[English] 日本語
Yorodumi
- PDB-5aj0: Cryo electron microscopy of actively translating human polysomes ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5aj0
TitleCryo electron microscopy of actively translating human polysomes (POST state).
Components
  • (40S ribosomal protein ...) x 31
  • (60S ribosomal protein ...) x 43
  • 18S ribosomal RNA
  • 28S ribosomal RNA
  • 5.8S ribosomal RNA
  • 5S ribosomal RNA
  • 60S acidic ribosomal protein P0
  • Guanine nucleotide-binding protein subunit beta-2-like 1
  • Nascent protein chain
  • Ubiquitin-40S ribosomal protein S27a
  • Ubiquitin-60S ribosomal protein L40
  • mRNAMessenger RNA
  • tRNATransfer RNA
KeywordsRIBOSOME / MAMMALIAN RIBOSOME / TRANSLATION / POLYSOME / CRYO ELECTRON MICROSCOPY / ELONGATION CYCLE
Function / homology
Function and homology information


positive regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis / negative regulation of endoplasmic reticulum unfolded protein response / embryonic brain development / oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of base-excision repair / eukaryotic 80S initiation complex / protein tyrosine kinase inhibitor activity / negative regulation of protein neddylation / translation at presynapse ...positive regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis / negative regulation of endoplasmic reticulum unfolded protein response / embryonic brain development / oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of base-excision repair / eukaryotic 80S initiation complex / protein tyrosine kinase inhibitor activity / negative regulation of protein neddylation / translation at presynapse / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of respiratory burst involved in inflammatory response / positive regulation of gastrulation / axial mesoderm development / regulation of G1 to G0 transition / negative regulation of formation of translation preinitiation complex / IRE1-RACK1-PP2A complex / nucleolus organization / ribosomal protein import into nucleus / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / regulation of translation involved in cellular response to UV / response to extracellular stimulus / positive regulation of endodeoxyribonuclease activity / positive regulation of Golgi to plasma membrane protein transport / exit from mitosis / protein-DNA complex disassembly / TNFR1-mediated ceramide production / 90S preribosome assembly / positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / negative regulation of DNA repair / negative regulation of RNA splicing / optic nerve development / TORC2 complex binding / oxidized purine DNA binding / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / supercoiled DNA binding / GAIT complex / G1 to G0 transition / neural crest cell differentiation / retinal ganglion cell axon guidance / NF-kappaB complex / rRNA modification in the nucleus and cytosol / negative regulation of phagocytosis / middle ear morphogenesis / ubiquitin-like protein conjugating enzyme binding / regulation of establishment of cell polarity / positive regulation of ubiquitin-protein transferase activity / Formation of the ternary complex, and subsequently, the 43S complex / laminin receptor activity / erythrocyte homeostasis / cytoplasmic side of rough endoplasmic reticulum membrane / A band / positive regulation of signal transduction by p53 class mediator / ubiquitin ligase inhibitor activity / alpha-beta T cell differentiation / pigmentation / protein kinase A binding / negative regulation of ubiquitin protein ligase activity / Ribosomal scanning and start codon recognition / ion channel inhibitor activity / Translation initiation complex formation / phagocytic cup / positive regulation of mitochondrial depolarization / response to aldosterone / negative regulation of Wnt signaling pathway / homeostatic process / positive regulation of T cell receptor signaling pathway / lung morphogenesis / macrophage chemotaxis / positive regulation of activated T cell proliferation / fibroblast growth factor binding / regulation of cell division / SARS-CoV-1 modulates host translation machinery / iron-sulfur cluster binding / Protein hydroxylation / TOR signaling / BH3 domain binding / mTORC1-mediated signalling / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Peptide chain elongation / Selenocysteine synthesis / protein-RNA complex assembly / monocyte chemotaxis / cysteine-type endopeptidase activator activity involved in apoptotic process / Formation of a pool of free 40S subunits / ribosomal small subunit export from nucleus / positive regulation of cyclic-nucleotide phosphodiesterase activity / Eukaryotic Translation Termination / blastocyst development / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / translation regulator activity / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / Viral mRNA Translation / protein localization to nucleus / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / cellular response to actinomycin D / GTP hydrolysis and joining of the 60S ribosomal subunit / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / negative regulation of respiratory burst involved in inflammatory response
