cycloheximide / Major pathway of rRNA processing in the nucleolus and cytosol / mRNA destabilization / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Formation of a pool of free 40S subunits / negative regulation of mRNA splicing, via spliceosome / preribosome, large subunit precursor / regulation of amino acid metabolic process / L13a-mediated translational silencing of Ceruloplasmin expression / translational elongation / ribosomal large subunit export from nucleus / 90S preribosome / G-protein alpha-subunit binding / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / regulation of translational fidelity / ribosomal subunit export from nucleus / ribosomal small subunit export from nucleus / translation regulator activity / translational termination / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / DNA-(apurinic or apyrimidinic site) endonuclease activity / maturation of LSU-rRNA / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rescue of stalled ribosome / ribosomal large subunit biogenesis / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / small-subunit processome / translational initiation / protein kinase C binding / macroautophagy / maintenance of translational fidelity / cytoplasmic stress granule / rRNA processing / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / large ribosomal subunit / ribosome binding / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / ribosomal large subunit assembly / cytoplasmic translation / cytosolic large ribosomal subunit / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / positive regulation of protein phosphorylation / G protein-coupled receptor signaling pathway / translation / negative regulation of gene expression / response to antibiotic / mRNA binding / nucleolus / mitochondrion / RNA binding / zinc ion binding / nucleoplasm / nucleus / metal ion binding / cytosol / cytoplasm
Similarity search - Function
60s Acidic ribosomal protein / 60S acidic ribosomal protein P0 / : / 50S ribosomal protein L10, insertion domain superfamily / Ribosomal protein L18/L18-A/B/e, conserved site / Ribosomal protein L18e signature. / : / 60S ribosomal protein L10P, insertion domain / Insertion domain in 60S ribosomal protein L10P / Ribosomal protein L18e ...60s Acidic ribosomal protein / 60S acidic ribosomal protein P0 / : / 50S ribosomal protein L10, insertion domain superfamily / Ribosomal protein L18/L18-A/B/e, conserved site / Ribosomal protein L18e signature. / : / 60S ribosomal protein L10P, insertion domain / Insertion domain in 60S ribosomal protein L10P / Ribosomal protein L18e / Ribosomal protein 60S L18 and 50S L18e / Ribosomal protein L1, conserved site / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / Ribosomal protein L1 signature. / Ribosomal protein L1 / Ribosomal protein S2, eukaryotic / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein L44e signature. / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / Ribosomal protein S25 / S25 ribosomal protein / Ribosomal protein L10e / Ribosomal protein L19, eukaryotic / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein S17e, conserved site / Ribosomal protein S17e signature. / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / : / Ribosomal protein L24e, conserved site / Ribosomal protein L19/L19e conserved site / Ribosomal protein L19e signature. / Ribosomal protein L24e signature. / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Ribosomal protein L44e / Ribosomal protein L44 / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / : / Ribosomal protein L30e signature 1. / Ribosomal protein L6e