6AH0: Precusor of Human Pre-catalytic Spliceosome

The Cryo-EM Structure of the Precusor of Human Pre-catalytic Spliceosome (pre-B complex). Determined by electron microscopy at 5.7 Å resolution. Released 14 Nov 2018.

Method: Electron microscopy
Resolution: 5.7 Å
Organism: Homo sapiens
Chains: 57
Atoms: 63,369
Mol. weight: 2500.76 kDa
Ligands: IHP, GTP, MG
Released: 14 Nov 2018

Explore 6AH0 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6AH0 contains 578 α-helices and 600 β-strands across 52 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: 74 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	103-107	5
α-helix	119-125	7
α-helix	174-189	16
α-helix	210-215	6
α-helix	227-234	8
α-helix	238-254	17
α-helix	302-324	23
α-helix	401-407	7
β-strand	413-414	2	68
α-helix	421-428	8
α-helix	430-433	4
α-helix	472-475	4
α-helix	476-478	3
α-helix	491-498	8
α-helix	500-505	6
α-helix	509-520	12
α-helix	523-526	4
α-helix	528-539	12
α-helix	547-562	16
α-helix	565-570	6
α-helix	571-582	12
α-helix	587-603	17
α-helix	606-613	8
α-helix	615-617	3
α-helix	622-639	18
α-helix	641-651	11
α-helix	658-675	18
α-helix	676-682	7
α-helix	683-694	12
α-helix	699-715	17
α-helix	721-727	7
α-helix	728-736	9
α-helix	741-753	13
α-helix	754-756	3
α-helix	761-775	15
α-helix	782-795	14
α-helix	803-805	3
α-helix	806-810	5
α-helix	811-813	3
α-helix	814-818	5
α-helix	821-825	5
α-helix	827-844	18
α-helix	847-854	8
α-helix	862-878	17
α-helix	881-883	3
α-helix	887-901	15
α-helix	908-921	14
α-helix	922-928	7
α-helix	929-941	13
α-helix	948-964	17
α-helix	968-981	14
α-helix	987-1001	15
α-helix	1006-1008	3
α-helix	1013-1020	8
α-helix	1021-1025	5
α-helix	1029-1045	17
α-helix	1052-1062	11
α-helix	1063-1067	5
α-helix	1071-1088	18
α-helix	1090-1097	8
α-helix	1111-1122	12
α-helix	1125-1135	11
α-helix	1141-1158	18
α-helix	1159-1163	5
α-helix	1166-1177	12
α-helix	1182-1198	17
α-helix	1205-1215	11
α-helix	1216-1219	4
α-helix	1224-1241	18
α-helix	1243-1250	8
α-helix	1259-1274	16
α-helix	1277-1280	4
α-helix	1281-1283	3
α-helix	1285-1286	2
α-helix	1299-1301	3

Chain 2: 11 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	464-467	4
α-helix	472-474	3
α-helix	477-481	5
α-helix	485-492	8
α-helix	499-501	3
α-helix	526-529	4
α-helix	533-536	4
α-helix	552-555	4
α-helix	568-579	12
β-strand	608	1	69
α-helix	611-617	7
α-helix	633-639	7
β-strand	648-649	2	70
β-strand	651	1	71
β-strand	655	1	71
β-strand	683	1	69
β-strand	686	1	69
β-strand	689-690	2	70

