6FF7

human Bact spliceosome core structure


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.5 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.2 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:  

  • 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 <sup>act </sup> spliceosome at 3.4 Å resolution. In the B <sup>act </sup> 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

    Bioanalytic Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany; Bioanalytics Group, Institute for Clinical Chemistry, University Medical Center Göttingen, Robert-Koch-Str. 40, 37073 Göttingen, Germany.,Department for Structural Dynamics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.,Department for Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.,Department for Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany. Electronic address: reinhard.luehrmann@mpi-bpc.mpg.de.,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: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RNA-binding motif protein, X-linked 2
1
322Homo sapiensMutation(s): 0 
Gene Names: RBMX2
Find proteins for Q9Y388 (Homo sapiens)
Go to Gene View: RBMX2
Go to UniProtKB:  Q9Y388
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
BUD13 homolog
3
619Homo sapiensMutation(s): 0 
Gene Names: BUD13
Find proteins for Q9BRD0 (Homo sapiens)
Go to Gene View: BUD13
Go to UniProtKB:  Q9BRD0
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Splicing factor 3A subunit 2
7
464Homo sapiensMutation(s): 0 
Gene Names: SF3A2 (SAP62)
Find proteins for Q15428 (Homo sapiens)
Go to Gene View: SF3A2
Go to UniProtKB:  Q15428
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Splicing factor 3B subunit 2
8
895Homo sapiensMutation(s): 0 
Gene Names: SF3B2 (SAP145)
Find proteins for Q13435 (Homo sapiens)
Go to Gene View: SF3B2
Go to UniProtKB:  Q13435
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-processing-splicing factor 8
A
2335Homo sapiensMutation(s): 0 
Gene Names: PRPF8 (PRPC8)
Find proteins for Q6P2Q9 (Homo sapiens)
Go to Gene View: PRPF8
Go to UniProtKB:  Q6P2Q9
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
116 kDa U5 small nuclear ribonucleoprotein component
B
972Homo sapiensMutation(s): 0 
Gene Names: EFTUD2 (KIAA0031, SNRP116)
Find proteins for Q15029 (Homo sapiens)
Go to Gene View: EFTUD2
Go to UniProtKB:  Q15029
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
SNW domain-containing protein 1
C
536Homo sapiensMutation(s): 0 
Gene Names: SNW1 (SKIIP, SKIP)
Find proteins for Q13573 (Homo sapiens)
Go to Gene View: SNW1
Go to UniProtKB:  Q13573
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
Pleiotropic regulator 1
D
514Homo sapiensMutation(s): 0 
Gene Names: PLRG1
Find proteins for O43660 (Homo sapiens)
Go to Gene View: PLRG1
Go to UniProtKB:  O43660
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-processing factor 17
E
579Homo sapiensMutation(s): 0 
Gene Names: CDC40 (EHB3, PRP17, PRPF17)
Find proteins for O60508 (Homo sapiens)
Go to Gene View: CDC40
Go to UniProtKB:  O60508
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
Cell division cycle 5-like protein
L
802Homo sapiensMutation(s): 0 
Gene Names: CDC5L (KIAA0432, PCDC5RP)
Find proteins for Q99459 (Homo sapiens)
Go to Gene View: CDC5L
Go to UniProtKB:  Q99459
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
Crooked neck-like protein 1
O
848Homo sapiensMutation(s): 0 
Gene Names: CRNKL1 (CRN)
Find proteins for Q9BZJ0 (Homo sapiens)
Go to Gene View: CRNKL1
Go to UniProtKB:  Q9BZJ0
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor RBM22
P
420Homo sapiensMutation(s): 0 
Gene Names: RBM22 (ZC3H16)
Find proteins for Q9NW64 (Homo sapiens)
Go to Gene View: RBM22
Go to UniProtKB:  Q9NW64
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
Protein BUD31 homolog
Q
144Homo sapiensMutation(s): 0 
Gene Names: BUD31 (EDG2)
Find proteins for P41223 (Homo sapiens)
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Go to UniProtKB:  P41223
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
Spliceosome-associated protein CWC15 homolog
R
229Homo sapiensMutation(s): 0 
Gene Names: CWC15 (C11orf5)
Find proteins for Q9P013 (Homo sapiens)
Go to Gene View: CWC15
Go to UniProtKB:  Q9P013
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
Serine/arginine repetitive matrix protein 2
S
2752Homo sapiensMutation(s): 0 
Gene Names: SRRM2 (KIAA0324, SRL300, SRM300)
