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- PDB-8y6o: Cryo-EM Structure of the human minor pre-B complex (pre-precataly... -

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Basic information

Entry
Database: PDB / ID: 8y6o
TitleCryo-EM Structure of the human minor pre-B complex (pre-precatalytic spliceosome) U11 and tri-snRNP part
Components
  • (Small nuclear ribonucleoprotein ...SnRNP) x 6
  • (U11/U12 small nuclear ribonucleoprotein ...) x 3
  • (U4/U6 small nuclear ribonucleoprotein ...) x 3
  • (U4/U6.U5 tri-snRNP-associated protein ...) x 2
  • (U5 small nuclear ribonucleoprotein ...) x 2
  • 116 kDa U5 small nuclear ribonucleoprotein component
  • Centrosomal AT-AC splicing factor
  • NHP2-like protein 1
  • Pre-mRNA-processing factor 6
  • Pre-mRNA-processing-splicing factor 8
  • Probable ATP-dependent RNA helicase DDX23
  • Programmed cell death protein 7
  • Serine/threonine-protein kinase PRP4 homolog
  • Small nuclear ribonucleoprotein-associated proteins B and B'
  • Thioredoxin-like protein 4B
  • U11 snRNAU11 spliceosomal RNA
  • U4atac snRNA
  • U5 snRNAU5 spliceosomal RNA
  • U6atac snRNA
  • Zinc finger matrin-type protein 5
  • pre-mRNAPrimary transcript
KeywordsSPLICING/RNA / spliceosome / minor spliceosome / U11 snRNP / U12 snRNP / U4atac / U6atac / CENATAC / TXNL4B / U11 snRNA / minor tri-snRNP / U12-type intron / SPLICING-RNA complex
Function / homology
Function and homology information


