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- PDB-6ff7: human Bact spliceosome core structure -

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Entry
Database: PDB / ID: 6ff7
Titlehuman Bact spliceosome core structure
Components
  • (Peptidyl-prolyl cis-trans isomerase ...Prolyl isomerase) x 2
  • (Pre-mRNA-processing factor ...) x 2
  • (Pre-mRNA-splicing factor ...) x 5
  • (Serine/arginine repetitive matrix protein ...) x 2
  • (Small nuclear ribonucleoprotein ...SnRNP) x 6
  • (Splicing factor 3A subunit ...) x 3
  • (Splicing factor 3B subunit ...) x 5
  • (U2 small nuclear ribonucleoprotein ...) x 2
  • (U5 small nuclear ribonucleoprotein ...) x 2
  • 116 kDa U5 small nuclear ribonucleoprotein component
  • BUD13 homolog
  • Cell division cycle 5-like protein
  • Crooked neck-like protein 1
  • Intron-binding protein aquarius
  • PHD finger-like domain-containing protein 5A
  • Peptidyl-prolyl cis-trans isomerase-like 1
  • Pleiotropic regulator 1
  • Pre-mRNA-processing-splicing factor 8
  • Protein BUD31 homolog
  • Putative pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16
  • RING finger protein 113A
  • RNA-binding motif protein, X-linked 2
  • SNW domain-containing protein 1
  • Smad nuclear-interacting protein 1
  • Small nuclear ribonucleoprotein-associated proteins B and B'
  • Spliceosome-associated protein CWC15 homolog
  • U2 snRNAU2 spliceosomal RNA
  • U5 snRNAU5 spliceosomal RNA
  • U6 snRNAU6 spliceosomal RNA
  • pre-mRNAPrimary transcript
KeywordsSPLICING / spliceosome / human / HELA / BACT / dynamics
Function / homologyDomain of unknown function DUF382 / LSM domain superfamily / PROCN domain / PRO8NT domain / Ribonuclease H-like superfamily / Tetratricopeptide-like helical domain superfamily / Armadillo-like helical / Domain of unknown function DUF1605 / DEAD/DEAH box helicase domain / Splicing factor 3B subunit 5/RDS3 complex subunit 10 ...Domain of unknown function DUF382 / LSM domain superfamily / PROCN domain / PRO8NT domain / Ribonuclease H-like superfamily / Tetratricopeptide-like helical domain superfamily / Armadillo-like helical / Domain of unknown function DUF1605 / DEAD/DEAH box helicase domain / Splicing factor 3B subunit 5/RDS3 complex subunit 10 / PROCT domain / Pre-mRNA-splicing factor Isy1 / Homeobox-like domain superfamily / Translation protein, beta-barrel domain superfamily / SMAD/FHA domain superfamily / Pre-mRNA-splicing factor SPF27 / Helicase-associated domain / U-box domain / Pre-mRNA-splicing factor Cwf15/Cwc15 / Nucleotide-binding alpha-beta plait domain superfamily / Tetratricopeptide repeat-containing domain / Translation elongation factor EFG/EF2, domain IV / Armadillo-type fold / Myb domain / Zinc finger, RING-type, conserved site / SKI-interacting protein, SKIP / Small ribonucleoprotein associated, SmB/SmN / Splicing factor 3B, subunit 5 / Sm-like protein Lsm6/SmF / Peptidyl-prolyl cis-trans isomerase E / MIF4G-like domain superfamily / Zinc finger, RING/FYVE/PHD-type / WD40/YVTN repeat-like-containing domain superfamily / Myb-like transcription factor / Splicing factor 3B subunit 1 / Immunoglobulin E-set / Ribosomal protein S5 domain 2-type fold, subgroup / Helicase superfamily 1/2, ATP-binding domain / Pre-mRNA-splicing factor 19 / mRNA splicing factor Cwf21 domain / PSP, proline-rich / PHF5-like / BUD31/G10-related, conserved site / RNA recognition motif domain / Transcription factor, GTP-binding domain / Ricin B, lectin domain / Matrin/U1-C, C2H2-type zinc finger / Elongation factor EFG, domain V-like / Ubiquitin