[English] 日本語
Yorodumi
- PDB-6yan: Mammalian 48S late-stage translation initiation complex with hist... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6yan
TitleMammalian 48S late-stage translation initiation complex with histone 4 mRNA
Components
  • (40S ribosomal protein ...) x 16
  • (Ribosomal protein ...) x 16
  • 18S ribosomal RNA
  • 60s ribosomal protein l41
  • Eukaryotic translation initiation factor 2 subunit 1
  • Ribosomal_S10 domain-containing protein
  • eukaryotic translation initiation factor 2 subunit gamma
  • histone 4 (H4) mRNA
  • initiator methionylated tRNA
KeywordsTRANSLATION / initiation complex / 48S / eukaryotic initiation factor 1A / rabbit
Function / homology
Function and homology information


eukaryotic translation initiation factor 2 complex / eukaryotic 48S preinitiation complex / cellular response to chemical stress / laminin receptor activity / ubiquitin ligase inhibitor activity / positive regulation of signal transduction by p53 class mediator / 90S preribosome / phagocytic cup / laminin binding / ribosomal small subunit export from nucleus ...eukaryotic translation initiation factor 2 complex / eukaryotic 48S preinitiation complex / cellular response to chemical stress / laminin receptor activity / ubiquitin ligase inhibitor activity / positive regulation of signal transduction by p53 class mediator / 90S preribosome / phagocytic cup / laminin binding / ribosomal small subunit export from nucleus / rough endoplasmic reticulum / translation regulator activity / gastrulation / MDM2/MDM4 family protein binding / translation initiation factor activity / cytosolic ribosome / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / response to endoplasmic reticulum stress / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / positive regulation of apoptotic signaling pathway / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / small-subunit processome / spindle / cytoplasmic stress granule / rRNA processing / rhythmic process / positive regulation of canonical Wnt signaling pathway / regulation of translation / ribosome binding / virus receptor activity / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / perikaryon / cytosolic large ribosomal subunit / cytoplasmic translation / cell differentiation / mitochondrial inner membrane / postsynaptic density / rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / cell division / DNA repair / mRNA binding / apoptotic process / synapse / dendrite / centrosome / nucleolus / perinuclear region of cytoplasm / Golgi apparatus / DNA binding / RNA binding / zinc ion binding / nucleus / membrane / plasma membrane / cytoplasm
Similarity search - Function
Ribosomal protein S26 / Ribosomal protein S8e, subdomain / Translation initiation factor 2; subunit 1; domain 2 / Phosducin; domain 2 / Ribosomal protein S21 / Hypothetical Cytosolic Protein; Chain: A; / Ribosomal protein S27 / first zn-finger domain of poly(adp-ribose) polymerase-1 / Alpha-Beta Plaits - #3370 / Ribosomal Protein S14/S29 ...Ribosomal protein S26 / Ribosomal protein S8e, subdomain / Translation initiation factor 2; subunit 1; domain 2 / Phosducin; domain 2 / Ribosomal protein S21 / Hypothetical Cytosolic Protein; Chain: A; / Ribosomal protein S27 / first zn-finger domain of poly(adp-ribose) polymerase-1 / Alpha-Beta Plaits - #3370 / Ribosomal Protein S14/S29 / 30s Ribosomal Protein S14; Chain N / Ribosomal Protein S8; Chain: A, domain 1 - #30 / Translation initiation factor 2, alpha subunit / Translation initiation factor 2, alpha subunit, middle domain superfamily / Translation initiation factor 2, alpha subunit, C-terminal / IF2a, S1-like domain / Eukaryotic translation initiation factor 2 alpha subunit / Dna Ligase; domain 1 - #10 / Ribosomal protein S11/S14 / S15/NS1, RNA-binding / K homology (KH) domain / Double Stranded RNA Binding Domain - #20 / Glucose-6-phosphate isomerase like protein; domain 1 / Ribosomal Protein S8; Chain: A, domain 1 / N-terminal domain of TfIIb / 40S ribosomal protein SA / Ribosomal Protein S5; domain 2 - #10 / 40S ribosomal protein SA, C-terminal domain / 40S ribosomal protein SA C-terminus / Ubiquitin-like protein FUBI / Translation factors / GMP Synthetase; Chain A, domain 3 / Ribosomal Protein S5; domain 2 / S1 domain profile. / Double Stranded RNA Binding Domain / : / Ribosomal protein S26e signature. / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein S21e, conserved site / Ribosomal protein S21e signature. / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / : / Ribosomal protein S12e signature. / Ribosomal protein S12e / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / Ribosomal protein S2, eukaryotic / S27a-like superfamily / 40S Ribosomal protein S10 / Plectin/S10, N-terminal / Plectin/S10 domain / : / Ribosomal protein S7e signature. / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein S30 / Ribosomal protein S30 / Ribosomal protein S17e, conserved site / Ribosomal protein S17e signature. / Ribosomal protein S25 / S25 ribosomal protein / Ribosomal protein S8e subdomain, eukaryotes / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein S3Ae, conserved site / Ribosomal protein S3Ae signature. / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein S3, eukaryotic/archaeal / Single Sheet / 40S ribosomal protein S4, C-terminal domain / 40S ribosomal protein S4 C-terminus / Ribosomal protein S27e signature. / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S4e signature. / Ribosomal protein S19A/S15e / Ribosomal protein S8e, conserved site / Ribosomal protein S8e signature. / Ribosomal protein S19e / Ribosomal protein S19e / Ribosomal_S19e / Ribosomal protein S17e / Ribosomal protein S17e-like superfamily / Ribosomal S17 / Ribosomal protein S6, eukaryotic / Elongation Factor Tu (Ef-tu); domain 3 / Ribosomal protein S7e / Ribosomal protein S7e / Ribosomal protein L7, eukaryotic / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein L30, N-terminal / Ribosomal L30 N-terminal domain / 40S ribosomal protein S11, N-terminal
Similarity search - Domain/homology
RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein eS32 / Small ribosomal subunit protein uS10 / 40S ribosomal protein S6 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein eS12 / Small ribosomal subunit protein uS9 ...RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein eS32 / Small ribosomal subunit protein uS10 / 40S ribosomal protein S6 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein eS12 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein RACK1 / Ubiquitin-ribosomal protein eS31 fusion protein / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein eS7 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS11 / Eukaryotic translation initiation factor 2 subunit 1 / Ubiquitin-like FUBI-ribosomal protein eS30 fusion protein / Small ribosomal subunit protein eS25 / Small ribosomal subunit protein eS26 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein eS28 / Small ribosomal subunit protein eS8 / Small ribosomal subunit protein eS4 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein eS6 / Small ribosomal subunit protein eS21 / Small ribosomal subunit protein eS19 / Small ribosomal subunit protein eS1 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein eS10 / Small ribosomal subunit protein uS17 / 40S ribosomal protein S24 / Small ribosomal subunit protein eS17 / Large ribosomal subunit protein uL30 / Small ribosomal subunit protein eS27 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein uS14
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
Mus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.48 Å
AuthorsBochler, A. / Simonetti, A. / Guca, E. / Hashem, Y.
Funding supportEuropean Union, France, 2items
OrganizationGrant numberCountry
European Research Council (ERC)759120European Union
French National Research AgencyANR-14-ACHN-0024 France
CitationJournal: Cell Rep / Year: 2020
Title: Structural Insights into the Mammalian Late-Stage Initiation Complexes.
Authors: Angelita Simonetti / Ewelina Guca / Anthony Bochler / Lauriane Kuhn / Yaser Hashem /
Abstract: In higher eukaryotes, the mRNA sequence in the direct vicinity of the start codon, called the Kozak sequence (CRCCaugG, where R is a purine), is known to influence the rate of the initiation process. ...In higher eukaryotes, the mRNA sequence in the direct vicinity of the start codon, called the Kozak sequence (CRCCaugG, where R is a purine), is known to influence the rate of the initiation process. However, the molecular basis underlying its role remains poorly understood. Here, we present the cryoelectron microscopy (cryo-EM) structures of mammalian late-stage 48S initiation complexes (LS48S ICs) in the presence of two different native mRNA sequences, β-globin and histone 4, at overall resolution of 3 and 3.5 Å, respectively. Our high-resolution structures unravel key interactions from the mRNA to eukaryotic initiation factors (eIFs): 1A, 2, 3, 18S rRNA, and several 40S ribosomal proteins. In addition, we are able to study the structural role of ABCE1 in the formation of native 48S ICs. Our results reveal a comprehensive map of ribosome/eIF-mRNA and ribosome/eIF-tRNA interactions and suggest the impact of mRNA sequence on the structure of the LS48S IC.
History
DepositionMar 12, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 8, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.last_update / _pdbx_entry_details.has_protein_modification

