[English] 日本語
Yorodumi
- PDB-5lqw: yeast activated spliceosome -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5lqw
Titleyeast activated spliceosome
Components
  • (Pre-mRNA-splicing factor ...) x 14
  • (Small nuclear ribonucleoprotein ...SnRNP) x 6
  • (U2 snRNP component ...) x 2
  • Pre-mRNA leakage protein 1
  • Pre-mRNA-processing protein 45
  • Pre-mRNA-splicing helicase BRR2
  • RDS3 complex subunit 10
  • Small nuclear ribonucleoprotein-associated protein B
  • U2 snRNAU2 spliceosomal RNA
  • U5 snRNAU5 spliceosomal RNA
  • U6 snRNAU6 spliceosomal RNA
  • actin pre-mRNA
KeywordsSPLICING / activated spliceosome / spliceosome / pre-mRNA splicing
Function / homology
Function and homology information


maintenance of RNA location / U2-type post-mRNA release spliceosomal complex / RES complex / snoRNA splicing / cellular bud site selection / post-mRNA release spliceosomal complex / cis assembly of pre-catalytic spliceosome / generation of catalytic spliceosome for first transesterification step / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / splicing factor binding ...maintenance of RNA location / U2-type post-mRNA release spliceosomal complex / RES complex / snoRNA splicing / cellular bud site selection / post-mRNA release spliceosomal complex / cis assembly of pre-catalytic spliceosome / generation of catalytic spliceosome for first transesterification step / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / splicing factor binding / U4/U6 snRNP / 7-methylguanosine cap hypermethylation / pre-mRNA binding / U2-type catalytic step 1 spliceosome / pICln-Sm protein complex / Prp19 complex / spliceosomal tri-snRNP complex / small nuclear ribonucleoprotein complex / ATP-dependent activity, acting on RNA / SMN-Sm protein complex / mRNA cis splicing, via spliceosome / U2-type spliceosomal complex / U2-type prespliceosome assembly / commitment complex / U2-type catalytic step 2 spliceosome / U4 snRNP / U2 snRNP / poly(U) RNA binding / U1 snRNP / U2-type prespliceosome / precatalytic spliceosome / spliceosomal complex assembly / Dual incision in TC-NER / DNA replication origin binding / generation of catalytic spliceosome for second transesterification step / Gap-filling DNA repair synthesis and ligation in TC-NER / mRNA 3'-splice site recognition / mRNA 5'-splice site recognition / DNA replication initiation / spliceosomal tri-snRNP complex assembly / U5 snRNA binding / U5 snRNP / spliceosomal snRNP assembly / U2 snRNA binding / U6 snRNA binding / mRNA export from nucleus / pre-mRNA intronic binding / positive regulation of cell cycle / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / positive regulation of RNA splicing / helicase activity / spliceosomal complex / mRNA splicing, via spliceosome / metallopeptidase activity / RNA helicase activity / nucleic acid binding / RNA helicase / response to xenobiotic stimulus / cell cycle / mRNA binding / GTPase activity / chromatin binding / chromatin / GTP binding / ATP hydrolysis activity / DNA binding / RNA binding / ATP binding / identical protein binding / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Ist3-like, RNA recognition motif / Bud13 / Pre-mRNA-splicing factor of RES complex / Slt11, RNA recognition motif / Torus domain / Pre-mRNA-splicing factor Cwc2, RNA recognition motif / Torus domain / : / STL11, N-terminal / WD repeat Prp46/PLRG1-like ...Ist3-like, RNA recognition motif / Bud13 / Pre-mRNA-splicing factor of RES complex / Slt11, RNA recognition motif / Torus domain / Pre-mRNA-splicing factor Cwc2, RNA recognition motif / Torus domain / : / STL11, N-terminal / WD repeat Prp46/PLRG1-like / BUD31/G10-related, conserved site / : / : / G10 protein signature 1. / G10 protein signature 2. / SKI-interacting protein SKIP, SNW domain / PHF5-like / SKI-interacting protein, SKIP / SKIP/SNW domain / PHF5-like protein / HAT (Half-A-TPR) repeat / Splicing factor 3B subunit 5/RDS3 complex subunit 10 / Splicing factor 3B subunit 10 (SF3b10) / Pre-mRNA-splicing factor Cwc2/Slt11 / Splicing factor 3B subunit 1-like / G10 protein / Pre-mRNA-splicing factor BUD31 / Pre-mRNA splicing factor component Cdc5p/Cef1, C-terminal / pre-mRNA splicing factor component / Initiation factor eIF-4 gamma, MA3 / MA3 domain / MI domain profile. / Domain in DAP-5, eIF4G, MA-3 and other proteins. / Pre-mRNA-splicing factor Syf1-like / Brr2, N-terminal helicase PWI domain / : / N-terminal helicase PWI domain / Pre-mRNA-splicing helicase BRR2 plug domain / Middle domain of eukaryotic initiation factor 4G (eIF4G) / MIF4G-like, type 3 / Snu114, GTP-binding domain / Sec63 Brl domain / 116kDa U5 small nuclear ribonucleoprotein component, N-terminal / 116kDa U5 small nuclear ribonucleoprotein component, C-terminal / 116 kDa U5 small nuclear ribonucleoprotein component N-terminus / : / Helicase associated domain (HA2), ratchet-like / DEAD-box helicase, OB fold / Oligonucleotide/oligosaccharide-binding (OB)-fold / Helicase-associated domain / Helicase associated domain (HA2), winged-helix / Helicase associated domain (HA2) Add an annotation / Small