6FF4

human Bact spliceosome core structure

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 2.4 of the entry. See complete history. 


Literature

Structure and Conformational Dynamics of the Human Spliceosomal BactComplex.

Haselbach, D., Komarov, I., Agafonov, D.E., Hartmuth, K., Graf, B., Dybkov, O., Urlaub, H., Kastner, B., Luhrmann, R., Stark, H.

(2018) Cell 172: 454-464.e11

  • DOI: 10.1016/j.cell.2018.01.010
  • Primary Citation of Related Structures:  
    6FF4, 6FF7

  • PubMed 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 act spliceosome at 3.4 Å resolution. In the B act state, the splic ...

    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 act spliceosome at 3.4 Å resolution. In the B act 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 act 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.

    Organizational Affiliation: 

    Department for Structural Dynamics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany. Electronic address: hstark1@gwdg.de.



Macromolecules

Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RNA-binding motif protein, X-linked 21322Homo sapiensMutation(s): 0 
Gene Names: RBMX2, CGI-79
Find proteins for Q9Y388 (Homo sapiens)
Explore Q9Y388 
Go to UniProtKB:  Q9Y388
NIH Common Fund Data Resources
PHAROS  Q9Y388
GTEx  ENSG00000134597
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
BUD13 homolog3619Homo sapiensMutation(s): 0 
Gene Names: BUD13
Find proteins for Q9BRD0 (Homo sapiens)
Explore Q9BRD0 
Go to UniProtKB:  Q9BRD0
NIH Common Fund Data Resources
PHAROS  Q9BRD0
GTEx  ENSG00000137656
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Splicing factor 3A subunit 27464Homo sapiensMutation(s): 0 
Gene Names: SF3A2, SAP62
Find proteins for Q15428 (Homo sapiens)
Explore Q15428 
Go to UniProtKB:  Q15428
NIH Common Fund Data Resources
PHAROS  Q15428
GTEx  ENSG00000104897
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Splicing factor 3B subunit 28895Homo sapiensMutation(s): 0 
Gene Names: SF3B2, SAP145
Find proteins for Q13435 (Homo sapiens)
Explore Q13435 
Go to UniProtKB:  Q13435
NIH Common Fund Data Resources
PHAROS  Q13435
GTEx  ENSG00000087365
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-processing-splicing factor 8A2335Homo sapiensMutation(s): 0 
Gene Names: PRPF8, PRPC8
Find proteins for Q6P2Q9 (Homo sapiens)
Explore Q6P2Q9 
Go to UniProtKB:  Q6P2Q9
NIH Common Fund Data Resources
PHAROS  Q6P2Q9
GTEx  ENSG00000174231
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
116 kDa U5 small nuclear ribonucleoprotein componentB972Homo sapiensMutation(s): 0 
Gene Names: EFTUD2, KIAA0031, SNRP116
Find proteins for Q15029 (Homo sapiens)
Explore Q15029 
Go to UniProtKB:  Q15029
NIH Common Fund Data Resources
PHAROS  Q15029
GTEx  ENSG00000108883
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
SNW domain-containing protein 1C536Homo sapiensMutation(s): 0 
Gene Names: SNW1, SKIIP, SKIP
Find proteins for Q13573 (Homo sapiens)
Explore Q13573 
Go to UniProtKB:  Q13573
NIH Common Fund Data Resources
PHAROS  Q13573
GTEx  ENSG00000100603
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Pleiotropic regulator 1D514Homo sapiensMutation(s): 0 
Gene Names: PLRG1
Find proteins for O43660 (Homo sapiens)
Explore O43660 
Go to UniProtKB:  O43660
NIH Common Fund Data Resources
PHAROS  O43660
GTEx  ENSG00000171566
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-processing factor 17E579Homo sapiensMutation(s): 0 
Gene Names: CDC40, EHB3, PRP17, PRPF17
Find proteins for O60508 (Homo sapiens)
Explore O60508 
Go to UniProtKB:  O60508
NIH Common Fund Data Resources
PHAROS  O60508
GTEx  ENSG00000168438
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Cell division cycle 5-like proteinL802Homo sapiensMutation(s): 0 
Gene Names: CDC5L, KIAA0432, PCDC5RP
Find proteins for Q99459 (Homo sapiens)
Explore Q99459 
Go to UniProtKB:  Q99459
NIH Common Fund Data Resources
PHAROS  Q99459
GTEx  ENSG00000096401
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
Crooked neck-like protein 1O848Homo sapiensMutation(s): 0 
Gene Names: CRNKL1, CRN, CGI-201, MSTP021
Find proteins for Q9BZJ0 (Homo sapiens)
Explore Q9BZJ0 
Go to UniProtKB:  Q9BZJ0
NIH Common Fund Data Resources
PHAROS  Q9BZJ0
GTEx  ENSG00000101343
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor RBM22P420Homo sapiensMutation(s): 0 
Gene Names: RBM22, ZC3H16, 199G4
Find proteins for Q9NW64 (Homo sapiens)
Explore Q9NW64 
Go to UniProtKB:  Q9NW64
NIH Common Fund Data Resources
PHAROS  Q9NW64
GTEx  ENSG00000086589
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
Protein BUD31 homologQ144Homo sapiensMutation(s): 0 
