PDB-7dvq: Cryo-EM Structure of the Activated Human Minor Spliceosome (minor...

Basic information

• Entry: Database: PDB / ID: 7dvq
• Title: Cryo-EM Structure of the Activated Human Minor Spliceosome (minor Bact Complex)

Components

• (Pre-mRNA-splicing factor ...) x 2
• (Serine/arginine repetitive matrix protein ...) x 2
• (Small nuclear ribonucleoprotein ...) x 6
• (Splicing factor 3B subunit ...) x 6
• (U5 small nuclear ribonucleoprotein ...) x 2
• 116 kDa U5 small nuclear ribonucleoprotein component
• Armadillo repeat-containing protein 7
• BUD13 homolog
• Cell division cycle 5-like protein
• Crooked neck-like protein 1
• Cysteine-rich PDZ-binding protein
• G-patch domain and KOW motifs-containing protein
• PHD finger-like domain-containing protein 5A
• Peptidyl-prolyl cis-trans isomerase CWC27 homolog
• Pleiotropic regulator 1
• Pre-mRNA-processing-splicing factor 8
• RING finger protein 113A
• RING-type E3 ubiquitin-protein ligase PPIL2
• RNA-binding motif protein, X-linked 2
• RNA-binding protein 48
• SNW domain-containing protein 1
• Smad nuclear-interacting protein 1
• Small nuclear ribonucleoprotein-associated proteins B and B'
• Sodium channel modifier 1
• Spliceosome-associated protein CWC15 homolog
• U12 snRNA
• U5 snRNA
• U6atac snRNA
• pre-mRNA

• Keywords: SPLICING / spliceosome / minor spliceosome / Bact complex / human spliceosome / PPIL2 / SCNM1 / RBM48-ARMC7 complex / U12-type intron / U6atac snRNA

Function / homology

Function:

regulation of postsynaptic density protein 95 clustering / RES complex / negative regulation of chemokine-mediated signaling pathway / snoRNA splicing / protein localization to microtubule / regulation of postsynaptic density assembly / U11/U12 snRNP / regulation of retinoic acid receptor signaling pathway / post-mRNA release spliceosomal complex / U2 snRNP binding / alternative mRNA splicing, via spliceosome / U7 snRNA binding / histone pre-mRNA DCP binding / U7 snRNP / B-WICH complex / regulation of vitamin D receptor signaling pathway / 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 / miRNA processing / splicing factor binding / protein methylation / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / U12-type spliceosomal complex / methylosome / nuclear retinoic acid receptor binding / 7-methylguanosine cap hypermethylation / Prp19 complex / U1 snRNP binding / pICln-Sm protein complex / mRNA 3'-end processing / blastocyst formation / sno(s)RNA-containing ribonucleoprotein complex / snRNP binding / U2-type catalytic step 1 spliceosome / RNA splicing, via transesterification reactions / small nuclear ribonucleoprotein complex / regulation of mRNA splicing, via spliceosome / C2H2 zinc finger domain binding / SMN-Sm protein complex / telomerase RNA binding / spliceosomal tri-snRNP complex / telomerase holoenzyme complex / P granule / U2-type spliceosomal complex / U2-type precatalytic spliceosome / positive regulation by host of viral transcription / mRNA cis splicing, via spliceosome / positive regulation of vitamin D receptor signaling pathway / transcription regulator inhibitor activity / commitment complex / U2-type prespliceosome assembly / nuclear vitamin D receptor binding / Transport of Mature mRNA derived from an Intron-Containing Transcript / U2-type catalytic step 2 spliceosome / Notch binding / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / U4 snRNP / positive regulation of mRNA splicing, via spliceosome / RUNX3 regulates NOTCH signaling / U2 snRNP / Basigin interactions / RHOBTB1 GTPase cycle / SAGA complex / NOTCH4 Intracellular Domain Regulates Transcription / RNA Polymerase II Transcription Termination / positive regulation of transcription by RNA polymerase III / U1 snRNP / ubiquitin-ubiquitin ligase activity / pattern recognition receptor activity / NOTCH3 Intracellular Domain Regulates Transcription / WD40-repeat domain binding / positive regulation of neurogenesis / U2-type prespliceosome / nuclear androgen receptor binding / precatalytic spliceosome / K63-linked polyubiquitin modification-dependent protein binding / positive regulation of transcription by RNA polymerase I / Notch-HLH transcription pathway / positive regulation of transforming growth factor beta receptor signaling pathway / Formation of paraxial mesoderm / mRNA Splicing - Minor Pathway / spliceosomal complex assembly / SMAD binding / regulation of RNA splicing / protein localization to nucleus / postsynaptic density, intracellular component / spliceosomal tri-snRNP complex assembly / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / U5 snRNA binding / U5 snRNP / RHOBTB2 GTPase cycle / positive regulation of G1/S transition of mitotic cell cycle / retinoic acid receptor signaling pathway / U2 snRNA binding / U6 snRNA binding / spliceosomal snRNP assembly / regulation of DNA repair / Cajal body

