Structure of PDB 6ff4 Chain A

Receptor sequence

>6ff4A (length=2238) Species: 9606 (Homo sapiens)

SEEKLQEKARKWQQLQAKRYAEKRKVDAQKEDMPPEHVRKIIRDHGDMTN
RKFRHDKRVYLGALKYMPHAVLKLLENMPMPWEQIRDVPVLYHITGAISF
VNEIPWVIEPVYISQWGSMWIMMRREKRDRRHFKRMRFPPFDDEEPPLDY
ADNILDVEPLEAIQLELDPEEDAPVLDWFYDHQPLRDSRKYVNGSTYQRW
QFTLPMMSTLYRLANQLLTDLVDDNYFYLFDLKAFFTSKALNMAIPGGPK
FEPLVRDINLQDEDWNEFNDINKIIIRQPIRTEYKIAFPYLYNNLPHHVH
LTWYHTPNVVFIKTEDPDLPAFYFDPLINPISHRHSVKSQEPLPDDDEEF
ELPEFVEPFLKDTPLYTDNTANGIALLWAPRPFNLRSGRTRRALDIPLVK
NWYREHCPAGQPVKVRVSYQKLLKYYVLNALKHRPPKAQKKRYLFRSFKA
TKFFQSTKLDWVEVGLQVCRQGYNMLNLLIHRKNLNYLHLDYNFNLKPVK
TLTTKERKKSRFGNAFHLCREVLRLTKLVVDSHVQYRLGNVDAFQLADGL
QYIFAHVGQLTGMYRYKYKLMRQIRMCKDLKHLIYYRFNTGPVGKGPGCG
FWAAGWRVWLFFMRGITPLLERWLGNLLARQFEGRHSKGVAKTVTKQRVE
SHFDLELRAAVMHDILDMMPEGIKQNKARTILQHLSEAWRCWKANIPWKV
PGLPTPIENMILRYVKAKADWWTNTAHYNRERIRRGATVDKTVCKKNLGR
LTRLYLKAEQERQHNYLKDGPYITAEEAVAVYTTTVHWLESRRFSPIPFP
PLSYKHDTKLLILALERLKEAYSVKSRLNQSQREELGLIEQAYDNPHEAL
SRIKRHLLTQRAFKEVGIEFMDLYSHLVPVYDVEPLEKITDAYLDQYLWY
EADKRRLFPPWIKPADTEPPPLLVYKWCQGINNLQDVWETSEGECNVMLE
SRFEKMYEKIDLTLLNRLLRLIVDHNIADYMTAKNNVVINYKDMNHTNSY
GIIRGLQFASFIVQYYGLVMDLLVLGLHRASEMAGPPQMPNDFLSFQDIA
TEAAHPIRLFCRYIDRIHIFFRFTADEARDLIQRYLTEHPDPNNENIVGY
NNKKCWPRDARMRLMKHDVNLGRAVFWDIKNRLPRSVTTVQWENSFVSVY
SKDNPNLLFNMCGFECRILPKCRTSYEEFTHKDGVWNLQNEVTKERTAQC
FLRVDDESMQRFHNRVRQILMASGSTTFTKIVNKWNTALIGLMTYFREAV
VNTQELLDLLVKCENKIQTRIKIGLNSKMPSRFPPVVFYTPKELGGLGML
SMGHVLIPQSDLRWSKQTDVGITHFRSGMSHEEDQLIPNLYRYIQPWESE
FIDSQRVWAEYALKRQEAIAQNRRLTLEDLEDSWDRGIPRINTLFQKDRH
TLAYDKGWRVRTDFKQYQVLKQNPFWWTHQRHDGKLWNLNNYRTDMIQAL
GGVEGILEHTLFKGTYFPTWEGLFWEKASGFEESMKWKKLTNAQRSGLNQ
IPNRRFTLWWSPTINRANVYVGFQVQLDLTGIFMHGKIPTLKISLIQIFR
AHLWQKIHESIVMDLCQVFDQELDALEIETVQKETIHPRKSYKMNSSCAD
ILLFASYKWNVSRPSLLADSKDVMDSTTTQKYWIDIQLRWGDYDSHDIER
YARAKFLDYTTDNMSIYPSPTGVLIAIDLAYNLHSAYGNWFPGSKPLIQQ
AMAKIMKANPALYVLRERIRKGLQLYSSEPTEPYLSSQNYGELFSNQIIW
FVDDTNVYRVTIHKTFEGNLTTKPINGAIFIFNPRTGQLFLKIIHTSVWA
GQKRLGQLAKWKTAEEVAALIRSLPVEEQPKQIIVTRKGMLDPLEVHLLD
FPNIVIKGSELQLPFQACLKVEKFGDLILKATEPQMVLFNLYDDWLKTIS
SYTAFSRLILILRALHVNNDRAKVILKPDKTTITEPHHIWPTLTDEEWIK
VEVQLKDLILADYGKKNNVNVASLTQSEIRDIILGMEIFSSKTEWRVRAI
SAANLHLRTNHIYVSSDDIKETGYTYILPKNVLKKFICISDLRAQIAGYL
YGVSPPDNPQVKEIRCIVMVPQWGTHQTVHLPGQLPQHEYLKEMEPLGWI
HTQPNESPQLSPQDVTTHAKIMADNPSWDGEKTIIITCSFTPGSCTLTAY
KLTPSGYEWGRQNTDKGNNPKGYLPSHYERVQMLLSDRFLGFFMVPAQSS
WNYNFMGVRHDPNMKYELQLANPKEFYHEVHRPSHFLN

