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- PDB-6ff4: human Bact spliceosome core structure -

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Basic information

Entry
Database: PDB / ID: 6ff4
Titlehuman Bact spliceosome core structure
Components
  • (Peptidyl-prolyl cis-trans ...) x 2
  • (Serine/arginine repetitive matrix protein ...) x 2
  • (Splicing factor 3B subunit ...) x 5
  • 116 kDa U5 small nuclear ribonucleoprotein component
  • BUD13 homolog
  • Cell division cycle 5-like protein
  • Crooked neck-like protein 1
  • PHD finger-like domain-containing protein 5A
  • Pleiotropic regulator 1
  • Pre-mRNA-processing factor 17
  • Pre-mRNA-processing-splicing factor 8
  • Pre-mRNA-splicing factor RBM22
  • Protein BUD31 homolog
  • RING finger protein 113A
  • RNA-binding motif protein, X-linked 2
  • SNW domain-containing protein 1
  • Spliceosome-associated protein CWC15 homolog
  • Splicing factor 3A subunit 2
  • U2 snRNA
  • U5 snRNA
  • U6 snRNA
  • pre mRNA
KeywordsSPLICING / spliceosome / human / HELA / BACT / dynamics
Function / homology
Function and homology information


RES complex / negative regulation of chemokine-mediated signaling pathway / snoRNA splicing / U11/U12 snRNP / regulation of retinoic acid receptor signaling pathway / post-mRNA release spliceosomal complex / regulation of vitamin D receptor signaling pathway / B-WICH complex / nuclear retinoic acid receptor binding / embryonic brain development ...RES complex / negative regulation of chemokine-mediated signaling pathway / snoRNA splicing / U11/U12 snRNP / regulation of retinoic acid receptor signaling pathway / post-mRNA release spliceosomal complex / regulation of vitamin D receptor signaling pathway / B-WICH complex / nuclear retinoic acid receptor binding / embryonic brain development / U12-type spliceosomal complex / mRNA 3'-end processing / RNA splicing, via transesterification reactions / C2H2 zinc finger domain binding / U2-type catalytic step 1 spliceosome / pre-mRNA binding / regulation of mRNA splicing, via spliceosome / positive regulation of mRNA splicing, via spliceosome / blastocyst formation / splicing factor binding / host-mediated activation of viral transcription / U2-type precatalytic spliceosome / positive regulation of vitamin D receptor signaling pathway / mRNA cis splicing, via spliceosome / U2-type spliceosomal complex / nuclear vitamin D receptor binding / U2-type prespliceosome assembly / Notch binding / Transport of Mature mRNA derived from an Intron-Containing Transcript / U2-type catalytic step 2 spliceosome / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / RUNX3 regulates NOTCH signaling / positive regulation of neurogenesis / NOTCH4 Intracellular Domain Regulates Transcription / RHOBTB1 GTPase cycle / SAGA complex / RNA Polymerase II Transcription Termination / U2 snRNP / NOTCH3 Intracellular Domain Regulates Transcription / U2-type prespliceosome / positive regulation of transcription by RNA polymerase III / WD40-repeat domain binding / protein peptidyl-prolyl isomerization / K63-linked polyubiquitin modification-dependent protein binding / nuclear androgen receptor binding / precatalytic spliceosome / Notch-HLH transcription pathway / Formation of paraxial mesoderm / SMAD binding / positive regulation of transforming growth factor beta receptor signaling pathway / regulation of RNA splicing / spliceosomal complex assembly / mRNA Splicing - Minor Pathway / mRNA 3'-splice site recognition / positive regulation of transcription by RNA polymerase I / spliceosomal tri-snRNP complex assembly / Prp19 complex / U5 snRNA binding / U5 snRNP / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / protein localization to nucleus / U2 snRNA binding / positive regulation of G1/S transition of mitotic cell cycle / U6 snRNA binding / pre-mRNA intronic binding / RHOBTB2 GTPase cycle / U1 snRNA binding / Cajal body / regulation of DNA repair / retinoic acid receptor signaling pathway / U4/U6 x U5 tri-snRNP complex / cellular response to retinoic acid / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / RNA splicing / DNA damage checkpoint signaling / positive regulation of RNA splicing / positive regulation of protein export from nucleus / nuclear receptor binding / response to cocaine / RNA polymerase II transcription regulatory region sequence-specific DNA binding / stem cell differentiation / peptidylprolyl isomerase / spliceosomal complex / peptidyl-prolyl cis-trans isomerase activity / Downregulation of SMAD2/3:SMAD4 transcriptional activity / positive regulation of neuron projection development / mRNA splicing, via spliceosome / RING-type E3 ubiquitin transferase / negative regulation of protein catabolic process / NOTCH1 Intracellular Domain Regulates Transcription / B-WICH complex positively regulates rRNA expression / positive regulation of protein import into nucleus / Pre-NOTCH Transcription and Translation / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / cellular response to xenobiotic stimulus / nuclear matrix / fibrillar center / mRNA processing
Similarity search - Function