negative regulation of centrosome duplication / spliceosomal snRNP complex / ribonucleoprotein complex localization / U4atac snRNP / positive regulation of cytotoxic T cell differentiation / maturation of 5S rRNA / R-loop processing / RNA localization / chromosome separation / U4atac snRNA binding ...negative regulation of centrosome duplication / spliceosomal snRNP complex / ribonucleoprotein complex localization / U4atac snRNP / positive regulation of cytotoxic T cell differentiation / maturation of 5S rRNA / R-loop processing / RNA localization / chromosome separation / U4atac snRNA binding / box C/D sno(s)RNA binding / snRNP binding / U2 snRNP binding / U7 snRNA binding / histone pre-mRNA DCP binding / dense fibrillar component / U7 snRNP / snRNA binding / 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 / U4/U6 snRNP / protein methylation / U12-type spliceosomal complex / methylosome / 7-methylguanosine cap hypermethylation / U2-type catalytic step 1 spliceosome / pICln-Sm protein complex / U1 snRNP binding / RNA splicing, via transesterification reactions / spliceosomal tri-snRNP complex / small nuclear ribonucleoprotein complex / P granule / sno(s)RNA-containing ribonucleoprotein complex / U4 snRNA binding / SMN-Sm protein complex / mRNA cis splicing, via spliceosome / U2-type spliceosomal complex / telomerase RNA binding / telomerase holoenzyme complex / U2-type precatalytic spliceosome / U2-type prespliceosome assembly / box C/D snoRNP assembly / commitment complex / U2-type catalytic step 2 spliceosome / U4 snRNP / rRNA modification in the nucleus and cytosol / U2 snRNP / RNA Polymerase II Transcription Termination / U1 snRNP / U3 snoRNA binding / U2-type prespliceosome / K63-linked polyubiquitin modification-dependent protein binding / precatalytic spliceosome / spliceosomal complex assembly / intercellular bridge / mRNA Splicing - Minor Pathway / regulation of protein catabolic process / single fertilization / MLL1 complex / spliceosomal tri-snRNP complex assembly / Major pathway of rRNA processing in the nucleolus and cytosol / U5 snRNA binding / U5 snRNP / Cajal body / U2 snRNA binding / spliceosomal snRNP assembly / U6 snRNA binding / RNA processing / ribonucleoprotein complex binding / pre-mRNA intronic binding / maturation of SSU-rRNA / U1 snRNA binding / maturation of LSU-rRNA / U4/U6 x U5 tri-snRNP complex / response to glucocorticoid / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / small-subunit processome / RNA splicing / response to cocaine / helicase activity / spliceosomal complex / ribosomal small subunit biogenesis / mRNA splicing, via spliceosome / mRNA processing / osteoblast differentiation / cellular response to xenobiotic stimulus / chromosome / cellular response to tumor necrosis factor / snRNP Assembly / cytosolic large ribosomal subunit / ATPase binding / SARS-CoV-2 modulates host translation machinery / ubiquitinyl hydrolase 1 / cellular response to lipopolysaccharide / RNA helicase activity
Similarity search - Function
CCDC84-like / Programmed cell death protein 7 / snRNP35, RNA recognition motif / Coiled coil protein 84 / Programmed cell death protein 7 / U11/U12 small nuclear ribonucleoprotein 25kDa protein / SNRNP25, ubiquitin-like domain / Ubiquitin-like domain / TRM13/UPF0224 family, U11-48K-like CHHC zinc finger domain / U11-48K-like CHHC zinc finger ...CCDC84-like / Programmed cell death protein 7 / snRNP35, RNA recognition motif / Coiled coil protein 84 / Programmed cell death protein 7 / U11/U12 small nuclear ribonucleoprotein 25kDa protein / SNRNP25, ubiquitin-like domain / Ubiquitin-like domain / TRM13/UPF0224 family, U11-48K-like CHHC zinc finger domain / U11-48K-like CHHC zinc finger / Zinc finger CHHC U11-48K-type profile. / USP39 / Serine/threonine-protein PRP4, catalytic domain / PRP4-like superfamily / pre-mRNA processing factor 4 (PRP4) like / SNU66/SART1 family / HIND motif / SART-1 family / HIND motif / PWI domain superfamily / PWI domain / PWI domain profile. / U1-C, C2H2-type zinc finger / U1 zinc finger / 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 / pre-mRNA processing factor 3 domain / PWI domain / PWI, domain in splicing factors / Small nuclear ribonucleoprotein Prp3, C-terminal domain / Small nuclear ribonucleoprotein Prp3, C-terminal domain / Dim1 family / Mitosis protein DIM1 / Mitosis protein DIM1 / PRP1 splicing factor, N-terminal / PRP1 splicing factor, N-terminal / Small ribonucleoprotein associated, SmB/SmN / Zinc finger C-x8-C-x5-C-x3-H type (and similar) / Small nuclear ribonucleoprotein D1 / 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. / Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger / Zinc finger, UBP-type / H/ACA ribonucleoprotein complex, subunit Nhp2-like / Zn-finger in ubiquitin-hydrolases and other protein / Zinc finger UBP-type profile. / Snu114, GTP-binding domain / Tetratricopeptide repeat / Sec63 Brl domain / Zinc finger, CCCH-type superfamily / 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 / zinc finger / 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 / Zinc finger, CCCH-type / Zinc finger C3H1-type profile. / LSM domain / LSM domain, eukaryotic/archaea-type / snRNP Sm proteins / Tetratricopeptide repeat / HAT (Half-A-TPR) repeat / HAT (Half-A-TPR) repeats / Peptidase C19, ubiquitin carboxyl-terminal hydrolase / Ubiquitin carboxyl-terminal hydrolase / Ubiquitin specific protease domain / Ubiquitin specific protease (USP) domain profile. / : / DEAD-box subfamily ATP-dependent helicases signature. / Sm domain profile. / ATP-dependent RNA helicase DEAD-box, conserved site / RNA helicase, DEAD-box type, Q motif / Elongation Factor G, domain II / Elongation Factor G, domain III / DEAD-box RNA helicase Q motif profile. / Translation elongation factor EFG/EF2, domain IV