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-10762
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
l: 60s ribosomal protein l41
C: 40S ribosomal protein SA
D: ribosomal protein eS1
E: 40S ribosomal protein uS5
F: Ribosomal protein S3
G: 40S ribosomal protein S4
H: Ribosomal protein S5
I: 40S ribosomal protein S6
J: ribosomal protein eS7
K: 40S ribosomal protein S8
L: Ribosomal protein S9 (Predicted)
M: 40S ribosomal protein eS10
N: Ribosomal protein S11
O: 40S ribosomal protein S12
P: ribosomal protein uS15
Q: 40S ribosomal protein uS11
S: ribosomal protein uS9
T: ribosomal protein eS17
V: 40S ribosomal protein eS19
W: Ribosomal_S10 domain-containing protein
X: 40S ribosomal protein S21
Y: Ribosomal protein S15a
Z: 40S ribosomal protein uS12
a: 40S ribosomal protein S24
b: 40S ribosomal protein eS26
c: 40S ribosomal protein S27
d: ribosomal protein eS28
e: ribosomal protein uS14
f: ribosomal protein eS31
g: ribosomal protein RACK1
h: ribosomal protein eS25
i: 40S ribosomal protein eS30
2: 18S ribosomal RNA
3: histone 4 (H4) mRNA
A: Eukaryotic translation initiation factor 2 subunit 1
B: eukaryotic translation initiation factor 2 subunit gamma
U: 40S ribosomal protein uS13
R: Ribosomal protein S15
1: initiator methionylated tRNA


