8UIB: Human INTS9-INTS11-BRAT1 complex

Structure of the human INTS9-INTS11-BRAT1 complex. Determined by electron microscopy at 3.21 Å resolution. Released 21 Aug 2024.

Method: Electron microscopy
Resolution: 3.21 Å
Organism: Homo sapiens
Chains: 3
Atoms: 11,868
Mol. weight: 229.97 kDa
Ligands: ZN
Released: 21 Aug 2024

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

Secondary structure: helices and β-sheets

8UIB contains 78 α-helices and 56 β-strands across 3 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 I: 13 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	3-4	2	1
β-strand	16	1	1
β-strand	24-25	2	2
α-helix	33-37	5
β-strand	38	1	3
β-strand	69-71	3	4
β-strand	74-76	3	4
β-strand	77	1	3
β-strand	83	1	5
β-strand	98-100	3	2
α-helix	110-114	5
β-strand	122-125	4	2
α-helix	127-145	19
β-strand	179	1	5
α-helix	184-191	8
β-strand	194-196	3	2
β-strand	210-215	6	6
β-strand	223-228	6	6
β-strand	234-235	2	6
β-strand	237	1	7
α-helix	248-250	3
β-strand	260-262	3	6
β-strand	263	1	7
α-helix	274-289	16
β-strand	295-296	2	8
α-helix	304-319	16
β-strand	326-329	4	8
α-helix	337-339	3
β-strand	373-376	4	8
α-helix	383-385	3
β-strand	392-393	2	8
α-helix	405-412	8
β-strand	419-422	4	8
α-helix	434-436	3
β-strand	442-445	4	8
α-helix	454-464	11
β-strand	468-470	3	6
β-strand	471-472	2	9
α-helix	473-475	3
β-strand	496-497	2	9
β-strand	502-503	2	1

Chain K: 15 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	5-8	4	10
β-strand	20-24	5	10
β-strand	27-30	4	10
α-helix	57-60	4
β-strand	61-65	5	10
α-helix	71-74	4
α-helix	77-79	3
α-helix	80-85	6
β-strand	90-91	2	10
β-strand	93	1	11
α-helix	96-113	18
α-helix	123-130	8
β-strand	133	1	10
β-strand	136	1	11
α-helix	137	1
β-strand	138	1	12
β-strand	141-143	3	13
β-strand	148-151	4	13
β-strand	152	1	12
β-strand	154	1	14
β-strand	164-168	5	13
β-strand	171-175	5	13
β-strand	191	1	14
β-strand	199-202	4	13
α-helix	216-227	12
β-strand	234-238	5	15
α-helix	245-258	14
β-strand	265	1	15
α-helix	277-287	11
β-strand	305	1	15
β-strand	319-323	5	15
α-helix	326-328	3
α-helix	332-340	9
β-strand	347-350	4	15
α-helix	359-365	7
β-strand	369-370	2	16
β-strand	378-379	2	16
β-strand	383-386	4	15
α-helix	395-405	11
β-strand	409-412	4	13
α-helix	417-429	13
β-strand	434-436	3	13
β-strand	444-445	2	10