signature. / Ribosomal protein S19e / Ribosomal protein S19e / Ribosomal_S19e / Ribosomal protein L23/L25, N-terminal / Ribosomal protein L23, N-terminal domain / Ribosomal protein L30e signature 2. / Ribosomal protein L30e, conserved site / Ribosomal protein S19A/S15e / Ribosomal protein L39e, conserved site / Ribosomal protein L39e signature. / Ribosomal protein S17e / Ribosomal protein S17e-like superfamily / Ribosomal S17 / Ribosomal protein L14e domain / 60S ribosomal protein L19 / Ribosomal protein L14 / Ribosomal protein L30/YlxQ / Ribosomal Protein L6, KOW domain / Ribosomal protein L7A/L8 / Ribosomal protein L13, eukaryotic/archaeal / 40S ribosomal protein S11, N-terminal / Ribosomal_S17 N-terminal / 60S ribosomal protein L35 / Ribosomal protein L6e / 60S ribosomal protein L6E / Ribosomal protein L14 / Ribosomal protein L1-like / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein L1p/L10e family / Ribosomal protein S23, eukaryotic/archaeal / Ribosomal protein L14, KOW motif / Ribosomal protein L37ae / Ribosomal L37ae protein family / 60S ribosomal protein L4, C-terminal domain / 60S ribosomal protein L4 C-terminal domain / Ribosomal protein L7, eukaryotic / Ribosomal protein L31e, conserved site / Ribosomal protein L31e signature. / Ribosomal_L19e / Ribosomal protein L30, N-terminal / Ribosomal L30 N-terminal domain / Ribosomal protein L19/L19e / Ribosomal protein L19/L19e, domain 1 / Ribosomal protein L19/L19e superfamily / Ribosomal protein L19e / Ribosomal protein S17, archaeal/eukaryotic / Ribosomal protein L39e / Ribosomal protein L39e domain superfamily / Ribosomal L39 protein / Ribosomal protein L5 eukaryotic/L18 archaeal / Ribosomal protein S28e conserved site / Ribosomal large subunit proteins 60S L5, and 50S L18 / Ribosomal protein S28e signature. / Ribosomal protein S28e / Ribosomal protein S28e
Similarity search - Domain/homology
osmium (III) hexammine / : / : / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) ...osmium (III) hexammine / : / : / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS4A / 60S ribosomal protein L42-A / Large ribosomal subunit protein uL15 / Small ribosomal subunit protein eS17A / Large ribosomal subunit protein eL24A / 60S ribosomal protein L23-B / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein eL39 / Large ribosomal subunit protein uL10 / 60S ribosomal protein L19-A / 60S ribosomal protein L2-A / Large ribosomal subunit protein uL30A / Large ribosomal subunit protein uL6A / Large ribosomal subunit protein uL22A / Large ribosomal subunit protein uL24A / Large ribosomal subunit protein eL15A / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein uS11A / 60S ribosomal protein L18-A / Small ribosomal subunit protein eS19A / Small ribosomal subunit protein uS8A / Large ribosomal subunit protein uL5A / Large ribosomal subunit protein eL31A / Large ribosomal subunit protein eL43B / Large ribosomal subunit protein eL42B / Small ribosomal subunit protein uS12B / Large ribosomal subunit protein uL14B / Large ribosomal subunit protein uL1A / Large ribosomal subunit protein uL2B / Small ribosomal subunit protein uS17B / Large ribosomal subunit protein eL18B / Small ribosomal subunit protein uS9B / Large ribosomal subunit protein uL11A / Small ribosomal subunit protein uS13B / Large ribosomal subunit protein eL19 / Large ribosomal subunit protein uL29A / Large ribosomal subunit protein uL4A / Large ribosomal subunit protein eL30 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein eL8A / 60S ribosomal protein L12-A / Small ribosomal subunit protein uS5 / Large ribosomal subunit