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- PDB-3jcr: 3D structure determination of the human*U4/U6.U5* tri-snRNP complex -

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Basic information

Entry
Database: PDB / ID: 3jcr
Title3D structure determination of the human*U4/U6.U5* tri-snRNP complex
Components
  • LSm2
  • LSm3
  • LSm4
  • LSm5
  • LSm6
  • LSm7
  • LSm8
  • SmB
  • SmD1
  • SmD2
  • SmD3
  • SmE
  • SmF
  • SmG
  • U4 snRNA
  • U5 snRNA
  • U5-40K
  • U6 snRNA
  • hBrr2
  • hDim1
  • hPrp28
  • hPrp3
  • hPrp31
  • hPrp4
  • hPrp6
  • hPrp8
  • hSad1
  • hSnu114
  • hSnu13
KeywordsSPLICING / snRNP / spliceosome / human
Function / homology
Function and homology information


Lsm2-8 complex / U6 snRNA 3'-end binding / spliceosomal snRNP complex / ribonucleoprotein complex localization / U4atac snRNP / RNA localization / U4atac snRNA binding / mRNA decay by 5' to 3' exoribonuclease / Lsm1-7-Pat1 complex / R-loop processing ...Lsm2-8 complex / U6 snRNA 3'-end binding / spliceosomal snRNP complex / ribonucleoprotein complex localization / U4atac snRNP / RNA localization / U4atac snRNA binding / mRNA decay by 5' to 3' exoribonuclease / Lsm1-7-Pat1 complex / R-loop processing / U6 snRNP / box C/D sno(s)RNA binding / PH domain binding / U2 snRNP binding / U7 snRNA binding / histone pre-mRNA DCP binding / U7 snRNP / dense fibrillar component / histone pre-mRNA 3'end processing complex / cis assembly of pre-catalytic spliceosome / SLBP independent Processing of Histone Pre-mRNAs / SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / box C/D methylation guide snoRNP complex / protein methylation / U4/U6 snRNP / U12-type spliceosomal complex / 7-methylguanosine cap hypermethylation / U1 snRNP binding / methylosome / RNA splicing, via transesterification reactions / pICln-Sm protein complex / U2-type catalytic step 1 spliceosome / snRNP binding / small nuclear ribonucleoprotein complex / sno(s)RNA-containing ribonucleoprotein complex / SMN-Sm protein complex / spliceosomal tri-snRNP complex / U4 snRNA binding / P granule / telomerase holoenzyme complex / U2-type precatalytic spliceosome / commitment complex / telomerase RNA binding / U2-type spliceosomal complex / U2-type prespliceosome assembly / U2-type catalytic step 2 spliceosome / box C/D snoRNP assembly / RNA Polymerase II Transcription Termination / P-body assembly / U2 snRNP / U1 snRNP / U4 snRNP / U2-type prespliceosome / rRNA modification in the nucleus and cytosol / U3 snoRNA binding / tRNA processing / K63-linked polyubiquitin modification-dependent protein binding / precatalytic spliceosome / mRNA catabolic process / spliceosomal complex assembly / mRNA Splicing - Minor Pathway / nuclear-transcribed mRNA catabolic process / MLL1 complex / spliceosomal tri-snRNP complex assembly / U5 snRNA binding / protein deubiquitination / U5 snRNP / U2 snRNA binding / U6 snRNA binding / pre-mRNA intronic binding / single fertilization / Major pathway of rRNA processing in the nucleolus and cytosol / spliceosomal snRNP assembly / ribonucleoprotein complex binding / RNA processing / U1 snRNA binding / Cajal body / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / RNA splicing / response to cocaine / maturation of SSU-rRNA / response to bacterium / spliceosomal complex / small-subunit processome / P-body / helicase activity / mRNA splicing, via spliceosome / small GTPase binding / cellular response to xenobiotic stimulus / mRNA processing / osteoblast differentiation / cellular response to tumor necrosis factor / cellular response to lipopolysaccharide / ATPase binding / ribosomal small subunit biogenesis / snRNP Assembly / protein-macromolecule adaptor activity
