9FMD: PRKR-interacting protein 1

Integrative model of the human post-catalytic spliceosome (P-complex). Determined by electron microscopy at 3.3 Å resolution. Released 10 Jul 2024.

Method: Electron microscopy
Resolution: 3.3 Å
Organisms: Homo sapiens, Human adenovirus 2
Chains: 63
Atoms: 120,489
Mol. weight: 3373.4 kDa
Ligands: MG, ATP, GTP, ZN
Released: 10 Jul 2024

Explore 9FMD in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9FMD contains 771 α-helices and 642 β-strands across 58 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain 1: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	27-39	13
α-helix	56-61	6
α-helix	80-93	14
α-helix	98-140	43

Chain 3: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	37-38	2	16
α-helix	40-55	16
α-helix	58-74	17
α-helix	77-86	10
α-helix	149-154	6
β-strand	156-157	2	16
α-helix	158-176	19

Chain 32: 6 helices, 0 β-strands

Element	Residues	Length
α-helix	55-59	5
α-helix	60-71	12
α-helix	73-80	8
α-helix	85-97	13
α-helix	105-107	3
α-helix	108-110	3

Chain 50: 9 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	72-118	47
α-helix	171-196	26
β-strand	198-206	9	36
β-strand	210-218	9	36
β-strand	222	1	37
α-helix	223-234	12
α-helix	240-243	4
α-helix	246-248	3
β-strand	249-253	5	36
β-strand	256-258	3	36
β-strand	263	1	37
α-helix	264-270	7
β-strand	273-274	2	38
β-strand	277-278	2	38
β-strand	289	1	39
α-helix	302-303	2
β-strand	304-308	5	36
α-helix	309-315	7
α-helix	321-323	3
β-strand	325-326	2	36

Chain 56: 2 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	28-32	5	45
β-strand	37-41	5	45
α-helix	45-47	3
β-strand	50	1	46
β-strand	57-60	4	46
β-strand	66-68	3	45
β-strand	71-81	11	46
β-strand	84-93	10	46
β-strand	99-103	5	46
β-strand	111-114	4	46
α-helix	115	1
β-strand	119-120	2	45

Chain 7: 20 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	40-42	3
α-helix	47-56	10
α-helix	63-73	11
β-strand	78-81	4	67
α-helix	88-98	11
β-strand	109-112	4	67
α-helix	116-129	14
α-helix	131-133	3
β-strand	137-140	4	67
α-helix	146-155	10
β-strand	159-162	4	67
α-helix	164-172	9
β-strand	183-187	5	67
α-helix	189-192	4
α-helix	198-205	8
β-strand	213-218	6	67
α-helix	223-226	4
α-helix	229-231	3
β-strand	237-239	3	67
α-helix	243-245	3
β-strand	251-258	8	68
α-helix	263-271	9
β-strand	279-283	5	68
α-helix	287-298	12
β-strand	305-306	2	68
α-helix	313-324	12
β-strand	330-333	4	68
α-helix	335-337	3
β-strand	346-351	6	68
α-helix	358-365	8
α-helix	370-372	3
β-strand	375-382	8	68
α-helix	386-396	11
β-strand	400-402	3	68

Chain 8: 4 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	66	1	71
β-strand	73-78	6	72
α-helix	86-93	8
α-helix	94-96	3
β-strand	101-103	3	72
β-strand	106	1	73
β-strand	113	1	73
α-helix	114	1
β-strand	116-121	6	72
α-helix	124-134	11
β-strand	138	1	74
β-strand	143	1	74
β-strand	145-148	4	72
β-strand	150-151	2	71

Chain 9: 9 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	7-17	11	71
β-strand	20-28	9	71
β-strand	33-39	7	71
α-helix	42-44	3
β-strand	48-54	7	71
α-helix	55	1
α-helix	56-69	14
α-helix	71-73	3
α-helix	76-78	3
α-helix	80-82	3
β-strand	87-94	8	71
β-strand	97-103	7	71
α-helix	109-114	6
α-helix	118-143	26
α-helix	145-146	2

50 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
PRKR-interacting protein 1	1	protein	184	Homo sapiens	Q9H875 (AlphaFold model)
U2 snRNA	2	RNA	187	Homo sapiens
Splicing factor ESS-2 homolog	3	protein	476	Homo sapiens	Q96DF8 (AlphaFold model)
Protein FAM32A	32	protein	112	Homo sapiens	Q9Y421 (AlphaFold model)
U5 snRNA	5	RNA	116	Homo sapiens
Protein FAM50A	50	protein	339	Homo sapiens	Q14320 (AlphaFold model)
STING ER exit protein	56	protein	222	Homo sapiens	Q9H5V9
U6 snRNA	6	RNA	106	Homo sapiens
Eukaryotic initiation factor 4A-III	7	protein	411	Homo sapiens	P38919
RNA-binding protein 8A	8	protein	174	Homo sapiens	Q9Y5S9
Protein mago nashi homolog	9	protein	146	Homo sapiens	P61326
Pre-mRNA-processing-splicing factor 8	A	protein	2335	Homo sapiens	Q6P2Q9

41 more molecules are not listed.

