[English] 日本語
Yorodumi
- PDB-3jcm: Cryo-EM structure of the spliceosomal U4/U6.U5 tri-snRNP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3jcm
TitleCryo-EM structure of the spliceosomal U4/U6.U5 tri-snRNP
Components
  • (Pre-mRNA-splicing factor ...) x 3
  • (Small nuclear ribonucleoprotein ...SnRNP) x 6
  • (U4/U6 small nuclear ribonucleoprotein ...) x 2
  • (U6 snRNA-associated Sm-like protein ...) x 7
  • 13 kDa ribonucleoprotein-associated protein
  • Pre-mRNA-processing factor 31
  • Pre-mRNA-splicing helicase BRR2
  • SNR14 snRNA
  • SNR6 snRNA
  • SNR7-L snRNA
  • Small nuclear ribonucleoprotein-associated protein B
  • Spliceosomal protein DIB1Spliceosome
  • pre-mRNAPrimary transcript
KeywordsTRANSCRIPTION / U4/U6.U5 tri-snRNP / pre-mRNA
Function / homology
Function and homology information


spliceosomal conformational changes to generate catalytic conformation / mRNA decay by 5' to 3' exoribonuclease / snoRNA splicing / Lsm1-7-Pat1 complex / U6 snRNP / snoRNA guided rRNA 2'-O-methylation / positive regulation of RNA binding / box C/D sno(s)RNA 3'-end processing / U4/U6 snRNP / generation of catalytic spliceosome for first transesterification step ...spliceosomal conformational changes to generate catalytic conformation / mRNA decay by 5' to 3' exoribonuclease / snoRNA splicing / Lsm1-7-Pat1 complex / U6 snRNP / snoRNA guided rRNA 2'-O-methylation / positive regulation of RNA binding / box C/D sno(s)RNA 3'-end processing / U4/U6 snRNP / generation of catalytic spliceosome for first transesterification step / deadenylation-dependent decapping of nuclear-transcribed mRNA / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / box C/D methylation guide snoRNP complex / splicing factor binding / P-body assembly / 7-methylguanosine cap hypermethylation / pICln-Sm protein complex / spliceosomal tri-snRNP complex / U4 snRNP / small nuclear ribonucleoprotein complex / sno(s)RNA-containing ribonucleoprotein complex / U4 snRNA binding / SMN-Sm protein complex / U2-type prespliceosome assembly / commitment complex / U2-type catalytic step 2 spliceosome / U2 snRNP / poly(U) RNA binding / nuclear-transcribed mRNA catabolic process / U3 snoRNA binding / U1 snRNP / U2-type prespliceosome / tRNA processing / precatalytic spliceosome / spliceosomal complex assembly / generation of catalytic spliceosome for second transesterification step / Major pathway of rRNA processing in the nucleolus and cytosol / mRNA 3'-splice site recognition / mRNA 5'-splice site recognition / spliceosomal tri-snRNP complex assembly / U5 snRNA binding / U5 snRNP / spliceosomal snRNP assembly / U2 snRNA binding / U6 snRNA binding / pre-mRNA intronic binding / maturation of SSU-rRNA / U1 snRNA binding / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / small-subunit processome / P-body / spliceosomal complex / mRNA splicing, via spliceosome / rRNA processing / metallopeptidase activity / cytosolic large ribosomal subunit / RNA helicase activity / nucleic acid binding / RNA helicase / mRNA binding / GTPase activity / GTP binding / nucleolus / ATP hydrolysis activity / mitochondrion / RNA binding / nucleoplasm / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Sec63 N-terminal domain-like domain / Sec63 N-terminal domain-like fold / Elongation Factor G (Translational Gtpase), domain 3 / Pre-mRNA processing factor 4 (PRP4)-like / Splicing Factor Motif, present in Prp18 and Pr04 / Prp31 C-terminal / U4/U6 small nuclear ribonucleoprotein Prp31 / Prp31 C terminal domain / Pre-mRNA-splicing factor 3 / U4/U6 small nuclear ribonucleoprotein Prp3 ...Sec63 N-terminal domain-like domain / Sec63 N-terminal domain-like fold / Elongation Factor G (Translational Gtpase), domain 3 / Pre-mRNA processing factor 4 (PRP4)-like / Splicing Factor Motif, present in Prp18 and Pr04 / Prp31 C-terminal / U4/U6 small nuclear ribonucleoprotein Prp31 / Prp31 C terminal domain / Pre-mRNA-splicing factor 3 / U4/U6 small nuclear ribonucleoprotein Prp3 / Sm-like protein Lsm8 / pre-mRNA processing factor 3 domain / Small nuclear ribonucleoprotein Prp3, C-terminal domain / Small nuclear ribonucleoprotein Prp3, C-terminal domain / U6 snRNA-associated Sm-like protein Lsm1/8 / Dim1 family / U6 snRNA-associated Sm-like protein LSm2 / Sm-like protein Lsm4 / Mitosis protein DIM1 / Mitosis protein DIM1 / Sm-like protein Lsm7 / PRP1 splicing factor, N-terminal / Sm-like protein LSm5 / Sm-like protein Lsm3 / U6 snRNA-associated Sm-like protein Lsm3 / PRP1 splicing factor, N-terminal / Pre-mRNA-splicing factor Syf1-like / NOSIC / Brr2, N-terminal helicase PWI domain / : / N-terminal helicase PWI domain / Pre-mRNA-splicing helicase BRR2 plug domain / NOSIC (NUC001) domain / Nop domain / Nop domain superfamily / Nop, C-terminal domain / snoRNA binding domain, fibrillarin / Nop domain profile. / H/ACA ribonucleoprotein complex, subunit Nhp2-like / 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 / Small nuclear ribonucleoprotein Sm D3 / Sec63 domain / Sec63 Brl domain / Small nuclear ribonucleoprotein Sm D2 / Small nuclear ribonucleoprotein E / Ribosomal protein L30/S12 / Small nuclear ribonucleoprotein G / Small nuclear ribonucleoprotein F / Sm-like protein Lsm7/SmG / Like-Sm (LSM) domain containing protein, LSm4/SmD1/SmD3 / SH3 type barrels. - #100 / Sm-like protein Lsm6/SmF / LSM domain / LSM domain, eukaryotic/archaea-type / snRNP Sm proteins / HAT (Half-A-TPR) repeat / HAT (Half-A-TPR) repeats / : / Sm domain profile. / C2 domain / 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 / Elongation factor EFG, domain V-like / Elongation factor G C-terminus / EF-G domain III/V-like / PROCT domain / Prp8 RNase domain IV, fingers region / PROCT (NUC072) domain / PRO8NT domain / PROCN domain / Pre-mRNA-processing-splicing factor 8, U6-snRNA-binding / Pre-mRNA-processing-splicing factor 8, U5-snRNA-binding / RNA recognition motif, spliceosomal PrP8 / PRP8 domain IV core / Pre-mRNA-processing-splicing factor 8, U5-snRNA-binding domain superfamily / Prp8 RNase domain IV, palm region / PRO8NT (NUC069), PrP8 N-terminal domain / PROCN (NUC071) domain / U6-snRNA interacting domain of PrP8 / U5-snRNA binding site 2 of PrP8 / RNA recognition motif of the spliceosomal PrP8 / PRP8 domain IV core / Pre-mRNA-processing-splicing factor 8 / 60s Ribosomal Protein L30; Chain: A; / Elongation factor Tu domain 2 / JAB/MPN domain / JAB1/MPN/MOV34 metalloenzyme domain / MPN domain / MPN domain profile. / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / Ribosomal protein L7Ae conserved site / Ribosomal protein L7Ae signature.
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / Chem-M7M / : / : / : / RNA / RNA (> 10) / RNA (> 100) / Pre-mRNA-splicing factor 6 / U4/U6 small nuclear ribonucleoprotein PRP4 ...GUANOSINE-5'-TRIPHOSPHATE / Chem-M7M / : / : / : / RNA / RNA (> 10) / RNA (> 100) / Pre-mRNA-splicing factor 6 / U4/U6 small nuclear ribonucleoprotein PRP4 / Pre-mRNA-splicing helicase BRR2 / Pre-mRNA-splicing factor 8 / Pre-mRNA-splicing factor SNU114 / U6 snRNA-associated Sm-like protein LSm2 / 13 kDa ribonucleoprotein-associated protein / Small nuclear ribonucleoprotein-associated protein B / U6 snRNA-associated Sm-like protein LSm4 / U6 snRNA-associated Sm-like protein LSm5 / Small nuclear ribonucleoprotein G / Small nuclear ribonucleoprotein Sm D3 / U6 snRNA-associated Sm-like protein LSm8 / Pre-mRNA-processing factor 31 / U6 snRNA-associated Sm-like protein LSm7 / Small nuclear ribonucleoprotein F / U6 snRNA-associated Sm-like protein LSm3 / Small nuclear ribonucleoprotein Sm D1 / U4/U6 small nuclear ribonucleoprotein PRP3 / Small nuclear ribonucleoprotein Sm D2 / U6 snRNA-associated Sm-like protein LSm6 / Spliceosomal protein DIB1 / Small nuclear ribonucleoprotein E
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288c (yeast)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsWan, R. / Yan, C. / Bai, R. / Wang, L. / Huang, M. / Wong, C.C. / Shi, Y.
CitationJournal: Science / Year: 2016
Title: The 3.8 Å structure of the U4/U6.U5 tri-snRNP: Insights into spliceosome assembly and catalysis.
Authors: Ruixue Wan / Chuangye Yan / Rui Bai / Lin Wang / Min Huang / Catherine C L Wong / Yigong Shi /