Chain 3: 14 helices, 104 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	72
α-helix	10-11	2
β-strand	14-20	7	73
β-strand	29-34	6	73
β-strand	37-42	6	73
β-strand	51-57	7	73
β-strand	62-67	6	74
β-strand	78-82	5	74
β-strand	86-93	8	74
β-strand	98-106	9	74
β-strand	120-123	4	75
β-strand	129-133	5	75
β-strand	136	1	76
β-strand	139-143	5	75
β-strand	144-146	3	77
β-strand	152-154	3	77
β-strand	165-172	8	76
β-strand	181-188	8	76
α-helix	190-193	4
β-strand	207-214	8	76
β-strand	219-227	9	76
β-strand	232-238	7	78
β-strand	247-252	6	78
β-strand	255-259	5	78
β-strand	267-270	4	78
β-strand	293-294	2	79
β-strand	299-300	2	79
β-strand	301-304	4	80
β-strand	309-318	10	80
β-strand	321-332	12	80
β-strand	336-338	3	81
β-strand	346-349	4	82
β-strand	350-351	2	81
β-strand	356-360	5	82
β-strand	372-374	3	80
β-strand	396-401	6	82
β-strand	407-413	7	83
α-helix	421	1
β-strand	422-427	6	83
α-helix	430-432	3
β-strand	434-438	5	83
β-strand	442-443	2	84
β-strand	444-450	7	85
β-strand	458-462	5	86
β-strand	473-477	5	86
β-strand	482-486	5	86
β-strand	492-493	2	86
β-strand	507-510	4	87
β-strand	516-520	5	87
β-strand	523-528	6	87
β-strand	532-534	3	87
α-helix	537-538	2
β-strand	544-549	6	88
β-strand	553-558	6	88
β-strand	562-567	6	88
β-strand	575	1	88
β-strand	582	1	88
β-strand	587	1	89
β-strand	592	1	90
α-helix	593-596	4
β-strand	605-608	4	90
β-strand	609	1	89
β-strand	613-617	5	90
β-strand	627-632	6	90
β-strand	637-641	5	91
β-strand	644	1	92
β-strand	663	1	92
β-strand	666-669	4	91
β-strand	674-676	3	91
β-strand	688-689	2	91
β-strand	700-706	7	93
β-strand	709-715	7	93
β-strand	719-724	6	93
β-strand	729-733	5	93
β-strand	734-735	2	84
β-strand	741-745	5	85
β-strand	753-758	6	85
β-strand	761-767	7	85
β-strand	776-780	5	83
β-strand	785-791	7	94
β-strand	796-804	9	94
α-helix	809-824	16
α-helix	839-844	6
β-strand	862-869	8	94
β-strand	876-881	6	94
β-strand	887-892	6	95
β-strand	905-911	7	95
β-strand	914	1	96
β-strand	919	1	96
β-strand	922-928	7	95
β-strand	931	1	97
β-strand	936	1	97
β-strand	939-945	7	95
β-strand	951-955	5	98
β-strand	958-963	6	98
β-strand	966-971	6	98
β-strand	978-983	6	98
β-strand	990-995	6	99
β-strand	999-1004	6	99
β-strand	1007	1	100
β-strand	1009-1014	6	99
β-strand	1021-1026	6	99
β-strand	1031	1	100
β-strand	1033-1040	8	101
β-strand	1043-1048	6	101
β-strand	1052-1057	6	101
β-strand	1088	1	99
β-strand	1090-1096	7	101
β-strand	1104-1107	4	72
β-strand	1116-1119	4	72
β-strand	1126-1131	6	72
α-helix	1135-1151	17
α-helix	1160-1164	5
β-strand	1173-1174	2	72
α-helix	1176-1179	4
α-helix	1180-1182	3
α-helix	1187-1197	11
α-helix	1201-1215	15

Chain 4: 2 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	14-18	5	102
α-helix	26-33	8
β-strand	39-43	5	102
β-strand	46-47	2	103
β-strand	52-53	2	103
β-strand	56-61	6	102
α-helix	64-74	11
β-strand	77-79	3	104
β-strand	82-84	3	104
β-strand	85-88	4	102

Chain 5: 3 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	20-24	5	68
α-helix	32-39	8
β-strand	45-50	6	68
β-strand	60-64	5	68
α-helix	67-76	10
β-strand	81-82	2	105
β-strand	85-86	2	105
β-strand	88-91	4	68
α-helix	106-115	10

Chain 6: 5 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	8-10	3	107
β-strand	18-19	2	108
α-helix	20	1
β-strand	22	1	109
α-helix	25-28	4
β-strand	30	1	110
β-strand	35	1	110
β-strand	42	1	111
β-strand	44-45	2	108
α-helix	52-54	3
β-strand	57	1	112
β-strand	64	1	112
β-strand	67	1	109
β-strand	70	1	111
α-helix	74-77	4
α-helix	80-82	3
β-strand	88-90	3	107

Chain 7: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	28-45	18
α-helix	47-56	10
α-helix	61-71	11

Chain a: 1 helix, 5 β-strands

Element	Residues	Length	Sheet
α-helix	27-37	11
β-strand	42-46	5	34
β-strand	51-59	9	34
β-strand	65-73	9	34
β-strand	93-101	9	34
β-strand	106-110	5	34