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / INOSITOL HEXAKISPHOSPHATE / : / : / : / RNA / RNA (> 10) / RNA (> 100) / U4/U6 small nuclear ribonucleoprotein Prp4 / U4/U6.U5 tri-snRNP-associated protein 1 ...GUANOSINE-5'-TRIPHOSPHATE / INOSITOL HEXAKISPHOSPHATE / : / : / : / RNA / RNA (> 10) / RNA (> 100) / U4/U6 small nuclear ribonucleoprotein Prp4 / U4/U6.U5 tri-snRNP-associated protein 1 / U4/U6 small nuclear ribonucleoprotein Prp3 / U5 small nuclear ribonucleoprotein 200 kDa helicase / Pre-mRNA-processing factor 6 / Small nuclear ribonucleoprotein-associated proteins B and B' / NHP2-like protein 1 / Small nuclear ribonucleoprotein E / Small nuclear ribonucleoprotein F / Small nuclear ribonucleoprotein G / Small nuclear ribonucleoprotein Sm D1 / Small nuclear ribonucleoprotein Sm D2 / Small nuclear ribonucleoprotein Sm D3 / Serine/threonine-protein kinase PRP4 homolog / 116 kDa U5 small nuclear ribonucleoprotein component / U11/U12 small nuclear ribonucleoprotein 35 kDa protein / Ubiquitin carboxyl-terminal hydrolase 39 / U11/U12 small nuclear ribonucleoprotein 48 kDa protein / Pre-mRNA-processing-splicing factor 8 / Centrosomal AT-AC splicing factor / Programmed cell death protein 7 / U4/U6 small nuclear ribonucleoprotein Prp31 / U5 small nuclear ribonucleoprotein 40 kDa protein / Probable ATP-dependent RNA helicase DDX23 / U11/U12 small nuclear ribonucleoprotein 25 kDa protein / Thioredoxin-like protein 4B / Zinc finger matrin-type protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.38 Å
AuthorsBai, R. / Yuan, M. / Zhang, P. / Luo, T. / Shi, Y. / Wan, R.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32171214 China
National Natural Science Foundation of China (NSFC)31930059 China
National Natural Science Foundation of China (NSFC)32100987 China
CitationJournal: Science / Year: 2024
Title: Structural basis of U12-type intron engagement by the fully assembled human minor spliceosome.
Authors: Rui Bai / Meng Yuan / Pu Zhang / Ting Luo / Yigong Shi / Ruixue Wan /
Abstract: The minor spliceosome, which is responsible for the splicing of U12-type introns, comprises five small nuclear RNAs (snRNAs), of which only one is shared with the major spliceosome. In this work, we ...The minor spliceosome, which is responsible for the splicing of U12-type introns, comprises five small nuclear RNAs (snRNAs), of which only one is shared with the major spliceosome. In this work, we report the 3.3-angstrom cryo-electron microscopy structure of the fully assembled human minor spliceosome pre-B complex. The atomic model includes U11 small nuclear ribonucleoprotein (snRNP), U12 snRNP, and U4atac/U6atac.U5 tri-snRNP. U11 snRNA is recognized by five U11-specific proteins (20K, 25K, 35K, 48K, and 59K) and the heptameric Sm ring. The 3' half of the 5'-splice site forms a duplex with U11 snRNA; the 5' half is recognized by U11-35K, U11-48K, and U11 snRNA. Two proteins, CENATAC and DIM2/TXNL4B, specifically associate with the minor tri-snRNP. A structural analysis uncovered how two conformationally similar tri-snRNPs are differentiated by the minor and major prespliceosomes for assembly.
History
DepositionFeb 2, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 20, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: pre-mRNA
B: U5 snRNA
C: Pre-mRNA-processing-splicing factor 8
D: 116 kDa U5 small nuclear ribonucleoprotein component
E: U5 small nuclear ribonucleoprotein 200 kDa helicase
F: U5 small nuclear ribonucleoprotein 40 kDa protein
G: Pre-mRNA-processing factor 6
H: Thioredoxin-like protein 4B
I: Probable ATP-dependent RNA helicase DDX23
a: Small nuclear ribonucleoprotein-associated proteins B and B'
b: Small nuclear ribonucleoprotein Sm D1
c: Small nuclear ribonucleoprotein Sm D2
d: Small nuclear ribonucleoprotein Sm D3
e: Small nuclear ribonucleoprotein E
f: Small nuclear ribonucleoprotein F
g: Small nuclear ribonucleoprotein G
J: U4atac snRNA
K: U6atac snRNA
L: U4/U6 small nuclear ribonucleoprotein Prp31
M: U4/U6 small nuclear ribonucleoprotein Prp4
N: U4/U6 small nuclear ribonucleoprotein Prp3
O: NHP2-like protein 1
R: Centrosomal AT-AC splicing factor
h: Small nuclear ribonucleoprotein-associated proteins B and B'
i: Small nuclear ribonucleoprotein Sm D1
j: Small nuclear ribonucleoprotein Sm D2
k: Small nuclear ribonucleoprotein Sm D3
l: Small nuclear ribonucleoprotein E
m: Small nuclear ribonucleoprotein F
n: Small nuclear ribonucleoprotein G
P: U11 snRNA
V: Zinc finger matrin-type protein 5
W: U11/U12 small nuclear ribonucleoprotein 35 kDa protein
X: U11/U12 small nuclear ribonucleoprotein 25 kDa protein
Y: U11/U12 small nuclear ribonucleoprotein 48 kDa protein
Z: Programmed cell death protein 7
o: Small nuclear ribonucleoprotein-associated proteins B and B'
p: Small nuclear ribonucleoprotein Sm D1
q: Small nuclear ribonucleoprotein Sm D2
r: Small nuclear ribonucleoprotein Sm D3
s: Small nuclear ribonucleoprotein E
t: Small nuclear ribonucleoprotein F
u: Small nuclear ribonucleoprotein G
S: U4/U6.U5 tri-snRNP-associated protein 1
U: U4/U6.U5 tri-snRNP-associated protein 2
Q: Serine/threonine-protein kinase PRP4 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,102,08756
Polymers2,100,46246
Non-polymers1,62410
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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RNA chain , 5 types, 5 molecules ABJKP