domain / Zinc finger, CCCH-type / JAB1/MPN/MOV34 metalloenzyme domain / Forkhead-associated (FHA) domain / LSM domain, eukaryotic/archaea-type / SWAP/Surp / Cwf15/Cwc15 cell cycle control protein / Breast carcinoma amplified sequence 2 (BCAS2) / Isy1-like splicing family / Splicing factor 3B subunit 10 (SF3b10) / Oligonucleotide/oligosaccharide-binding (OB)-fold / Helicase associated domain (HA2) / PRO8NT (NUC069), PrP8 N-terminal domain / SANT/Myb domain / Leucine-rich repeat / Small GTP-binding protein domain / Matrin/U1-C-like, C2H2-type zinc finger / Cleavage/polyadenylation specificity factor, A subunit, C-terminal / Sec63 domain / Translation elongation factor EFTu-like, domain 2 / SKI-interacting protein SKIP, SNW domain / Initiation factor eIF-4 gamma, MA3 / MIF4G-like, type 3 / U box domain / U2A'/phosphoprotein 32 family A, C-terminal / Helicase, C-terminal / HAT (Half-A-TPR) repeat / SAP domain / PWI domain / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain / Zinc finger, RING-type / G10 protein / WD40 repeat / WD40-repeat-containing domain / Bud13 / PROCT (NUC072) domain / Splicing factor 3B subunit 1-like / Ubiquitin family / Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD / RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) / Elongation factor Tu GTP binding domain / Pre-mRNA-splicing factor CWC24-like / Pre-mRNA-splicing factor Cwc2/Slt11 / Pre-mRNA-processing factor 19 / MPN domain / Helicase conserved C-terminal domain / Pre-mRNA-splicing factor Isy1 superfamily / Zinc finger, CCCH-type superfamily / PWI domain superfamily / Winged helix DNA-binding domain superfamily / WD40-repeat-containing domain superfamily
Function and homology information
Specimen sourceHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 4.5 Å resolution
AuthorsHaselbach, D. / Komarov, I. / Agafonov, D. / Hartmuth, K. / Graf, B. / Kastner, B. / Luehrmann, R. / Stark, H.
CitationJournal: Cell / Year: 2018
Title: Structure and Conformational Dynamics of the Human Spliceosomal B Complex.
Authors: David Haselbach / Ilya Komarov / Dmitry E Agafonov / Klaus Hartmuth / Benjamin Graf / Olexandr Dybkov / Henning Urlaub / Berthold Kastner / Reinhard Lührmann / Holger Stark
Abstract: The spliceosome is a highly dynamic macromolecular complex that precisely excises introns from pre-mRNA. Here we report the cryo-EM 3D structure of the human B spliceosome at 3.4 Å resolution. In ...The spliceosome is a highly dynamic macromolecular complex that precisely excises introns from pre-mRNA. Here we report the cryo-EM 3D structure of the human B spliceosome at 3.4 Å resolution. In the B state, the spliceosome is activated but not catalytically primed, so that it is functionally blocked prior to the first catalytic step of splicing. The spliceosomal core is similar to the yeast B spliceosome; important differences include the presence of the RNA helicase aquarius and peptidyl prolyl isomerases. To examine the overall dynamic behavior of the purified spliceosome, we developed a principal component analysis-based approach. Calculating the energy landscape revealed eight major conformational states, which we refined to higher resolution. Conformational differences of the highly flexible structural components between these eight states reveal how spliceosomal components contribute to the assembly of the spliceosome, allowing it to generate a dynamic interaction network required for its subsequent catalytic activation.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jan 3, 2018 / Release: Mar 13, 2019

