Structure of PDB 5gm6 Chain A

Receptor sequence

>5gm6A (length=2200) Species: 559292 (Saccharomyces cerevisiae S288C)

AYTPKAEMPPEHLRKIINTHSDMASKMYNTDKKAFLGALKYLPHAILKLL
ENMPHPWEQAKEVKVLYHTSGAITFVNETPRVIEPVYTAQWSATWIAMRR
EKRDRTHFKRMRFPPFDDDEPPLSYEQHIENIEPLDPINLPLDSQDDEYV
KDWLYDSRPLEEDSKKVNGTSYKKWSFDLPEMSNLYRLSTPLRDEVTDKN
YYYLFDKKSFFNGKALNNAIPGGPKFEPLYPREEEEDYNEFNSIDRVIFR
VPIRSEYKVAFPHLYNSRPRSVRIPWYNNPVSCIIQNDEEYDTPALFFDP
SLNPIDFTLPEDFAPLLAEEEELILPNTKDAMSLYHSPFPFNRTKGKMVR
AQDVALAKKWFLQHPDEEYPVKVKVSYQKLLKNYVLNELHPTLPTNHNKT
KLLKSLKNTKYFQQTTIDWVEAGLQLCRQGHNMLNLLIHRKGLTYLHLDY
NFNLKPTKTLTTKERKKSRLGNSFHLMRELLKMMKLIVDTHVQFRLGNVD
AFQLADGIHYILNHIGQLTGIYRYKYKVMHQIRACKDLKHIIYYKFNKNL
GKGPGCGFWQPAWRVWLNFLRGTIPLLERYIGNLITRQFEGRSNEIVKTT
TKQRLDAYYDLELRNSVMDDILEMMPESIRQKKARTILQHLSEAWRCWKA
NIPWDVPGMPAPIKKIIERYIKSKADAWVSAAHYNRERIKRGAHVEKTMV
KKNLGRLTRLWIKNEQERQRQIQKNGPEITPEEATTIFSVMVEWLESRSF
SPIPFPPLTYKNDTKILVLALEDLKDVYASKVRLNASEREELALIEEAYD
NPHDTLNRIKKYLLTQRVFKPVDITMMENYQNISPVYSVDPLEKITDAYL
DQYLWYEADQRKLFPNWIKPSDSEIPPLLVYKWTQGINNLSEIWDVSRGQ
SAVLLETTLGEMAEKIDFTLLNRLLRLIVDPNIADYITAKNNVVINFKDM
SHVNKYGLIRGLKFASFIFQYYGLVIDLLLLGQERATDLAGPANNPNEFM
QFKSKEVEKAHPIRLYTRYLDRIYMLFHFEEDEGEELTDEYLAENPDPNF
ENSIGYNNRKCWPKDSRMRLIRQDVNLGRAVFWEIQSRVPTSLTSIKWEN
AFVSVYSKNNPNLLFSMCGFEVRILPRQRMEEVVSNDEGVWDLVDERTKQ
RTAKAYLKVSEEEIKKFDSRIRGILMASGSTTFTKVAAKWNTSLISLFTY
FREAIVATEPLLDILVKGETRIQNRVKLGLNSKMPTRFPPAVFYTPKELG
GLGMISASHILIPASDLSWSKQTDTGITHFRAGMTHEDEKLIPTIFRYIT
TWENEFLDSQRVWAEYATKRQEAIQQNRRLAFEELEGSWDRGIPRISTLF
QRDRHTLAYDRGHRIRREFKQYSLERNSPFWWTNSHHDGKLWNLNAYRTD
VIQALGGIETILEHTLFKGTGFNSWEGLFWEKASGFEDSMQFKKLTHAQR
TGLSQIPNRRFTLWWSPTINRANVYVGFLVQLDLTGIFLHGKIPTLKISL
IQIFRAHLWQKIHESIVFDICQILDGELDVLQIESVTKETVHPRKSYKMN
SSAADITMESVHEWEVSKPSLLHETNDSFKGLITNKMWFDVQLRYGDYDS
HDISRYVRAKFLDYTTDNVSMYPSPTGVMIGIDLAYNMYDAYGNWFNGLK
PLIQNSMRTIMKANPALYVLRERIRKGLQIYQSSVQEPFLNSSNYAELFN
NDIKLFVDDTNVYRVTVHKTFEGNVATKAINGCIFTLNPKTGHLFLKIIH
TSVWAGQKRLSQLAKWKTAEEVSALVRSLPKEEQPKQIIVTRKAMLDPLE
VHMLDFPNIAIRPTELRLPFSAAMSIDKLSDVVMKATEPQMVLFNIYDDW
LDRISSYTAFSRLTLLLRALKTNEESAKMILLSDPTITIKSYHLWPSFTD
EQWITIESQMRDLILTEYGRKYNVNISALTQTEIKDIILGKNEWRKSAIA
NTLLYLRLKNIYVSADDFVEEQNVYVLPKNLLKKFIEISDVKIQVAAFIY
GMSAKDHPKVKEIKTVVLVPQLGHVGSVQISNIPDIGDLPDTEGLELLGW
IHTQTEELKFMAASEVATHSKLFADKKRDCIDISIFSTPGSVSLSAYNLT
DEGYQWGEENKDIMNVLSEGFEPTFSTHAQLLLSDRITGNFIIPSGNVWN
YTFMGTAFNQEGDYNFKYGIPLEFYNEMHRPVHFLQFSEELEAEQIDVFS

3D structure

• PDB: 5gm6 Structure of a yeast activated spliceosome at 3.5 angstrom resolution
• Chain: A
• Resolution: 3.5 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	Y128 P130 K174 K190 T205 R207 R284 T296 S297 K334 K340 E353 L355 R358 W402 F484 R488 R495 K503 K527 N528 N532 H535 P539 N541 K544 K546 K549 K670 Y671 K672 H675 R709 N713 R716 G717 H839	Y2 P4 K48 K64 T79 R81 R158 T170 S171 K208 K214 E227 L229 R232 W276 F339 R343 R350 K358 K382 N383 N387 H390 P394 N396 K399 K401 K404 K525 Y526 K527 H530 R564 N568 R571 G572 H694
BS02	rna	A	K586 E609 K611 R614 G616 S618 Y725 N728 R732 R737 T744 Q748 R749 Y753 L756 T1591 H1592	K441 E464 K466 R469 G471 S473 Y580 N583 R587 R592 T599 Q603 R604 Y608 L611 T1446 H1447
BS03	rna	A	D755 K777 Q784 S787 K847 R851 R854 N930 K1093 D1094 F1587 K1588 R1595	D610 K632 Q639 S642 K702 R706 R709 N785 K948 D949 F1442 K1443 R1450
BS04	rna	A	K351 T607 R610 R614 R668 Y671 S1377 K1378 M1379 Y1620 K1637	K225 T462 R465 R469 R523 Y526 S1232 K1233 M1234 Y1475 K1492
BS05	peptide	A	N343 N344 P357 E359 R380 S381 K1362 T1365 D1411 I1422 H1424 F1425 R1426 A1427 G1428	N217 N218 P231 E233 R254 S255 K1217 T1220 D1266 I1277 H1279 F1280 R1281 A1282 G1283

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:5gm6, PDBe:5gm6, PDBj:5gm6
• PDBsum: 5gm6
• PubMed: 27445306
• UniProt: P33334|PRP8_YEAST Pre-mRNA-splicing factor 8 (Gene Name=PRP8)