44 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
U5snRNA	B	RNA	117	Homo sapiens
U5 small nuclear ribonucleoprotein 200 kDa helicase	D	protein	2136	Homo sapiens	O75643 (AlphaFold model)
U5 small nuclear ribonucleoprotein 40 kDa protein	E	protein	357	Homo sapiens	Q96DI7 (AlphaFold model)
Small nuclear ribonucleoprotein Sm D2	P, a, k	protein	118	Homo sapiens	P62316 (AlphaFold model)
Small nuclear ribonucleoprotein F	Q, b, m	protein	86	Homo sapiens	P62306 (AlphaFold model)
Small nuclear ribonucleoprotein E	R, c, l	protein	92	Homo sapiens	P62304
Small nuclear ribonucleoprotein G	S, d, n	protein	76	Homo sapiens	P62308
Small nuclear ribonucleoprotein Sm D3	T, e, h	protein	126	Homo sapiens	P62318
Small nuclear ribonucleoprotein-associated proteins B and B'	U, f, i	protein	231	Homo sapiens	P14678
Small nuclear ribonucleoprotein Sm D1	V, g, j	protein	119	Homo sapiens	P62314
U6snRNA	F	RNA	107	Homo sapiens
U6 snRNA-associated Sm-like protein LSm2	q	protein	95	Homo sapiens	Q9Y333

31 more molecules are not listed.

Sequence of entity 1 (B), FASTA

>6AH0_1 U5snRNA (chains B)
AUACUCUGGUUUCUCUUCAGAUCGCAUAAAUCUUUCGCCUUUUACUAAAGAUUUCCGUGG
AGAGGAACAACUCUGAGUCUUAACCCAAUUUUUUGAGGCCUUGCUUUGGCAAGGCUA

Sequence of entity 2 (D), FASTA

>6AH0_2 U5 small nuclear ribonucleoprotein 200 kDa helicase (chains D)
MADVTARSLQYEYKANSNLVLQADRSLIDRTRRDEPTGEVLSLVGKLEGTRMGDKAQRTK
PQMQEERRAKRRKRDEDRHDINKMKGYTLLSEGIDEMVGIIYKPKTKETRETYEVLLSFI
QAALGDQPRDILCGAADEVLAVLKNEKLRDKERRKEIDLLLGQTDDTRYHVLVNLGKKIT
DYGGDKEIQNMDDNIDETYGVNVQFESDEEEGDEDVYGEVREEASDDDMEGDEAVVRCTL
SANLVASGELMSSKKKDLHPRDIDAFWLQRQLSRFYDDAIVSQKKADEVLEILKTASDDR
ECENQLVLLLGFNTFDFIKVLRQHRMMILYCTLLASAQSEAEKERIMGKMEADPELSKFL
YQLHETEKEDLIREERSRRERVRQSRMDTDLETMDLDQGGEALAPRQVLDLEDLVFTQGS
HFMANKRCQLPDGSFRRQRKGYEEVHVPALKPKPFGSEEQLLPVEKLPKYAQAGFEGFKT
LNRIQSKLYRAALETDENLLLCAPTGAGKTNVALMCMLREIGKHINMDGTINVDDFKIIY
IAPMRSLVQEMVGSFGKRLATYGITVAELTGDHQLCKEEISATQIIVCTPEKWDIITRKG
GERTYTQLVRLIILDEIHLLHDDRGPVLEALVARAIRNIEMTQEDVRLIGLSATLPNYED
VATFLRVDPAKGLFYFDNSFRPVPLEQTYVGITEKKAIKRFQIMNEIVYEKIMEHAGKNQ
VLVFVHSRKETGKTARAIRDMCLEKDTLGLFLREGSASTEVLRTEAEQCKNLELKDLLPY
GFAIHHAGMTRVDRTLVEDLFADKHIQVLVSTATLAWGVNLPAHTVIIKGTQVYSPEKGR
WTELGALDILQMLGRAGRPQYDTKGEGILITSHGELQYYLSLLNQQLPIESQMVSKLPDM
LNAEIVLGNVQNAKDAVNWLGYAYLYIRMLRSPTLYGISHDDLKGDPLLDQRRLDLVHTA
ALMLDKNNLVKYDKKTGNFQVTELGRIASHYYITNDTVQTYNQLLKPTLSEIELFRVFSL
SSEFKNITVREEEKLELQKLLERVPIPVKESIEEPSAKINVLLQAFISQLKLEGFALMAD
MVYVTQSAGRLMRAIFEIVLNRGWAQLTDKTLNLCKMIDKRMWQSMCPLRQFRKLPEEVV
KKIEKKNFPFERLYDLNHNEIGELIRMPKMGKTIHKYVHLFPKLELSVHLQPITRSTLKV
ELTITPDFQWDEKVHGSSEAFWILVEDVDSEVILHHEYFLLKAKYAQDEHLITFFVPVFE
PLPPQYFIRVVSDRWLSCETQLPVSFRHLILPEKYPPPTELLDLQPLPVSALRNSAFESL
YQDKFPFFNPIQTQVFNTVYNSDDNVFVGAPTGSGKTICAEFAILRMLLQSSEGRCVYIT
PMEALAEQVYMDWYEKFQDRLNKKVVLLTGETSTDLKLLGKGNIIISTPEKWDILSRRWK
QRKNVQNINLFVVDEVHLIGGENGPVLEVICSRMRYISSQIERPIRIVALSSSLSNAKDV
AHWLGCSATSTFNFHPNVRPVPLELHIQGFNISHTQTRLLSMAKPVYHAITKHSPKKPVI
VFVPSRKQTRLTAIDILTTCAADIQRQRFLHCTEKDLIPYLEKLSDSTLKETLLNGVGYL
HEGLSPMERRLVEQLFSSGAIQVVVASRSLCWGMNVAAHLVIIMDTQYYNGKIHAYVDYP
IYDVLQMVGHANRPLQDDEGRCVIMCQGSKKDFFKKFLYEPLPVESHLDHCMHDHFNAEI
VTKTIENKQDAVDYLTWTFLYRRMTQNPNYYNLQGISHRHLSDHLSELVEQTLSDLEQSK
CISIEDEMDVAPLNLGMIAAYYYINYTTIELFSMSLNAKTKVRGLIEIISNAAEYENIPI
RHHEDNLLRQLAQKVPHKLNNPKFNDPHVKTNLLLQAHLSRMQLSAELQSDTEEILSKAI
RLIQACVDVLSSNGWLSPALAAMELAQMVTQAMWSKDSYLKQLPHFTSEHIKRCTDKGVE
SVFDIMEMEDEERNALLQLTDSQIADVARFCNRYPNIELSYEVVDKDSIRSGGPVVVLVQ
LEREEEVTGPVIAPLFPQKREEGWWVVIGDAKSNSLISIKRLTLQQKAKVKLDFVAPATG
AHNYTLYFMSDAYMGCDQEYKFSVDVKEAETDSDSD

