7BFQ: Integrator complex subunit 9

Structure of the Integrator cleavage module with extended INTS4 and rigid body docked INTS9/11 CTD. Determined by electron microscopy at 4.15 Å resolution. Released 24 Mar 2021.

Method: Electron microscopy
Resolution: 4.15 Å
Organism: Homo sapiens
Chains: 4
Atoms: 11,924
Mol. weight: 271.32 kDa
Released: 24 Mar 2021

Explore 7BFQ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7BFQ contains 72 α-helices and 72 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: 26 helices, 39 β-strands

Element	Residues	Length	Sheet
β-strand	2-5	4	1
β-strand	15-19	5	1
β-strand	22-25	4	1
α-helix	33-37	5
α-helix	39-40	2
α-helix	47-51	5
β-strand	54	1	2
β-strand	68-71	4	2
β-strand	74-77	4	2
β-strand	83	1	3
α-helix	93-96	4
β-strand	97-99	3	1
β-strand	100	1	4
α-helix	110-116	7
β-strand	124-125	2	4
α-helix	127-145	19
α-helix	159-164	6
α-helix	167-170	4
β-strand	179	1	3
α-helix	180-183	4
α-helix	184-193	10
α-helix	194	1
β-strand	195-196	2	4
β-strand	203-205	3	5
β-strand	209-215	7	5
β-strand	223-228	6	5
β-strand	233-237	5	5
α-helix	248-250	3
β-strand	260-263	4	5
α-helix	274-291	18
β-strand	295-298	4	6
α-helix	304-319	16
β-strand	326-329	4	6
α-helix	333-342	10
β-strand	373-376	4	6
α-helix	382-386	5
β-strand	392-395	4	6
α-helix	405-413	9
β-strand	419-422	4	6
α-helix	429-433	5
β-strand	442-445	4	6
α-helix	454-464	11
β-strand	468-470	3	5
β-strand	471-472	2	7
α-helix	473-476	4
α-helix	478-479	2
α-helix	494-495	2
β-strand	496-497	2	7
β-strand	501-504	4	1
β-strand	511-516	6	8
α-helix	521-524	4
β-strand	529-530	2	8
β-strand	536-539	4	8
β-strand	542	1	9
β-strand	543-547	5	8
β-strand	550-554	5	8
β-strand	585-586	2	10
α-helix	591-600	10
β-strand	606-611	6	11
β-strand	614-619	6	11
α-helix	620-622	3
β-strand	624-629	6	11
β-strand	632-638	7	11
α-helix	641-652	12
β-strand	656-657	2	10

Chain B: 22 helices, 31 β-strands

Element	Residues	Length	Sheet
β-strand	3-8	6	13
β-strand	20-23	4	13
β-strand	29-30	2	13
α-helix	57-60	4
β-strand	63-65	3	13
α-helix	71-74	4
α-helix	79-81	3
β-strand	90-92	3	13
α-helix	94-113	20
α-helix	120-122	3
α-helix	123-130	8
β-strand	133-135	3	13
β-strand	141-143	3	14
β-strand	149-151	3	14
β-strand	154	1	15
β-strand	162	1	15
β-strand	165-167	3	14
β-strand	172-176	5	14
β-strand	199-203	5	14
α-helix	213-229	17
β-strand	235-238	4	16
α-helix	242-258	17
α-helix	272-281	10
α-helix	288-296	9
α-helix	305-311	7
β-strand	320-323	4	16
α-helix	332-340	9
β-strand	347-350	4	16
α-helix	358-365	8
β-strand	369-371	3	17
β-strand	377-379	3	17
β-strand	383-386	4	16
α-helix	395-405	11
β-strand	409-413	5	14
α-helix	417-430	14
β-strand	434-436	3	14
β-strand	444-447	4	13
β-strand	453-457	5	8
α-helix	458-469	12
β-strand	479	1	9
β-strand	482-484	3	8
β-strand	491-493	3	8
α-helix	495-502	8
β-strand	508-517	10	11
α-helix	523-525	3
α-helix	526-537	12
β-strand	543-545	3	11
β-strand	551-553	3	11
β-strand	556-560	5	11
α-helix	561-562	2
β-strand	570-577	8	11
α-helix	578-580	3
α-helix	581-591	11

Chain C: 16 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	36-44	9
α-helix	49-60	12
α-helix	66-82	17
α-helix	86-100	15
α-helix	111-119	9
α-helix	124-140	17
α-helix	144-158	15
α-helix	164-177	14
α-helix	195-204	10
α-helix	209-223	15
α-helix	231-239	9
α-helix	246-262	17
β-strand	267-268	2	12
β-strand	277-278	2	12
α-helix	279-291	13
α-helix	298-308	11
α-helix	314-318	5
α-helix	329-343	15

Chain U: 8 helices, 0 β-strands

Element	Residues	Length
α-helix	351-359	9
α-helix	366-368	3
α-helix	369-380	12
α-helix	422-437	16
α-helix	441-455	15
α-helix	460-479	20
α-helix	486-495	10
α-helix	505-516	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Integrator complex subunit 9	A	protein	658	Homo sapiens	Q9NV88 (AlphaFold model)
Integrator complex subunit 4	C	protein	979	Homo sapiens	Q96HW7 (AlphaFold model)
Integrator complex subunit 11	B	protein	645	Homo sapiens	Q5TA45 (AlphaFold model)
Unknown	U	protein	171	Homo sapiens