#1: RNA chain pre-mRNA / Primary transcript


Mass: 89522.656 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: RNA chain U5 snRNA / U5 spliceosomal RNA


Mass: 37254.855 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: 20330981
#17: RNA chain U4atac snRNA


Mass: 42049.789 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#18: RNA chain U6atac snRNA


Mass: 40221.832 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: 187960111
#24: RNA chain U11 snRNA / U11 spliceosomal RNA


Mass: 43505.629 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: 161169046

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Protein , 11 types, 13 molecules CDGHIahoORVZQ

#3: Protein Pre-mRNA-processing-splicing factor 8 / 220 kDa U5 snRNP-specific protein / PRP8 homolog / Splicing factor Prp8 / p220


Mass: 273974.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q6P2Q9
#4: Protein 116 kDa U5 small nuclear ribonucleoprotein component / Elongation factor Tu GTP-binding domain-containing protein 2 / SNU114 homolog / hSNU114 / U5 snRNP- ...Elongation factor Tu GTP-binding domain-containing protein 2 / SNU114 homolog / hSNU114 / U5 snRNP-specific protein / 116 kDa / U5-116 kDa


Mass: 109560.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q15029
#7: Protein Pre-mRNA-processing factor 6 / Androgen receptor N-terminal domain-transactivating protein 1 / ANT-1 / PRP6 homolog / U5 snRNP- ...Androgen receptor N-terminal domain-transactivating protein 1 / ANT-1 / PRP6 homolog / U5 snRNP-associated 102 kDa protein / U5-102 kDa protein


Mass: 107092.242 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O94906
#8: Protein Thioredoxin-like protein 4B / Dim1-like protein


Mass: 17034.611 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9NX01
#9: Protein Probable ATP-dependent RNA helicase DDX23 / 100 kDa U5 snRNP-specific protein / DEAD box protein 23 / PRP28 homolog / U5-100kD


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
#10: Protein Small nuclear ribonucleoprotein-associated proteins B and B' / snRNP-B / Sm protein B/B' / Sm-B/B' / SmB/B'


Mass: 24642.131 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P14678
#22: Protein NHP2-like protein 1 / High mobility group-like nuclear protein 2 homolog 1 / OTK27 / SNU13 homolog / hSNU13 / U4/U6.U5 ...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


Mass: 14191.524 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P55769
#23: Protein Centrosomal AT-AC splicing factor / Coiled-coil domain-containing protein 84


Mass: 38034.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q86UT8
#25: Protein Zinc finger matrin-type protein 5 / U11/U12 small nuclear ribonucleoprotein 20 kDa protein / U11/U12 snRNP 20 kDa protein / U11/U12-20K


Mass: 20002.801 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9UDW3
#29: Protein Programmed cell death protein 7 / / ES18 / hES18


Mass: 54791.984 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q8N8D1
#32: Protein Serine/threonine-protein kinase PRP4 homolog / PRP4 kinase / PRP4 pre-mRNA-processing factor 4 homolog


Mass: 117264.977 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: Q13523, non-specific serine/threonine protein kinase

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U5 small nuclear ribonucleoprotein ... , 2 types, 2 molecules EF

#5: Protein U5 small nuclear ribonucleoprotein 200 kDa helicase / Activating signal cointegrator 1 complex subunit 3-like 1 / BRR2 homolog / U5 snRNP-specific 200 ...Activating signal cointegrator 1 complex subunit 3-like 1 / BRR2 homolog / U5 snRNP-specific 200 kDa protein / U5-200KD