Similarity search - Function
USP39 / DDX23-like domain / PRP4-like superfamily / pre-mRNA processing factor 4 (PRP4) like / Sm-like protein Lsm8 / PWI domain superfamily / PWI domain / PWI domain profile. / Pre-mRNA processing factor 4 (PRP4)-like / U6 snRNA-associated Sm-like protein LSm2 ...USP39 / DDX23-like domain / PRP4-like superfamily / pre-mRNA processing factor 4 (PRP4) like / Sm-like protein Lsm8 / PWI domain superfamily / PWI domain / PWI domain profile. / Pre-mRNA processing factor 4 (PRP4)-like / U6 snRNA-associated Sm-like protein LSm2 / Sm-like protein Lsm4 / Splicing Factor Motif, present in Prp18 and Pr04 / Sm-like protein Lsm7 / U6 snRNA-associated Sm-like protein Lsm1/8 / Sm-like protein LSm5 / Sm-like protein Lsm3 / U6 snRNA-associated Sm-like protein Lsm3 / Pre-mRNA-splicing factor 3 / U4/U6 small nuclear ribonucleoprotein Prp3 / pre-mRNA processing factor 3 domain / Prp31 C-terminal / U4/U6 small nuclear ribonucleoprotein Prp31 / Prp31 C terminal domain / Small nuclear ribonucleoprotein Prp3, C-terminal domain / Small nuclear ribonucleoprotein Prp3, C-terminal domain / PWI domain / PWI, domain in splicing factors / Dim1 family / Mitosis protein DIM1 / Mitosis protein DIM1 / PRP1 splicing factor, N-terminal / PRP1 splicing factor, N-terminal / : / : / Small ribonucleoprotein associated, SmB/SmN / Small nuclear ribonucleoprotein D1 / Brr2, N-terminal helicase PWI domain / : / N-terminal helicase PWI domain / Pre-mRNA-splicing helicase BRR2 plug domain / Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger / Zinc finger, UBP-type / Zn-finger in ubiquitin-hydrolases and other protein / Zinc finger UBP-type profile. / Winged Helix-turn-helix domain / Sec63 Brl domain / NOSIC / : / NOSIC (NUC001) domain / Nop domain / Nop domain superfamily / Nop, C-terminal domain / snoRNA binding domain, fibrillarin / Nop domain profile. / Tetratricopeptide repeat / H/ACA ribonucleoprotein complex, subunit Nhp2-like / 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 / 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 / LSM domain / Tetratricopeptide repeat / LSM domain, eukaryotic/archaea-type / snRNP Sm proteins / Peptidase C19, ubiquitin carboxyl-terminal hydrolase / Ubiquitin carboxyl-terminal hydrolase / DEAD-box subfamily ATP-dependent helicases signature. / HAT (Half-A-TPR) repeat / HAT (Half-A-TPR) repeats / Ubiquitin specific protease domain / Ubiquitin specific protease (USP) domain profile. / ATP-dependent RNA helicase DEAD-box, conserved site / RNA helicase, DEAD-box type, Q motif / : / Sm domain profile. / DEAD-box RNA helicase Q motif profile. / Elongation Factor G, domain II / Elongation Factor G, domain III / LSM domain superfamily / JAB1/Mov34/MPN/PAD-1 ubiquitin protease / Translation elongation factor EFG/EF2, domain IV / Elongation factor G, domain IV / Elongation factor G, domain IV / Elongation factor G C-terminus / Elongation factor EFG, domain V-like / Elongation factor G C-terminus / Tetratricopeptide repeat / EF-G domain III/V-like / PROCT domain
Similarity search - Domain/homology