Similarity search - Function
Ubiquitin-like protein FUBI / 60s Acidic ribosomal protein / 60S acidic ribosomal protein P0 / Ribosomal protein L6, N-terminal / 40S ribosomal protein SA / Ribosomal protein L6, N-terminal domain / Ribosomal protein L30e / Ribosomal protein L28e / Ribosomal protein L2, archaeal-type / 40S ribosomal protein SA, C-terminal domain ...Ubiquitin-like protein FUBI / 60s Acidic ribosomal protein / 60S acidic ribosomal protein P0 / Ribosomal protein L6, N-terminal / 40S ribosomal protein SA / Ribosomal protein L6, N-terminal domain / Ribosomal protein L30e / Ribosomal protein L28e / Ribosomal protein L2, archaeal-type / 40S ribosomal protein SA, C-terminal domain / Ribosomal L15/L27a, N-terminal / 40S ribosomal protein SA C-terminus / Ribosomal protein L23 / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / : / Ribosomal protein S12e / 50S ribosomal protein L10, insertion domain superfamily / 60S ribosomal protein L10P, insertion domain / Insertion domain in 60S ribosomal protein L10P / metallochaperone-like domain / Small (40S) ribosomal subunit Asc1/RACK1 / TRASH domain / Ribosomal protein S19e, conserved site / : / S27a-like superfamily / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein S25 / Ribosomal protein S26e signature. / Ribosomal protein S17e, conserved site / : / Ribosomal protein S30 / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein L29e / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein S8e subdomain, eukaryotes / S25 ribosomal protein / Ribosomal protein L10e, conserved site / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Ribosomal protein L10e / Ribosomal protein L27e, conserved site / Ribosomal protein S19A/S15e / Ribosomal protein S21e, conserved site / Ribosomal protein S21e signature. / Ribosomal L29e protein family / Ribosomal protein S30 / Ribosomal protein S3Ae, conserved site / Ribosomal protein S12e signature. / Ribosomal protein S17e / Ribosomal protein S17e-like superfamily / Ribosomal protein S27a / Ribosomal protein S19e / Ribosomal_S19e / Ribosomal protein S8e, conserved site / Ribosomal protein S5, eukaryotic/archaeal / 40S ribosomal protein S11, N-terminal / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein S6, eukaryotic / Ribosomal protein S2, eukaryotic / Ribosomal protein L24e, conserved site / Ribosomal protein S7e / 40S ribosomal protein S4, C-terminal domain / Ribosomal protein L34e, conserved site / Ribosomal protein L1, conserved site / Eukaryotic Ribosomal Protein L27, KOW domain / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal S17 / Ribosomal protein S19e signature. / Ribosomal protein L44e / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal protein L27e / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein L27e superfamily / Ribosomal protein S21e / Ribosomal protein S19e / Ribosomal protein S27, zinc-binding domain superfamily / Ribosomal L38e protein family / Ribosomal protein L23/L25, N-terminal / 40S Ribosomal protein S10 / 60S ribosomal protein L35 / Ribosomal protein L1 / Ribosomal protein S17, archaeal/eukaryotic / Ribosomal protein S27 / Ribosomal protein S28e conserved site / Ribosomal protein S6/S6e/A/B/2, conserved site / Ribosomal protein S28e / Ribosomal protein L35Ae, conserved site / Ribosomal protein L30e, conserved site / 40S ribosomal protein S4 C-terminus / Ribosomal protein S4e, N-terminal / Ribosomal protein S23, eukaryotic/archaeal / Ribosomal_S17 N-terminal
Similarity search - Domain/homology
: / : / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL10 ...: / : / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL10 / 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 eS4, Y isoform 1 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein eS12 / Large ribosomal subunit protein eL13 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL11 / 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 uS12 / 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 / 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 uL1 / 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)
Yersinia pseudotuberculosis (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsBehrmann, E. / Loerke, J. / Budkevich, T.V. / Yamamoto, K. / Schmidt, A. / Penczek, P.A. / Vos, M.R. / Burger, J. / Mielke, T. / Scheerer, P. / Spahn, C.M.T.
CitationJournal: Cell / Year: 2015
Title: Structural snapshots of actively translating human ribosomes.
Authors: Elmar Behrmann / Justus Loerke / Tatyana V Budkevich / Kaori Yamamoto / Andrea Schmidt / Pawel A Penczek / Matthijn R Vos / Jörg Bürger / Thorsten Mielke / Patrick Scheerer / Christian M T Spahn /