3D structure

• PDB: 6ff4 Structure and Conformational Dynamics of the Human Spliceosomal BactComplex.
• 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	D682 R686 W717 K721 K774 R778 R781 L856 N857 Q858 R861 K1020 D1021 W1515 R1523	D654 R658 W689 K693 K746 R750 R753 L828 N829 Q830 R833 K992 D993 W1487 R1495
BS02	rna	A	A56 H97 G222 S223 T224 K267 E280 R409 R417 R419 R420 D423 P425 K428 K452 N457 H461 P464 K469 R470 R474 K595 Y596 K597 R600 Q601 R635 F639 R642 G643 P646 L647 V767 D768 K769 R1298	A28 H69 G194 S195 T196 K239 E252 R381 R389 R391 R392 D395 P397 K400 K424 N429 H433 P436 K441 R442 R446 K567 Y568 K569 R572 Q573 R607 F611 R614 G615 P618 L619 V739 D740 K741 R1270
BS03	rna	A	R35 E534 K536 K537 R539 G541 A543 W651 N654 R658 R663 K666 K670 T673 Q675 R676 S679 T1519 N1520	R10 E506 K508 K509 R511 G513 A515 W623 N626 R630 R635 K638 K642 T645 Q647 R648 S651 T1491 N1492
BS04	rna	A	R82 H83 K85 K278 V441 N512 T532 R535 R539 Y592 R593 N1304 S1305 K1306 S1358	R54 H55 K57 K250 V413 N484 T504 R507 R511 Y564 R565 N1276 S1277 K1278 S1330
BS05	IHP	A	R163 K442 H584 K609 H610 Y613 Y614 K623	R135 K414 H556 K581 H582 Y585 Y586 K595

Gene Ontology

Molecular Function

• GO:0003723 RNA 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:0070530 K63-linked polyubiquitin modification-dependent protein binding
• GO:0097157 pre-mRNA intronic binding
• GO:0140492 metal-dependent deubiquitinase activity

Biological Process

• GO:0000244 spliceosomal tri-snRNP complex assembly
• GO:0000375 RNA splicing, via transesterification reactions
• GO:0000398 mRNA splicing, via spliceosome
• GO:0006397 mRNA processing
• GO:0008380 RNA splicing
• GO:0071222 cellular response to lipopolysaccharide
• GO:0071356 cellular response to tumor necrosis factor

Cellular Component

• GO:0005634 nucleus
• GO:0005654 nucleoplasm
• GO:0005681 spliceosomal complex
• GO:0005682 U5 snRNP
• GO:0016020 membrane
• GO:0016607 nuclear speck
• GO:0030532 small nuclear ribonucleoprotein complex
• GO:0046540 U4/U6 x U5 tri-snRNP complex
• GO:0071005 U2-type precatalytic spliceosome
• GO:0071006 U2-type catalytic step 1 spliceosome
• GO:0071007 U2-type catalytic step 2 spliceosome
• GO:0071013 catalytic step 2 spliceosome

External links

• PDB: RCSB:6ff4, PDBe:6ff4, PDBj:6ff4
• PDBsum: 6ff4
• PubMed: 29361316
• UniProt: Q6P2Q9|PRP8_HUMAN Pre-mRNA-processing-splicing factor 8 (Gene Name=PRPF8)