RNA / RNA (> 10) / RNA (> 100) / U4/U6 small nuclear ribonucleoprotein Prp4 / U4/U6 small nuclear ribonucleoprotein Prp3 / U5 small nuclear ribonucleoprotein 200 kDa helicase / Pre-mRNA-processing factor 6 / U6 snRNA-associated Sm-like protein LSm8 / Small nuclear ribonucleoprotein-associated proteins B and B' / NHP2-like protein 1 ...RNA / RNA (> 10) / RNA (> 100) / U4/U6 small nuclear ribonucleoprotein Prp4 / U4/U6 small nuclear ribonucleoprotein Prp3 / U5 small nuclear ribonucleoprotein 200 kDa helicase / Pre-mRNA-processing factor 6 / U6 snRNA-associated Sm-like protein LSm8 / Small nuclear ribonucleoprotein-associated proteins B and B' / NHP2-like protein 1 / Small nuclear ribonucleoprotein E / Small nuclear ribonucleoprotein F / Small nuclear ribonucleoprotein G / U6 snRNA-associated Sm-like protein LSm3 / U6 snRNA-associated Sm-like protein LSm6 / Small nuclear ribonucleoprotein Sm D1 / Small nuclear ribonucleoprotein Sm D2 / Small nuclear ribonucleoprotein Sm D3 / Thioredoxin-like protein 4A / 116 kDa U5 small nuclear ribonucleoprotein component / Ubiquitin carboxyl-terminal hydrolase 39 / U4/U6 small nuclear ribonucleoprotein Prp4 / Pre-mRNA-processing-splicing factor 8 / U4/U6 small nuclear ribonucleoprotein Prp31 / U5 small nuclear ribonucleoprotein 40 kDa protein / Probable ATP-dependent RNA helicase DDX23 / U6 snRNA-associated Sm-like protein LSm7 / U6 snRNA-associated Sm-like protein LSm2 / U6 snRNA-associated Sm-like protein LSm5 / U6 snRNA-associated Sm-like protein LSm4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7 Å
AuthorsAgafonov, D.E. / Kastner, B. / Dybkov, O. / Hofele, R.V. / Liu, W.T. / Urlaub, H. / Luhrmann, R. / Stark, H.
CitationJournal: Science / Year: 2016
Title: Molecular architecture of the human U4/U6.U5 tri-snRNP.
Authors: Dmitry E Agafonov / Berthold Kastner / Olexandr Dybkov / Romina V Hofele / Wen-Ti Liu / Henning Urlaub / Reinhard Lührmann / Holger Stark /
Abstract: The U4/U6.U5 triple small nuclear ribonucleoprotein (tri-snRNP) is a major spliceosome building block. We obtained a three-dimensional structure of the 1.8-megadalton human tri-snRNP at a resolution ...The U4/U6.U5 triple small nuclear ribonucleoprotein (tri-snRNP) is a major spliceosome building block. We obtained a three-dimensional structure of the 1.8-megadalton human tri-snRNP at a resolution of 7 angstroms using single-particle cryo-electron microscopy (cryo-EM). We fit all known high-resolution structures of tri-snRNP components into the EM density map and validated them by protein cross-linking. Our model reveals how the spatial organization of Brr2 RNA helicase prevents premature U4/U6 RNA unwinding in isolated human tri-snRNPs and how the ubiquitin C-terminal hydrolase-like protein Sad1 likely tethers the helicase Brr2 to its preactivation position. Comparison of our model with cryo-EM three-dimensional structures of the Saccharomyces cerevisiae tri-snRNP and Schizosaccharomyces pombe spliceosome indicates that Brr2 undergoes a marked conformational change during spliceosome activation, and that the scaffolding protein Prp8 is also rearranged to accommodate the spliceosome's catalytic RNA network.
History
DepositionJan 21, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 23, 2016Group: Structure summary
Revision 1.2Apr 6, 2016Group: Database references
Revision 1.3Jul 18, 2018Group: Data collection / Category: em_software / Item: _em_software.image_processing_id / _em_software.name
Revision 1.4Feb 21, 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
G: hPrp6
D: U5-40K
C: hBrr2
E: hDim1
A: hPrp8
F: hPrp28
B: hSnu114
O: SmB
P: SmD1
Q: SmD2
R: SmD3
S: SmE
T: SmF
U: SmG
8: LSm8
6: LSm6
5: LSm5
4: LSm4
3: LSm3
2: LSm2
7: LSm7
K: hPrp3
L: hPrp4
J: hPrp31
I: hSnu13
o: SmB
p: SmD1
q: SmD2
r: SmD3
s: SmE
t: SmF
u: SmG
V: hSad1
M: U4 snRNA
N: U6 snRNA
H: U5 snRNA


