8R2D: Integrator cleavage module assembly intermediate

Integrator cleavage module assembly intermediate. Determined by electron microscopy at 3.9 Å resolution. Released 31 Jul 2024.

Method: Electron microscopy
Resolution: 3.9 Å
Organism: Homo sapiens
Chains: 4
Atoms: 18,276
Mol. weight: 341.06 kDa
Ligands: ZN
Released: 31 Jul 2024

Explore 8R2D in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8R2D contains 123 α-helices and 75 β-strands across 4 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 A: 44 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	3-6	4
α-helix	9-17	9
α-helix	22-23	2
α-helix	26-40	15
α-helix	47-51	5
α-helix	55-61	7
α-helix	72-83	12
α-helix	87-93	7
α-helix	98-102	5
α-helix	105-109	5
α-helix	117-130	14
α-helix	134-139	6
α-helix	140-144	5
α-helix	146-152	7
β-strand	157	1	1
α-helix	158-175	18
α-helix	193-206	14
α-helix	211-227	17
β-strand	228	1	2
α-helix	231-245	15
α-helix	256-267	12
α-helix	278-289	12
α-helix	295-304	10
α-helix	310-327	18
β-strand	331	1	3
α-helix	349-354	6
α-helix	358-374	17
α-helix	388-402	15
β-strand	407	1	3
α-helix	410-419	10
α-helix	424-435	12
α-helix	443-457	15
α-helix	464-478	15
α-helix	494-505	12
α-helix	514-530	17
α-helix	535-543	9
α-helix	547-553	7
α-helix	559-573	15
α-helix	590-601	12
α-helix	607-622	16
α-helix	631-642	12
α-helix	649-665	17
α-helix	688-697	10
α-helix	700-706	7
α-helix	713-732	20
α-helix	769-777	9
α-helix	782-789	8
α-helix	799-807	9

Chain B: 23 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	2-5	4	4
β-strand	15-18	4	4
β-strand	23-26	4	4
α-helix	33-36	4
β-strand	38	1	5
α-helix	39-40	2
α-helix	47-50	4
β-strand	54	1	6
α-helix	64-66	3
β-strand	69-71	3	6
β-strand	74-76	3	6
β-strand	77	1	5
β-strand	83	1	7
β-strand	98-99	2	4
α-helix	104-106	3
α-helix	110-114	5
β-strand	124-125	2	8
α-helix	127-144	18
α-helix	155-157	3
α-helix	159-162	4
α-helix	169-171	3
α-helix	175-177	3
β-strand	179	1	7
α-helix	184-190	7
α-helix	191-193	3
β-strand	195-196	2	8
β-strand	203-205	3	9
β-strand	209-215	7	9
β-strand	223-228	6	9
β-strand	233-234	2	9
β-strand	237-238	2	10
α-helix	248-250	3
β-strand	260	1	9
β-strand	261-262	2	11
β-strand	263-264	2	10
α-helix	274-289	16
β-strand	296-298	3	12
α-helix	304-316	13
β-strand	326-329	4	12
α-helix	333-341	9
β-strand	373-376	4	12
α-helix	383-385	3
β-strand	393-395	3	12
α-helix	405-411	7
β-strand	419-422	4	12
α-helix	429-433	5
α-helix	434-436	3
β-strand	442-445	4	12
α-helix	454-464	11
β-strand	469-472	4	11
α-helix	473-476	4
β-strand	497-499	3	11
β-strand	503-505	3	4

Chain C: 12 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	4-8	5	13
β-strand	20-23	4	13
β-strand	28-31	4	13
α-helix	48-50	3
α-helix	57-60	4
β-strand	61-65	5	13
α-helix	77-80	4
β-strand	90-91	2	13
α-helix	94-113	20
α-helix	123-130	8
β-strand	133	1	13
β-strand	137	1	14
β-strand	140	1	14
β-strand	142-144	3	15
β-strand	148-151	4	15
β-strand	154	1	16
β-strand	163-167	5	15
β-strand	172-176	5	15
β-strand	191	1	16
β-strand	200-203	4	15
α-helix	216-229	14
β-strand	234-236	3	17
α-helix	246-257	12
β-strand	265-267	3	17
α-helix	278-282	5
β-strand	305-306	2	17
β-strand	319-322	4	17
α-helix	332-339	8
β-strand	347-349	3	17
α-helix	359-362	4
β-strand	370	1	18
β-strand	378	1	18
β-strand	383-385	3	17
α-helix	395-405	11
β-strand	410-413	4	15
α-helix	417-430	14
β-strand	435-436	2	15
β-strand	442	1	1
β-strand	444-446	3	13