Abstract: Macromolecular machines, such as the ribosome, undergo large-scale conformational changes during their functional cycles. Although their mode of action is often compared to that of mechanical ...Macromolecular machines, such as the ribosome, undergo large-scale conformational changes during their functional cycles. Although their mode of action is often compared to that of mechanical machines, a crucial difference is that, at the molecular dimension, thermodynamic effects dominate functional cycles, with proteins fluctuating stochastically between functional states defined by energetic minima on an energy landscape. Here, we have used cryo-electron microscopy to image ex-vivo-derived human polysomes as a source of actively translating ribosomes. Multiparticle refinement and 3D variability analysis allowed us to visualize a variety of native translation intermediates. Significantly populated states include not only elongation cycle intermediates in pre- and post-translocational states, but also eEF1A-containing decoding and termination/recycling complexes. Focusing on the post-translocational state, we extended this assessment to the single-residue level, uncovering striking details of ribosome-ligand interactions and identifying both static and functionally important dynamic elements.
History
DepositionFeb 19, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 20, 2015Provider: repository / Type: Initial release
Revision 1.1May 27, 2015Group: Other
Revision 1.2Jul 1, 2015Group: Database references
Revision 1.3Jan 11, 2017Group: Structure summary
Revision 1.4Aug 23, 2017Group: Data collection / Derived calculations / Category: em_image_scans / em_software / struct_conn / Item: _em_software.image_processing_id
Revision 1.5Nov 8, 2017Group: Structure summary / Category: entity / Item: _entity.pdbx_description
Revision 1.6Jun 20, 2018Group: Advisory / Data collection / Derived calculations
Category: database_PDB_caveat / diffrn ...database_PDB_caveat / diffrn / diffrn_radiation / diffrn_radiation_wavelength / struct_conn
Revision 1.7Oct 24, 2018Group: Advisory / Data collection / Derived calculations / Category: pdbx_validate_close_contact / struct_conn
Revision 1.8Nov 21, 2018Group: Advisory / Data collection / Derived calculations / Category: pdbx_validate_close_contact / struct_conn
Revision 1.9Dec 18, 2019Group: Other / Category: atom_sites
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3]
Remark 700SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW ...SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "VB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "FA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A3: 5.8S ribosomal RNA
A4: 5S ribosomal RNA
AA: 60S ribosomal protein L8
AB: 60S ribosomal protein L3
AC: 60S ribosomal protein L4
AD: 60S ribosomal protein L5
AE: 60S ribosomal protein L6
AF: 60S ribosomal protein L7
AG: 60S ribosomal protein L7a
AH: 60S ribosomal protein L9
AI: 60S ribosomal protein L10
AJ: 60S ribosomal protein L11
AK: 60S acidic ribosomal protein P0
AL: 60S ribosomal protein L13
AM: 60S ribosomal protein L14
AN: 60S ribosomal protein L15
AO: 60S ribosomal protein L13a
AP: 60S ribosomal protein L17
AQ: 60S ribosomal protein L18
AR: 60S ribosomal protein L19
AS: 60S ribosomal protein L18a
AT: 60S ribosomal protein L21
AU: 60S ribosomal protein L22
AV: 60S ribosomal protein L23
AW: 60S ribosomal protein L24
AX: 60S ribosomal protein L23a
AY: 60S ribosomal protein L26
AZ: 60S ribosomal protein L27
Aa: 60S ribosomal protein L27a
Ab: 60S ribosomal protein L29
Ac: 60S ribosomal protein L30
Ad: 60S ribosomal protein L31
Ae: 60S ribosomal protein L32
Af: 60S ribosomal protein L35a
Ag: 60S ribosomal protein L34
Ah: 60S ribosomal protein L35
Ai: 60S ribosomal protein L36
Aj: 60S ribosomal protein L37
Ak: 60S ribosomal protein L38
Al: 60S ribosomal protein L39
Am: Ubiquitin-60S ribosomal protein L40
An: 60S ribosomal protein L41
Ao: 60S ribosomal protein L36a
Ap: 60S ribosomal protein L37a
Aq: 60S ribosomal protein L12
At: 60S ribosomal protein L28
Au: 60S ribosomal protein L10a
A2: 28S ribosomal RNA
B1: 18S ribosomal RNA
BA: 40S ribosomal protein SA
BB: 40S ribosomal protein S3a
BC: 40S ribosomal protein S2
BD: 40S ribosomal protein S3
BE: 40S ribosomal protein S4, Y isoform 1
BF: 40S ribosomal protein S5
BG: 40S ribosomal protein S6
BH: 40S ribosomal protein S7
BI: 40S ribosomal protein S8
BJ: 40S ribosomal protein S9
BK: 40S ribosomal protein S10
BL: 40S ribosomal protein S11
BM: 40S ribosomal protein S12
BN: 40S ribosomal protein S13
BO: 40S ribosomal protein S14
BP: 40S ribosomal protein S15
BQ: 40S ribosomal protein S16
BR: 40S ribosomal protein S17-like
BS: 40S ribosomal protein S18
BT: 40S ribosomal protein S19
BU: 40S ribosomal protein S20
BV: 40S ribosomal protein S21
BW: 40S ribosomal protein S15a
BX: 40S ribosomal protein S23
BY: 40S ribosomal protein S24
BZ: 40S ribosomal protein S25
Ba: 40S ribosomal protein S26
Bb: 40S ribosomal protein S27
Bc: 40S ribosomal protein S28
Bd: 40S ribosomal protein S29
Be: 40S ribosomal protein S30
Bf: Ubiquitin-40S ribosomal protein S27a
Bg: Guanine nucleotide-binding protein subunit beta-2-like 1
Bv: tRNA
Bw: tRNA
Bx: mRNA
By: Nascent protein chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,924,116417
Polymers3,915,86686
Non-polymers8,250331
Water0
1