PWI domain / PWI domain / : / Pre-mRNA-splicing factor CWC24-like / Ist3-like, RNA recognition motif / : / Bud13 / : / Pre-mRNA-splicing factor of RES complex / HAT (Half-A-TPR) repeat ...PWI domain / PWI domain / : / Pre-mRNA-splicing factor CWC24-like / Ist3-like, RNA recognition motif / : / Bud13 / : / Pre-mRNA-splicing factor of RES complex / HAT (Half-A-TPR) repeat / : / SF3B6, RNA recognition motif / PWI domain superfamily / PWI domain / PWI domain profile. / Cactus-binding C-terminus of cactin protein / PWI domain / PWI, domain in splicing factors / : / SF3A2 domain / : / Pre-mRNA-splicing factor SF3a complex subunit 2 (Prp11) / mRNA splicing factor Cwf21 domain / cwf21 domain / Pre-mRNA-processing factor 17 / Zinc finger C-x8-C-x5-C-x3-H type (and similar) / : / Domain of unknown function DUF382 / Domain of unknown function (DUF382) / G10 protein signature 2. / Splicing factor 3B, subunit 5 / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, cyclophilin A-like / BUD31/G10-related, conserved site / G10 protein signature 1. / Splicing factor 3B subunit 1 / Splicing factor 3B subunit 1 / Zinc-finger of C2H2 type / : / STL11, N-terminal / : / Pre-mRNA-splicing factor Syf1/CRNKL1 C-terminal HAT repeat / SKI-interacting protein SKIP, SNW domain / PSP, proline-rich / SKI-interacting protein, SKIP / SKIP/SNW domain / PSP / proline-rich domain in spliceosome associated proteins / Pre-mRNA-splicing factor Cwf15/Cwc15 / Cwf15/Cwc15 cell cycle control protein / WD repeat Prp46/PLRG1-like / Pre-mRNA-splicing factor Cwc2/Slt11 / Matrin/U1-C, C2H2-type zinc finger / : / Zinc finger matrin-type profile. / G10 protein / Pre-mRNA-splicing factor BUD31 / PHF5-like / Pre-mRNA splicing factor component Cdc5p/Cef1, C-terminal / : / : / PHF5-like protein / pre-mRNA splicing factor component / Splicing factor 3B subunit 5/RDS3 complex subunit 10 / Splicing factor 3B subunit 10 (SF3b10) / Splicing factor 3B subunit 1-like / Myb-like DNA-binding domain / Spt5 C-terminal domain / Spt5 C-terminal nonapeptide repeat binding Spt4 / Zinc finger, CCCH-type superfamily / zinc finger / : / PPP2R1A-like HEAT repeat / SAP motif profile. / 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 / SAP domain / Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation / SAP domain / Matrin/U1-C-like, C2H2-type zinc finger / U1-like zinc finger / Myb-type HTH DNA-binding domain profile. / Zinc finger, CCCH-type / Zinc finger C3H1-type profile. / Cyclophilin-like / Cyclophilin / HAT (Half-A-TPR) repeat / HAT (Half-A-TPR) repeats / Myb domain / Cyclophilin-type peptidyl-prolyl cis-trans isomerase / RSE1/DDB1/CPSF1 second beta-propeller / Cleavage/polyadenylation specificity factor, A subunit, C-terminal / Cleavage/polyadenylation specificity factor, A subunit, N-terminal / : / CPSF A subunit region / RSE1/DDB1/CPSF1 first beta-propeller / Zinc finger, C3HC4 type (RING finger) / Elongation Factor G, domain II
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / INOSITOL HEXAKISPHOSPHATE / : / : / RNA / RNA (> 10) / RNA (> 100) / E3 ubiquitin-protein ligase RNF113A / Pleiotropic regulator 1 / Pre-mRNA-processing factor 17 ...GUANOSINE-5'-TRIPHOSPHATE / INOSITOL HEXAKISPHOSPHATE / : / : / RNA / RNA (> 10) / RNA (> 100) / E3 ubiquitin-protein ligase RNF113A / Pleiotropic regulator 1 / Pre-mRNA-processing factor 17 / Splicing factor 3B subunit 1 / Protein BUD31 homolog / Splicing factor 3B subunit 2 / SNW domain-containing protein 1 / 116 kDa U5 small nuclear ribonucleoprotein component / Splicing factor 3B subunit 3 / Splicing factor 3A subunit 2 / Pre-mRNA-processing-splicing factor 8 / Spliceosome-associated protein CWC27 homolog / PHD finger-like domain-containing protein 5A / Serine/arginine repetitive matrix protein 1 / Cell division cycle 5-like protein / BUD13 homolog / Splicing factor 3B subunit 5 / Crooked neck-like protein 1 / Pre-mRNA-splicing factor RBM22 / Spliceosome-associated protein CWC15 homolog / Serine/arginine repetitive matrix protein 2 / RNA-binding motif protein, X-linked 2 / Splicing factor 3B subunit 6 / Peptidyl-prolyl cis-trans isomerase-like 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
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.
History
DepositionJan 3, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 29, 2018Provider: repository / Type: Initial release
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Revision 2.0Dec 19, 2018Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Polymer sequence / Structure summary
Category: em_entity_assembly / entity ...em_entity_assembly / entity / entity_poly / entity_poly_seq / pdbx_poly_seq_scheme / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_unobs_or_zero_occ_residues
Item: _em_entity_assembly.entity_id_list / _entity.formula_weight ..._em_entity_assembly.entity_id_list / _entity.formula_weight / _entity_poly.nstd_monomer / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details
Revision 2.1Jan 2, 2019Group: Data collection / Data processing / Source and taxonomy
Category: em_3d_reconstruction / em_entity_assembly_naturalsource / em_particle_selection
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Revision 2.2Mar 13, 2019Group: Data collection
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Revision 2.3Dec 11, 2019Group: Other / Category: atom_sites / cell
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Revision 2.4Oct 7, 2020Group: Derived calculations / Structure summary / Category: chem_comp / pdbx_struct_conn_angle / struct_conn
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Revision 2.5Nov 6, 2024Group: Data collection / Database references / Structure summary
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Structure visualization

