Structure of PDB 5lqw Chain A

Receptor sequence

>5lqwA (length=2130) Species: 4932 (Saccharomyces cerevisiae)

KAEMPPEHLRKIINTHSDMASKNYNTDKKAFLGALKYLPHAILKLLENMP
HPWEQAKEVKVLYHTSGAITFVNETPRVIEPVYTAQWSATWIAMRREKRD
RTHFKRMRFPPFDDDEPPLSYEQHIENIEPLDPINLPLDSQDDEYVKDWL
YDSRPLEEDSKKVNGTSYKKWSFDLPEMSNLYRLSTPLRDEVTDKNYYYL
FDKKSFFNGKALNNAIPGGPKFEPLYPREEEEDYNEFNSIDRVIFRVPIR
SEYKVAFPHLYNSRPRSVRIPWYNNPVSCIIQNDEEYDTPALFFDPSLEE
EELILPNTKDAMSLYHSPFPFNRTKGKMVRAQDVALAKKWFLQHPDEEYP
VKVKVSYQKLLKNYVLNELHPTLPTNHNKTKLLKSLKNTKYFQQTTIDWV
EAGLQLCRQGHNMLNLLIHRKGLTYLHLDYNFNLKPTKTLTTKERKKSRL
GNSFHLMRELLKMMKLIVDTHVQFRLGNVDAFQLADGIHYILNHIGQLTG
IYRYKYKVMHQIRACKDLKHIIYYKFNKNLGKGPGCGFWQPAWRVWLNFL
RGTIPLLERYIGNLITRQFEGRSNEIVKTTTKQRLDAYYDLELRNSVMDD
ILEMMPESIRQKKARTILQHLSEAWRCWKANIPWDVPGMPAPIKKIIERY
IKSKADAWVSAAHYNRERIKRGAHVEKTMVKKNLGRLTRLWIKNEQERQR
QIQKNGPEITPEEATTIFSVMVEWLESRSFSPIPFPPLTYKNDTKILVLA
LEDLKDVYASKVRLNASEREELALIEEAYDNPHDTLNRIKKYLLTQRVFK
PVDITMMENYQNISPVYSVDPLEKITDAYLDQYLWYEADQRKLFPNWIKP
SDSEIPPLLVYKWTQGINNLSEIWDVSRGQSAVLLETTLGEMAEKIDFTL
LNRLLRLIVDPNIADYITAKNNVVINFKDMSHVNKYGLIRGLKFASFIFQ
YYGLVIDLLLLGQERATDLAGPANNPNEFMQFKSKEVEKAHPIRLYTRYL
DRIYMLFHFEEDEGEELTDEYLAENPDPNFENSIGYNNRKCWPKDSRMRL
IRQDVNLGRAVFWEIQSRVPTSLTSIKWENAFVSVYSKNNPNLLFSMCGF
EVRILPRQRMEEVVSNDEGVWDLVDERTKQRTAKAYLKVSEEEIKKFDSR
IRGILMASGSTTFTKVAAKWNTSLISLFTYFREAIVATEPLLDILVKGET
RIQNRVKLGLNSKMPTRFPPAVFYTPKELGGLGMISASHILIPAEKLIPT
IFRYITTWENEFLDSQRVWAEYATKRQEAIQQNRRLAFEELEGSWDRGIP
RISTLFQRDRHTLAYDRGHRIRREFKQYSLERNSPFWWTNSHHDGKLWNL
NAYRTDVIQALGGIETILEHTLFKGTGFNSWEGLFWEKASGFEDSMQFKK
LTHAQRTGLSQIPNRRFTLWWSPTINRANVYVGFLVQLDLTGIFLHGKIP
TLKISLIQIFRAHLWQKIHESIVFDICQILDGELDVLQIESVTKETVHPR
KSYKMNSSAADITMESWEVSKPSLLHETNDSLITNKMWFDVQLRYGDYDS
HDISRYVRAKFLDYTTDNVSMYPSPTGVMIGIDLAYNMYDAYGNWFNGLK
PLIQNSMRTIMKANPALYVLRERIRKGLQIYQSPFLNSSNYAELFNNDIK
LFVDDTNVYRVTVHKTFEGNVATKAINGCIFTLNPKTGHLFLKIIHTSVW
AGQKRLSQLAKWKTAEEVSALVRSLPKEEQPKQIIVTRKAMLDPLEVHML
DFPNIAIRPTELRLPFSAAMSIDKLSDVVMKATEPQMVLFNIYDDWLDRI
SSYTAFSRLTLLLRALKTNEESAKMILLSDPTITIKSYHLWPSFTDEQWI
TIESQMRDLILTEYGRKYNVNISALTQTESKNEWRKSAIANTLLYLRLKN
IYVSADDFVEEQNVYVLPKNLLKKFIEISDVKIQVAAFIYGMSAKDHPKV
KEIKTVVLVPQLGHVGSVQISNIPDIGDLPDTEGLELLGWIHTQTEELKF
MAASEVATHSKLFADKKRDCIDISIFSTPGSVSLSAYNLTDEGYQWGEEN
KDIMNVLSEGFEPTFSTHAQLLLSDRITGNFIIPSGNVWNYTFMGTAFNQ
EGDYNFKYGIPLEFYNEMHRPVHFLQFSEL

3D structure

• PDB: 5lqw Molecular architecture of the Saccharomyces cerevisiae activated spliceosome
• Chain: A
• Resolution: 5.8 Å

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	K847 G850 K1093 D1094	K682 G685 K928 D929
BS02	rna	A	E204 G295 S297 F352 E353 L355 F484 P485 N532 Y671 K672 N713 F714 G717 V840 E841	E74 G165 S167 F222 E223 L225 F319 P320 N367 Y506 K507 N548 F549 G552 V675 E676
BS03	rna	A	N728 V742 T744 T746 R749 A752	N563 V577 T579 T581 R584 A587
BS04	rna	A	R668 S1377 K1378 M1379	R503 S1212 K1213 M1214

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

External links

• PDB: RCSB:5lqw, PDBe:5lqw, PDBj:5lqw
• PDBsum: 5lqw
• PubMed: 27562955
• UniProt: P33334|PRP8_YEAST Pre-mRNA-splicing factor 8 (Gene Name=PRP8)