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

-
Components

-
RNA chain , 6 types, 7 molecules A3A4A2B1BvBwBx

#1: RNA chain 5.8S ribosomal RNA /


Mass: 62616.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK 293T / References: GenBank: 51477016
#2: RNA chain 5S ribosomal RNA /


Mass: 38998.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK 293T / References: GenBank: 23898
#48: RNA chain 28S ribosomal RNA /


Mass: 1627178.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK 293T / References: GenBank: 337381
#49: RNA chain 18S ribosomal RNA /


Mass: 602776.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK 293T / References: GenBank: 36162
#83: RNA chain tRNA / Transfer RNA


Mass: 24485.539 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: MIXTURE OF ALL ENDOGENOUS PRESENT / Source: (natural) Yersinia pseudotuberculosis (bacteria) / Cell line: HEK 293T / References: GenBank: 755367513
#84: RNA chain mRNA / Messenger RNA


Mass: 8527.686 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: MIXTURE OF ALL ENDOGENOUS PRESENT / Source: (natural) Homo sapiens (human) / Cell line: HEK 293T

+
60S ribosomal protein ... , 43 types, 43 molecules AAABACADAEAFAGAHAIAJALAMANAOAPAQARASATAUAVAWAXAYAZAaAbAcAdAe...

#3: Protein 60S ribosomal protein L8 /


Mass: 28088.863 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK 293T / References: UniProt: P62917
#4: Protein 60S ribosomal protein L3 / / HIV-1 TAR RNA-binding protein B / TARBP-B


Mass: 46211.113 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK 293T / References: UniProt: P39023
#5: Protein 60S ribosomal protein L4 / / 60S ribosomal protein L1


Mass: 47804.621 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK 293T / References: UniProt: P36578
#6: Protein 60S ribosomal protein L5 /


Mass: 34426.789 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK 293T / References: UniProt: P46777
#7: Protein 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) / Cell line: HEK 293T / References: UniProt: Q02878
#8: Protein 60S ribosomal protein L7 /


Mass: 29290.973 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK 293T / References: UniProt: P18124
#9: Protein 60S ribosomal protein L7a / / 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) / Cell line: HEK 293T / References: UniProt: P62424
#10: Protein 60S ribosomal protein L9 /