Sequence of entity 3 (E), FASTA

>6AH0_3 U5 small nuclear ribonucleoprotein 40 kDa protein (chains E)
MIEQQKRKGPELPLVPVKRQRHELLLGAGSGPGAGQQQATPGALLQAGPPRCSSLQAPIM
LLSGHEGEVYCCKFHPNGSTLASAGFDRLILLWNVYGDCDNYATLKGHSGAVMELHYNTD
GSMLFSASTDKTVAVWDSETGERVKRLKGHTSFVNSCYPARRGPQLVCTGSDDGTVKLWD
IRKKAAIQTFQNTYQVLAVTFNDTSDQIISGGIDNDIKVWDLRQNKLTYTMRGHADSVTG
LSLSSEGSYLLSNAMDNTVRVWDVRPFAPKERCVKIFQGNVHNFEKNLLRCSWSPDGSKI
AAGSADRFVYVWDTTSRRILYKLPGHAGSINEVAFHPDEPIIISASSDKRLYMGEIQ

Sequence of entity 4 (P, a, k), FASTA

>6AH0_4 Small nuclear ribonucleoprotein Sm D2 (chains P, a, k)
MSLLNKPKSEMTPEELQKREEEEFNTGPLSVLTQSVKNNTQVLINCRNNKKLLGRVKAFD
RHCNMVLENVKEMWTEVPKSGKGKKKSKPVNKDRYISKMFLRGDSVIVVLRNPLIAGK

Sequence of entity 5 (Q, b, m), FASTA

>6AH0_5 Small nuclear ribonucleoprotein F (chains Q, b, m)
MSLPLNPKPFLNGLTGKPVMVKLKWGMEYKGYLVSVDGYMNMQLANTEEYIDGALSGHLG
EVLIRCNNVLYIRGVEEEEEDGEMRE

Sequence of entity 6 (R, c, l), FASTA

>6AH0_6 Small nuclear ribonucleoprotein E (chains R, c, l)
MAYRGQGQKVQKVMVQPINLIFRYLQNRSRIQVWLYEQVNMRIEGCIIGFDEYMNLVLDD
AEEIHSKTKSRKQLGRIMLKGDNITLLQSVSN