Abstract: Splicing of precursor messenger RNA is accomplished by a dynamic megacomplex known as the spliceosome. Assembly of a functional spliceosome requires a preassembled U4/U6.U5 tri-snRNP complex, which ...Splicing of precursor messenger RNA is accomplished by a dynamic megacomplex known as the spliceosome. Assembly of a functional spliceosome requires a preassembled U4/U6.U5 tri-snRNP complex, which comprises the U5 small nuclear ribonucleoprotein (snRNP), the U4 and U6 small nuclear RNA (snRNA) duplex, and a number of protein factors. Here we report the three-dimensional structure of a Saccharomyces cerevisiae U4/U6.U5 tri-snRNP at an overall resolution of 3.8 angstroms by single-particle electron cryomicroscopy. The local resolution for the core regions of the tri-snRNP reaches 3.0 to 3.5 angstroms, allowing construction of a refined atomic model. Our structure contains U5 snRNA, the extensively base-paired U4/U6 snRNA, and 30 proteins including Prp8 and Snu114, which amount to 8495 amino acids and 263 nucleotides with a combined molecular mass of ~1 megadalton. The catalytic nucleotide U80 from U6 snRNA exists in an inactive conformation, stabilized by its base-pairing interactions with U4 snRNA and protected by Prp3. Pre-messenger RNA is bound in the tri-snRNP through base-pairing interactions with U6 snRNA and loop I of U5 snRNA. This structure, together with that of the spliceosome, reveals the molecular choreography of the snRNAs in the activation process of the spliceosomal ribozyme.
History
DepositionDec 23, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 24, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: cell / database_2 ...cell / database_2 / em_image_scans / struct_conn
Item: _cell.Z_PDB / _cell.length_a ..._cell.Z_PDB / _cell.length_a / _cell.length_b / _cell.length_c / _struct_conn.pdbx_leaving_atom_flag
Revision 1.2Mar 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: atom_sites / chem_comp_atom ...atom_sites / chem_comp_atom / chem_comp_bond / database_2 / struct_sheet / struct_site
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-6561
  • Imaged by UCSF Chimera
  • Download
  • Superimposition on EM map
  • EMDB-6562
  • Imaged by UCSF Chimera
  • Download
  • Superimposition on EM map
  • EMDB-6563
  • Imaged by UCSF Chimera
  • Download
  • Superimposition on EM map
  • EMDB-6564
  • Imaged by UCSF Chimera
  • Download
  • Superimposition on EM map
  • EMDB-6565
  • Imaged by UCSF Chimera
  • Download
  • Superimposition on EM map
  • EMDB-6566
  • Imaged by UCSF Chimera
  • Download
  • Superimposition on EM map
  • EMDB-6567
  • Imaged by UCSF Chimera
  • Download
  • Superimposition on EM map
  • EMDB-6568
  • Imaged by UCSF Chimera
  • Download
  • Superimposition on EM map
  • EMDB-6569
  • Imaged by UCSF Chimera
  • Download
  • Superimposition on EM map
  • EMDB-6570
  • Imaged by UCSF Chimera
  • Download
  • Superimposition on EM map
  • EMDB-6571
  • Imaged by UCSF Chimera
  • Download
  • Superimposition on EM map
  • EMDB-6572
  • Imaged by UCSF Chimera
  • Download
  • Superimposition on EM map
  • EMDB-6573
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Pre-mRNA-splicing factor 8
B: U4/U6 small nuclear ribonucleoprotein PRP4
I: Pre-mRNA-processing factor 31
G: Pre-mRNA-splicing factor 6
K: U4/U6 small nuclear ribonucleoprotein PRP3
L: Spliceosomal protein DIB1
M: 13 kDa ribonucleoprotein-associated protein
H: Pre-mRNA-splicing factor SNU114
N: Pre-mRNA-splicing helicase BRR2
R: Small nuclear ribonucleoprotein Sm D3
S: Small nuclear ribonucleoprotein-associated protein B
T: Small nuclear ribonucleoprotein Sm D1
U: Small nuclear ribonucleoprotein Sm D2
V: Small nuclear ribonucleoprotein E
W: Small nuclear ribonucleoprotein F
X: Small nuclear ribonucleoprotein G
J: Small nuclear ribonucleoprotein Sm D3
O: Small nuclear ribonucleoprotein-associated protein B
P: Small nuclear ribonucleoprotein Sm D1
Q: Small nuclear ribonucleoprotein Sm D2
Y: Small nuclear ribonucleoprotein E
Z: Small nuclear ribonucleoprotein F
a: Small nuclear ribonucleoprotein G
b: U6 snRNA-associated Sm-like protein LSm8
c: U6 snRNA-associated Sm-like protein LSm2
d: U6 snRNA-associated Sm-like protein LSm3
e: U6 snRNA-associated Sm-like protein LSm6
f: U6 snRNA-associated Sm-like protein LSm5
g: U6 snRNA-associated Sm-like protein LSm7
h: U6 snRNA-associated Sm-like protein LSm4
C: pre-mRNA
D: SNR6 snRNA
E: SNR14 snRNA
F: SNR7-L snRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,373,83336
Polymers1,372,82234
Non-polymers1,0102
Water0
1