Theoretical massNumber of molelcules
Total (without water)1,544,41336
Polymers1,544,41336
Non-polymers00
Water00
1


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

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Components

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Protein , 26 types, 33 molecules GDCEAFBOoPpQqRrSsTtUu8654327KL...

#1: Protein hPrp6 / Pre-mRNA-processing factor 6 / Androgen receptor N-terminal domain-transactivating protein 1 / ANT- ...Pre-mRNA-processing factor 6 / Androgen receptor N-terminal domain-transactivating protein 1 / ANT-1 / PRP6 homolog / U5 snRNP-associated 102 kDa protein / U5-102 kDa protein / Coordinate model: Cα atoms only


Mass: 107092.242 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O94906
#2: Protein U5-40K / U5 small nuclear ribonucleoprotein 40 kDa protein / U5 snRNP 40 kDa protein / U5-40K / 38 kDa- ...U5 small nuclear ribonucleoprotein 40 kDa protein / U5 snRNP 40 kDa protein / U5-40K / 38 kDa-splicing factor / Prp8-binding protein / hPRP8BP / U5 snRNP-specific 40 kDa protein / WD repeat-containing protein 57 / Coordinate model: Cα atoms only


Mass: 39359.492 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q96DI7
#3: Protein hBrr2 / U5 small nuclear ribonucleoprotein 200 kDa helicase / Activating signal cointegrator 1 complex ...U5 small nuclear ribonucleoprotein 200 kDa helicase / Activating signal cointegrator 1 complex subunit 3-like 1 / BRR2 homolog / U5 snRNP-specific 200 kDa protein / U5-200KD / Coordinate model: Cα atoms only


Mass: 244823.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O75643, RNA helicase
#4: Protein hDim1 / Thioredoxin-like protein 4A / DIM1 protein homolog / Spliceosomal U5 snRNP-specific 15 kDa protein ...Thioredoxin-like protein 4A / DIM1 protein homolog / Spliceosomal U5 snRNP-specific 15 kDa protein / Thioredoxin-like U5 snRNP protein U5-15kD / Coordinate model: Cα atoms only


Mass: 16807.346 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P83876
#5: Protein hPrp8 / Pre-mRNA-processing-splicing factor 8 / 220 kDa U5 snRNP-specific protein / PRP8 homolog / Splicing ...Pre-mRNA-processing-splicing factor 8 / 220 kDa U5 snRNP-specific protein / PRP8 homolog / Splicing factor Prp8 / p220 / Coordinate model: Cα atoms only


Mass: 273974.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q6P2Q9
#6: Protein hPrp28 / Probable ATP-dependent RNA helicase DDX23 / 100 kDa U5 snRNP-specific protein / DEAD box protein 23 ...Probable ATP-dependent RNA helicase DDX23 / 100 kDa U5 snRNP-specific protein / DEAD box protein 23 / PRP28 homolog / U5-100kD / Coordinate model: Cα atoms only


Mass: 95785.148 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BUQ8, RNA helicase
#7: Protein hSnu114 / 116 kDa U5 small nuclear ribonucleoprotein component / Elongation factor Tu GTP-binding domain- ...116 kDa U5 small nuclear ribonucleoprotein component / Elongation factor Tu GTP-binding domain-containing protein 2 / SNU114 homolog / hSNU114 / U5 snRNP-specific protein / 116 kDa / U5-116 kDa / Coordinate model: Cα atoms only


Mass: 109560.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q15029
#8: Protein SmB / Small nuclear ribonucleoprotein-associated proteins B and B' / snRNP-B / Sm protein B/B' / Sm-B/B' / SmB/B' / Coordinate model: Cα atoms only


Mass: 24642.131 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P14678
#9: Protein SmD1 / Small nuclear ribonucleoprotein Sm D1 / Sm-D1 / Sm-D autoantigen / snRNP core protein D1 / Coordinate model: Cα atoms only


Mass: 13310.653 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62314
#10: Protein SmD2 / Small nuclear ribonucleoprotein Sm D2 / Sm-D2 / snRNP core protein D2 / Coordinate model: Cα atoms only


Mass: 13551.928 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62316
#11: Protein SmD3 / Small nuclear ribonucleoprotein Sm D3 / Sm-D3 / snRNP core protein D3 / Coordinate model: Cα atoms only


Mass: 13940.308 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62318
#12: Protein SmE / Small nuclear ribonucleoprotein E / snRNP-E / Sm protein E / Sm-E / SmE / Coordinate model: Cα atoms only


Mass: 10817.601 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62304
#13: Protein SmF / Small nuclear ribonucleoprotein F / snRNP-F / Sm protein F / Sm-F / SmF / Coordinate model: Cα atoms only


Mass: 9734.171 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62306
#14: Protein SmG / Small nuclear ribonucleoprotein G / snRNP-G / Sm protein G / Sm-G / SmG / Coordinate model: Cα atoms only


Mass: 8508.084 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62308
#15: Protein LSm8 / U6 snRNA-associated Sm-like protein LSm8 / Coordinate model: Cα atoms only


Mass: 10410.589 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O95777
#16: Protein LSm6 / U6 snRNA-associated Sm-like protein LSm6 / Coordinate model: Cα atoms only


Mass: 9139.571 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62312
#17: Protein LSm5 / U6 snRNA-associated Sm-like protein LSm5 / Coordinate model: Cα atoms only


Mass: 9945.448 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y4Y9
#18: Protein LSm4 / U6 snRNA-associated Sm-like protein LSm4 / Glycine-rich protein / GRP / Coordinate model: Cα atoms only


Mass: 15375.775 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y4Z0
#19: Protein LSm3 / U6 snRNA-associated Sm-like protein LSm3 / Coordinate model: Cα atoms only