protein uL18 / 40S ribosomal protein S11-B / Small ribosomal subunit protein uS7 / Large ribosomal subunit protein uL13A / 40S ribosomal protein S23-A / Small ribosomal subunit protein uS2A / 40S ribosomal protein S18-A / Large ribosomal subunit protein eL14A / Small ribosomal subunit protein RACK1 / Large ribosomal subunit protein eL32 / Small ribosomal subunit protein uS10 / 60S ribosomal protein L35-A / 40S ribosomal protein S16-B / Small ribosomal subunit protein uS14A / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein eL37A / 60S ribosomal protein L43-A / 60S ribosomal protein L1-B / Small ribosomal subunit protein uS19 / Large ribosomal subunit protein eL6A / Large ribosomal subunit protein eL21A / Small ribosomal subunit protein eS25A / Small ribosomal subunit protein eS28A
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Saccharomyces cerevisiae S288c (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement, SAD / Resolution: 4 Å
AuthorsBen-Shem, A. / Jenner, L. / Yusupova, G. / Yusupov, M.
CitationJournal: Science / Year: 2010
Title: Crystal structure of the eukaryotic ribosome.
Authors: Ben-Shem, A. / Jenner, L. / Yusupova, G. / Yusupov, M.
History
DepositionJul 23, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
SupersessionDec 10, 2014ID: 3O2Z, 3O30, 3O58, 3O5H
Revision 1.1Dec 10, 2014Group: Other
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A1: 18S ribosomal RNA
AA: 40S ribosomal protein S0-A
AB: 40S ribosomal protein S2
AC: 40S ribosomal protein S3
AD: 40S ribosomal protein S5
AE: 40S ribosomal protein S9-A
AF: 40S ribosomal protein S11
AG: 40S ribosomal protein S13
AH: 40S ribosomal protein S14-A
AI: 40S ribosomal protein S15
AJ: 40S ribosomal protein S16
AK: 40S ribosomal protein S17-A
AL: 40S ribosomal protein S18
AM: 40S ribosomal protein S19-A
AN: 40S ribosomal protein S20
AO: 40S ribosomal protein S22-A
AP: 40S ribosomal protein S23
AQ: 40S ribosomal protein S25-A
AR: 40S ribosomal protein S28-A
AS: 40S ribosomal protein S29-A
AT: Guanine nucleotide-binding protein subunit beta-like protein; RACK-1
Aa: Unassigned secondary structure
Ab: Unassigned secondary structure
Ac: Unassigned secondary structure
Ad: Unassigned secondary structure
Ae: Unassigned secondary structure
Af: Unassigned secondary structure
Ah: Unassigned secondary structure
B1: 25S ribosomal RNA
B2: 5S ribosomal RNA
B3: 5.8S ribosomal RNA
BA: 60S ribosomal protein L1
BB: 60S ribosomal protein L2
BC: 60S ribosomal protein L3
BD: 60S ribosomal protein L4-A
BE: 60S ribosomal protein L5
BF: 60S ribosomal protein L6-A
BG: 60S ribosomal protein L7-A
BH: 60S ribosomal protein L8-A
BI: 60S ribosomal protein L9-A
BJ: 60S ribosomal protein L10
BK: 60S ribosomal protein L11-A
BN: 60S ribosomal protein L14-A
BO: 60S ribosomal protein L15-A
BP: 60S ribosomal protein L16-A
BQ: 60S ribosomal protein L17-A
BR: 60S ribosomal protein L18
BS: 60S ribosomal protein L19
BT: 60S ribosomal protein L21-A
BU: 60S ribosomal protein L23
BV: 60S ribosomal protein L24-A
BW: 60S ribosomal protein L25
BX: 60S ribosomal protein L26-A
BY: 60S ribosomal protein L28
BZ: 60S ribosomal protein L30
Ba: 60S ribosomal protein L31-A
Bb: 60S ribosomal protein L32
Bc: 60S ribosomal protein L35
Bd: 60S ribosomal protein L37-A
Be: 60S ribosomal protein L39
Bf: 60S ribosomal protein L42
Bg: 60S ribosomal protein L43
Bh: Unassigned secondary structure
Bi: Unassigned secondary structure
Bj: Unassigned secondary structure
Bk: Unassigned secondary structure
Bl: Unassigned secondary structure
Bm: Unassigned secondary structure
Bn: Unassigned secondary structure