Sequence of entity 7 (S, d, n), FASTA

>6AH0_7 Small nuclear ribonucleoprotein G (chains S, d, n)
MSKAHPPELKKFMDKKLSLKLNGGRHVQGILRGFDPFMNLVIDECVEMATSGQQNNIGMV
VIRGNSIIMLEALERV

Sequence of entity 8 (T, e, h), FASTA

>6AH0_8 Small nuclear ribonucleoprotein Sm D3 (chains T, e, h)
MSIGVPIKVLHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGRVAQLEQ
VYIRGSKIRFLILPDMLKNAPMLKSMKNKNQGSGAGRGKAAILKAQVAARGRGRGMGRGN
IFQKRR

Sequence of entity 9 (U, f, i), FASTA

>6AH0_9 Small nuclear ribonucleoprotein-associated proteins B and B' (chains U, f, i)
MTVGKSSKMLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAE
REEKRVLGLVLLRGENLVSMTVEGPPPKDTGIARVPLAGAAGGPGIGRAAGRGIPAGVPM
PQAPAGLAGPVRGVGGPSQQVMTPQGRGTVAAAAAAATASIAGAPTQYPPGRGGPPPPMG
RGAPPPGMMGPPPGMRPPMGPPMGIPPGRGTPMGMPPPGMRPPPPGMRGLL

Sequence of entity 10 (V, g, j), FASTA

>6AH0_10 Small nuclear ribonucleoprotein Sm D1 (chains V, g, j)
MKLVRFLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREPVQLETLSI
RGNNIRYFILPDSLPLDTLLVDVEPKVKSKKREAVAGRGRGRGRGRGRGRGRGRGGPRR

Sequence of entity 11 (F), FASTA

>6AH0_11 U6snRNA (chains F)
GUGCUCGCUUCGGCAGCACAUAUACUAAAAUUGGAACGAUACAGAGAAGAUUAGCAUGGC
CCCUGCGCAAGGAUGACACGCAAAUUCGUGAAGCGUUCCAUAUUUUU

Sequence of entity 12 (q), FASTA

>6AH0_12 U6 snRNA-associated Sm-like protein LSm2 (chains q)
MLFYSFFKSLVGKDVVVELKNDLSICGTLHSVDQYLNIKLTDISVTDPEKYPHMLSVKNC
FIRGSVVRYVQLPADEVDTQLLQDAARKEALQQKQ

Ligands and cofactors

ID	Name	Formula	Copies
IHP	Inositol hexakisphosphate	C6 H18 O24 P6	1
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	1
MG	Magnesium ion	Mg	1

Primary citation

Structures of the human pre-catalytic spliceosome and its precursor spliceosome. Zhan, X., Yan, C., Zhang, X. et al. Cell Res (2018) 28:1129-1140. DOI 10.1038/s41422-018-0094-7 · PubMed

Other PDB entries of the same protein (UniProt O75643 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2Q0Z 2.0 Å, Crystal structure of Q9P172/Sec63 from Homo sapiens. Northeast Structural Genomics…
8BCE 2.05 Å, Human Brr2 Helicase Region in complex with C-tail deleted Jab1 and compound 76
8BC9 2.3 Å, Human Brr2 Helicase Region in complex with C-tail deleted Jab1 and compound 24
8BCC 2.35 Å, Human Brr2 Helicase Region in complex with C-tail deleted Jab1 and compound 39
8BCB 2.38 Å, Human Brr2 Helicase Region in complex with C-tail deleted Jab1 and compound 34
8BC8 2.39 Å, Human Brr2 Helicase Region in complex with C-tail deleted Jab1 and compound 18
8BCG 2.39 Å, Human Brr2 Helicase Region in complex with C-tail deleted Jab1 and compound 86
6S8Q 2.39 Å, Human Brr2 Helicase Region in complex with C-tail deleted Jab1
9S2E 2.4 Å, Human intron-lariat spliceosome-Aquarius (ILSaqr)
8BCF 2.42 Å, Human Brr2 Helicase Region in complex with C-tail deleted Jab1 and compound 78
7BDK 2.52 Å, Human Brr2 Helicase Region in complex with C-tail deleted Jab1 and ADP
7BDJ 2.59 Å, Human Brr2 Helicase Region in complex with C-tail deleted Jab1 and mant-ATPgammaS

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