Chain D: 44 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	69-82	14
α-helix	86-99	14
α-helix	107-110	4
α-helix	111-118	8
α-helix	125-138	14
α-helix	145-158	14
α-helix	164-176	13
α-helix	196-201	6
α-helix	202-205	4
α-helix	209-224	16
α-helix	232-237	6
α-helix	238-242	5
α-helix	246-262	17
β-strand	267-269	3	19
β-strand	276-278	3	19
α-helix	279-291	13
α-helix	296-305	10
α-helix	306-308	3
α-helix	314-319	6
α-helix	323-325	3
α-helix	378-383	6
α-helix	388-404	17
α-helix	406-418	13
α-helix	419-421	3
α-helix	425-437	13
α-helix	446-453	8
α-helix	454-457	4
α-helix	461-471	11
α-helix	479-495	17
α-helix	500-511	12
α-helix	515-518	4
α-helix	521-525	5
α-helix	542-557	16
α-helix	561-563	3
α-helix	567-580	14
α-helix	609-620	12
α-helix	633-649	17
α-helix	654-671	18
α-helix	695-705	11
α-helix	706-710	5
β-strand	711-712	2	20
α-helix	716-734	19
α-helix	753-764	12
α-helix	769-771	3
β-strand	818-819	2	20
β-strand	821-826	6	21
β-strand	835-837	3	22
β-strand	844-852	9	21
α-helix	857-860	4
β-strand	861-866	6	22
β-strand	873-875	3	22
α-helix	876-878	3
α-helix	879-881	3
β-strand	882-886	5	21
β-strand	889-897	9	21
β-strand	907-917	11	22
β-strand	944-946	3	22
β-strand	952-958	7	22

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
BRCA1-associated ATM activator 1	A	protein	827	Homo sapiens	Q6PJG6 (AlphaFold model)
Integrator complex subunit 9	B	protein	658	Homo sapiens	Q9NV88 (AlphaFold model)
Integrator complex subunit 11	C	protein	612	Homo sapiens	Q5TA45 (AlphaFold model)
Integrator complex subunit 4	D	protein	973	Homo sapiens	Q96HW7 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8R2D_1 BRCA1-associated ATM activator 1 (chains A)
GPSQSNMDPECAQLLPALCAVLVDPRQPVADDTCLEKLLDWFKTVTEGESSVVLLQEHPC
LVELLSHVLKVQDLSSGVLSFSLRLAGTFAAQENCFQYLQQGELLPGLFGEPGPLGRATW
AVPTVRSGWIQGLRSLAQHPSALRFLADHGAVDTIFSLQGDSSLFVASAASQLLVHVLAL
SMRGGAEGQPCLPGGDWPACAQKIMDHVEESLCSAATPKVTQALNVLTTTFGRCQSPWTE
ALWVRLSPRVACLLERDPIPAAHSFVDLLLCVARSPVFSSSDGSLWETVARALSCLGPTH
MGPLALGILKLEHCPQALRTQAFQVLLQPLACVLKATVQAPGPPGLLDGTADDATTVDTL
LASKSSCAGLLCRTLAHLEELQPLPQRPSPWPQASLLGATVTVLRLCDGSAAPASSVGGH
LCGTLAGCVRVQRAALDFLGTLSQGTGPQELVTQALAVLLECLESPGSSPTVLKKAFQAT
LRWLLSSPKTPGCSDLGPLIPQFLRELFPVLQKRLCHPCWEVRDSALEFLTQLSRHWGGQ
ADFRCALLASEVPQLALQLLQDPESYVRASAVTAMGQLSSQGLHAPTSPEHAEARQSLFL
ELLHILSVDSEGFPRRAVMQVFTEWLRDGHADAAQDTEQFVATVLQAASRDLDWEVRAQG
LELALVFLGQTLGPPRTHCPYAVALPEVAPAQPLTEALRALCHVGLFDFAFCALFDCDRP
VAQKSCDLLLFLRDKIASYSSLREARGSPNTASAEATLPRWRAGEQAQPPGDQEPEAVLA
MLRSLDLEGLRSTLAESSDHVEKSPQSLLQDMLATGGFLQGDEADCY

Sequence of entity 2 (B), FASTA

>8R2D_2 Integrator complex subunit 9 (chains B)
MKLYCLSGHPTLPCNVLKFKSTTIMLDCGLDMTSTLNFLPLPLVQSPRLSNLPGWSLKDG
NAFLDKELKECSGHVFVDSVPEFCLPETELIDLSTVDVILISNYHCMMALPYITEHTGFT
GTVYATEPTVQIGRLLMEELVNFIERVPKAQSASLWKNKDIQRLLPSPLKDAVEVSTWRR
CYTMQEVNSALSKIQLVGYSQKIELFGAVQVTPLSSGYALGSSNWIIQSHYEKVSYVSGS
SLLTTHPQPMDQASLKNSDVLVLTGLTQIPTANPDGMVGEFCSNLALTVRNGGNVLVPCY
PSGVIYDLLECLYQYIDSAGLSSVPLYFISPVANSSLEFSQIFAEWLCHNKQSKVYLPEP
PFPHAELIQTNKLKHYPSIHGDFSNDFRQPCVVFTGHPSLRFGDVVHFMELWGKSSLNTV
IFTEPDFSYLEALAPYQPLAMKCIYCPIDTRLNFIQVSKLLKEVQPLHVVCPEQYTQPPP
AQSHRMDLMIDCQPPAMSYRRAEVLALPFKRRYEKIEIMPELADSLVPMEIKPGISLATV
SAVLHTKDNKHLLQPPPRPAQPTSGKKRKRVSDDVPDCKVLKPLLSGSIPVEQFVQTLEK
HGFSDIKVEDTAKGHIVLLQEAETLIQIEEDSTHIICDNDEMLRVRLRDLVLKFLQKF