Domain/homology:

RBM48, RNA recognition motif / RNA-binding protein 48 / Armadillo repeat-containing protein 7 / Sodium channel modifier 1, zinc-finger / Sodium channel modifier 1, acidic C-terminal domain / Sodium channel modifier 1 / Zinc-finger of sodium channel modifier 1 / Acidic C-terminal region of sodium channel modifier 1 SCNM1 / G-patch domain and KOW motifs-containing protein, KOW 1 / G-patch domain and KOW motifs-containing protein, KOW 2 / PDZ-binding protein, CRIPT / Microtubule-associated protein CRIPT / Pre-mRNA-splicing factor Spp2-like / Peptidyl-prolyl cis-trans isomerase like 2, U-box domain / : / Spp2/MOS2, G-patch domain / G-patch domain / Pre-mRNA-splicing factor CWC24-like / Ist3-like, RNA recognition motif / : / Bud13 / : / Pre-mRNA-splicing factor of RES complex / : / SF3B6, RNA recognition motif / : / PWI domain superfamily / PWI domain / PWI domain profile. / SF3B4, RNA recognition motif 2 / : / : / mRNA splicing factor Cwf21 domain / cwf21 domain / PWI domain / G-patch domain profile. / PWI, domain in splicing factors / G-patch domain / SF3B4, RNA recognition motif 1 / : / HAT (Half-A-TPR) repeat / glycine rich nucleic binding domain / Zinc finger C-x8-C-x5-C-x3-H type (and similar) / Splicing factor 3B, subunit 5 / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, cyclophilin A-like / Splicing factor 3B subunit 1 / : / Splicing factor 3B subunit 1 / Domain of unknown function DUF382 / Domain of unknown function (DUF382) / SKI-interacting protein SKIP, SNW domain / SKI-interacting protein, SKIP / SKIP/SNW domain / Pre-mRNA-splicing factor Cwf15/Cwc15 / Cwf15/Cwc15 cell cycle control protein / WD repeat Prp46/PLRG1-like / : / Pre-mRNA splicing factor component Cdc5p/Cef1, C-terminal / : / : / pre-mRNA splicing factor component / PHF5-like / PHF5-like protein / PSP, proline-rich / PSP / proline-rich domain in spliceosome associated proteins / Myb-like DNA-binding domain / 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 / MIF4G domain / : / Small ribonucleoprotein associated, SmB/SmN / Spt5 C-terminal domain / Spt5 C-terminal nonapeptide repeat binding Spt4 / Small nuclear ribonucleoprotein D1 / Middle domain of eukaryotic initiation factor 4G (eIF4G) / MIF4G-like, type 3 / U-box domain profile. / Modified RING finger domain / Zinc finger, CCCH-type superfamily / U-box domain / PPP2R1A-like HEAT repeat / Brr2, N-terminal helicase PWI domain / : / N-terminal helicase PWI domain / Pre-mRNA-splicing helicase BRR2 plug domain / SAP domain / SAP motif profile. / Sec63 Brl domain / Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation / SAP domain / zinc finger / : / Helicase associated domain (HA2), ratchet-like / :

Component:

Chem-G5J / GUANOSINE-5'-TRIPHOSPHATE / INOSITOL HEXAKISPHOSPHATE / : / : / : / : / RNA / RNA (> 10) / RNA (> 100) / E3 ubiquitin-protein ligase RNF113A / Pleiotropic regulator 1 / Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16 / Splicing factor 3B subunit 1 / U5 small nuclear ribonucleoprotein 200 kDa helicase / Small nuclear ribonucleoprotein-associated proteins B and B' / 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 / RING-type E3 ubiquitin-protein ligase PPIL2 / Splicing factor 3B subunit 2 / SNW domain-containing protein 1 / 116 kDa U5 small nuclear ribonucleoprotein component / Splicing factor 3B subunit 3 / Splicing factor 3B subunit 4 / RNA-binding protein 48 / Pre-mRNA-processing-splicing factor 8 / Spliceosome-associated protein CWC27 homolog / PHD finger-like domain-containing protein 5A / Serine/arginine repetitive matrix protein 1 / Smad nuclear-interacting protein 1 / G-patch domain and KOW motifs-containing protein / U5 small nuclear ribonucleoprotein 40 kDa protein / Cell division cycle 5-like protein / BUD13 homolog / Sodium channel modifier 1 / Splicing factor 3B subunit 5 / Crooked neck-like protein 1 / Armadillo repeat-containing protein 7 / Pre-mRNA-splicing factor CWC22 homolog / Spliceosome-associated protein CWC15 homolog / Cysteine-rich PDZ-binding protein / Serine/arginine repetitive matrix protein 2 / RNA-binding motif protein, X-linked 2 / Splicing factor 3B subunit 6

• Biological species: Homo sapiens (human)
• Method: ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.89 Å
• Authors: Bai, R. / Wan, R. / Wang, L. / Xu, K. / Zhang, Q. / Lei, J. / Shi, Y.

Funding support

China, 1items

Organization	Grant number	Country
National Natural Science Foundation of China (NSFC)	31930059	China

• Citation: Journal: Science / Year: 2021; Title: Structure of the activated human minor spliceosome.; Authors: Rui Bai / Ruixue Wan / Lin Wang / Kui Xu / Qiangfeng Zhang / Jianlin Lei / Yigong Shi / ; Abstract: The minor spliceosome mediates splicing of the rare but essential U12-type precursor messenger RNA. Here, we report the atomic features of the activated human minor spliceosome determined by cryo-electron microscopy at 2.9-angstrom resolution. The 5' splice site and branch point sequence of the U12-type intron are recognized by the U6atac and U12 small nuclear RNAs (snRNAs), respectively. Five newly identified proteins stabilize the conformation of the catalytic center: The zinc finger protein SCNM1 functionally mimics the SF3a complex of the major spliceosome, the RBM48-ARMC7 complex binds the γ-monomethyl phosphate cap at the 5' end of U6atac snRNA, the U-box protein PPIL2 coordinates loop I of U5 snRNA and stabilizes U5 small nuclear ribonucleoprotein (snRNP), and CRIPT stabilizes U12 snRNP. Our study provides a framework for the mechanistic understanding of the function of the human minor spliceosome.

History

Deposition	Jan 14, 2021	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Mar 31, 2021	Provider: repository / Type: Initial release

Assembly

Deposited unit

A: Pre-mRNA-processing-splicing factor 8

B: U5 snRNA

C: 116 kDa U5 small nuclear ribonucleoprotein component

D: U5 small nuclear ribonucleoprotein 200 kDa helicase

E: U5 small nuclear ribonucleoprotein 40 kDa protein

a: Small nuclear ribonucleoprotein Sm D3

b: Small nuclear ribonucleoprotein-associated proteins B and B'

c: Small nuclear ribonucleoprotein Sm D1

d: Small nuclear ribonucleoprotein Sm D2

f: Small nuclear ribonucleoprotein F

e: Small nuclear ribonucleoprotein E

g: Small nuclear ribonucleoprotein G

F: U6atac snRNA

G: pre-mRNA

H: U12 snRNA

h: Small nuclear ribonucleoprotein Sm D3

i: Small nuclear ribonucleoprotein-associated proteins B and B'