Chain T: 50 helices, 0 β-strands

Element	Residues	Length
α-helix	9-16	8
α-helix	22-25	4
α-helix	26-42	17
α-helix	45-51	7
α-helix	54-64	11
α-helix	70-83	14
α-helix	87-92	6
α-helix	99-103	5
α-helix	108-110	3
α-helix	112-115	4
α-helix	117-130	14
α-helix	134-142	9
α-helix	147-152	6
α-helix	158-175	18
α-helix	193-206	14
α-helix	211-227	17
α-helix	231-245	15
α-helix	246-249	4
α-helix	253	1
α-helix	256-266	11
α-helix	277-279	3
α-helix	280-289	10
α-helix	295-303	9
α-helix	310-321	12
α-helix	322-324	3
α-helix	348-354	7
α-helix	358-375	18
α-helix	387-401	15
α-helix	410-418	9
α-helix	423-435	13
α-helix	443-457	15
α-helix	464-478	15
α-helix	495-509	15
α-helix	514-527	14
α-helix	535-538	4
α-helix	547-550	4
α-helix	552-555	4
α-helix	559-566	8
α-helix	568-574	7
α-helix	592-602	11
α-helix	607-622	16
α-helix	625-627	3
α-helix	631-643	13
α-helix	648-665	18
α-helix	694-696	3
α-helix	703-708	6
α-helix	713-724	12
α-helix	774-778	5
α-helix	781-787	7
α-helix	799-807	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Integrator complex subunit 9	I	protein	658	Homo sapiens	Q9NV88 (AlphaFold model)
Integrator complex subunit 11	K	protein	600	Homo sapiens	Q5TA45 (AlphaFold model)
BRCA1-associated ATM activator 1	T	protein	821	Homo sapiens	Q6PJG6 (AlphaFold model)

Sequence of entity 1 (I), FASTA

>8UIB_1 Integrator complex subunit 9 (chains I)
MKLYCLSGHPTLPCNVLKFKSTTIMLDCGLDMTSTLNFLPLPLVQSPRLSNLPGWSLKDG
NAFLDKELKECSGHVFVDSVPEFCLPETELIDLSTVDVILISNYHCMMALPYITEHTGFT
GTVYATEPTVQIGRLLMEELVNFIERVPKAQSASLWKNKDIQRLLPSPLKDAVEVSTWRR
CYTMQEVNSALSKIQLVGYSQKIELFGAVQVTPLSSGYALGSSNWIIQSHYEKVSYVSGS
SLLTTHPQPMDQASLKNSDVLVLTGLTQIPTANPDGMVGEFCSNLALTVRNGGNVLVPCY
PSGVIYDLLECLYQYIDSAGLSSVPLYFISPVANSSLEFSQIFAEWLCHNKQSKVYLPEP
PFPHAELIQTNKLKHYPSIHGDFSNDFRQPCVVFTGHPSLRFGDVVHFMELWGKSSLNTV
IFTEPDFSYLEALAPYQPLAMKCIYCPIDTRLNFIQVSKLLKEVQPLHVVCPEQYTQPPP
AQSHRMDLMIDCQPPAMSYRRAEVLALPFKRRYEKIEIMPELADSLVPMEIKPGISLATV
SAVLHTKDNKHLLQPPPRPAQPTSGKKRKRVSDDVPDCKVLKPLLSGSIPVEQFVQTLEK
HGFSDIKVEDTAKGHIVLLQEAETLIQIEEDSTHIICDNDEMLRVRLRDLVLKFLQKF

Sequence of entity 2 (K), FASTA

>8UIB_2 Integrator complex subunit 11 (chains K)
MPEIRVTPLGAGQDVGRSCILVSIAGKNVMLDCGMHMGFNDDRRFPDFSYITQNGRLTDF
LDCVIISHFHLDHCGALPYFSEMVGYDGPIYMTHPTQAICPILLEDYRKIAVDKKGEANF
FTSQMIKDCMKKVVAVHLHQTVQVDDELEIKAYYAGHVLGAAMFQIKVGSESVVYTGDYN
MTPDRHLGAAWIDKCRPNLLITESTYATTIRDSKRCRERDFLKKVHETVERGGKVLIPVF
ALGRAQELCILLETFWERMNLKVPIYFSTGLTEKANHYYKLFIPWTNQKIRKTFVQRNMF
EFKHIKAFDRAFADNPGPMVVFATPGMLHAGQSLQIFRKWAGNEKNMVIMPGYCVQGTVG
HKILSGQRKLEMEGRQVLEVKMQVEYMSFSAHADAKGIMQLVGQAEPESVLLVHGEAKKM
EFLKQKIEQELRVNCYMPANGETVTLPTSPSIPVGISLGLLKREMAQGLLPEAKKPRLLH
GTLIMKDSNFRLVSSEQALKELGLAEHQLRFTCRVHLHDTRKEQETALRVYSHLKSVLKD
HCVQHLPDGSVTVESVLLQAAAPSEDPGTKVLLVSWTYQDEELGSFLTSLLKKGLPQAPS