nuclear ribonucleoprotein Sm D3 / Sec63 domain / Sec63 Brl domain / Small nuclear ribonucleoprotein Sm D2 / Small nuclear ribonucleoprotein E / Small nuclear ribonucleoprotein G / Small nuclear ribonucleoprotein F / Sm-like protein Lsm7/SmG / Like-Sm (LSM) domain containing protein, LSm4/SmD1/SmD3 / Sm-like protein Lsm6/SmF / Myb-type HTH DNA-binding domain profile. / Zinc finger, CCCH-type / Zinc finger C3H1-type profile. / LSM domain / LSM domain, eukaryotic/archaea-type / snRNP Sm proteins / HAT (Half-A-TPR) repeat / HAT (Half-A-TPR) repeats / Forkhead associated domain / Forkhead-associated (FHA) domain profile. / FHA domain / Cleavage/polyadenylation specificity factor, A subunit, N-terminal / Mono-functional DNA-alkylating methyl methanesulfonate N-term / Myb domain / Cleavage/polyadenylation specificity factor, A subunit, C-terminal / CPSF A subunit region / : / Forkhead-associated (FHA) domain / Sm domain profile. / Myb-like DNA-binding domain / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / DEAH-box subfamily ATP-dependent helicases signature. / Translation elongation factor EFG/EF2, domain IV / Elongation factor G, domain IV / Elongation factor G, domain IV / LSM domain superfamily / Elongation factor G C-terminus / SMAD/FHA domain superfamily / Elongation factor EFG, domain V-like / Elongation factor G C-terminus / EF-G domain III/V-like / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / PROCT domain / Prp8 RNase domain IV, fingers region / PROCT (NUC072) domain / PRO8NT domain / PROCN domain
Similarity search - Domain/homology
RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / RDS3 complex subunit 10 / Pre-mRNA-splicing factor ATP-dependent RNA helicase-like protein PRP2 / Pre-mRNA-splicing factor BUD31 / Pre-mRNA-processing protein 45 / Pre-mRNA-splicing helicase BRR2 / Pre-mRNA-splicing factor 8 ...RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / RDS3 complex subunit 10 / Pre-mRNA-splicing factor ATP-dependent RNA helicase-like protein PRP2 / Pre-mRNA-splicing factor BUD31 / Pre-mRNA-processing protein 45 / Pre-mRNA-splicing helicase BRR2 / Pre-mRNA-splicing factor 8 / Pre-mRNA-splicing factor SNU114 / Pre-mRNA-splicing factor SLT11 / Small nuclear ribonucleoprotein-associated protein B / Small nuclear ribonucleoprotein G / U2 snRNP component IST3 / Small nuclear ribonucleoprotein Sm D3 / Pre-mRNA-splicing factor CWC26 / U2 snRNP component HSH155 / Pre-mRNA-splicing factor CWC22 / Small nuclear ribonucleoprotein F / Small nuclear ribonucleoprotein Sm D1 / Pre-mRNA-splicing factor CEF1 / Pre-mRNA-splicing factor SYF1 / Pre-mRNA-splicing factor RSE1 / Small nuclear ribonucleoprotein Sm D2 / Pre-mRNA-splicing factor RDS3 / Pre-mRNA leakage protein 1 / Pre-mRNA-splicing factor CWC2 / Pre-mRNA-splicing factor CLF1 / Small nuclear ribonucleoprotein E / Pre-mRNA-splicing factor PRP46
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.8 Å
AuthorsRauhut, R. / Luehrmann, R.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationSFB 860 Germany
CitationJournal: Science / Year: 2016
Title: Molecular architecture of the Saccharomyces cerevisiae activated spliceosome.
Authors: Reinhard Rauhut / Patrizia Fabrizio / Olexandr Dybkov / Klaus Hartmuth / Vladimir Pena / Ashwin Chari / Vinay Kumar / Chung-Tien Lee / Henning Urlaub / Berthold Kastner / Holger Stark / Reinhard Lührmann /
Abstract: The activated spliceosome (B) is in a catalytically inactive state and is remodeled into a catalytically active machine by the RNA helicase Prp2, but the mechanism is unclear. Here, we describe a 3D ...The activated spliceosome (B) is in a catalytically inactive state and is remodeled into a catalytically active machine by the RNA helicase Prp2, but the mechanism is unclear. Here, we describe a 3D electron cryomicroscopy structure of the Saccharomyces cerevisiae B complex at 5.8-angstrom resolution. Our model reveals that in B, the catalytic U2/U6 RNA-Prp8 ribonucleoprotein core is already established, and the 5' splice site (ss) is oriented for step 1 catalysis but occluded by protein. The first-step nucleophile-the branchsite adenosine-is sequestered within the Hsh155 HEAT domain and is held 50 angstroms away from the 5'ss. Our structure suggests that Prp2 adenosine triphosphatase-mediated remodeling leads to conformational changes in Hsh155's HEAT domain that liberate the first-step reactants for catalysis.
History
DepositionAug 17, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 5, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2017Group: Author supporting evidence / Data collection / Derived calculations
Category: em_image_scans / em_software ...em_image_scans / em_software / pdbx_audit_support / struct_conn
Item: _em_software.name / _pdbx_audit_support.funding_organization
Revision 1.2Oct 24, 2018Group: Advisory / Data collection / Derived calculations / Category: pdbx_validate_close_contact / struct_conn
Revision 1.3Nov 21, 2018Group: Advisory / Data collection / Derived calculations
Category: pdbx_validate_close_contact / struct_conn / struct_conn_type