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Assembly

Deposited unit
1: RNA-binding motif protein, X-linked 2
2: U2 snRNA
3: BUD13 homolog
5: U5 snRNA
6: U6 snRNA
7: Splicing factor 3A subunit 2
8: Splicing factor 3B subunit 2
A: Pre-mRNA-processing-splicing factor 8
B: 116 kDa U5 small nuclear ribonucleoprotein component
C: SNW domain-containing protein 1
D: Pleiotropic regulator 1
E: Pre-mRNA-processing factor 17
L: Cell division cycle 5-like protein
O: Crooked neck-like protein 1
P: Pre-mRNA-splicing factor RBM22
Q: Protein BUD31 homolog
R: Spliceosome-associated protein CWC15 homolog
S: Serine/arginine repetitive matrix protein 2
V: Peptidyl-prolyl cis-trans isomerase-like 1
Y: Serine/arginine repetitive matrix protein 1
Z: pre-mRNA
s: Peptidyl-prolyl cis-trans isomerase CWC27 homolog
t: RING finger protein 113A
u: Splicing factor 3B subunit 1
v: Splicing factor 3B subunit 3
x: Splicing factor 3B subunit 5
y: PHD finger-like domain-containing protein 5A
z: Splicing factor 3B subunit 6
0: Smad nuclear-interacting protein 1
9: Splicing factor 3A subunit 3
F: U5 small nuclear ribonucleoprotein 40 kDa protein
G: Pre-mRNA-processing factor 19
H: Pre-mRNA-processing factor 19
I: Pre-mRNA-processing factor 19
J: Pre-mRNA-processing factor 19
K: Pre-mRNA-splicing factor SPF27
M: Pre-mRNA-splicing factor SYF1
T: Pre-mRNA-splicing factor CWC22 homolog
U: Intron-binding protein aquarius
W: U2 small nuclear ribonucleoprotein A'
X: U2 small nuclear ribonucleoprotein B''
a: Small nuclear ribonucleoprotein Sm D2
b: Small nuclear ribonucleoprotein F
c: Small nuclear ribonucleoprotein E
d: Small nuclear ribonucleoprotein G
e: Small nuclear ribonucleoprotein Sm D3
f: Small nuclear ribonucleoprotein-associated proteins B and B'
g: Small nuclear ribonucleoprotein Sm D1
h: Small nuclear ribonucleoprotein Sm D2
i: Small nuclear ribonucleoprotein F
j: Small nuclear ribonucleoprotein E
k: Small nuclear ribonucleoprotein G
l: Small nuclear ribonucleoprotein Sm D3
m: Small nuclear ribonucleoprotein-associated proteins B and B'
n: Small nuclear ribonucleoprotein Sm D1
o: Peptidyl-prolyl cis-trans isomerase E
p: Splicing factor 3A subunit 1
q: Putative pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16
r: U5 small nuclear ribonucleoprotein 200 kDa helicase
w: Pre-mRNA-splicing factor ISY1 homolog
N: Splicing factor 3B subunit 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,741,13281
Polyers3,738,25461
Non-polymers2,87920
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein/peptide , 17 types, 18 molecules 13ABCDLOQRVty0Ufmq

#1: Protein/peptide RNA-binding motif protein, X-linked 2


Mass: 37425.984 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y388
#3: Protein/peptide BUD13 homolog


Mass: 70669.211 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BRD0
#8: Protein/peptide 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: (natural) Homo sapiens (human) / References: UniProt: Q6P2Q9
#9: Protein/peptide 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


Mass: 109560.625 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q15029
#10: Protein/peptide SNW domain-containing protein 1 / Nuclear protein SkiP / Nuclear receptor coactivator NCoA-62 / Ski-interacting protein


Mass: 61610.703 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q13573
#11: Protein/peptide Pleiotropic regulator 1


Mass: 57280.758 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: O43660
#13: Protein/peptide Cell division cycle 5-like protein / Cdc5-like protein / Pombe cdc5-related protein


Mass: 92406.883 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q99459
#14: Protein/peptide Crooked neck-like protein 1 / Crooked neck homolog / hCrn


Mass: 100610.008 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BZJ0
#16: Protein/peptide Protein BUD31 homolog / Protein EDG-2 / Protein G10 homolog


Mass: 17032.850 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: P41223
#17: Protein/peptide Spliceosome-associated protein CWC15 homolog


Mass: 26674.447 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q9P013
#19: Protein/peptide Peptidyl-prolyl cis-trans isomerase-like 1 / PPIase / Rotamase PPIL1


Mass: 18257.805 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y3C6, peptidylprolyl isomerase
#23: Protein/peptide RING finger protein 113A / / Zinc finger protein 183


Mass: 38847.199 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: O15541
#27: Protein/peptide PHD finger-like domain-containing protein 5A / PHD finger-like domain protein 5A / Splicing factor 3B-associated 14 kDa protein / SF3b14b


Mass: 12427.524 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q7RTV0
#29: Protein/peptide Smad nuclear-interacting protein 1 / FHA domain-containing protein SNIP1


Mass: 45880.738 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q8TAD8
#36: Protein/peptide Intron-binding protein aquarius / Intron-binding protein of 160 kDa / IBP160