Sequence of entity 1 (1), FASTA

>9FMD_1 PRKR-interacting protein 1 (chains 1)
MASPAASSVRPPRPKKEPQTLVIPKNAAEEQKLKLERLMKNPDKAVPIPEKMSEWAPRPP
PEFVRDVMGSSAGAGSGEFHVYRHLRRREYQRQDYMDAMAEKQKLDAEFQKRLEKNKIAA
EEQTAKRRKKRQKLKEKKLLAKKMKLEQKKQEGPGQPKEQGSSSSAEASGTEEEEEVPSF
TMGR

Sequence of entity 2 (2), FASTA

>9FMD_2 U2 snRNA (chains 2)
AUCGCUUCUCGGCCUUUUGGCUAAGAUCAAGUGUAGUAUCUGUUCUUAUCAGUUUAAUAU
CUGAUACGUCCUCUAUCCGAGGACAAUAUAUUAAAAGAUUUUUGGAACUGGGAGAUGGAA
UAGGAGCUUGCUCCGUCCACUCCACGCAUCGACCUGGUAUUGCAGUACCUCCAGGAACGG
UGCACCC

Sequence of entity 3 (3), FASTA

>9FMD_3 Splicing factor ESS-2 homolog (chains 3)
METPGASASSLLLPAASRPPRKREAGEAGAATSKQRVLDEEEYIEGLQTVIQRDFFPDVE
KLQAQKEYLEAEENGDLERMRQIAIKFGSALGKMSREPPPPYVTPATFETPEVHAGTGVV
GNKPRPRGRGLEDGEAGEEEEKEPLPSLDVFLSRYTSEDNASFQEIMEVAKERSRARHAW
LYQAEEEFEKRQKDNLELPSAEHQAIESSQASVETWKYKAKNSLMYYPEGVPDEEQLFKK
PRQVVHKNTRFLRDPFSQALSRCQLQQAAALNAQHKQGKVGPDGKELIPQESPRVGGFGF
VATPSPAPGVNESPMMTWGEVENTPLRVEGSETPYVDRTPGPAFKILEPGRRERLGLKMA
NEAAAKNRAKKQEALRRVTENLASLTPKGLSPAMSPALQRLVSRTASKYTDRALRASYTP
SPARSTHLKTPASGLQTPTSTPAPGSATRTPLTQDPASITDNLLQLPARRKASDFF

Sequence of entity 4 (32), FASTA

>9FMD_4 Protein FAM32A (chains 32)
MEAYEQVQKGPLKLKGVAELGVTKRKKKKKDKDKAKLLEAMGTSKKNEEEKRRGLDKRTP
AQAAFEKMQEKRQMERILKKASKTHKQRVEDFNRHLDTLTEHYDIPKVSWTK

Sequence of entity 5 (5), FASTA

>9FMD_5 U5 snRNA (chains 5)
AUACUCUGGUUUCUCUUCAGAUCGCAUAAAUCUUUCGCCUUUUACUAAAGAUUUCCGUGG
AGAGGAACAACUCUGAGUCUUAACCCAAUUUUUUGAGCCUUGCCUUGGCAAGGCUA

Sequence of entity 6 (50), FASTA

>9FMD_6 Protein FAM50A (chains 50)
MAQYKGAASEAGRAMHLMKKREKQREQMEQMKQRIAEENIMKSNIDKKFSAHYDAVEAEL
KSSTVGLVTLNDMKAKQEALVKEREKQLAKKEQSKELQMKLEKLREKERKKEAKRKISSL
SFTLEEEEEGGEEEEEAAMYEEEMEREEITTKKRKLGKNPDVDTSFLPDRDREEEENRLR
EELRQEWEAKQEKIKSEEIEITFSYWDGSGHRRTVKMRKGNTMQQFLQKALEILRKDFSE
LRSAGVEQLMYIKEDLIIPHHHSFYDFIVTKARGKSGPLFNFDVHDDVRLLSDATVEKDE
SHAGKVVLRSWYEKNKHIFPASRWEPYDPEKKWDKYTIR