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
#6: Protein U5 small nuclear ribonucleoprotein 40 kDa protein / U5 snRNP 40 kDa protein / U5-40K / 38 kDa-splicing factor / Prp8-binding protein / hPRP8BP / U5 ...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


Mass: 39359.492 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q96DI7

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Small nuclear ribonucleoprotein ... , 6 types, 18 molecules bipcjqdkrelsfmtgnu

#11: Protein Small nuclear ribonucleoprotein Sm D1 / Sm-D1 / Sm-D autoantigen / snRNP core protein D1


Mass: 13310.653 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62314
#12: Protein Small nuclear ribonucleoprotein Sm D2 / Sm-D2 / snRNP core protein D2


Mass: 13551.928 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62316
#13: Protein Small nuclear ribonucleoprotein Sm D3 / Sm-D3 / snRNP core protein D3


Mass: 13940.308 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62318
#14: Protein Small nuclear ribonucleoprotein E / snRNP-E / Sm protein E / Sm-E / SmE


Mass: 10817.601 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62304
#15: Protein Small nuclear ribonucleoprotein F / snRNP-F / Sm protein F / Sm-F / SmF


Mass: 9734.171 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62306
#16: Protein Small nuclear ribonucleoprotein G / snRNP-G / Sm protein G / Sm-G / SmG


Mass: 8508.084 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62308

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U4/U6 small nuclear ribonucleoprotein ... , 3 types, 3 molecules LMN

#19: Protein U4/U6 small nuclear ribonucleoprotein Prp31 / Pre-mRNA-processing factor 31 / Serologically defined breast cancer antigen NY-BR-99 / U4/U6 snRNP ...Pre-mRNA-processing factor 31 / Serologically defined breast cancer antigen NY-BR-99 / U4/U6 snRNP 61 kDa protein / Protein 61K / hPrp31


Mass: 55528.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q8WWY3
#20: Protein U4/U6 small nuclear ribonucleoprotein Prp4 / PRP4 homolog / hPrp4 / U4/U6 snRNP 60 kDa protein / WD splicing factor Prp4


Mass: 58536.105 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O43172
#21: Protein U4/U6 small nuclear ribonucleoprotein Prp3 / Pre-mRNA-splicing factor 3 / hPrp3 / U4/U6 snRNP 90 kDa protein


Mass: 77669.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O43395

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U11/U12 small nuclear ribonucleoprotein ... , 3 types, 3 molecules WXY

#26: Protein U11/U12 small nuclear ribonucleoprotein 35 kDa protein / U11/U12 snRNP 35 kDa protein / U11/U12-35K / Protein HM-1 / U1 snRNP-binding protein homolog


Mass: 29514.471 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q16560
#27: Protein U11/U12 small nuclear ribonucleoprotein 25 kDa protein / U11/U12 snRNP 25 kDa protein / U11/U12-25K / Minus-99 protein


Mass: 15290.729 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BV90
#28: Protein U11/U12 small nuclear ribonucleoprotein 48 kDa protein / U11/U12 snRNP 48 kDa protein / U11/U12-48K


Mass: 40042.621 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q6IEG0

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U4/U6.U5 tri-snRNP-associated protein ... , 2 types, 2 molecules SU

#30: Protein U4/U6.U5 tri-snRNP-associated protein 1 / SNU66 homolog / hSnu66 / Squamous cell carcinoma antigen recognized by T-cells 1 / SART-1 / hSART-1 ...SNU66 homolog / hSnu66 / Squamous cell carcinoma antigen recognized by T-cells 1 / SART-1 / hSART-1 / U4/U6.U5 tri-snRNP-associated 110 kDa protein


Mass: 90414.117 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O43290
#31: Protein 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


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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Non-polymers , 4 types, 10 molecules

#33: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#34: Chemical ChemComp-IHP / INOSITOL HEXAKISPHOSPHATE / MYO-INOSITOL HEXAKISPHOSPHATE / INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE / Phytic acid


Mass: 660.035 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H18O24P6
#35: 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
#36: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn

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Details

Has ligand of interestN

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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: human minor pre-B complex / Type: COMPLEX
Entity ID: #1-#9, #17-#22, #24, #32, #23, #30-#31, #25-#29, #10-#16
Source: RECOMBINANT
Molecular weightValue: 1.8 MDa / Experimental value: YES
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.9
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: NITROGEN

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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 FIELDBright-field microscopy / Nominal magnification: 81000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 500 nm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.38 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 388888 / Symmetry type: POINT

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