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-4099
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Pre-mRNA-splicing factor 8
B: Pre-mRNA-splicing factor SNU114
C: Pre-mRNA-splicing helicase BRR2
D: Pre-mRNA-splicing factor SLT11
E: Pre-mRNA-splicing factor BUD31
F: Pre-mRNA-splicing factor CWC2
H: Pre-mRNA-splicing factor CWC22
J: U2 snRNP component IST3
K: Pre-mRNA-splicing factor PRP46
L: Pre-mRNA-splicing factor CWC26
M: Pre-mRNA-processing protein 45
N: Pre-mRNA leakage protein 1
O: Pre-mRNA-splicing factor ATP-dependent RNA helicase-like protein PRP2
P: Pre-mRNA-splicing factor SYF1
Q: U2 snRNP component HSH155
R: Pre-mRNA-splicing factor CLF1
W: Pre-mRNA-splicing factor CEF1
X: Pre-mRNA-splicing factor RSE1
Y: Pre-mRNA-splicing factor RDS3
Z: RDS3 complex subunit 10
b: Small nuclear ribonucleoprotein-associated protein B
d: Small nuclear ribonucleoprotein Sm D3
e: Small nuclear ribonucleoprotein E
f: Small nuclear ribonucleoprotein F
g: Small nuclear ribonucleoprotein G
h: Small nuclear ribonucleoprotein Sm D1
j: Small nuclear ribonucleoprotein Sm D2
2: U2 snRNA
5: U5 snRNA
6: U6 snRNA
9: actin pre-mRNA