Sequence of entity 7 (56), FASTA

>9FMD_7 STING ER exit protein (chains 56)
MPKVVSRSVVCSDTRDREEYDDGEKPLHVYYCLCGQMVLVLDCQLEKLPMRPRDRSRVID
AAKHAHKFCNTEDEETMYLRRPEGIERQYRKKCAKCGLPLFYQSQPKNAPVTFIVDGAVV
KFGQGFGKTNIYTQKQEPPKKVMMTKRTKDMGKFSSVTVSTIDEEEEEIEAREVADSYAQ
NAKVIEKQLERKGMSKRRLQELAELEAKKAKMKGTLIDNQFK

Sequence of entity 8 (6), FASTA

>9FMD_8 U6 snRNA (chains 6)
GUGCUCGCUUCGGCAGCACAUAUACUAAAAUUGGAACGAUACAGAGAAGAUUAGCAUGGC
CCCUGCGCAAGGAUGACACGCAAAUUCGUGAAGCGUUCCAUAUUUU

Sequence of entity 9 (7), FASTA

>9FMD_9 Eukaryotic initiation factor 4A-III (chains 7)
MATTATMATSGSARKRLLKEEDMTKVEFETSEEVDVTPTFDTMGLREDLLRGIYAYGFEK
PSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQVRETQALILAPTRELAV
QIQKGLLALGDYMNVQCHACIGGTNVGEDIRKLDYGQHVVAGTPGRVFDMIRRRSLRTRA
IKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQVVLISATLPHEILEMTNKFMTDPIRIL
VKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKVDWLTEKMREA
NFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLIINYDLPNNREL
YIHRIGRSGRYGRKGVAINFVKNDDIRILRDIEQYYSTQIDEMPMNVADLI

Sequence of entity 10 (8), FASTA

>9FMD_10 RNA-binding protein 8A (chains 8)
MADVLDLHEAGGEDFAMDEDGDESIHKLKEKAKKRKGRGFGSEEGSRARMREDYDSVEQD
GDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVE
YETYKEAQAAMEGLNGQDLMGQPISVDWCFVRGPPKGKRRGGRRRSRSPDRRRR

Sequence of entity 11 (9), FASTA

>9FMD_11 Protein mago nashi homolog (chains 9)
MESDFYLRYYVGHKGKFGHEFLEFEFRPDGKLRYANNSNYKNDVMIRKEAYVHKSVMEEL
KRIIDDSEITKEDDALWPPPDRVGRQELEIVIGDEHISFTTSKIGSLIDVNQSKDPEGLR
VFYYLVQDLKCLVFSLIGLHFKIKPI