Mass: 171502.453 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: O60306
#44: Protein/peptide Small nuclear ribonucleoprotein-associated proteins B and B' / snRNP-B / Sm protein B/B' / SmB/B'


Mass: 24642.131 Da / Num. of mol.: 2 / Source: (natural) Homo sapiens (human) / References: UniProt: P14678
#48: Protein/peptide Putative pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16 / ATP-dependent RNA helicase #3 / DEAH-box protein 16


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

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RNA chain , 4 types, 4 molecules 256Z

#2: RNA chain U2 snRNA / U2 spliceosomal RNA


Mass: 60186.445 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: GenBank: 36516
#4: RNA chain U5 snRNA / U5 spliceosomal RNA


Mass: 36908.668 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: GenBank: 36515
#5: RNA chain U6 snRNA / U6 spliceosomal RNA


Mass: 34404.438 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: GenBank: 254540252
#21: RNA chain pre-mRNA / Primary transcript


Mass: 118377.562 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human)

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Splicing factor 3A subunit ... , 3 types, 3 molecules 79p

#6: Protein/peptide Splicing factor 3A subunit 2 / SF3a66 / Spliceosome-associated protein 62 / SAP 62


Mass: 49327.355 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q15428
#30: Protein/peptide Splicing factor 3A subunit 3 / SF3a60 / Spliceosome-associated protein 61 / SAP 61


Mass: 58934.844 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q12874
#47: Protein/peptide Splicing factor 3A subunit 1 / SF3a120 / Spliceosome-associated protein 114 / SAP 114


Mass: 88991.094 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q15459

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Splicing factor 3B subunit ... , 5 types, 6 molecules 8uvxzN

#7: Protein/peptide Splicing factor 3B subunit 2 / Pre-mRNA-splicing factor SF3b 145 kDa subunit / SF3b145 / Spliceosome-associated protein 145 / SAP 145


Mass: 100377.812 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q13435
#24: Protein/peptide Splicing factor 3B subunit 1 / Pre-mRNA-splicing factor SF3b 155 kDa subunit / SF3b155 / Spliceosome-associated protein 155 / SAP 155


Mass: 146024.938 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: O75533
#25: Protein/peptide Splicing factor 3B subunit 3 / Pre-mRNA-splicing factor SF3b 130 kDa subunit / SF3b130 / STAF130 / Spliceosome-associated protein 130 / SAP 130


Mass: 135718.844 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q15393
#26: Protein/peptide Splicing factor 3B subunit 5 / SF3b5 / Pre-mRNA-splicing factor SF3b 10 kDa subunit


Mass: 10149.369 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BWJ5
#28: Protein/peptide 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


Mass: 14606.900 Da / Num. of mol.: 2 / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y3B4

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Pre-mRNA-processing factor ... , 2 types, 5 molecules EGHIJ

#12: Protein/peptide Pre-mRNA-processing factor 17 / Cell division cycle 40 homolog / EH-binding protein 3 / Ehb3 / PRP17 homolog / hPRP17


Mass: 65612.180 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: O60508
#32: Protein/peptide
Pre-mRNA-processing factor 19 / Nuclear matrix protein 200 / PRP19/PSO4 homolog / hPso4 / RING-type E3 ubiquitin transferase PRP19 / Senescence evasion factor


Mass: 55245.547 Da / Num. of mol.: 4 / Source: (natural) Homo sapiens (human)
References: UniProt: Q9UMS4, RING-type E3 ubiquitin transferase

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Pre-mRNA-splicing factor ... , 5 types, 5 molecules PKMTw

#15: Protein/peptide Pre-mRNA-splicing factor RBM22 / RNA-binding motif protein 22 / Zinc finger CCCH domain-containing protein 16


Mass: 46959.555 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q9NW64
#33: Protein/peptide Pre-mRNA-splicing factor SPF27 / Breast carcinoma-amplified sequence 2 / DNA amplified in mammary carcinoma 1 protein / Spliceosome-associated protein SPF 27


Mass: 26163.420 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: O75934
#34: Protein/peptide Pre-mRNA-splicing factor SYF1 / Protein HCNP / XPA-binding protein 2


Mass: 100148.711 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q9HCS7
#35: Protein/peptide Pre-mRNA-splicing factor CWC22 homolog / Nucampholin homolog / fSAPb


Mass: 105646.578 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q9HCG8
#50: Protein/peptide Pre-mRNA-splicing factor ISY1 homolog