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

-
Components

-
Pre-mRNA-splicing factor ... , 3 types, 3 molecules AGH

#1: Protein Pre-mRNA-splicing factor 8


Mass: 279867.469 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Genus: PRP8 / Strain: S288c / References: UniProt: P33334
#4: Protein Pre-mRNA-splicing factor 6


Mass: 104370.133 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Genus: PRP6 / Strain: S288c / References: UniProt: P19735
#8: Protein Pre-mRNA-splicing factor SNU114 / 114 kDa U5 small nuclear ribonucleoprotein component / Growth inhibitory protein 10


Mass: 114174.008 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Genus: SNU114 / Strain: S288c / References: UniProt: P36048

-
U4/U6 small nuclear ribonucleoprotein ... , 2 types, 2 molecules BK

#2: Protein U4/U6 small nuclear ribonucleoprotein PRP4 / Pre-mRNA-processing protein 4


Mass: 52506.984 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Genus: PRP4 / Strain: S288c / References: UniProt: P20053
#5: Protein U4/U6 small nuclear ribonucleoprotein PRP3 / Pre-mRNA-splicing factor 3


Mass: 55974.320 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Genus: PRP3 / Strain: S288c / References: UniProt: Q03338

-
Protein , 5 types, 6 molecules ILMNSO

#3: Protein Pre-mRNA-processing factor 31


Mass: 56382.516 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Genus: PRP31 / Strain: S288c / References: UniProt: P49704
#6: Protein Spliceosomal protein DIB1 / Spliceosome


Mass: 16798.387 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Genus: DIB1 / Strain: S288c / References: UniProt: Q06819
#7: Protein 13 kDa ribonucleoprotein-associated protein / Small nuclear ribonucleoprotein-associated protein 1


Mass: 13582.855 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Genus: SNU13NHP2L1 / Strain: S288c / References: UniProt: P39990
#9: Protein Pre-mRNA-splicing helicase BRR2 / Protein Snu246