Mass: 21899.471 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK 293T / References: UniProt: P32969
#11: Protein 60S ribosomal protein L10 / / Laminin receptor homolog / Protein QM / Tumor suppressor QM


Mass: 24657.084 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK 293T / References: UniProt: P27635
#12: Protein 60S ribosomal protein L11 / / CLL-associated antigen KW-12


Mass: 20288.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK 293T / References: UniProt: P62913
#14: Protein 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) / Cell line: HEK 293T / References: UniProt: P26373
#15: Protein 60S ribosomal protein L14 / / CAG-ISL 7


Mass: 23485.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK 293T / References: UniProt: P50914
#16: Protein 60S ribosomal protein L15 /


Mass: 24207.285 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK 293T / References: UniProt: P61313
#17: Protein 60S ribosomal protein L13a / / 23 kDa highly basic protein


Mass: 23633.412 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK 293T / References: UniProt: P40429
#18: Protein 60S ribosomal protein L17 / / 60S ribosomal protein L23 / PD-1


Mass: 21443.170 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK 293T / References: UniProt: P18621
#19: Protein 60S ribosomal protein L18 /


Mass: 21687.676 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK 293T / References: UniProt: Q07020
#20: Protein 60S ribosomal protein L19 /


Mass: 23535.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK 293T / References: UniProt: P84098
#21: Protein 60S ribosomal protein L18a /


Mass: 20808.514 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK 293T / References: UniProt: Q02543
#22: Protein 60S ribosomal protein L21 /


Mass: 18609.988 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK 293T / References: UniProt: P46778
#23: 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


Mass: 14813.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK 293T / References: UniProt: P35268
#24: Protein 60S ribosomal protein L23 / / 60S ribosomal protein L17


Mass: 14892.505 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK 293T / References: UniProt: P62829
#25: Protein 60S ribosomal protein L24 / / 60S ribosomal protein L30


Mass: 17825.111 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK 293T / References: UniProt: P83731
#26: Protein 60S ribosomal protein L23a /


Mass: 17740.193 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK 293T / References: UniProt: P62750
#27: Protein 60S ribosomal protein L26 /


Mass: 17303.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK 293T / References: UniProt: P61254
#28: Protein 60S ribosomal protein L27 /


Mass: 15835.831 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK 293T / References: UniProt: P61353
#29: Protein 60S ribosomal protein L27a /


Mass: 16604.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK 293T / References: UniProt: P46776
#30: Protein 60S ribosomal protein L29 / / Cell surface heparin-binding protein HIP


Mass: 17804.275 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK 293T / References: UniProt: P47914
#31: Protein 60S ribosomal protein L30 /


Mass: 12805.092 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK 293T / References: UniProt: P62888
#32: Protein 60S ribosomal protein L31 /


Mass: 14494.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK 293T / References: UniProt: P62899
#33: Protein 60S ribosomal protein L32 /


Mass: 15898.932 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK 293T / References: UniProt: P62910
#34: Protein 60S ribosomal protein L35a / / Cell growth-inhibiting gene 33 protein


Mass: 12564.743 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK 293T / References: UniProt: P18077
#35: Protein 60S ribosomal protein L34 /


Mass: 13326.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK 293T / References: UniProt: P49207
#36: Protein 60S ribosomal protein L35 /


Mass: 14593.624 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK 293T / References: UniProt: P42766
#37: Protein 60S ribosomal protein L36 /


Mass: 12290.859 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK 293T / References: UniProt: Q9Y3U8
#38: Protein 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) / Cell line: HEK 293T / References: UniProt: P61927
#39: Protein 60S ribosomal protein L38 /


Mass: 8238.948 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK 293T / References: UniProt: P63173
#40: Protein 60S ribosomal protein L39 /


Mass: 6426.759 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK 293T / References: UniProt: P62891
#42: Protein/peptide 60S ribosomal protein L41 / / HG12


Mass: 3473.451 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK 293T / References: UniProt: P62945
#43: Protein 60S ribosomal protein L36a / / 60S ribosomal protein L44 / Cell growth-inhibiting gene 15 protein / Cell migration-inducing gene 6 protein


Mass: 12476.973 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK 293T / References: UniProt: P83881
#44: Protein 60S ribosomal protein L37a /


Mass: 10299.350 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK 293T / References: UniProt: P61513
#45: Protein 60S ribosomal protein L12 /