Theoretical massNumber of molelcules
Total (without water)2,351,19031
Polymers2,351,19031
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

-
Pre-mRNA-splicing factor ... , 14 types, 14 molecules ABDEFHKLOPRWXY

#1: Protein Pre-mRNA-splicing factor 8 / Coordinate model: Cα atoms only


Mass: 279850.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P33334
#2: Protein Pre-mRNA-splicing factor SNU114 / 114 kDa U5 small nuclear ribonucleoprotein component / Growth inhibitory protein 10 / Coordinate model: Cα atoms only


Mass: 114174.008 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P36048
#4: Protein Pre-mRNA-splicing factor SLT11 / Extracellular mutant protein 2 / Synthetic lethality with U2 protein 11 / Coordinate model: Cα atoms only


Mass: 40988.590 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P38241
#5: Protein Pre-mRNA-splicing factor BUD31 / Bud site selection protein 31 / Complexed with CEF1 protein 14 / Coordinate model: Cα atoms only


Mass: 18484.502 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P25337
#6: Protein Pre-mRNA-splicing factor CWC2 / Complexed with CEF1 protein 2 / PRP19-associated complex protein 40 / Synthetic lethal with CLF1 protein 3 / Coordinate model: Cα atoms only


Mass: 38486.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q12046
#7: Protein Pre-mRNA-splicing factor CWC22 / Complexed with CEF1 protein 22 / Coordinate model: Cα atoms only


Mass: 67386.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P53333
#9: Protein Pre-mRNA-splicing factor PRP46 / Complexed with CEF1 protein 1 / PRP nineteen-associated complex protein 50 / PRP19-associated ...Complexed with CEF1 protein 1 / PRP nineteen-associated complex protein 50 / PRP19-associated complex protein 50 / Pre-mRNA-processing protein 46 / Coordinate model: Cα atoms only


Mass: 50771.289 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q12417
#10: Protein Pre-mRNA-splicing factor CWC26 / Bud site selection protein 13 / Complexed with CEF1 protein 26 / Synthetic lethal with CLF1 protein 7 / Coordinate model: Cα atoms only


Mass: 30529.141 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P46947
#13: Protein Pre-mRNA-splicing factor ATP-dependent RNA helicase-like protein PRP2 / Pre-mRNA-processing protein 2 / Coordinate model: Cα atoms only


Mass: 99947.492 Da / Num. of mol.: 1 / Mutation: G551N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: PRP2, RNA2, YNR011C, N2048 / Production host: Escherichia coli (E. coli) / References: UniProt: P20095, RNA helicase
#14: Protein Pre-mRNA-splicing factor SYF1 / PRP19-associated complex protein 90 / Synthetic lethal with CDC40 protein 1 / Coordinate model: Cα atoms only


Mass: 100344.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q04048
#16: Protein Pre-mRNA-splicing factor CLF1 / Crooked neck-like factor 1 / PRP19-associated complex protein 77 / Synthetic lethal with CDC40 protein 3 / Coordinate model: Cα atoms only


Mass: 82555.859 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q12309
#17: Protein Pre-mRNA-splicing factor CEF1 / PRP nineteen-associated complex protein 85 / PRP19-associated complex protein 85 / Coordinate model: Cα atoms only


Mass: 67837.773 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q03654
#18: Protein Pre-mRNA-splicing factor RSE1 / RNA splicing and ER to Golgi transport factor 1 / Spliceosome-associated protein 130 / Coordinate model: Cα atoms only