Mass: 33046.254 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q9ULR0

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Serine/arginine repetitive matrix protein ... , 2 types, 2 molecules SY

#18: Protein/peptide 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


Mass: 300255.312 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q9UQ35
#20: Protein/peptide Serine/arginine repetitive matrix protein 1 / SR-related nuclear matrix protein of 160 kDa / SRm160 / Ser/Arg-related nuclear matrix protein


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

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Peptidyl-prolyl cis-trans isomerase ... , 2 types, 2 molecules so

#22: Protein/peptide Peptidyl-prolyl cis-trans isomerase CWC27 homolog / PPIase CWC27 / Antigen NY-CO-10 / Serologically defined colon cancer antigen 10


Mass: 53941.227 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q6UX04, peptidylprolyl isomerase
#46: Protein/peptide Peptidyl-prolyl cis-trans isomerase E / PPIase E / Cyclophilin E / Cyclophilin-33 / Rotamase E


Mass: 33475.773 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q9UNP9, peptidylprolyl isomerase

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

#31: Protein/peptide 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


Mass: 39359.492 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q96DI7
#49: Protein/peptide 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


Mass: 244823.422 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: O75643, RNA helicase

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U2 small nuclear ribonucleoprotein ... , 2 types, 2 molecules WX

#37: Protein/peptide U2 small nuclear ribonucleoprotein A' / U2 snRNP A'


Mass: 28484.592 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: P09661
#38: Protein/peptide U2 small nuclear ribonucleoprotein B'' / U2 snRNP B''


Mass: 25524.367 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: P08579

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Small nuclear ribonucleoprotein ... , 6 types, 12 molecules ahbicjdkelgn

#39: Protein/peptide Small nuclear ribonucleoprotein Sm D2 / Sm-D2 / snRNP core protein D2


Mass: 13551.928 Da / Num. of mol.: 2 / Source: (natural) Homo sapiens (human) / References: UniProt: P62316
#40: Protein/peptide Small nuclear ribonucleoprotein F / snRNP-F / Sm protein F / SmF


Mass: 9734.171 Da / Num. of mol.: 2 / Source: (natural) Homo sapiens (human) / References: UniProt: P62306
#41: Protein/peptide Small nuclear ribonucleoprotein E / snRNP-E / Sm protein E / SmE


Mass: 10817.601 Da / Num. of mol.: 2 / Source: (natural) Homo sapiens (human) / References: UniProt: P62304
#42: Protein/peptide Small nuclear ribonucleoprotein G / snRNP-G / Sm protein G / SmG


Mass: 8508.084 Da / Num. of mol.: 2 / Source: (natural) Homo sapiens (human) / References: UniProt: P62308
#43: Protein/peptide Small nuclear ribonucleoprotein Sm D3 / Sm-D3 / snRNP core protein D3


Mass: 13940.308 Da / Num. of mol.: 2 / Source: (natural) Homo sapiens (human) / References: UniProt: P62318
#45: Protein/peptide Small nuclear ribonucleoprotein Sm D1 / Sm-D1 / Sm-D autoantigen / snRNP core protein D1


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

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Non-polymers , 5 types, 20 molecules

#51: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 11 / Formula: Zn / Zinc
#52: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Formula: Mg / Magnesium
#53: Chemical ChemComp-IHP / INOSITOL HEXAKISPHOSPHATE


Mass: 660.035 Da / Num. of mol.: 1 / Formula: C6H18O24P6 / Phytic acid
#54: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Formula: C10H16N5O14P3 / Guanosine triphosphate / Comment: GTP (energy-carrying molecule) *YM
#55: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Formula: C10H15N5O10P2 / Adenosine diphosphate / Comment: ADP (energy-carrying molecule) *YM

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: human Bact spliceosome / Type: COMPLEX
Entity ID: 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50
Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 7.6
SpecimenEmbedding applied: YES / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 / Grid type: Quantifoil R3.5/1
EM embeddingMaterial: ice
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 40 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k)
Image scansSampling size: 14 microns / Width: 4096 / Height: 4096

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Processing

EM software
IDNameVersionCategory
7UCSF Chimeramodel fitting
10EMAN2initial Euler assignment
11RELION2final Euler assignment
CTF correctionType: PHASE FLIPPING ONLY
SymmetryPoint symmetry: C1
3D reconstructionResolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 165853 / Symmetry type: POINT

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