Gene Names: BUD31, EDG2
Find proteins for P41223 (Homo sapiens)
Explore P41223 
Go to UniProtKB:  P41223
NIH Common Fund Data Resources
PHAROS  P41223
GTEx  ENSG00000106245
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
Spliceosome-associated protein CWC15 homologR229Homo sapiensMutation(s): 0 
Gene Names: CWC15, C11orf5, AD-002, HSPC148
Find proteins for Q9P013 (Homo sapiens)
Explore Q9P013 
Go to UniProtKB:  Q9P013
NIH Common Fund Data Resources
PHAROS  Q9P013
GTEx  ENSG00000150316
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
Serine/arginine repetitive matrix protein 2S2752Homo sapiensMutation(s): 0 
Gene Names: SRRM2, KIAA0324, SRL300, SRM300, HSPC075
Find proteins for Q9UQ35 (Homo sapiens)
Explore Q9UQ35 
Go to UniProtKB:  Q9UQ35
NIH Common Fund Data Resources
PHAROS  Q9UQ35
GTEx  ENSG00000167978
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomerase-like 1V166Homo sapiensMutation(s): 0 
Gene Names: PPIL1, CYPL1, CGI-124, UNQ2425/PRO4984
EC: 5.2.1.8
Find proteins for Q9Y3C6 (Homo sapiens)
Explore Q9Y3C6 
Go to UniProtKB:  Q9Y3C6
NIH Common Fund Data Resources
PHAROS  Q9Y3C6
GTEx  ENSG00000137168
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
Serine/arginine repetitive matrix protein 1Y904Homo sapiensMutation(s): 0 
Gene Names: SRRM1, SRM160
Find proteins for Q8IYB3 (Homo sapiens)
Explore Q8IYB3 
Go to UniProtKB:  Q8IYB3
NIH Common Fund Data Resources
PHAROS  Q8IYB3
GTEx  ENSG00000133226
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomerase CWC27 homologs472Homo sapiensMutation(s): 0 
Gene Names: CWC27, SDCCAG10, UNQ438/PRO871
EC: 5.2.1.8
Find proteins for Q6UX04 (Homo sapiens)
Explore Q6UX04 
Go to UniProtKB:  Q6UX04
NIH Common Fund Data Resources
PHAROS  Q6UX04
GTEx  ENSG00000153015
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
RING finger protein 113At343Homo sapiensMutation(s): 0 
Gene Names: RNF113A, RNF113, ZNF183
EC: 2.3.2.27
Find proteins for O15541 (Homo sapiens)
Explore O15541 
Go to UniProtKB:  O15541
NIH Common Fund Data Resources
PHAROS  O15541
GTEx  ENSG00000125352
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
Splicing factor 3B subunit 1u1304Homo sapiensMutation(s): 0 
Gene Names: SF3B1, SAP155
Find proteins for O75533 (Homo sapiens)
Explore O75533 
Go to UniProtKB:  O75533
NIH Common Fund Data Resources
PHAROS  O75533
GTEx  ENSG00000115524
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
Splicing factor 3B subunit 3v1217Homo sapiensMutation(s): 0 
Gene Names: SF3B3, KIAA0017, SAP130
Find proteins for Q15393 (Homo sapiens)
Explore Q15393 
Go to UniProtKB:  Q15393
NIH Common Fund Data Resources
PHAROS  Q15393
GTEx  ENSG00000189091
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
Splicing factor 3B subunit 5x86Homo sapiensMutation(s): 0 
Gene Names: SF3B5, SF3B10
Find proteins for Q9BWJ5 (Homo sapiens)
Explore Q9BWJ5 
Go to UniProtKB:  Q9BWJ5
NIH Common Fund Data Resources
PHAROS  Q9BWJ5
GTEx  ENSG00000169976
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
PHD finger-like domain-containing protein 5Ay110Homo sapiensMutation(s): 0 
Gene Names: PHF5A
Find proteins for Q7RTV0 (Homo sapiens)
Explore Q7RTV0 
Go to UniProtKB:  Q7RTV0
NIH Common Fund Data Resources
PHAROS  Q7RTV0
GTEx  ENSG00000100410
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
Splicing factor 3B subunit 6z125Homo sapiensMutation(s): 0 
Gene Names: SF3B6, SAP14, SF3B14, SF3B14A, CGI-110, HSPC175, HT006
Find proteins for Q9Y3B4 (Homo sapiens)
Explore Q9Y3B4 
Go to UniProtKB:  Q9Y3B4
NIH Common Fund Data Resources
PHAROS  Q9Y3B4
GTEx  ENSG00000115128
Protein Feature View
Expand
  • Reference Sequence
Find similar nucleic acids by: 
(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsLengthOrganismImage
U2 snRNA2188Homo sapiens
Find similar nucleic acids by: 
(by identity cutoff)  |  Structure
Entity ID: 4
MoleculeChainsLengthOrganismImage
U5 snRNA5116Homo sapiens
Find similar nucleic acids by: 
(by identity cutoff)  |  Structure
Entity ID: 5
MoleculeChainsLengthOrganismImage
U6 snRNA6107Homo sapiens
Find similar nucleic acids by: 
(by identity cutoff)  |  Structure
Entity ID: 21
MoleculeChainsLengthOrganismImage
pre mRNAZ478Homo sapiens
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-08-29
    Type: Initial release
  • Version 2.0: 2018-12-19
    Changes: Advisory, Data collection, Derived calculations, Polymer sequence, Structure summary
  • Version 2.1: 2019-01-02
    Changes: Data collection, Data processing, Source and taxonomy
  • Version 2.2: 2019-03-13
    Changes: Data collection
  • Version 2.3: 2019-12-11
    Changes: Other
  • Version 2.4: 2020-10-07
    Changes: Derived calculations, Structure summary