Mass: 153956.781 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q04693
#19: Protein Pre-mRNA-splicing factor RDS3 / Regulator of drug sensitivity 3 / Coordinate model: Cα atoms only


Mass: 12283.573 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q06835

-
Protein , 5 types, 5 molecules CMNZb

#3: Protein Pre-mRNA-splicing helicase BRR2 / Protein Snu246 / Coordinate model: Cα atoms only


Mass: 246470.266 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P32639, RNA helicase
#11: Protein Pre-mRNA-processing protein 45 / Coordinate model: Cα atoms only


Mass: 42548.727 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P28004
#12: Protein Pre-mRNA leakage protein 1 / Coordinate model: Cα atoms only


Mass: 23685.682 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q07930
#20: Protein RDS3 complex subunit 10 / Splicing factor 3b subunit / Coordinate model: Cα atoms only


Mass: 10045.401 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0C074
#21: Protein Small nuclear ribonucleoprotein-associated protein B / snRNP-B / Sm protein B / SmB / Coordinate model: Cα atoms only


Mass: 22426.990 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P40018

-
U2 snRNP component ... , 2 types, 2 molecules JQ

#8: Protein U2 snRNP component IST3 / Increased sodium tolerance protein 3 / U2 snRNP protein SNU17 / Coordinate model: Cα atoms only


Mass: 17121.127 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P40565
#15: Protein U2 snRNP component HSH155 / Coordinate model: Cα atoms only


Mass: 110166.672 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P49955

-
Small nuclear ribonucleoprotein ... , 6 types, 6 molecules defghj

#22: Protein Small nuclear ribonucleoprotein Sm D3 / Sm-D3 / snRNP core protein D3 / Coordinate model: Cα atoms only


Mass: 11240.139 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P43321
#23: Protein Small nuclear ribonucleoprotein E / snRNP-E / Sm protein E / SmE / Coordinate model: Cα atoms only


Mass: 10385.098 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q12330
#24: Protein Small nuclear ribonucleoprotein F / snRNP-F / Sm protein F / SmF / Coordinate model: Cα atoms only


Mass: 9669.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P54999
#25: Protein Small nuclear ribonucleoprotein G / snRNP-G / Sm protein G / SmG / Coordinate model: Cα atoms only


Mass: 8490.809 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P40204
#26: Protein Small nuclear ribonucleoprotein Sm D1 / Sm-D1 / snRNP core protein D1 / Coordinate model: Cα atoms only


Mass: 16296.798 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q02260
#27: Protein Small nuclear ribonucleoprotein Sm D2 / Sm-D2 / snRNP core protein D2 / Coordinate model: Cα atoms only


Mass: 12876.066 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q06217

-
RNA chain , 4 types, 4 molecules 2569

#28: RNA chain U2 snRNA / U2 spliceosomal RNA


Mass: 376267.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
#29: RNA chain U5 snRNA / U5 spliceosomal RNA


Mass: 57444.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
#30: RNA chain U6 snRNA / U6 spliceosomal RNA


Mass: 35883.176 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
#31: RNA chain actin pre-mRNA


Mass: 182574.875 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast)

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: yeast activated spliceosome (BACT) / Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightValue: 3.8 MDa / Experimental value: NO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: prp2-1
Buffer solutionpH: 7.3
Buffer component
IDConc.NameBuffer-ID
120 mMHepes1
21.5 mMMgCl21
375 mMKCl1
42 mMIPTG1
50.5 mMDTT1
SpecimenConc.: 0.05 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R3.5/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Calibrated magnification: 74000 X / Cs: 0.001 mm / C2 aperture diameter: 100 µm / Alignment procedure: ZEMLIN TABLEAU
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 1 sec. / Electron dose: 40 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k) / Num. of grids imaged: 1
EM imaging opticsSpherical aberration corrector: Cs corrector with two hexapoles

-
Processing

EM software
IDNameVersionCategory
4CTFFIND3CTF correction
11RELION3final Euler assignment
13RELION33D reconstruction
CTF correctionType: PHASE FLIPPING ONLY
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 5.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 122000 / Symmetry type: POINT

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more