Sequence of entity 12 (A), FASTA

>9FMD_12 Pre-mRNA-processing-splicing factor 8 (chains A)
MAGVFPYRGPGNPVPGPLAPLPDYMSEEKLQEKARKWQQLQAKRYAEKRKFGFVDAQKED
MPPEHVRKIIRDHGDMTNRKFRHDKRVYLGALKYMPHAVLKLLENMPMPWEQIRDVPVLY
HITGAISFVNEIPWVIEPVYISQWGSMWIMMRREKRDRRHFKRMRFPPFDDEEPPLDYAD
NILDVEPLEAIQLELDPEEDAPVLDWFYDHQPLRDSRKYVNGSTYQRWQFTLPMMSTLYR
LANQLLTDLVDDNYFYLFDLKAFFTSKALNMAIPGGPKFEPLVRDINLQDEDWNEFNDIN
KIIIRQPIRTEYKIAFPYLYNNLPHHVHLTWYHTPNVVFIKTEDPDLPAFYFDPLINPIS
HRHSVKSQEPLPDDDEEFELPEFVEPFLKDTPLYTDNTANGIALLWAPRPFNLRSGRTRR
ALDIPLVKNWYREHCPAGQPVKVRVSYQKLLKYYVLNALKHRPPKAQKKRYLFRSFKATK
FFQSTKLDWVEVGLQVCRQGYNMLNLLIHRKNLNYLHLDYNFNLKPVKTLTTKERKKSRF
GNAFHLCREVLRLTKLVVDSHVQYRLGNVDAFQLADGLQYIFAHVGQLTGMYRYKYKLMR
QIRMCKDLKHLIYYRFNTGPVGKGPGCGFWAAGWRVWLFFMRGITPLLERWLGNLLARQF
EGRHSKGVAKTVTKQRVESHFDLELRAAVMHDILDMMPEGIKQNKARTILQHLSEAWRCW
KANIPWKVPGLPTPIENMILRYVKAKADWWTNTAHYNRERIRRGATVDKTVCKKNLGRLT
RLYLKAEQERQHNYLKDGPYITAEEAVAVYTTTVHWLESRRFSPIPFPPLSYKHDTKLLI
LALERLKEAYSVKSRLNQSQREELGLIEQAYDNPHEALSRIKRHLLTQRAFKEVGIEFMD
LYSHLVPVYDVEPLEKITDAYLDQYLWYEADKRRLFPPWIKPADTEPPPLLVYKWCQGIN
NLQDVWETSEGECNVMLESRFEKMYEKIDLTLLNRLLRLIVDHNIADYMTAKNNVVINYK
DMNHTNSYGIIRGLQFASFIVQYYGLVMDLLVLGLHRASEMAGPPQMPNDFLSFQDIATE
AAHPIRLFCRYIDRIHIFFRFTADEARDLIQRYLTEHPDPNNENIVGYNNKKCWPRDARM
RLMKHDVNLGRAVFWDIKNRLPRSVTTVQWENSFVSVYSKDNPNLLFNMCGFECRILPKC
RTSYEEFTHKDGVWNLQNEVTKERTAQCFLRVDDESMQRFHNRVRQILMASGSTTFTKIV
NKWNTALIGLMTYFREAVVNTQELLDLLVKCENKIQTRIKIGLNSKMPSRFPPVVFYTPK
ELGGLGMLSMGHVLIPQSDLRWSKQTDVGITHFRSGMSHEEDQLIPNLYRYIQPWESEFI
DSQRVWAEYALKRQEAIAQNRRLTLEDLEDSWDRGIPRINTLFQKDRHTLAYDKGWRVRT
DFKQYQVLKQNPFWWTHQRHDGKLWNLNNYRTDMIQALGGVEGILEHTLFKGTYFPTWEG
LFWEKASGFEESMKWKKLTNAQRSGLNQIPNRRFTLWWSPTINRANVYVGFQVQLDLTGI
FMHGKIPTLKISLIQIFRAHLWQKIHESIVMDLCQVFDQELDALEIETVQKETIHPRKSY
KMNSSCADILLFASYKWNVSRPSLLADSKDVMDSTTTQKYWIDIQLRWGDYDSHDIERYA
RAKFLDYTTDNMSIYPSPTGVLIAIDLAYNLHSAYGNWFPGSKPLIQQAMAKIMKANPAL
YVLRERIRKGLQLYSSEPTEPYLSSQNYGELFSNQIIWFVDDTNVYRVTIHKTFEGNLTT
KPINGAIFIFNPRTGQLFLKIIHTSVWAGQKRLGQLAKWKTAEEVAALIRSLPVEEQPKQ
IIVTRKGMLDPLEVHLLDFPNIVIKGSELQLPFQACLKVEKFGDLILKATEPQMVLFNLY
DDWLKTISSYTAFSRLILILRALHVNNDRAKVILKPDKTTITEPHHIWPTLTDEEWIKVE
VQLKDLILADYGKKNNVNVASLTQSEIRDIILGMEISAPSQQRQQIAEIEKQTKEQSQLT
ATQTRTVNKHGDEIITSTTSNYETQTFSSKTEWRVRAISAANLHLRTNHIYVSSDDIKET
GYTYILPKNVLKKFICISDLRAQIAGYLYGVSPPDNPQVKEIRCIVMVPQWGTHQTVHLP
GQLPQHEYLKEMEPLGWIHTQPNESPQLSPQDVTTHAKIMADNPSWDGEKTIIITCSFTP
GSCTLTAYKLTPSGYEWGRQNTDKGNNPKGYLPSHYERVQMLLSDRFLGFFMVPAQSSWN
YNFMGVRHDPNMKYELQLANPKEFYHEVHRPSHFLNFALLQEGEVYSADREDLYA

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	6
ATP	Adenosine-5'-triphosphate	C10 H16 N5 O13 P3	1
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	1
ZN	Zinc ion	Zn	6
IHP	Inositol hexakisphosphate	C6 H18 O24 P6	1

Water and common crystallization additives (K) are not listed.

Primary citation

Mechanism for the initiation of spliceosome disassembly. Vorlander, M.K., Rothe, P., Kleifeld, J. et al. Nature (2024) 632:443-450. DOI 10.1038/s41586-024-07741-1 · PubMed

Other PDB entries of the same protein (UniProt Q9H875 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8C6J 2.8 Å, Human spliceosomal PM5 C* complex
6ICZ 3.0 Å, Cryo-EM structure of a human post-catalytic spliceosome (P complex) at 3.0 angstrom
6QDV 3.3 Å, Human post-catalytic P complex spliceosome
5XJC 3.6 Å, Cryo-EM structure of the human spliceosome just prior to exon ligation at 3.6 angstrom
7W5A 3.6 Å, The cryo-EM structure of human pre-C*-II complex
7W5B 4.3 Å, The cryo-EM structure of human C* complex

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