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- PDB-5lqw: yeast activated spliceosome -

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Basic information

Entry
Database: PDB / ID: 5lqw
Titleyeast activated spliceosome
Components
  • (Pre-mRNA-splicing factor ...) x 14
  • (Small nuclear ribonucleoprotein ...) 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 snRNA
  • U5 snRNA
  • U6 snRNA
  • actin pre-mRNA
KeywordsSPLICING / activated spliceosome / spliceosome / pre-mRNA splicing
Function / homology
Function and homology information


maintenance of RNA location / RES complex / U2-type post-mRNA release spliceosomal complex / cellular bud site selection / snoRNA splicing / post-mRNA release spliceosomal complex / generation of catalytic spliceosome for first transesterification step / cis assembly of pre-catalytic spliceosome / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / U4/U6 snRNP ...maintenance of RNA location / RES complex / U2-type post-mRNA release spliceosomal complex / cellular bud site selection / snoRNA splicing / post-mRNA release spliceosomal complex / generation of catalytic spliceosome for first transesterification step / cis assembly of pre-catalytic spliceosome / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / U4/U6 snRNP / 7-methylguanosine cap hypermethylation / ATP-dependent activity, acting on RNA / pICln-Sm protein complex / U2-type catalytic step 1 spliceosome / pre-mRNA binding / snRNP binding / splicing factor binding / SMN-Sm protein complex / small nuclear ribonucleoprotein complex / spliceosomal tri-snRNP complex / commitment complex / mRNA cis splicing, via spliceosome / U2-type spliceosomal complex / U2-type prespliceosome assembly / U2-type catalytic step 2 spliceosome / U2 snRNP / U1 snRNP / U4 snRNP / poly(U) RNA binding / U2-type prespliceosome / precatalytic spliceosome / generation of catalytic spliceosome for second transesterification step / Formation of TC-NER Pre-Incision Complex / mRNA 5'-splice site recognition / spliceosomal complex assembly / mRNA 3'-splice site recognition / Gap-filling DNA repair synthesis and ligation in TC-NER / DNA replication origin binding / spliceosomal tri-snRNP complex assembly / Dual incision in TC-NER / Prp19 complex / U5 snRNA binding / U5 snRNP / DNA replication initiation / U2 snRNA binding / U6 snRNA binding / pre-mRNA intronic binding / spliceosomal snRNP assembly / mRNA export from nucleus / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / positive regulation of cell cycle / catalytic step 2 spliceosome / positive regulation of RNA splicing / spliceosomal complex / helicase activity / mRNA splicing, via spliceosome / metallopeptidase activity / nucleic acid binding / RNA helicase activity / RNA helicase / response to xenobiotic stimulus / GTPase activity / mRNA binding / chromatin binding / chromatin / GTP binding / ATP hydrolysis activity / DNA binding / RNA binding / zinc ion binding / ATP binding / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Ist3-like, RNA recognition motif / : / Bud13 / : / Pre-mRNA-splicing factor of RES complex / HAT (Half-A-TPR) repeat / Slt11, RNA recognition motif / Pre-mRNA-splicing factor Cwc2, RNA recognition motif / : / Torus domain ...Ist3-like, RNA recognition motif / : / Bud13 / : / Pre-mRNA-splicing factor of RES complex / HAT (Half-A-TPR) repeat / Slt11, RNA recognition motif / Pre-mRNA-splicing factor Cwc2, RNA recognition motif / : / Torus domain / Torus domain / : / : / Pre-mRNA-splicing factor SYF1 middle HAT repeat / G10 protein signature 2. / BUD31/G10-related, conserved site / G10 protein signature 1. / : / : / STL11, N-terminal / : / Pre-mRNA-splicing factor Syf1/CRNKL1 C-terminal HAT repeat / SKI-interacting protein SKIP, SNW domain / SKI-interacting protein, SKIP / SKIP/SNW domain / : / Pre-mRNA-splicing factor Syf1/CNRKL1 N-terminal HAT repeat / WD repeat Prp46/PLRG1-like / Pre-mRNA-splicing factor Cwc2/Slt11 / G10 protein / Pre-mRNA-splicing factor BUD31 / PHF5-like / Pre-mRNA splicing factor component Cdc5p/Cef1, C-terminal / : / : / PHF5-like protein / pre-mRNA splicing factor component / Splicing factor 3B subunit 5/RDS3 complex subunit 10 / Splicing factor 3B subunit 10 (SF3b10) / Initiation factor eIF-4 gamma, MA3 / MA3 domain / MI domain profile. / Domain in DAP-5, eIF4G, MA-3 and other proteins. / Splicing factor 3B subunit 1-like / Middle domain of eukaryotic initiation factor 4G (eIF4G) / MIF4G-like, type 3 / Brr2, N-terminal helicase PWI domain / : / N-terminal helicase PWI domain / Pre-mRNA-splicing helicase BRR2 plug domain / Winged Helix-turn-helix domain / Sec63 Brl domain / : / : / PPP2R1A-like HEAT repeat / 116kDa U5 small nuclear ribonucleoprotein component, N-terminal / 116kDa U5 small nuclear ribonucleoprotein component, C-terminal / Snu114, GTP-binding domain / 116 kDa U5 small nuclear ribonucleoprotein component N-terminus / Pre-mRNA-splicing factor Syf1-like / Sec63 domain / Sec63 Brl domain / : / Small nuclear ribonucleoprotein Sm D3 / Helicase associated domain (HA2), ratchet-like / DEAD-box helicase, OB fold / Oligonucleotide/oligosaccharide-binding (OB)-fold / Helicase associated domain (HA2), winged-helix / Small nuclear ribonucleoprotein Sm D2 / Small nuclear ribonucleoprotein E / Helicase-associated domain / Small nuclear ribonucleoprotein G / Helicase associated domain (HA2) Add an annotation / 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. / Forkhead associated domain / Forkhead-associated (FHA) domain profile. / LSM domain / LSM domain, eukaryotic/archaea-type / snRNP Sm proteins / FHA domain / Forkhead-associated (FHA) domain / HAT (Half-A-TPR) repeat / HAT (Half-A-TPR) repeats / Myb domain / RSE1/DDB1/CPSF1 second beta-propeller / Cleavage/polyadenylation specificity factor, A subunit, C-terminal / Cleavage/polyadenylation specificity factor, A subunit, N-terminal / : / CPSF A subunit region / RSE1/DDB1/CPSF1 first beta-propeller / : / Sm domain profile. / Myb-like DNA-binding domain / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site
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
Revision 1.4May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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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
Water00
1


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

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Components

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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

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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

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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

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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

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RNA chain , 4 types, 4 molecules 2569

#28: RNA chain U2 snRNA


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


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


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)

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Experimental details

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Experiment

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

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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

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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 / 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

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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

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