Mass: 17847.619 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK 293T / References: UniProt: P30050
#46: Protein 60S ribosomal protein L28 /


Mass: 15784.622 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK 293T / References: UniProt: P46779
#47: Protein 60S ribosomal protein L10a / / CSA-19 / Neural precursor cell expressed developmentally down-regulated protein 6 / NEDD-6


Mass: 24879.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK 293T / References: UniProt: P62906

-
Protein , 4 types, 4 molecules AKAmBfBg

#13: Protein 60S acidic ribosomal protein P0 / / 60S ribosomal protein L10E


Mass: 34309.418 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK 293T / References: UniProt: P05388
#41: Protein Ubiquitin-60S ribosomal protein L40 / CEP52 / Ubiquitin A-52 residue ribosomal protein fusion product 1


Mass: 14758.394 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK 293T / References: UniProt: P62987
#81: Protein Ubiquitin-40S ribosomal protein S27a / Ubiquitin carboxyl extension protein 80


Mass: 18004.041 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK 293T / References: UniProt: P62979
#82: Protein Guanine nucleotide-binding protein subunit beta-2-like 1 / Cell proliferation-inducing gene 21 protein / Guanine nucleotide-binding protein subunit beta-like ...Cell proliferation-inducing gene 21 protein / Guanine nucleotide-binding protein subunit beta-like protein 12.3 / Human lung cancer oncogene 7 protein / HLC-7 / Receptor for activated C kinase / Receptor of activated protein kinase C 1 / RACK1


Mass: 35115.652 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK 293T / References: UniProt: P63244

+
40S ribosomal protein ... , 31 types, 31 molecules BABBBCBDBEBFBGBHBIBJBKBLBMBNBOBPBQBRBSBTBUBVBWBXBYBZBaBbBcBdBe

#50: 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


Mass: 32883.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK 293T / References: UniProt: P08865
#51: Protein 40S ribosomal protein S3a / / 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) / Cell line: HEK 293T / References: UniProt: P61247
#52: Protein 40S ribosomal protein S2 / / 40S ribosomal protein S4 / Protein LLRep3


Mass: 31376.516 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK 293T / References: UniProt: P15880
#53: Protein 40S ribosomal protein S3 /


Mass: 26729.369 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK 293T
References: UniProt: P23396, DNA-(apurinic or apyrimidinic site) lyase
#54: Protein 40S ribosomal protein S4, Y isoform 1 / Ribosome


Mass: 29512.756 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK 293T / References: UniProt: P22090
#55: Protein 40S ribosomal protein S5 /


Mass: 22913.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK 293T / References: UniProt: P46782
#56: Protein 40S ribosomal protein S6 / / Phosphoprotein NP33


Mass: 28751.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK 293T / References: UniProt: P62753
#57: Protein 40S ribosomal protein S7 /


Mass: 22168.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK 293T / References: UniProt: P62081
#58: Protein 40S ribosomal protein S8 /


Mass: 24263.387 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK 293T / References: UniProt: P62241
#59: Protein 40S ribosomal protein S9 /


Mass: 22641.564 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK 293T / References: UniProt: P46781
#60: Protein 40S ribosomal protein S10 /


Mass: 18933.846 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK 293T / References: UniProt: P46783
#61: Protein 40S ribosomal protein S11 /


Mass: 18468.826 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK 293T / References: UniProt: P62280
#62: Protein 40S ribosomal protein S12 /


Mass: 14538.987 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK 293T / References: UniProt: P25398
#63: Protein 40S ribosomal protein S13 /


Mass: 17259.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK 293T / References: UniProt: P62277
#64: Protein 40S ribosomal protein S14 /


Mass: 16302.772 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK 293T / References: UniProt: P62263
#65: Protein 40S ribosomal protein S15 / / RIG protein


Mass: 17076.207 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK 293T / References: UniProt: P62841
#66: Protein 40S ribosomal protein S16 /


Mass: 16477.377 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK 293T / References: UniProt: P62249
#67: Protein 40S ribosomal protein S17-like /


Mass: 15578.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK 293T / References: UniProt: P08708
#68: Protein 40S ribosomal protein S18 / / Ke-3 / Ke3


Mass: 17759.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK 293T / References: UniProt: P62269
#69: Protein 40S ribosomal protein S19 /