Sequence of entity 3 (C), FASTA

>8R2D_3 Integrator complex subunit 11 (chains C)
GPSDPGPKRAEFMPEIRVTPLGAGQDVGRSCILVSIAGKNVMLDCGMHMGFNDDRRFPDF
SYITQNGRLTDFLDCVIISHFHLDHCGALPYFSEMVGYDGPIYMTHPTQAICPILLEDYR
KIAVDKKGEANFFTSQMIKDCMKKVVAVHLHQTVQVDDELEIKAYYAGHVLGAAMFQIKV
GSESVVYTGDYNMTPDRHLGAAWIDKCRPNLLITESTYATTIRDSKRCRERDFLKKVHET
VERGGKVLIPVFALGRAQELCILLETFWERMNLKVPIYFSTGLTEKANHYYKLFIPWTNQ
KIRKTFVQRNMFEFKHIKAFDRAFADNPGPMVVFATPGMLHAGQSLQIFRKWAGNEKNMV
IMPGYCVQGTVGHKILSGQRKLEMEGRQVLEVKMQVEYMSFSAHADAKGIMQLVGQAEPE
SVLLVHGEAKKMEFLKQKIEQELRVNCYMPANGETVTLPTSPSIPVGISLGLLKREMAQG
LLPEAKKPRLLHGTLIMKDSNFRLVSSEQALKELGLAEHQLRFTCRVHLHDTRKEQETAL
RVYSHLKSVLKDHCVQHLPDGSVTVESVLLQAAAPSEDPGTKVLLVSWTYQDEELGSFLT
SLLKKGLPQAPS

Sequence of entity 4 (D), FASTA

>8R2D_4 Integrator complex subunit 4 (chains D)
GPSDPGPKRAMAAHLKKRVYEEFTKVVQPQEEIATKKLRLTKPSKSAALHIDLCKATSPA
DALQYLLQFARKPVEAESVEGVVRILLEHYYKENDPSVRLKIASLLGLLSKTAGFSPDCI
MDDAINILQNEKSHQVLAQLLDTLLAIGTKLPENQAIQMRLVDVACKHLTDTSHGVRNKC
LQLLGNLGSLEKSVTKDAEGLAARDVQKIIGDYFSDQDPRVRTAAIKAMLQLHERGLKLH
QTIYNQACKLLSDDYEQVRSAAVQLIWVVSQLYPESIVPIPSSNEEIRLVDDAFGKICHM
VSDGSWVVRVQAAKLLGSMEQVSSHFLEQTLDKKLMSDLRRKRTAHERAKELYSSGEFSS
GRKWGDDAPKEEVDTGAVNLIESGACGAFVHGLEDEMYEVRIAAVEALCMLAQSSPSFAE
KCLDFLVDMFNDEIEEVRLQSIHTMRKISNNITLREDQLDTVLAVLEDSSRDIREALHEL
LCCTNVSTKEGIHLALVELLKNLTKYPTDRDSIWKCLKFLGSRHPTLVLPLVPELLSTHP
FFDTAEPDMDDPAYIAVLVLIFNAAKTCPTMPALFSDHTFRHYAYLRDSLSHLVPALRLP
GRKLVSSAVSPSIIPQEDPSQQFLQQSLERVYSLQHLDPQGAQELLEFTIRDLQRLGELQ
SELAGVADFSATYLRCQLLLIKALQEKLWNVAAPLYLKQSDLASAAAKQIMEETYKMEFM
YSGVENKQVVIIHHMRLQAKALQLIVTARTTRGLDPLFGMCEKFLQEVDFFQRYFIADLP
HLQDSFVDKLLDLMPRLMTSKPAEVVKILQTMLRQSAFLHLPLPEQIHKASATIIEPAGE
SDNPLRFTSGLVVALDVDATLEHVQDPQNTVKVQVLYPDGQAQMIHPKPADFRNPGPGRH
RLITQVYLSHTAWTEACQVEVRLLLAYNSSARIPKCPWMEGGEMSPQVETSIEGTIPFSK
PVKVYIMPKPARR

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2

Primary citation

Assembly mechanism of Integrator's RNA cleavage module. Sabath, K., Qiu, C., Jonas, S. Mol Cell (2024) 84:2882-2899.e10. DOI 10.1016/j.molcel.2024.06.032 · PubMed

Other PDB entries of the same protein (UniProt Q6PJG6 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4IFI 2.2 Å, Structure of human BRCA1 BRCT in complex with BAAT peptide
8R23 3.2 Å, INTS9-INTS11-BRAT1 complex
8UIB 3.21 Å, Structure of the human INTS9-INTS11-BRAT1 complex
8R22 3.9 Å, INTS9-INTS11-BRAT1-WDR73 complex

Browse structure collections

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