9FMD

Integrative model of the human post-catalytic spliceosome (P-complex)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Mechanism for the initiation of spliceosome disassembly.

Vorlander, M.K.Rothe, P.Kleifeld, J.Cormack, E.Veleti, L.Riabov-Bassat, D.Fin, L.Phillips, A.W.Cochella, L.Plaschka, C.

(2024) Nature 

  • DOI: https://doi.org/10.1038/s41586-024-07741-1
  • Primary Citation of Related Structures:  
    8RO0, 8RO1, 8RO2, 9FMD

  • PubMed Abstract: 

    Pre-mRNA splicing requires the assembly, remodeling, and disassembly of the multi-megadalton ribonucleoprotein complex called the spliceosome 1 . Recent studies have shed light on spliceosome assembly and remodeling for catalysis 2-6 , but the mechanism of disassembly remains unclear. Here, we report 2.6 to 3.2 Å resolution cryo-electron microscopy structures of nematode and human terminal intron-lariat spliceosomes along with biochemical and genetic data. Our results uncover how four disassembly factors and the conserved RNA helicase DHX15 initiate spliceosome disassembly. The disassembly factors probe large inner and outer spliceosome surfaces to detect the release of ligated mRNA. Two of these factors, TFIP11 and C19L1, and three general spliceosome subunits, SYF1, SYF2 and SDE2, then dock and activate DHX15 on the catalytic U6 snRNA to initiate disassembly. U6 thus controls both the start 5 and end of pre-mRNA splicing. Taken together, our results explain the molecular basis of canonical spliceosome disassembly and provide a framework to understand general spliceosomal RNA helicase control and the discard of aberrant spliceosomes.