Bo: Unassigned secondary structure
Bp: Unassigned secondary structure
Bq: Unassigned secondary structure
Br: Unassigned secondary structure
C1: 18S ribosomal RNA
CA: 40S ribosomal protein S0-A
CB: 40S ribosomal protein S2
CC: 40S ribosomal protein S3
CD: 40S ribosomal protein S5
CE: 40S ribosomal protein S9-A
CF: 40S ribosomal protein S11
CG: 40S ribosomal protein S13
CH: 40S ribosomal protein S14-A
CI: 40S ribosomal protein S15
CJ: 40S ribosomal protein S16
CK: 40S ribosomal protein S17-A
CL: 40S ribosomal protein S18
CM: 40S ribosomal protein S19-A
CN: 40S ribosomal protein S20
CO: 40S ribosomal protein S22-A
CP: 40S ribosomal protein S23
CQ: 40S ribosomal protein S25-A
CR: 40S ribosomal protein S28-A
CS: 40S ribosomal protein S29-A
CT: Guanine nucleotide-binding protein subunit beta-like protein; RACK-1
Ca: Unassigned secondary structure
Cb: Unassigned secondary structure
Cc: Unassigned secondary structure
Cd: Unassigned secondary structure
Ch: Unassigned secondary structure
D1: 25S ribosomal RNA
D2: 5S ribosomal RNA
D3: 5.8S ribosomal RNA
DA: 60S ribosomal protein L1
DB: 60S ribosomal protein L2
DC: 60S ribosomal protein L3
DD: 60S ribosomal protein L4-A
DE: 60S ribosomal protein L5
DF: 60S ribosomal protein L6-A
DG: 60S ribosomal protein L7-A
DH: 60S ribosomal protein L8-A
DI: 60S ribosomal protein L9-A
DJ: 60S ribosomal protein L10
DK: 60S ribosomal protein L11-A
DL: 60S ribosomal protein L12
DM: 60S acidic ribosomal protein P0
DN: 60S ribosomal protein L14-A
DO: 60S ribosomal protein L15-A
DP: 60S ribosomal protein L16-A
DQ: 60S ribosomal protein L17-A
DR: 60S ribosomal protein L18
DS: 60S ribosomal protein L19
DT: 60S ribosomal protein L21-A
DU: 60S ribosomal protein L23
DV: 60S ribosomal protein L24-A
DW: 60S ribosomal protein L25
DX: 60S ribosomal protein L26-A
DY: 60S ribosomal protein L28
DZ: 60S ribosomal protein L30
Da: 60S ribosomal protein L31-A
Db: 60S ribosomal protein L32
Dc: 60S ribosomal protein L35
Dd: 60S ribosomal protein L37-A
De: 60S ribosomal protein L39
Df: 60S ribosomal protein L42
Dg: 60S ribosomal protein L43
Dh: Unassigned secondary structure
Di: Unassigned secondary structure
Dj: Unassigned secondary structure
Dk: Unassigned secondary structure
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,851,649854
Polymers5,646,898139
Non-polymers204,751715
Water00
1
A1: 18S ribosomal RNA
AA: 40S ribosomal protein S0-A
AB: 40S ribosomal protein S2
AC: 40S ribosomal protein S3
AD: 40S ribosomal protein S5
AE: 40S ribosomal protein S9-A
AF: 40S ribosomal protein S11
AG: 40S ribosomal protein S13
AH: 40S ribosomal protein S14-A
AI: 40S ribosomal protein S15
AJ: 40S ribosomal protein S16
AK: 40S ribosomal protein S17-A
AL: 40S ribosomal protein S18
AM: 40S ribosomal protein S19-A
AN: 40S ribosomal protein S20
AO: 40S ribosomal protein S22-A
AP: 40S ribosomal protein S23
AQ: 40S ribosomal protein S25-A
AR: 40S ribosomal protein S28-A
AS: 40S ribosomal protein S29-A
AT: Guanine nucleotide-binding protein subunit beta-like protein; RACK-1
Aa: Unassigned secondary structure
Ab: Unassigned secondary structure
Ac: Unassigned secondary structure
Ad: Unassigned secondary structure
Ae: Unassigned secondary structure
Af: Unassigned secondary structure
Ah: Unassigned secondary structure
B1: 25S ribosomal RNA
B2: 5S ribosomal RNA
B3: 5.8S ribosomal RNA
BA: 60S ribosomal protein L1
BB: 60S ribosomal protein L2
BC: 60S ribosomal protein L3
BD: 60S ribosomal protein L4-A
BE: 60S ribosomal protein L5
BF: 60S ribosomal protein L6-A
BG: 60S ribosomal protein L7-A
BH: 60S ribosomal protein L8-A
BI: 60S ribosomal protein L9-A
BJ: 60S ribosomal protein L10