Find proteins for Q9UQ35 (Homo sapiens)
Go to Gene View: SRRM2
Go to UniProtKB:  Q9UQ35
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
Peptidyl-prolyl cis-trans isomerase-like 1
V
166Homo sapiensMutation(s): 0 
Gene Names: PPIL1 (CYPL1)
EC: 5.2.1.8
Find proteins for Q9Y3C6 (Homo sapiens)
Go to Gene View: PPIL1
Go to UniProtKB:  Q9Y3C6
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
Serine/arginine repetitive matrix protein 1
Y
904Homo sapiensMutation(s): 0 
Gene Names: SRRM1 (SRM160)
Find proteins for Q8IYB3 (Homo sapiens)
Go to Gene View: SRRM1
Go to UniProtKB:  Q8IYB3
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
Peptidyl-prolyl cis-trans isomerase CWC27 homolog
s
472Homo sapiensMutation(s): 0 
Gene Names: CWC27 (SDCCAG10)
Find proteins for Q6UX04 (Homo sapiens)
Go to Gene View: CWC27
Go to UniProtKB:  Q6UX04
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
RING finger protein 113A
t
343Homo sapiensMutation(s): 0 
Gene Names: RNF113A (RNF113, ZNF183)
EC: 2.3.2.27
Find proteins for O15541 (Homo sapiens)
Go to Gene View: RNF113A
Go to UniProtKB:  O15541
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
Splicing factor 3B subunit 1
u
1304Homo sapiensMutation(s): 0 
Gene Names: SF3B1 (SAP155)
Find proteins for O75533 (Homo sapiens)
Go to Gene View: SF3B1
Go to UniProtKB:  O75533
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
Splicing factor 3B subunit 3
v
1217Homo sapiensMutation(s): 0 
Gene Names: SF3B3 (KIAA0017, SAP130)
Find proteins for Q15393 (Homo sapiens)
Go to Gene View: SF3B3
Go to UniProtKB:  Q15393
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
Splicing factor 3B subunit 5
x
86Homo sapiensMutation(s): 0 
Gene Names: SF3B5 (SF3B10)
Find proteins for Q9BWJ5 (Homo sapiens)
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Go to UniProtKB:  Q9BWJ5
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
PHD finger-like domain-containing protein 5A
y
110Homo sapiensMutation(s): 0 
Gene Names: PHF5A
Find proteins for Q7RTV0 (Homo sapiens)
Go to Gene View: PHF5A
Go to UniProtKB:  Q7RTV0
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
Splicing factor 3B subunit 6
z, N
125Homo sapiensMutation(s): 0 
Gene Names: SF3B6 (SAP14, SF3B14, SF3B14A)
Find proteins for Q9Y3B4 (Homo sapiens)
Go to Gene View: SF3B6
Go to UniProtKB:  Q9Y3B4
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
Smad nuclear-interacting protein 1
0
396Homo sapiensMutation(s): 0 
Gene Names: SNIP1
Find proteins for Q8TAD8 (Homo sapiens)
Go to Gene View: SNIP1
Go to UniProtKB:  Q8TAD8
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
Splicing factor 3A subunit 3
9
501Homo sapiensMutation(s): 0 
Gene Names: SF3A3 (SAP61)
Find proteins for Q12874 (Homo sapiens)
Go to Gene View: SF3A3
Go to UniProtKB:  Q12874
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
U5 small nuclear ribonucleoprotein 40 kDa protein
F
357Homo sapiensMutation(s): 0 
Gene Names: SNRNP40 (PRP8BP, SFP38, WDR57)
Find proteins for Q96DI7 (Homo sapiens)
Go to Gene View: SNRNP40
Go to UniProtKB:  Q96DI7
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-processing factor 19
G, H, I, J
504Homo sapiensMutation(s): 0 
Gene Names: PRPF19 (NMP200, PRP19, SNEV)
EC: 2.3.2.27
Find proteins for Q9UMS4 (Homo sapiens)
Go to Gene View: PRPF19
Go to UniProtKB:  Q9UMS4
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor SPF27
K
225Homo sapiensMutation(s): 0 
Gene Names: BCAS2 (DAM1)
Find proteins for O75934 (Homo sapiens)
Go to Gene View: BCAS2
Go to UniProtKB:  O75934
Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor SYF1
M
855Homo sapiensMutation(s): 0 
Gene Names: XAB2 (HCNP, KIAA1177, SYF1)
Find proteins for Q9HCS7 (Homo sapiens)
Go to Gene View: XAB2
Go to UniProtKB:  Q9HCS7
Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor CWC22 homolog
T
908Homo sapiensMutation(s): 0 
Gene Names: CWC22 (KIAA1604, NCM)
Find proteins for Q9HCG8 (Homo sapiens)
Go to Gene View: CWC22
Go to UniProtKB:  Q9HCG8
Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
Intron-binding protein aquarius
U
1485Homo sapiensMutation(s): 0 
Gene Names: AQR (KIAA0560)
EC: 3.6.4.13
Find proteins for O60306 (Homo sapiens)
Go to Gene View: AQR
Go to UniProtKB:  O60306
Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
U2 small nuclear ribonucleoprotein A'
W
255Homo sapiensMutation(s): 0 
Gene Names: SNRPA1
Find proteins for P09661 (Homo sapiens)