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,229,57444
Polymers2,227,64028
Non-polymers1,93516
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: cross-linking
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area165530 Å2
ΔGint-898 kcal/mol
Surface area375910 Å2
MethodPISA

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Components

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Protein , 15 types, 15 molecules 137ABCDELOPQRty

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


Mass: 37425.984 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HeLa S3 / References: UniProt: Q9Y388
#3: Protein BUD13 homolog


Mass: 70669.211 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HeLa S3 / References: UniProt: Q9BRD0
#6: Protein Splicing factor 3A subunit 2 / SF3a66 / Spliceosome-associated protein 62 / SAP 62


Mass: 49327.355 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HeLa S3 / References: UniProt: Q15428
#8: 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) / Cell line: HeLa S3 / References: UniProt: Q6P2Q9
#9: 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) / Cell line: HeLa S3 / References: UniProt: Q15029
#10: Protein 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 method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HeLa S3 / References: UniProt: Q13573
#11: Protein Pleiotropic regulator 1


Mass: 57280.758 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HeLa S3 / References: UniProt: O43660
#12: Protein 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 method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HeLa S3 / References: UniProt: O60508
#13: Protein Cell division cycle 5-like protein / Cdc5-like protein / Pombe cdc5-related protein


Mass: 92406.883 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HeLa S3 / References: UniProt: Q99459
#14: Protein Crooked neck-like protein 1 / Crooked neck homolog / hCrn


Mass: 100610.008 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HeLa S3 / References: UniProt: Q9BZJ0
#15: Protein 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 method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HeLa S3 / References: UniProt: Q9NW64
#16: Protein Protein BUD31 homolog / Protein EDG-2 / Protein G10 homolog


Mass: 17032.850 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HeLa S3 / References: UniProt: P41223
#17: Protein Spliceosome-associated protein CWC15 homolog