Sequence of entity 3 (T), FASTA

>8UIB_3 BRCA1-associated ATM activator 1 (chains T)
MDPECAQLLPALCAVLVDPRQPVADDTCLEKLLDWFKTVTEGESSVVLLQEHPCLVELLS
HVLKVQDLSSGVLSFSLRLAGTFAAQENCFQYLQQGELLPGLFGEPGPLGRATWAVPTVR
SGWIQGLRSLAQHPSALRFLADHGAVDTIFSLQGDSSLFVASAASQLLVHVLALSMRGGA
EGQPCLPGGDWPACAQKIMDHVEESLCSAATPKVTQALNVLTTTFGRCQSPWTEALWVRL
SPRVACLLERDPIPAAHSFVDLLLCVARSPVFSSSDGSLWETVARALSCLGPTHMGPLAL
GILKLEHCPQALRTQAFQVLLQPLACVLKATVQAPGPPGLLDGTADDATTVDTLLASKSS
CAGLLCRTLAHLEELQPLPQRPSPWPQASLLGATVTVLRLCDGSAAPASSVGGHLCGTLA
GCVRVQRAALDFLGTLSQGTGPQELVTQALAVLLECLESPGSSPTVLKKAFQATLRWLLS
SPKTPGCSDLGPLIPQFLRELFPVLQKRLCHPCWEVRDSALEFLTQLSRHWGGQADFRCA
LLASEVPQLALQLLQDPESYVRASAVTAMGQLSSQGLHAPTSPEHAEARQSLFLELLHIL
SVDSEGFPRRAVMQVFTEWLRDGHADAAQDTEQFVATVLQAASRDLDWEVRAQGLELALV
FLGQTLGPPRTHCPYAVALPEVAPAQPLTEALRALCHVGLFDFAFCALFDCDRPVAQKSC
DLLLFLRDKIASYSSLREARGSPNTASAEATLPRWRAGEQAQPPGDQEPEAVLAMLRSLD
LEGLRSTLAESSDHVEKSPQSLLQDMLATGGFLQGDEADCY

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2

Primary citation

Cytoplasmic binding partners of the Integrator endonuclease INTS11 and its paralog CPSF73 are required for their nuclear function. Lin, M.H., Jensen, M.K., Elrod, N.D. et al. Mol Cell (2024) 84:2900-2917.e10. DOI 10.1016/j.molcel.2024.06.017 · PubMed

Other PDB entries of the same protein (UniProt Q9NV88 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5V8W 2.1 Å, Crystal structure of human Integrator IntS9-IntS11 CTD complex
8RC4 3.1 Å, Structure of Integrator-PP2A complex
8R23 3.2 Å, INTS9-INTS11-BRAT1 complex
7CUN 3.5 Å, The structure of human Integrator-PP2A complex
7BFP 3.56 Å, Structure of the Integrator cleavage module with INTS4/9/11
7PKS 3.6 Å, Structural basis of Integrator-mediated transcription regulation
8RBZ 3.7 Å, Structure of Integrator-PP2A-SOSS-CTD post-termination complex
8R22 3.9 Å, INTS9-INTS11-BRAT1-WDR73 complex
8R2D 3.9 Å, Integrator cleavage module assembly intermediate
8RBX 4.1 Å, Structure of Integrator-PP2A bound to a paused RNA polymerase II-DSIF-NELF-nucleosome…
8YJB 4.1 Å, Cryo-EM structure of the human DSS1-INTAC complex
7BFQ 4.15 Å, Structure of the Integrator cleavage module with extended INTS4 and rigid body docked…

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