j: Small nuclear ribonucleoprotein Sm D1

k: Small nuclear ribonucleoprotein Sm D2

m: Small nuclear ribonucleoprotein F

l: Small nuclear ribonucleoprotein E

n: Small nuclear ribonucleoprotein G

v: Sodium channel modifier 1

1: Splicing factor 3B subunit 1

2: Splicing factor 3B subunit 2

3: Splicing factor 3B subunit 3

4: Splicing factor 3B subunit 4

5: Splicing factor 3B subunit 6

6: PHD finger-like domain-containing protein 5A

7: Splicing factor 3B subunit 5

L: Cell division cycle 5-like protein

J: Crooked neck-like protein 1

P: Spliceosome-associated protein CWC15 homolog

R: SNW domain-containing protein 1

T: Pleiotropic regulator 1

X: Smad nuclear-interacting protein 1

Y: RNA-binding motif protein, X-linked 2

Z: BUD13 homolog

9: RING-type E3 ubiquitin-protein ligase PPIL2

z: Peptidyl-prolyl cis-trans isomerase CWC27 homolog

x: Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16

y: G-patch domain and KOW motifs-containing protein

M: RING finger protein 113A

U: Serine/arginine repetitive matrix protein 2

V: Pre-mRNA-splicing factor CWC22 homolog

8: Serine/arginine repetitive matrix protein 1

0: Cysteine-rich PDZ-binding protein

I: RNA-binding protein 48

K: Armadillo repeat-containing protein 7

hetero molecules

Summary:

• 2.92 MDa, 49 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	2,918,376	66
Polymers	2,915,998	49
Non-polymers	2,378	17
Water	54	3

1

Summary:

• Idetical with deposited unit
• defined by author

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555		1

Components

Protein , 20 types, 21 molecules A C b i v 6 L J P R T X Y Z 9 z y M 0 I K

#1: Protein

A Pre-mRNA-processing-splicing factor 8 / 220 kDa U5 snRNP-specific protein / PRP8 homolog / Splicing factor Prp8 / p220

Details:

Mass: 273974.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q6P2Q9

#3: Protein

C 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

Details:

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

b i Small nuclear ribonucleoprotein-associated proteins B and B' / snRNP-B / Sm protein B/B' / SmB/B'

Details:

Mass: 24642.131 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P14678

#16: Protein

v Sodium channel modifier 1

Details:

Mass: 25993.537 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BWG6

#22: Protein

6 PHD finger-like domain-containing protein 5A / PHD finger-like domain protein 5A / Splicing factor 3B-associated 14 kDa protein / SF3b14b

Details:

Mass: 12427.524 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q7RTV0

#24: Protein

L Cell division cycle 5-like protein / Cdc5-like protein / Pombe cdc5-related protein

Details:

Mass: 92406.883 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q99459

#25: Protein

J Crooked neck-like protein 1 / Crooked neck homolog / hCrn

Details:

Mass: 100610.008 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BZJ0

#26: Protein

P Spliceosome-associated protein CWC15 homolog

Details:

Mass: 26674.447 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9P013

#27: Protein

R SNW domain-containing protein 1 / Nuclear protein SkiP / Nuclear receptor coactivator NCoA-62 / Ski-interacting protein

Details:

Mass: 61610.703 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q13573

#28: Protein

T Pleiotropic regulator 1

Details:

Mass: 57280.758 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O43660

#29: Protein

X Smad nuclear-interacting protein 1 / FHA domain-containing protein SNIP1

Details:

Mass: 45880.738 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q8TAD8

#30: Protein

Y RNA-binding motif protein, X-linked 2

Details:

Mass: 37425.984 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y388

#31: Protein

Z BUD13 homolog

Details:

Mass: 70669.211 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BRD0

#32: Protein

9 RING-type E3 ubiquitin-protein ligase PPIL2 / CYC4 / Cyclophilin-60 / Cyclophilin-like protein Cyp-60 / Cyp60 / hCyP-60 / Probable inactive peptidyl-prolyl cis-trans isomerase-like 2 / PPIase / Rotamase PPIL2

Details:

Mass: 58910.379 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: Q13356, RING-type E3 ubiquitin transferase

#33: Protein

z Peptidyl-prolyl cis-trans isomerase CWC27 homolog / PPIase CWC27 / Antigen NY-CO-10 / Serologically defined colon cancer antigen 10

Details:

Mass: 53941.227 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q6UX04, peptidylprolyl isomerase

#35: Protein

y G-patch domain and KOW motifs-containing protein / G-patch domain-containing protein 5 / Protein MOS2 homolog / Protein T54

Details:

Mass: 52299.711 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q92917

#36: Protein

M RING finger protein 113A / Zinc finger protein 183

Details:

Mass: 38847.199 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O15541

#40: Protein

0 Cysteine-rich PDZ-binding protein / Cysteine-rich interactor of PDZ three / Cysteine-rich interactor of PDZ3

Details:

Mass: 11239.073 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9P021

#41: Protein

I RNA-binding protein 48

Details:

Mass: 41878.523 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q5RL73

#42: Protein

K Armadillo repeat-containing protein 7

Details:

Mass: 21946.039 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9H6L4

RNA chain , 4 types, 4 molecules B F G H

#2: RNA chain

B U5 snRNA

Details:

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

#13: RNA chain

F U6atac snRNA

Details:

Mass: 39876.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: 187960111

#14: RNA chain

G pre-mRNA

Details:

Mass: 44322.848 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

#15: RNA chain

H U12 snRNA

Details:

Mass: 48353.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: 951206

U5 small nuclear ribonucleoprotein ... , 2 types, 2 molecules D E

#4: Protein

D 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

Details:

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

#5: Protein

E U5 small nuclear ribonucleoprotein 40 kDa protein / U5-40K / 38 kDa-splicing factor / Prp8-binding protein / hPRP8BP / U5 snRNP-specific 40 kDa protein / WD repeat-containing protein 57

Details:

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

Small nuclear ribonucleoprotein ... , 6 types, 12 molecules a h c j d k f m e l g n

#6: Protein

a h Small nuclear ribonucleoprotein Sm D3 / Sm-D3 / snRNP core protein D3

Details:

Mass: 13940.308 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62318

#8: Protein

c j Small nuclear ribonucleoprotein Sm D1 / Sm-D1 / Sm-D autoantigen / snRNP core protein D1

Details:

Mass: 13310.653 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62314

#9: Protein

d k Small nuclear ribonucleoprotein Sm D2 / Sm-D2 / snRNP core protein D2

Details:

Mass: 13551.928 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62316

#10: Protein

f m Small nuclear ribonucleoprotein F / snRNP-F / Sm protein F / SmF

Details:

Mass: 9734.171 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62306

#11: Protein

e l Small nuclear ribonucleoprotein E / snRNP-E / Sm protein E / SmE

Details:

Mass: 10817.601 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62304

#12: Protein

g n Small nuclear ribonucleoprotein G / snRNP-G / Sm protein G / SmG

Details:

Mass: 8508.084 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62308

Splicing factor 3B subunit ... , 6 types, 6 molecules 1 2 3 4 5 7

#17: Protein

1 Splicing factor 3B subunit 1 / Pre-mRNA-splicing factor SF3b 155 kDa subunit / SF3b155 / Spliceosome-associated protein 155 / SAP 155

Details:

Mass: 146104.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O75533

#18: Protein

2 Splicing factor 3B subunit 2 / Pre-mRNA-splicing factor SF3b 145 kDa subunit / SF3b145 / Spliceosome-associated protein 145 / SAP 145

Details:

Mass: 100377.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q13435

#19: Protein

3 Splicing factor 3B subunit 3 / Pre-mRNA-splicing factor SF3b 130 kDa subunit / SF3b130 / STAF130 / Spliceosome-associated protein 130 / SAP 130

Details:

Mass: 135798.828 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q15393

#20: Protein

4 Splicing factor 3B subunit 4 / Pre-mRNA-splicing factor SF3b 49 kDa subunit / Spliceosome-associated protein 49 / SAP 49

Details:

Mass: 44436.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q15427

#21: Protein

5 Splicing factor 3B subunit 6 / Pre-mRNA branch site protein p14 / SF3b 14 kDa subunit / SF3B14a / Spliceosome-associated protein / 14-kDa / Splicing factor 3b / subunit 6 / 14kDa

Details:

Mass: 14606.900 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y3B4

#23: Protein

7 Splicing factor 3B subunit 5 / SF3b5 / Pre-mRNA-splicing factor SF3b 10 kDa subunit

Details:

Mass: 10149.369 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BWJ5

Pre-mRNA-splicing factor ... , 2 types, 2 molecules x V

#34: Protein

x Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16 / ATP-dependent RNA helicase #3 / DEAH-box protein 16

Details:

Mass: 119443.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O60231, RNA helicase

#38: Protein

V Pre-mRNA-splicing factor CWC22 homolog / Nucampholin homolog / fSAPb

Details:

Mass: 105646.578 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9HCG8

Serine/arginine repetitive matrix protein ... , 2 types, 2 molecules U 8

#37: Protein

U Serine/arginine repetitive matrix protein 2 / 300 kDa nuclear matrix antigen / Serine/arginine-rich splicing factor-related nuclear matrix protein of 300 kDa / Ser/Arg-related nuclear matrix protein of 300 kDa / Splicing coactivator subunit SRm300 / Tax-responsive enhancer element-binding protein 803 / TaxREB803

Details:

Mass: 300255.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9UQ35

#39: Protein

8 Serine/arginine repetitive matrix protein 1 / SR-related nuclear matrix protein of 160 kDa / SRm160 / Ser/Arg-related nuclear matrix protein

Details:

Mass: 102600.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q8IYB3

Non-polymers , 7 types, 20 molecules

#43: Chemical

A-3000 ChemComp-IHP / INOSITOL HEXAKISPHOSPHATE / MYO-INOSITOL HEXAKISPHOSPHATE / INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE

Details:

Mass: 660.035 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₁₈O₂₄P₆ / Feature type: SUBJECT OF INVESTIGATION

#44: Chemical

C-1500 ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE

Details:

Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₀H₁₆N₅O₁₄P₃ / Feature type: SUBJECT OF INVESTIGATION / Comment: GTP, energy-carrying molecule*YM

#45: Chemical

C-1501 F-201 F-202 F-203 F-204
ChemComp-MG / MAGNESIUM ION

Details:

Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION

#46: Chemical

F-205 F-206 ChemComp-K / POTASSIUM ION

Details:

Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION

#47: Chemical

F-207 ChemComp-G5J / 5'-O-[(S)-hydroxy{[(R)-hydroxy{[(S)-hydroxy(methoxy)phosphoryl]oxy}phosphoryl]oxy}phosphoryl]guanosine

Details:

Mass: 537.207 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₁H₁₈N₅O₁₄P₃ / Feature type: SUBJECT OF INVESTIGATION

#48: Chemical

v-300 6-201 6-202 6-203 M-500 0-200 0-201
ChemComp-ZN / ZINC ION

Details:

Mass: 65.409 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION

#49: Water

ChemComp-HOH / water

Details:

Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H₂O

Details

• Has ligand of interest: Y

Experimental details

Experiment

• Experiment: Method: ELECTRON MICROSCOPY
• EM experiment: Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

Sample preparation

• Component: Name: the activated human minor spliceosome (human minor Bact complex); Type: COMPLEX / Entity ID: #1-#12, #14-#42 / Source: NATURAL
• Molecular weight: Experimental value: NO
• Source (natural): Organism: Homo sapiens (human)
• Buffer solution: pH: 7.9
• Specimen: Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
• Vitrification: Cryogen name: ETHANE

Electron microscopy imaging

• Experimental equipment: Model: Titan Krios / Image courtesy: FEI Company
• Microscopy: Model: FEI TITAN KRIOS
• Electron gun: Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
• Electron lens: Mode: BRIGHT FIELD
• Image recording: Electron dose: 50 e/Ų / Film or detector model: GATAN K3 (6k x 4k)

Processing

• CTF correction: Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
• 3D reconstruction: Resolution: 2.89 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 101443 / Symmetry type: POINT