Mass: 26674.447 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HeLa S3 / References: UniProt: Q9P013
#23: Protein RING finger protein 113A / Zinc finger protein 183


Mass: 38847.199 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HeLa S3 / References: UniProt: O15541
#27: Protein 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 method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HeLa S3 / References: UniProt: Q7RTV0

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RNA chain , 4 types, 4 molecules 256Z

#2: RNA chain U2 snRNA


Mass: 60186.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HeLA S3 / References: GenBank: 36516
#4: RNA chain U5 snRNA


Mass: 36908.668 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HeLa S3 / References: GenBank: 36515
#5: RNA chain U6 snRNA


Mass: 34404.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HeLa S3
#21: RNA chain pre mRNA


Mass: 153787.984 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HeLa S3

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Splicing factor 3B subunit ... , 5 types, 5 molecules 8uvxz

#7: Protein 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 method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HeLa S3 / References: UniProt: Q13435
#24: Protein 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 method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HeLa S3 / References: UniProt: O75533
#25: Protein Splicing factor 3B subunit 3 / Pre-mRNA-splicing factor SF3b 130 kDa subunit / SF3b130 / STAF130 / Spliceosome-associated protein ...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 method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HeLa S3 / References: UniProt: Q15393
#26: Protein Splicing factor 3B subunit 5 / SF3b5 / Pre-mRNA-splicing factor SF3b 10 kDa subunit


Mass: 10149.369 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HeLa S3 / References: UniProt: Q9BWJ5
#28: Protein Splicing factor 3B subunit 6 / Pre-mRNA branch site protein p14 / SF3b 14 kDa subunit / SF3B14a / Spliceosome-associated protein / ...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.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HeLa S3 / References: UniProt: Q9Y3B4

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

#18: Protein Serine/arginine repetitive matrix protein 2 / 300 kDa nuclear matrix antigen / Serine/arginine-rich splicing factor-related nuclear matrix ...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 method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HeLa S3 / References: UniProt: Q9UQ35
#20: Protein 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 method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HeLa S3 / References: UniProt: Q8IYB3

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Peptidyl-prolyl cis-trans ... , 2 types, 2 molecules Vs

#19: Protein Peptidyl-prolyl cis-trans isomerase-like 1 / PPIase / Rotamase PPIL1


Mass: 18257.805 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HeLa S3 / References: UniProt: Q9Y3C6, peptidylprolyl isomerase
#22: Protein 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 method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HeLa S3 / References: UniProt: Q6UX04, peptidylprolyl isomerase

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Non-polymers , 4 types, 16 molecules

#29: Chemical
ChemComp-MG / MAGNESIUM ION


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


Mass: 660.035 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H18O24P6
#31: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#32: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Zn

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Details

Has protein modificationY

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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 Bact spliceosome state 1 unmasked / Type: COMPLEX / Entity ID: #1-#4, #6-#28 / Source: NATURAL
Molecular weightValue: 4.5 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human) / Cell: HeLa
Buffer solutionpH: 7.9
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMHEPES1
2150 mMNaCl1
31.5 mMMgCl21
SpecimenConc.: 0.05 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R3.5/1
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 75 % / Chamber temperature: 277 K / Details: blot with blotting sensor

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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: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal magnification: 59000 X / Nominal defocus max: 4500 nm / Nominal defocus min: 800 nm / Cs: 0.001 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Residual tilt: 14 mradians
Image recordingAverage exposure time: 1 sec. / Electron dose: 40 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 32000
EM imaging opticsSpherical aberration corrector: Microscope was modified with a Cs corrector with two hexapoles elements
Image scansSampling size: 14 µm / Width: 4096 / Height: 4096

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Processing

SoftwareName: PHENIX / Version: 1.12_2829: / Classification: refinement
EM software
IDNameCategory
4GctfCTF correction
7UCSF Chimeramodel fitting
9EMAN2initial Euler assignment
10RELIONfinal Euler assignment
11RELIONclassification
12RELION3D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING ONLY
Particle selectionNum. of particles selected: 308000
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 17000 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01174604
ELECTRON MICROSCOPYf_angle_d1.263102254
ELECTRON MICROSCOPYf_dihedral_angle_d12.41444497
ELECTRON MICROSCOPYf_chiral_restr0.0711358
ELECTRON MICROSCOPYf_plane_restr0.00912180

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