Mass: 11859.390 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62310
#20: Protein LSm2 / U6 snRNA-associated Sm-like protein LSm2 / Protein G7b / Small nuclear ribonuclear protein D ...U6 snRNA-associated Sm-like protein LSm2 / Protein G7b / Small nuclear ribonuclear protein D homolog / snRNP core Sm-like protein Sm-x5 / Coordinate model: Cα atoms only


Mass: 10847.495 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y333
#21: Protein LSm7 / U6 snRNA-associated Sm-like protein LSm7 / Coordinate model: Cα atoms only


Mass: 11617.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9UK45
#22: Protein hPrp3 / U4/U6 small nuclear ribonucleoprotein Prp3 / Pre-mRNA-splicing factor 3 / hPrp3 / U4/U6 snRNP 90 kDa protein / Coordinate model: Cα atoms only


Mass: 77669.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O43395
#23: Protein hPrp4 / 60 kDa U4/U6 snRNP-specific spliceosomal protein / PRP4 pre-mRNA processing factor 4 homolog (Yeast) ...60 kDa U4/U6 snRNP-specific spliceosomal protein / PRP4 pre-mRNA processing factor 4 homolog (Yeast) / isoform CRA_b / Coordinate model: Cα atoms only


Mass: 58407.980 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q5T1M7, UniProt: O43172*PLUS
#24: Protein hPrp31 / U4/U6 small nuclear ribonucleoprotein Prp31 / Pre-mRNA-processing factor 31 / Serologically defined ...U4/U6 small nuclear ribonucleoprotein Prp31 / Pre-mRNA-processing factor 31 / Serologically defined breast cancer antigen NY-BR-99 / U4/U6 snRNP 61 kDa protein / Protein 61K / hPrp31 / Coordinate model: Cα atoms only


Mass: 55528.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q8WWY3
#25: Protein hSnu13 / NHP2-like protein 1 / High mobility group-like nuclear protein 2 homolog 1 / OTK27 / SNU13 homolog ...NHP2-like protein 1 / High mobility group-like nuclear protein 2 homolog 1 / OTK27 / SNU13 homolog / hSNU13 / U4/U6.U5 small nuclear ribonucleoprotein SNU13 / U4/U6.U5 tri-snRNP 15.5 kDa protein / NHP2-like protein 1 / N-terminally processed / Coordinate model: Cα atoms only


Mass: 14191.524 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P55769
#26: Protein hSad1 / U4/U6.U5 tri-snRNP-associated protein 2 / Inactive ubiquitin-specific peptidase 39 / SAD1 homolog / ...U4/U6.U5 tri-snRNP-associated protein 2 / Inactive ubiquitin-specific peptidase 39 / SAD1 homolog / U4/U6.U5 tri-snRNP-associated 65 kDa protein / 65K / Coordinate model: Cα atoms only


Mass: 65481.426 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q53GS9

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RNA chain , 3 types, 3 molecules MNH

#27: RNA chain U4 snRNA / Coordinate model: P atoms only


Mass: 46536.492 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#28: RNA chain U6 snRNA / Coordinate model: P atoms only


Mass: 34098.270 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#29: RNA chain U5 snRNA / Coordinate model: P atoms only


Mass: 36891.684 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)

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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

Component
IDNameTypeDetailsParent-ID
1human U4/U6.U5 tri-snRNPCOMPLEXmonomer0
2human U4/U6.U5 tri-snRNP1
Molecular weightValue: 1.8 MDa / Experimental value: YES
Buffer solutionName: 20 mM HEPES, pH 7.9, 100 mM KCl, 5 mM MgCl2, 0.1 mM EDTA
pH: 7.9
Details: 20 mM HEPES, pH 7.9, 100 mM KCl, 5 mM MgCl2, 0.1 mM EDTA
SpecimenConc.: 0.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 200 mesh copper grid with carbon support film
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Details: Plunged into liquid ethane (FEI VITROBOT MARK IV).

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS / Date: Sep 10, 2015
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Calibrated magnification: 74000 X / Nominal defocus max: 5350 nm / Nominal defocus min: 1000 nm / Cs: 0.0001 mm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 45 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)
Image scansNum. digital images: 4688

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Processing

EM softwareName: RELION / Category: 3D reconstruction
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 141109 / Nominal pixel size: 2 Å / Actual pixel size: 2 Å / Details: (Single particle--Applied symmetry: C1) / Symmetry type: POINT
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms9200 203 0 0 9403

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Jul 12, 2017. Major update of PDB

Major update of PDB

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

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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

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