Theoretical massNumber of molelcules
Total (without water)1,273,88039
Polymers1,273,88039
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

-
Protein/peptide , 1 types, 1 molecules l

#1: Protein/peptide 60s ribosomal protein l41 / eL41


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 ... , 16 types, 16 molecules CEGIKMOQVXZabciU

#2: 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: 23360.791 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TLT8
#4: Protein 40S ribosomal protein uS5


Mass: 24814.285 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TUT9*PLUS
#6: Protein 40S ribosomal protein S4


Mass: 29658.920 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TK17
#8: Protein 40S ribosomal protein S6


Mass: 27471.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TM55, UniProt: A0A5K1UJS7*PLUS
#10: Protein 40S ribosomal protein S8


Mass: 23902.871 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TJW1
#12: Protein 40S ribosomal protein eS10


Mass: 11773.953 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TPV3
#14: Protein 40S ribosomal protein S12


Mass: 13766.122 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SFR8
#16: Protein 40S ribosomal protein uS11


Mass: 14544.659 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1T1F0
#19: Protein 40S ribosomal protein eS19


Mass: 15812.286 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TN62
#21: Protein 40S ribosomal protein S21


Mass: 8896.102 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TM82
#23: Protein 40S ribosomal protein uS12


Mass: 15757.587 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SZ47
#24: Protein 40S ribosomal protein S24


Mass: 14575.199 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TS40
#25: Protein 40S ribosomal protein eS26


Mass: 11315.428 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TFE8
#26: 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: G1TZ76
#32: Protein 40S ribosomal protein eS30


Mass: 6741.048 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1T8A2
#37: Protein 40S ribosomal protein uS13


Mass: 16642.307 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TPG3

-
Ribosomal protein ... , 16 types, 16 molecules DFHJLNPSTYdefghR

#3: Protein ribosomal protein eS1


Mass: 24944.408 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TN72
#5: Protein Ribosomal protein S3


Mass: 25158.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TNM3
#7: Protein Ribosomal protein S5


Mass: 21525.941 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TFM5
#9: Protein ribosomal protein eS7


Mass: 21716.387 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SVB0
#11: Protein Ribosomal protein S9 (Predicted)


Mass: 21266.166 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: B7NZS8
#13: Protein 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
#15: Protein ribosomal protein uS15


Mass: 17128.191 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SP51
#17: Protein ribosomal protein uS9


Mass: 15975.753 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SGX4
#18: Protein ribosomal protein eS17


Mass: 14578.988 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TU13
#22: Protein Ribosomal protein S15a


Mass: 14734.357 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TG89
#27: Protein ribosomal protein eS28


Mass: 7263.394 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TIB4
#28: Protein ribosomal protein uS14


Mass: 6364.426 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1U7M4
#29: Protein ribosomal protein eS31


Mass: 8358.903 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SK22
#30: Protein ribosomal protein RACK1


Mass: 34669.113 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SJB4
#31: Protein ribosomal protein eS25


Mass: 8526.119 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TDB3
#38: Protein Ribosomal protein S15


Mass: 15873.732 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1U0Q2

-
Protein , 3 types, 3 molecules WAB

#20: Protein Ribosomal_S10 domain-containing protein


Mass: 11765.890 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: A0A5F9CX53, UniProt: G1SIZ2*PLUS
#35: Protein Eukaryotic translation initiation factor 2 subunit 1


Mass: 30633.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1T2G4
#36: Protein eukaryotic translation initiation factor 2 subunit gamma


Mass: 45862.441 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)

-
RNA chain , 3 types, 3 molecules 231

#33: RNA chain 18S ribosomal RNA


Mass: 601015.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: U at position 1244 is modified / Source: (natural) Oryctolagus cuniculus (rabbit)
#34: RNA chain histone 4 (H4) mRNA


Mass: 11685.985 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse)
#39: RNA chain initiator methionylated tRNA


Mass: 24376.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: adenine at position 37 is modified (threonyl-carbomoyl-adenosine (t6A))
Source: (natural) Oryctolagus cuniculus (rabbit)

-
Details

Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1LS48S IC with histone 4 mRNACOMPLEXall0MULTIPLE SOURCES
2LS48S ICRIBOSOME#1-#33, #35-#391NATURAL
3histone 4 mRNACOMPLEX#341RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Oryctolagus cuniculus (rabbit)9986
23Mus musculus (house mouse)10090
Source (recombinant)Organism: synthetic construct (others)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 26 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

-
Processing

CTF correctionType: NONE
3D reconstructionResolution: 3.48 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 372000 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT

+
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