Structure of PDB 5gap Chain A

Receptor sequence
>5gapA (length=1349) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence]
DAYYDLELRNSVMDDILEMMPESIRQKKARTILQHLSEAWRCWKANIPWD
VPGMPAPIKKIIERYIKSKADAWVSAAHYNRERIKRGAHVEKTMVKKNLG
RLTRLWIKNEQERQRQIQKNGPEITPEEATTIFSVMVEWLESRSFSPIPF
PPLTYKNDTKILVLALEDLKDVYASKVRLNASEREELALIEEAYDNPHDT
LNRIKKYLLTQRVFKPVDITMMENYQNISPVYSVDPLEKITDAYLDQYLW
YEADQRKLFPNWIKPSDSEIPPLLVYKWTQGINNLSEIWDVSRGQSAVLL
ETTLGEMAEKIDFTLLNRLLRLIVDPNIADYITAKNNVVINFKDMSHVNK
YGLIRGLKFASFIFQYYGLVIDLLLLGQERATDLAGPANNPNEFMQFKSK
EVEKAHPIRLYTRYLDRIYMLFHFEEDEGEELTDEYLAENPDPNFENSIG
YNNRKCWPKDSRMRLIRQDVNLGRAVFWEIQSRVPTSLTSIKWENAFVSV
YSKNNPNLLFSMCGFEVRILPRQRMEEVVSNDEGVWDLVDERTKQRTAKA
YLKVSEEEIKKFDSRIRGILMASGSTTFTKVAAKWNTSLISLFTYFREAI
VATEPLLDILVKGETRIQNRVKLGLNSKMPTRFPPAVFYTPKELGGLGMI
SASHILIPASDLSWSKQTDTGITHFRADEKLIPTIFRYITTWENEFLDSQ
RVWAEYATKRQEAIQQNRRLAFEELEGSWDRGIPRISTLFQRDRHTLAYD
RGHRIRREFKQYSLERNSPFWWTNSHHDGKLWNLNAYRTDVIQALGGIET
ILEHTLFKGTGFNSWEGLFWEKASGFEDSMQFKKLTHAQRTGLSQIPNRR
FTLWWSPTINRANVYVGFLVQLDLTGIFLHGKIPTLKISLIQIFRAHLWQ
KIHESIVFDICQILDGELDVLQIESVTKETVHPRKSYKMNSSAADITMES
VHEWEVSKPSLLHETNDSFKGLITNKMWFDVQLRYGDYDSHDISRYVRAK
FLDYTTDNVSMYPSPTGVMIGIDLAYNMYDAYGNWFNGLKPLIQNSMRTI
MKANPALYVLRERIRKGLQIYQSSVQEPFLNSSNYAELFNNDIKLFVDDT
NVYRVTVHKTFEGNVATKAINGCIFTLNPKTGHLFLKIIHTSVWAGQKRL
SQLAKWKTAEEVSALVRSLPKEEQPKQIIVTRKAMLDPLEVHMLDFPNIA
IRPTELRLPFSAAMSIDKLSDVVMKATEPQMVLFNIYDDWLDRISSYTAF
SRLTLLLRALKTNEESAKMILLSDPTITIKSYHLWPSFTDEQWITIESQM
RDLILTEYGRKYNVNISALTQTEIKDIILGQNIKAPSVKRQKMAELEAA
3D structure
PDB5gap Cryo-EM structure of the yeast U4/U6.U5 tri-snRNP at 3.7 angstrom resolution.
ChainA
Resolution3.6 Å
3D
structure
[Spin on]
[Spin off]
[Reset orientation]

[High quality]
[Low quality]

[White background]
[Black background]

[Download]
[Download structure with residue number starting from 1]
Enzymatic activity
Enzyme Commision number ?
Interaction with ligand
Site
#		 Ligand Ligand
chain		 Binding residues on receptor
(original residue number in PDB)		 Binding residues on receptor
(residue number reindexed from 1)		 Binding affinity
BS01 rna A F1587 K1588 K1589 L2074 F832 K833 K834 L1319
BS02 rna A S1377 K1378 G1622 F1623 V1625 D1628 L1629 G1636 K1637 I1646 Q1647 R1650 A1651 H1652 S627 K628 G867 F868 V870 D873 L874 G881 K882 I891 Q892 R895 A896 H897
BS03 rna A R1366 M1379 R616 M629
Gene Ontology
Molecular Function
GO:0000386 second spliceosomal transesterification activity
GO:0003723 RNA binding
GO:0003729 mRNA binding
GO:0005515 protein binding
GO:0008233 peptidase activity
GO:0008237 metallopeptidase activity
GO:0017070 U6 snRNA binding
GO:0030619 U1 snRNA binding
GO:0030620 U2 snRNA binding
GO:0030623 U5 snRNA binding
GO:0097157 pre-mRNA intronic binding
Biological Process
GO:0000244 spliceosomal tri-snRNP complex assembly
GO:0000350 generation of catalytic spliceosome for second transesterification step
GO:0000387 spliceosomal snRNP assembly
GO:0000389 mRNA 3'-splice site recognition
GO:0000395 mRNA 5'-splice site recognition
GO:0000398 mRNA splicing, via spliceosome
GO:0006397 mRNA processing
GO:0008380 RNA splicing
Cellular Component
GO:0005634 nucleus
GO:0005681 spliceosomal complex
GO:0005682 U5 snRNP
GO:0005737 cytoplasm
GO:0046540 U4/U6 x U5 tri-snRNP complex
GO:0071013 catalytic step 2 spliceosome

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5gap, PDBe:5gap, PDBj:5gap
PDBsum5gap
PubMed26829225
UniProtP33334|PRP8_YEAST Pre-mRNA-splicing factor 8 (Gene Name=PRP8)

[Back to BioLiP]