Mass: 246470.266 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Genus: BRR2 / Strain: S288c / References: UniProt: P32639, RNA helicase
#11: Protein Small nuclear ribonucleoprotein-associated protein B / snRNP-B / Sm protein B / Sm-B / SmB


Mass: 22426.990 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Genus: SMB1 / Strain: S288c / References: UniProt: P40018

-
Small nuclear ribonucleoprotein ... , 6 types, 12 molecules RJTPUQVYWZXa

#10: Protein Small nuclear ribonucleoprotein Sm D3 / Sm-D3 / snRNP core protein D3


Mass: 11240.139 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Genus: SMD3 / Strain: S288c / References: UniProt: P43321
#12: Protein Small nuclear ribonucleoprotein Sm D1 / Sm-D1 / snRNP core protein D1


Mass: 16296.798 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Genus: SMD1 / Strain: S288c / References: UniProt: Q02260
#13: Protein Small nuclear ribonucleoprotein Sm D2 / Sm-D2 / snRNP core protein D2


Mass: 12876.066 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Genus: SMD2 / Strain: S288c / References: UniProt: Q06217
#14: Protein Small nuclear ribonucleoprotein E / snRNP-E / Sm protein E / Sm-E / SmE


Mass: 10385.098 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Genus: SME1 / Strain: S288c / References: UniProt: Q12330
#15: Protein Small nuclear ribonucleoprotein F / snRNP-F / Sm protein F / Sm-F / SmF


Mass: 9669.945 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Genus: SMX3 / Strain: S288c / References: UniProt: P54999
#16: Protein Small nuclear ribonucleoprotein G / snRNP-G / Sm protein G / Sm-G / SmG


Mass: 8490.809 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Genus: SMX2 / Strain: S288c / References: UniProt: P40204

-
U6 snRNA-associated Sm-like protein ... , 7 types, 7 molecules bcdefgh

#17: Protein U6 snRNA-associated Sm-like protein LSm8


Mass: 12403.378 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Genus: LSM8 / Strain: S288c / References: UniProt: P47093
#18: Protein U6 snRNA-associated Sm-like protein LSm2 / Small nuclear ribonucleoprotein D homolog SNP3


Mass: 11177.888 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Genus: LSM2 / Strain: S288c / References: UniProt: P38203
#19: Protein U6 snRNA-associated Sm-like protein LSm3 / SmX4 protein


Mass: 10039.262 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Genus: LSM3 / Strain: S288c / References: UniProt: P57743
#20: Protein U6 snRNA-associated Sm-like protein LSm6


Mass: 9406.579 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Genus: LSM6 / Strain: S288c / References: UniProt: Q06406
#21: Protein U6 snRNA-associated Sm-like protein LSm5


Mass: 10432.954 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Genus: LSM5 / Strain: S288c / References: UniProt: P40089
#22: Protein U6 snRNA-associated Sm-like protein LSm7


Mass: 13027.045 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Genus: LSM7 / Strain: S288c / References: UniProt: P53905
#23: Protein U6 snRNA-associated Sm-like protein LSm4


Mass: 21298.070 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Genus: LSM4 / Strain: S288c / References: UniProt: P40070

-
RNA chain , 4 types, 4 molecules CDEF

#24: RNA chain pre-mRNA / Primary transcript


Mass: 6425.880 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#25: RNA chain SNR6 snRNA / U6 snRNA


Mass: 35883.176 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / References: GenBank: 831416131
#26: RNA chain SNR14 snRNA / U4 snRNA


Mass: 51186.023 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / References: GenBank: 831416092
#27: RNA chain SNR7-L snRNA / U5 snRNA


Mass: 68643.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / References: GenBank: 831416109

-
Non-polymers , 2 types, 2 molecules

#28: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#29: Chemical ChemComp-M7M / N,N,7-trimethylguanosine 5'-(trihydrogen diphosphate)


Mass: 487.296 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H23N5O11P2

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: U4/U6.U5 tri-snRNP / Type: COMPLEX
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

-
Electron microscopy imaging

MicroscopyModel: FEI TITAN / Date: Aug 8, 2015
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k)

-
Processing

SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 172134 / Actual pixel size: 1.32 Å / Symmetry type: POINT
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms52625 5565 63 0 58253

+
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