BK: 60S ribosomal protein L11-A
BN: 60S ribosomal protein L14-A
BO: 60S ribosomal protein L15-A
BP: 60S ribosomal protein L16-A
BQ: 60S ribosomal protein L17-A
BR: 60S ribosomal protein L18
BS: 60S ribosomal protein L19
BT: 60S ribosomal protein L21-A
BU: 60S ribosomal protein L23
BV: 60S ribosomal protein L24-A
BW: 60S ribosomal protein L25
BX: 60S ribosomal protein L26-A
BY: 60S ribosomal protein L28
BZ: 60S ribosomal protein L30
Ba: 60S ribosomal protein L31-A
Bb: 60S ribosomal protein L32
Bc: 60S ribosomal protein L35
Bd: 60S ribosomal protein L37-A
Be: 60S ribosomal protein L39
Bf: 60S ribosomal protein L42
Bg: 60S ribosomal protein L43
Bh: Unassigned secondary structure
Bi: Unassigned secondary structure
Bj: Unassigned secondary structure
Bk: Unassigned secondary structure
Bl: Unassigned secondary structure
Bm: Unassigned secondary structure
Bn: Unassigned secondary structure
Bo: Unassigned secondary structure
Bp: Unassigned secondary structure
Bq: Unassigned secondary structure
Br: Unassigned secondary structure
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,905,961428
Polymers2,804,30273
Non-polymers101,660355
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C1: 18S ribosomal RNA
CA: 40S ribosomal protein S0-A
CB: 40S ribosomal protein S2
CC: 40S ribosomal protein S3
CD: 40S ribosomal protein S5
CE: 40S ribosomal protein S9-A
CF: 40S ribosomal protein S11
CG: 40S ribosomal protein S13
CH: 40S ribosomal protein S14-A
CI: 40S ribosomal protein S15
CJ: 40S ribosomal protein S16
CK: 40S ribosomal protein S17-A
CL: 40S ribosomal protein S18
CM: 40S ribosomal protein S19-A
CN: 40S ribosomal protein S20
CO: 40S ribosomal protein S22-A
CP: 40S ribosomal protein S23
CQ: 40S ribosomal protein S25-A
CR: 40S ribosomal protein S28-A
CS: 40S ribosomal protein S29-A
CT: Guanine nucleotide-binding protein subunit beta-like protein; RACK-1
Ca: Unassigned secondary structure
Cb: Unassigned secondary structure
Cc: Unassigned secondary structure
Cd: Unassigned secondary structure
Ch: Unassigned secondary structure
D1: 25S ribosomal RNA
D2: 5S ribosomal RNA
D3: 5.8S ribosomal RNA
DA: 60S ribosomal protein L1
DB: 60S ribosomal protein L2
DC: 60S ribosomal protein L3
DD: 60S ribosomal protein L4-A
DE: 60S ribosomal protein L5
DF: 60S ribosomal protein L6-A
DG: 60S ribosomal protein L7-A
DH: 60S ribosomal protein L8-A
DI: 60S ribosomal protein L9-A
DJ: 60S ribosomal protein L10
DK: 60S ribosomal protein L11-A
DL: 60S ribosomal protein L12
DM: 60S acidic ribosomal protein P0
DN: 60S ribosomal protein L14-A
DO: 60S ribosomal protein L15-A
DP: 60S ribosomal protein L16-A
DQ: 60S ribosomal protein L17-A
DR: 60S ribosomal protein L18
DS: 60S ribosomal protein L19
DT: 60S ribosomal protein L21-A
DU: 60S ribosomal protein L23
DV: 60S ribosomal protein L24-A
DW: 60S ribosomal protein L25
DX: 60S ribosomal protein L26-A
DY: 60S ribosomal protein L28
DZ: 60S ribosomal protein L30
Da: 60S ribosomal protein L31-A
Db: 60S ribosomal protein L32
Dc: 60S ribosomal protein L35
Dd: 60S ribosomal protein L37-A
De: 60S ribosomal protein L39
Df: 60S ribosomal protein L42
Dg: 60S ribosomal protein L43
Dh: Unassigned secondary structure
Di: Unassigned secondary structure
Dj: Unassigned secondary structure
Dk: Unassigned secondary structure
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,945,688426
Polymers2,842,59766
Non-polymers103,091360
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)437.110, 288.380, 306.560
Angle α, β, γ (deg.)90.00, 99.13, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
RNA chain , 4 types, 8 molecules A1C1B1D1B2D2B3D3