Go to Gene View: SNRPA1
Go to UniProtKB:  P09661
Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
U2 small nuclear ribonucleoprotein B''
X
225Homo sapiensMutation(s): 0 
Gene Names: SNRPB2
Find proteins for P08579 (Homo sapiens)
Go to Gene View: SNRPB2
Go to UniProtKB:  P08579
Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein Sm D2
a, h
118Homo sapiensMutation(s): 0 
Gene Names: SNRPD2 (SNRPD1)
Find proteins for P62316 (Homo sapiens)
Go to Gene View: SNRPD2
Go to UniProtKB:  P62316
Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein F
b, i
86Homo sapiensMutation(s): 0 
Gene Names: SNRPF (PBSCF)
Find proteins for P62306 (Homo sapiens)
Go to Gene View: SNRPF
Go to UniProtKB:  P62306
Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein E
c, j
92Homo sapiensMutation(s): 0 
Gene Names: SNRPE
Find proteins for P62304 (Homo sapiens)
Go to Gene View: SNRPE
Go to UniProtKB:  P62304
Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein G
d, k
76Homo sapiensMutation(s): 0 
Gene Names: SNRPG (PBSCG)
Find proteins for P62308 (Homo sapiens)
Go to Gene View: SNRPG
Go to UniProtKB:  P62308
Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein Sm D3
e, l
126Homo sapiensMutation(s): 0 
Gene Names: SNRPD3
Find proteins for P62318 (Homo sapiens)
Go to Gene View: SNRPD3
Go to UniProtKB:  P62318
Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein-associated proteins B and B'
f, m
240Homo sapiensMutation(s): 0 
Gene Names: SNRPB (COD, SNRPB1)
Find proteins for P14678 (Homo sapiens)
Go to Gene View: SNRPB
Go to UniProtKB:  P14678
Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
Small nuclear ribonucleoprotein Sm D1
g, n
119Homo sapiensMutation(s): 0 
Gene Names: SNRPD1
Find proteins for P62314 (Homo sapiens)
Go to Gene View: SNRPD1
Go to UniProtKB:  P62314
Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
Peptidyl-prolyl cis-trans isomerase E
o
301Homo sapiensMutation(s): 0 
Gene Names: PPIE (CYP33)
EC: 5.2.1.8
Find proteins for Q9UNP9 (Homo sapiens)
Go to Gene View: PPIE
Go to UniProtKB:  Q9UNP9
Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
Splicing factor 3A subunit 1
p
793Homo sapiensMutation(s): 0 
Gene Names: SF3A1 (SAP114)
Find proteins for Q15459 (Homo sapiens)
Go to Gene View: SF3A1
Go to UniProtKB:  Q15459
Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
Putative pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16
q
1041Homo sapiensMutation(s): 0 
Gene Names: DHX16 (DBP2, DDX16, KIAA0577, PRP2)
EC: 3.6.4.13
Find proteins for O60231 (Homo sapiens)
Go to Gene View: DHX16
Go to UniProtKB:  O60231
Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
U5 small nuclear ribonucleoprotein 200 kDa helicase
r
2136Homo sapiensMutation(s): 0 
Gene Names: SNRNP200 (ASCC3L1, HELIC2, KIAA0788)
EC: 3.6.4.13
Find proteins for O75643 (Homo sapiens)
Go to Gene View: SNRNP200
Go to UniProtKB:  O75643
Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
Pre-mRNA-splicing factor ISY1 homolog
w
285Homo sapiensMutation(s): 0 
Gene Names: ISY1 (KIAA1160)
Find proteins for Q9ULR0 (Homo sapiens)
Go to Gene View: ISY1
Go to UniProtKB:  Q9ULR0
Entity ID: 2
MoleculeChainsLengthOrganism
U2 snRNA2188Homo sapiens
Entity ID: 4
MoleculeChainsLengthOrganism
U5 snRNA5116Homo sapiens
Entity ID: 5
MoleculeChainsLengthOrganism
U6 snRNA6107Homo sapiens
Entity ID: 21
MoleculeChainsLengthOrganism
pre-mRNAZ369Homo sapiens
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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2, P, Q, y, Z
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
ADP
Query on ADP

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r
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
GTP
Query on GTP

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Download CCD File 
B
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
 Ligand Interaction
MG
Query on MG

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6, r
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
IHP
Query on IHP

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A
INOSITOL HEXAKISPHOSPHATE
C6 H18 O24 P6
IMQLKJBTEOYOSI-GPIVLXJGSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.5 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-03-13
    Type: Initial release
  • Version 1.1: 2019-04-03
    Type: Advisory, Data collection, Derived calculations
  • Version 1.2: 2019-12-11
    Type: Other