  • Organizational Affiliation

    Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, Vienna, Austria.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PRKR-interacting protein 1A [auth 1]184Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000128563 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Splicing factor ESS-2 homologC [auth 3]476Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000100056 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Protein FAM32AD [auth 32]112Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000105058 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Protein FAM50AF [auth 50]339Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000071859 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
STING ER exit proteinG [auth 56]222Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000018610 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic initiation factor 4A-IIII [auth 7]411Homo sapiensMutation(s): 0 
EC: 3.6.4.13
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GTEx:  ENSG00000141543 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
RNA-binding protein 8AJ [auth 8]174Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000265241 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Protein mago nashi homologK [auth 9]146Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000162385 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-processing-splicing factor 8L [auth A]2,335Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000174231 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
U5 small nuclear ribonucleoprotein 200 kDa helicaseM [auth B]2,136Homo sapiensMutation(s): 0 
EC: 3.6.4.13
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GTEx:  ENSG00000144028 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
116 kDa U5 small nuclear ribonucleoprotein componentN [auth C]972Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000108883 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor ISY1 homologO [auth D]285Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000240682 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
U5 small nuclear ribonucleoprotein 40 kDa proteinP [auth E]357Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000060688 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Splicing factor CactinR [auth F]758Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000105298 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor CWC22 homologS [auth H]908Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000163510 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SYF1T [auth I]855Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000076924 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Crooked neck-like protein 1V [auth J]848Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000101343 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SPF27W [auth K]225Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000116752 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Cell division cycle 5-like proteinX [auth L]802Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000096401 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SYF2Y [auth M]243Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000117614 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Protein BUD31 homologZ [auth N]144Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000106245 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Nitric oxide synthase-interacting proteinAA [auth NO]301Homo sapiensMutation(s): 0 
EC: 2.3.2.27
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GTEx:  ENSG00000142546 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor RBM22BA [auth O]420Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000086589 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Spliceosome-associated protein CWC15 homologCA [auth P]229Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000150316 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
Intron-binding protein aquariusDA [auth Q]1,485Homo sapiensMutation(s): 0 
EC: 3.6.4.13
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GTEx:  ENSG00000021776 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
SNW domain-containing protein 1EA [auth R]536Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000100603 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomerase-like 1FA [auth S]166Homo sapiensMutation(s): 0 
EC: 5.2.1.8
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GTEx:  ENSG00000137168 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/arginine repetitive matrix protein 2GA [auth SR]2,752Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000167978 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
Pleiotropic regulator 1HA [auth T]514Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000171566 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SLU7IA [auth U]586Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000164609 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
ATP-dependent RNA helicase DHX8JA [auth V]1,220Homo sapiensMutation(s): 0 
EC: 3.6.4.13
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GTEx:  ENSG00000067596 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-processing factor 17KA [auth W]579Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000168438 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
Splicing regulator SDE2LA [auth X]451Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000143751 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
Coiled-coil domain-containing protein 12MA [auth Z]166Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000160799 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D3NA [auth a],
UA [auth h]
126Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000100028 
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UniProt GroupP62318
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein-associated proteins B and B'OA [auth b],
VA [auth i]
240Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000125835 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D1PA [auth c],
WA [auth j]
119Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000167088 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D2QA [auth d],
XA [auth k]
118Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000125743 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein ERA [auth e],
YA [auth l]
92Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000182004 
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UniProt GroupP62304
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein FSA [auth f],
ZA [auth m]
86Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000139343 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein GAB [auth n],
TA [auth g]
76Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000143977 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
U2 small nuclear ribonucleoprotein A'BB [auth o]255Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000131876 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
U2 small nuclear ribonucleoprotein B''CB [auth p]225Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000125870 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-processing factor 19DB [auth q],
EB [auth r],
FB [auth s],
GB [auth t]
504Homo sapiensMutation(s): 0 
EC: 2.3.2.27
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Find proteins for Q9UMS4 (Homo sapiens)
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GTEx:  ENSG00000110107 
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
Peptidylprolyl isomerase domain and WD repeat-containing protein 1HB [auth w]646Homo sapiensMutation(s): 0 
EC: 5.2.1.8
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Find proteins for Q96BP3 (Homo sapiens)
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GTEx:  ENSG00000113593 
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
Splicing factor C9orf78IB [auth x]289Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000136819 
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomerase EJB [auth y]301Homo sapiensMutation(s): 0 
EC: 5.2.1.8
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Find proteins for Q9UNP9 (Homo sapiens)
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GTEx:  ENSG00000084072 
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
NF-kappa-B-activating proteinKB [auth z]415Homo sapiensMutation(s): 0 
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Find proteins for Q8N5F7 (Homo sapiens)
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GTEx:  ENSG00000101882 
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Entity ID: 2
MoleculeChains LengthOrganismImage
U2 snRNAB [auth 2]187Homo sapiens
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Entity ID: 5
MoleculeChains LengthOrganismImage
U5 snRNAE [auth 5]116Homo sapiens
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Entity ID: 8
MoleculeChains LengthOrganismImage
U6 snRNAH [auth 6]106Homo sapiens
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Entity ID: 17
MoleculeChains LengthOrganismImage
ExonQ [auth EX]14Human adenovirus 2
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Entity ID: 21
MoleculeChains LengthOrganismImage
INTRONU [auth IN]113Human adenovirus 2
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Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
IHP
Query on IHP

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AC [auth U]INOSITOL HEXAKISPHOSPHATE
C6 H18 O24 P6
IMQLKJBTEOYOSI-GPIVLXJGSA-N
GTP
Query on GTP

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TB [auth C]GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
ATP
Query on ATP

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SB [auth 7]ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
ZN
Query on ZN

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UB [auth N]
VB [auth N]
WB [auth N]
XB [auth O]
YB [auth O]
UB [auth N],
VB [auth N],
WB [auth N],
XB [auth O],
YB [auth O],
ZB [auth O]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
K
Query on K

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PB [auth 6]POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG
Query on MG

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LB [auth 6]
MB [auth 6]
NB [auth 6]
OB [auth 6]
QB [auth 6]
LB [auth 6],
MB [auth 6],
NB [auth 6],
OB [auth 6],
QB [auth 6],
RB [auth 7]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
SEP
Query on SEP
EA [auth R]L-PEPTIDE LINKINGC3 H8 N O6 PSER
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)European Union--

Revision History  (Full details and data files)

  • Version 1.0: 2024-07-10
    Type: Initial release