#1: RNA chain 18S ribosomal RNA


Mass: 579761.938 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: GenBank: Z75578
#29: RNA chain 25S ribosomal RNA


Mass: 1097493.875 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: GenBank: BK006945.1
#30: RNA chain 5S ribosomal RNA


Mass: 38951.105 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: GenBank: J01360.1, GenBank: AE016820.4
#31: RNA chain 5.8S ribosomal RNA


Mass: 50682.922 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: GenBank: HQ026735.1

-
40S ribosomal protein ... , 19 types, 38 molecules AACAABCBACCCADCDAECEAFCFAGCGAHCHAICIAJCJAKCKALCLAMCMANCNAOCO...

#2: Protein 40S ribosomal protein S0-A


Mass: 28051.330 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P32905
#3: Protein 40S ribosomal protein S2


Mass: 27490.826 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P25443
#4: Protein 40S ribosomal protein S3


Mass: 26542.789 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05750
#5: Protein 40S ribosomal protein S5


Mass: 25072.600 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P26783
#6: Protein 40S ribosomal protein S9-A


Mass: 22487.893 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: O13516
#7: Protein 40S ribosomal protein S11


Mass: 17785.934 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P26781, UniProt: P0CX48*PLUS
#8: Protein 40S ribosomal protein S13


Mass: 17059.945 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05756
#9: Protein 40S ribosomal protein S14-A


Mass: 14562.655 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P06367
#10: Protein 40S ribosomal protein S15


Mass: 16031.907 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q01855
#11: Protein 40S ribosomal protein S16


Mass: 15877.490 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P40213, UniProt: P0CX52*PLUS
#12: Protein 40S ribosomal protein S17-A


Mass: 15820.413 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P02407
#13: Protein 40S ribosomal protein S18


Mass: 17071.641 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P35271, UniProt: P0CX56*PLUS
#14: Protein 40S ribosomal protein S19-A


Mass: 15942.125 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P07280
#15: Protein 40S ribosomal protein S20


Mass: 13929.044 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P38701
#16: Protein 40S ribosomal protein S22-A


Mass: 14650.062 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0C0W1
#17: Protein 40S ribosomal protein S23


Mass: 16073.896 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P32827, UniProt: P0CX30*PLUS
#18: Protein 40S ribosomal protein S25-A


Mass: 12067.272 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q3E792
#19: Protein 40S ribosomal protein S28-A


Mass: 7605.847 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q3E7X9
#20: Protein 40S ribosomal protein S29-A


Mass: 6675.723 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P41057

-
Protein , 2 types, 3 molecules ATCTDM

#21: Protein Guanine nucleotide-binding protein subunit beta-like protein; RACK-1 / Receptor of activated protein kinase C 1 / RACK1 / Receptor for activated C kinase


Mass: 34841.219 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P38011
#73: Protein 60S acidic ribosomal protein P0 / A0 / L10E


Mass: 33798.191 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05317

-
Unassigned secondary ... , 16 types, 27 molecules AaBoCaAbCbAcCcAdCdAeBjDjAfAhChBhDhBiDiBkDkBlBmBnBpBqBr

#22: Protein/peptide Unassigned secondary structure


Mass: 1720.111 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
#23: Protein Unassigned secondary structure


Mass: 8954.028 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
#24: Protein Unassigned secondary structure


Mass: 7932.770 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
#25: Protein/peptide Unassigned secondary structure


Mass: 2996.685 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
#26: Protein/peptide Unassigned secondary structure


Mass: 1805.216 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
#27: Protein/peptide Unassigned secondary structure


Mass: 954.168 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
#28: Protein/peptide Unassigned secondary structure


Mass: 3507.314 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
#63: Protein/peptide Unassigned secondary structure


Mass: 3762.629 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
#64: Protein/peptide Unassigned secondary structure


Mass: 1039.273 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
#65: Protein/peptide Unassigned secondary structure


Mass: 1379.692 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
#66: Protein/peptide Unassigned secondary structure


Mass: 1635.006 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
#67: Protein/peptide Unassigned secondary structure


Mass: 783.958 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
#68: Protein/peptide Unassigned secondary structure


Mass: 2315.846 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
#69: Protein/peptide Unassigned secondary structure


Mass: 698.854 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
#70: Protein/peptide Unassigned secondary structure


Mass: 1464.797 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
#71: Protein/peptide Unassigned secondary structure


Mass: 1975.426 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)

+
60S ribosomal protein ... , 32 types, 63 molecules BADABBDBBCDCBDDDBEDEBFDFBGDGBHDHBIDIBJDJBKDKBNDNBODOBPDPBQDQ...

#32: Protein 60S ribosomal protein L1 / L10a


Mass: 24524.799 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P53030, UniProt: P0CX43*PLUS
#33: Protein 60S ribosomal protein L2 / L5 / RP8 / YL6


Mass: 27463.574 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05736, UniProt: P0CX46*PLUS
#34: Protein 60S ribosomal protein L3


Mass: 43850.793 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P14126
#35: Protein 60S ribosomal protein L4-A


Mass: 39159.125 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P10664
#36: Protein 60S ribosomal protein L5


Mass: 33792.844 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P26321
#37: Protein 60S ribosomal protein L6-A / L17 / RP18 / YL16


Mass: 20000.564 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q02326
#38: Protein 60S ribosomal protein L7-A / L6 / RP11 / YL8


Mass: 27686.281 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05737
#39: Protein 60S ribosomal protein L8-A / L4 / L4-2 / L7a-1 /


Mass: 28175.820 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P17076
#40: Protein 60S ribosomal protein L9-A / L8 / RP24 / YL11