Mass: 16091.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK 293T / References: UniProt: P39019
#70: Protein 40S ribosomal protein S20 /


Mass: 13398.763 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK 293T / References: UniProt: P60866
#71: Protein 40S ribosomal protein S21 /


Mass: 9124.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK 293T / References: UniProt: P63220
#72: Protein 40S ribosomal protein S15a /


Mass: 14865.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK 293T / References: UniProt: P62244
#73: Protein 40S ribosomal protein S23 /


Mass: 15844.666 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK 293T / References: UniProt: P62266
#74: Protein 40S ribosomal protein S24 /


Mass: 15463.333 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK 293T / References: UniProt: P62847
#75: Protein 40S ribosomal protein S25 /


Mass: 13776.224 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK 293T / References: UniProt: P62851
#76: Protein 40S ribosomal protein S26 /


Mass: 13047.532 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK 293T / References: UniProt: P62854
#77: Protein 40S ribosomal protein S27 / / Metallopan-stimulin 1 / MPS-1


Mass: 9480.186 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK 293T / References: UniProt: P42677
#78: Protein 40S ribosomal protein S28 /


Mass: 7855.052 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK 293T / References: UniProt: P62857
#79: Protein 40S ribosomal protein S29 /


Mass: 6690.821 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK 293T / References: UniProt: P62273
#80: Protein 40S ribosomal protein S30 /


Mass: 6668.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK 293T / References: UniProt: P62861

-
Protein/peptide , 1 types, 1 molecules By

#85: Protein/peptide Nascent protein chain


Mass: 2060.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: MIXTURE OF ALL ENDOGENOUS PRESENT / Source: (natural) Homo sapiens (human) / Cell line: HEK 293T

-
Non-polymers , 2 types, 331 molecules

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


Mass: 24.305 Da / Num. of mol.: 326 / Source method: obtained synthetically / Formula: Mg
#87: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn

-
Details

Sequence detailsCGCGACCUCAGAUCAGACGUGGCGACCCGCUGAAUUUAAGCAUAUUAGUCAGCGGAGGAAAAGAAACU

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: NATIVE RIBOSOMAL COMPLEX FROM POLYSOMES - POST STATE / Type: RIBOSOME
Buffer solutionName: 20 MM HEPES-KOH, PH 7.5, 100 MM KCL, 1.5 MM MGCL2, 0.5 MM SPERMIDINE, 0.04 MM SPERMINE, 1 MM DTT
pH: 7.5
Details: 20 MM HEPES-KOH, PH 7.5, 100 MM KCL, 1.5 MM MGCL2, 0.5 MM SPERMIDINE, 0.04 MM SPERMINE, 1 MM DTT
SpecimenConc.: 3.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: OTHER
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE
Details: VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 100, TEMPERATURE- 93, INSTRUMENT- FEI VITROBOT MARK II, METHOD- BLOT FOR 2-4 SECONDS BEFORE PLUNGING,

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS / Date: Aug 20, 2012 / Details: DATA WAS COLLECTED AUTOMATICALLY WITH LEGINON
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 115000 X / Calibrated magnification: 205000 X / Nominal defocus max: 4500 nm / Nominal defocus min: 2000 nm / Cs: 2 mm
Image recordingElectron dose: 20 e/Å2 / Film or detector model: TVIPS TEMCAM-F416 (4k x 4k)

-
Processing

EM software
IDNameVersionCategory
1CTFFIND3CTF correction
2Signatureparticle selection
3SPARX3D reconstruction
4SPIDER3D reconstruction
CTF correctionDetails: DEFOCUS GROUPS
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionMethod: MULTI-REFERENCE TEMPLATE MATCHING / Resolution: 3.5 Å / Num. of particles: 313321 / Actual pixel size: 0.945 Å
Magnification calibration: CROSS- -CORRELATION DENSITIES WITHIN SPHERICAL SHELL
Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2875. (DEPOSITION ID: 13060).
Symmetry type: POINT
Atomic model buildingSpace: REAL
Atomic model buildingPDB-ID: 4UJE

4uje

RefinementHighest resolution: 3.5 Å
Refinement stepCycle: LAST / Highest resolution: 3.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms55858 5878 3 0 61739

+
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