Structure of PDB 5gmk Chain A

Receptor sequence

>5gmkA (length=1910) Species: 559292 (Saccharomyces cerevisiae S288C)

LYTPKAEMPPEHLRKIINTHSDMASKMYNTDKKAFLGALKYLPHAILKLL
ENMPHPWEQAKEVKVLYHTSGAITFVNETPRVIEPVYTAQWSATWIAMRR
EKRDRTHFKRMRFPPFDDDEPPLSYEQHIENIEPLDPINLPLDSQDDEYV
KDWLYDSRPLEEDSKKVNGTSYKKWSFDLPEMSNLYRLSTPLRDEVTDKN
YYYLFDKKSFFNGKALNNAIPGGPKFEPLYPREEEEDYNEFNSIDRVIFR
VPIRSEYKVAFPHLYNSRPRSVRIPWYNNPVSCIIQNDEEYDTPALFFDP
SLNPIGDFTLPEDFAPLLAEEEELILPNTKDAMSLYHSPFPFNRTKGKMV
RAQDVALAKKWFLQHPDEEYPVKVKVSYQKLLKNYVLNELHPTLPTNHNK
TKLLKSLKNTKYFQQTTIDWVEAGLQLCRQGHNMLNLLIHRKGLTYLHLD
YNFNLKPTKTLTTKERKKSRLGNSFHLMRELLKMMKLIVDTHVQFRLGNV
DAFQLADGIHYILNHIGQLTGIYRYKYKVMHQIRACKDLKHIIYYKFNKN
LGKGPGCGFWQPAWRVWLNFLRGTIPLLERYIGNLITRQFEGRSNEIVKT
TTKQRLDAYYDLELRNSVMDDILEMMPESIRQKKARTILQHLSEAWRCWK
ANIPWDVPGMPAPIKKIIERYIKSKADAWVSAAHYNRERIKRGAHVEKTM
VKKNLGRLTRLWIKNEQERQRQIQKNGPEITPEEATTIFSVMVEWLESRS
FSPIPFPPLTYKNDTKILVLALEDLKDVYASKVRLNASEREELALIEEAY
DNPHDTLNRIKKYLLTQRVFKPVDITMMENYQNISPVYSVDPLEKITDAY
LDQYLWYEADQRKLFPNWIKPSDSEIPPLLVYKWTQGINNLSEIWDVSRG
QSAVLLETTLGEMAEKIDFTLLNRLLRLIVDPNIADYITAKNNVVINFKD
MSHVNKYGLIRGLKFASFIFQYYGLVIDLLLLGQERATDLAGPANNPNEF
MQFKSKEVEKAHPIRLYTRYLDRIYMLFHFEEDEGEELTDEYLAENPDPN
FENSIGYNNRKCWPKDSRMRLIRQDVNLGRAVFWEIQSRVPTSLTSIKWE
NAFVSVYSKNNPNLLFSMCGFEVRILPRQRMEEVVSNDEGVWDLVDERTK
QRTAKAYLKVSEEEIKKFDSRIRGILMASGSTTFTKVAAKWNTSLISLFT
YFREAIVATEPLLDILVKGETRIQNRVKLGLNSKMPTRFPPAVFYTPKEL
GGLGMISASHILIPASDLSWSKQTDTGITHFRAGMTHEDEKLIPTIFRYI
TTWENEFLDSQRVWAEYATKRQEAIQQNRRLAFEELEGSWDRGIPRISTL
FQRDRHTLAYDRGHRIRREFKQYSLERNSPFWWTNSHHDGKLWNLNAYRT
DVIQALGGIETILEHTLFKGTGFNSWEGLFWEKSQIPNRRFTLWWSPTIN
RANVYVGFLVQLDLTGIFLHGKIPTLKISLIQIFRAHLWQKIHESIVFDI
CQILDGELDVLQIESVTKETVHPRKSYKMNSSAADITMESVHEWEVSKPS
LLHETNDSFKGLITNKMWFDVQLRYGDYDSHDISRYVRAKFLDYTTDNVS
MYPSPTGVMIGIDLAYNMYDAYGNWFNGLKPLIQNSMRTIMKANPALYVL
RERIRKGLQIYQSSYAELFNNDIKLFVDDTNVYRVTVHKTFEGNVATKAI
NGCIFTLNPKTGHLFLKIIHTSVWAGQKRLSQLAKWKTAEEVSALVRSLP
KEEQPKQIIVTRKAMLDPLEVHMLDFPNIAIRPTELRLPFSAAMSIDKLS
DVVMKATEPQMVLFNIYDDWLDRISSYTAFSRLTLLLRALKTNEESAKMI
LLSDPTITIKSYHLWPSFTDEQWITIESQMRDLILTEYGRKYNVNISALT
QTEIKDIILG

3D structure

• PDB: 5gmk Structure of a yeast catalytic step I spliceosome at 3.4 angstrom resolution
• Chain: A
• Resolution: 3.4 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 K190 T205 R284 T296 S297 K333 K340 F352 E353 L355 W402 F484 R488 R495 D498 K503 N532 H535 L538 P539 N541 K546 K549 K670 Y671 K672 H675 R709 N713 R716 G717 P720 L721 H839 K842	Y2 K64 T79 R158 T170 S171 K207 K214 F226 E227 L229 W276 F340 R344 R351 D354 K359 N388 H391 L394 P395 N397 K402 K405 K526 Y527 K528 H531 R565 N569 R572 G573 P576 L577 H695 K698
BS02	rna	A	K152 M153 K586 K608 E609 K611 R614 G616 S618 Y725 N728 R732 R737 T744 Q748 R749	K26 M27 K442 K464 E465 K467 R470 G472 S474 Y581 N584 R588 R593 T600 Q604 R605
BS03	rna	A	D755 K777 R780 Q784 S787 K794 K846 K847 R851 R854 R928 R934 K1093 D1094 T1327 P1602 N1603 P1639 T1640 I1643 V1870	D611 K633 R636 Q640 S643 K650 K702 K703 R707 R710 R784 R790 K949 D950 T1183 P1437 N1438 P1474 T1475 I1478 V1695
BS04	rna	A	S925 M972 A1322 T1337 R1521 P1524 K1535 R1650 K1903 R1904 S1906 Q1907	S781 M828 A1178 T1193 R1377 P1380 K1391 R1485 K1728 R1729 S1731 Q1732
BS05	rna	A	K351 E512 V520 Q523 K524 R614 Y667 Y671 S1377 K1378 M1379 P1380 T1430 Y1620 K1637	K225 E368 V376 Q379 K380 R470 Y523 Y527 S1233 K1234 M1235 P1236 T1286 Y1455 K1472
BS06	rna	A	T607 R610	T463 R466
BS07	peptide	A	N343 N344 P347 F352 P354 E359 E382 K1362 T1365 D1411 T1423 H1424 F1425 R1426 A1427	N217 N218 P221 F226 P228 E233 E256 K1218 T1221 D1267 T1279 H1280 F1281 R1282 A1283

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:5gmk, PDBe:5gmk, PDBj:5gmk
• PDBsum: 5gmk
• PubMed: 27445308
• UniProt: P33334|PRP8_YEAST Pre-mRNA-splicing factor 8 (Gene Name=PRP8)