Mass: 21605.061 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05738
#41: Protein 60S ribosomal protein L10


Mass: 25410.465 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P41805
#42: Protein 60S ribosomal protein L11-A / L16 / RP39 / YL22


Mass: 19755.691 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0C0W9
#43: Protein 60S ribosomal protein L14-A


Mass: 15195.066 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P36105
#44: Protein 60S ribosomal protein L15-A / L13 / RP15R / YL10 / YP18


Mass: 24482.357 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05748
#45: Protein 60S ribosomal protein L16-A / L13a / L21 / RP22 / YL15


Mass: 22247.227 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P26784
#46: Protein 60S ribosomal protein L17-A / L20A / YL17


Mass: 20589.518 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05740
#47: Protein 60S ribosomal protein L18 / RP28


Mass: 20609.252 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P07279, UniProt: P0CX50*PLUS
#48: Protein 60S ribosomal protein L19 / L23 / RP15L / RP33 / YL14


Mass: 21762.316 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05735, UniProt: P0CX83*PLUS
#49: Protein 60S ribosomal protein L21-A


Mass: 18279.266 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q02753
#50: Protein 60S ribosomal protein L23 / L17a / YL32


Mass: 14493.950 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P04451, UniProt: P0CX42*PLUS
#51: Protein 60S ribosomal protein L24-A / L30 / RP29 / YL21


Mass: 17661.717 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P04449
#52: Protein 60S ribosomal protein L25 / RP16L / YL25 / YP42'


Mass: 15787.612 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P04456
#53: Protein 60S ribosomal protein L26-A / L33 / YL33


Mass: 14265.784 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P05743
#54: Protein 60S ribosomal protein L28 / L27a / L29 / RP44 / RP62 / YL24


Mass: 16762.650 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P02406
#55: Protein 60S ribosomal protein L30 / L32 / RP73 / YL38


Mass: 11430.364 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P14120
#56: Protein 60S ribosomal protein L31-A / L34 / YL28


Mass: 12980.158 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0C2H8
#57: Protein 60S ribosomal protein L32


Mass: 14809.441 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P38061
#58: Protein 60S ribosomal protein L35


Mass: 13942.640 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P39741, UniProt: P0CX84*PLUS
#59: Protein 60S ribosomal protein L37-A / L43 / YL35 / YP55


Mass: 9877.395 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P49166
#60: Protein 60S ribosomal protein L39 / L46 / YL40


Mass: 6358.640 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P04650
#61: Protein 60S ribosomal protein L42


Mass: 12246.658 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P02405, UniProt: P0CX28*PLUS
#62: Protein 60S ribosomal protein L43 / L37a / YL35


Mass: 10112.952 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P49631, UniProt: P0CX26*PLUS
#72: Protein 60S ribosomal protein L12 / L15 / YL23


Mass: 17850.621 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P17079, UniProt: P0CX53*PLUS

-
Non-polymers , 1 types, 715 molecules

#74: Chemical...
ChemComp-OHX / osmium (III) hexammine / osmium(6+) hexaazanide


Mass: 286.365 Da / Num. of mol.: 715 / Source method: obtained synthetically / Formula: H12N6Os

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.38 Å3/Da / Density % sol: 63.59 %
Crystal growTemperature: 297 K / Method: vapor diffusion / pH: 7
Details: PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine, pH 7, VAPOR DIFFUSION, temperature 297K

-
Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.999 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 16, 2009
RadiationMonochromator: 0.999 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999 Å / Relative weight: 1
ReflectionResolution: 4→268 Å / Num. all: 630832 / Num. obs: 619044 / % possible obs: 98.1 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3
Reflection shell
Resolution (Å)Mean I/σ(I) obsDiffraction-ID% possible all
4-4.151184.5
4.15-4.352197.9

-
Processing

Software
NameClassification
XDSdata scaling
PHASERphasing
DMmodel building
DMMultimodel building
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
DMphasing
DMMultiphasing
RefinementMethod to determine structure: molecular replacement, SAD / Resolution: 4→268 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.341 12352 RANDOM 2%
Rwork0.278 --
obs0.28 605235 -
all-619044 -
Refinement stepCycle: LAST / Resolution: 4→268 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14656 38107 2485 0 55248
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONfhenix bond distance0.011
X-RAY DIFFRACTIONfhenix bond angle degree1.4

+
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