Sequence of entity 1 (A), FASTA

>7BFQ_1 Integrator complex subunit 9 (chains A)
MKLYCLSGHPTLPCNVLKFKSTTIMLDCGLDMTSTLNFLPLPLVQSPRLSNLPGWSLKDG
NAFLDKELKECSGHVFVDSVPEFCLPETELIDLSTVDVILISNYHCMMALPYITEHTGFT
GTVYATEPTVQIGRLLMEELVNFIERVPKAQSASLWKNKDIQRLLPSPLKDAVEVSTWRR
CYTMQEVNSALSKIQLVGYSQKIELFGAVQVTPLSSGYALGSSNWIIQSHYEKVSYVSGS
SLLTTHPQPMDQASLKNSDVLVLTGLTQIPTANPDGMVGEFCSNLALTVRNGGNVLVPCY
PSGVIYDLLECLYQYIDSAGLSSVPLYFISPVANSSLEFSQIFAEWLCHNKQSKVYLPEP
PFPHAELIQTNKLKHYPSIHGDFSNDFRQPCVVFTGHPSLRFGDVVHFMELWGKSSLNTV
IFTEPDFSYLEALAPYQPLAMKCIYCPIDTRLNFIQVSKLLKEVQPLHVVCPEQYTQPPP
AQSHRMDLMIDCQPPAMSYRRAEVLALPFKRRYEKIEIMPELADSLVPMEIKPGISLATV
SAVLHTKDNKHLLQPPPRPAQPTSGKKRKRVSDDVPDCKVLKPLLSGSIPVEQFVQTLEK
HGFSDIKVEDTAKGHIVLLQEAETLIQIEEDSTHIICDNDEMLRVRLRDLVLKFLQKF

Sequence of entity 2 (C), FASTA

>7BFQ_2 Integrator complex subunit 4 (chains C)
MHHHHHHHHPPSGADPMAAHLKKRVYEEFTKVVQPQEEIATKKLRLTKPSKSAALHIDLC
KATSPADALQYLLQFARKPVEAESVEGVVRILLEHYYKENDPSVRLKIASLLGLLSKTAG
FSPDCIMDDAINILQNEKSHQVLAQLLDTLLAIGTKLPENQAIQMRLVDVACKHLTDTSH
GVRNKCLQLLGNLGSLEKSVTKDAEGLAARDVQKIIGDYFSDQDPRVRTAAIKAMLQLHE
RGLKLHQTIYNQACKLLSDDYEQVRSAAVQLIWVVSQLYPESIVPIPSSNEEIRLVDDAF
GKICHMVSDGSWVVRVQAAKLLGSMEQVSSHFLEQTLDKKLMSDLRRKRTAHERAKELYS
SGEFSSGRKWGDDAPKEEVDTGAVNLIESGACGAFVHGLEDEMYEVRIAAVEALCMLAQS
SPSFAEKCLDFLVDMFNDEIEEVRLQSIHTMRKISNNITLREDQLDTVLAVLEDSSRDIR
EALHELLCCTNVSTKEGIHLALVELLKNLTKYPTDRDSIWKCLKFLGSRHPTLVLPLVPE
LLSTHPFFDTAEPDMDDPAYIAVLVLIFNAAKTCPTMPALFSDHTFRHYAYLRDSLSHLV
PALRLPGRKLVSSAVSPSIIPQEDPSQQFLQQSLERVYSLQHLDPQGAQELLEFTIRDLQ
RLGELQSELAGVADFSATYLRCQLLLIKALQEKLWNVAAPLYLKQSDLASAAAKQIMEET
YKMEFMYSGVENKQVVIIHHMRLQAKALQLIVTARTTRGLDPLFGMCEKFLQEVDFFQRY
FIADLPHLQDSFVDKLLDLMPRLMTSKPAEVVKILQTMLRQSAFLHLPLPEQIHKASATI
IEPAGESDNPLRFTSGLVVALDVDATLEHVQDPQNTVKVQVLYPDGQAQMIHPKPADFRN
PGPGRHRLITQVYLSHTAWTEACQVEVRLLLAYNSSARIPKCPWMEGGEMSPQVETSIEG
TIPFSKPVKVYIMPKPARR

Sequence of entity 3 (B), FASTA

>7BFQ_3 Integrator complex subunit 11 (chains B)
MDEKTTGWRGGHVVEGLAGELEQLRARLEHHPQGQREPPPSGADPMPEIRVTPLGAGQDV
GRSCILVSIAGKNVMLDCGMHMGFNDDRRFPDFSYITQNGRLTDFLDCVIISHFHLDHCG
ALPYFSEMVGYDGPIYMTHPTQAICPILLEDYRKIAVDKKGEANFFTSQMIKDCMKKVVA
VHLHQTVQVDDELEIKAYYAGHVLGAAMFQIKVGSESVVYTGDYNMTPDRHLGAAWIDKC
RPNLLITESTYATTIRDSKRCRERDFLKKVHETVERGGKVLIPVFALGRAQELCILLETF
WERMNLKVPIYFSTGLTEKANHYYKLFIPWTNQKIRKTFVQRNMFEFKHIKAFDRAFADN
PGPMVVFATPGMLHAGQSLQIFRKWAGNEKNMVIMPGYCVQGTVGHKILSGQRKLEMEGR
QVLEVKMQVEYMSFSAHADAKGIMQLVGQAEPESVLLVHGEAKKMEFLKQKIEQELRVNC
YMPANGETVTLLTSPSIPVGISLGLLKREMAQGLLPEAKKPRLLHGTLIMKDSNFRLVSS
EQALKELGLAEHQLRFTCRVHLHDTRKEQETALRVYSHLKSVLKDHCVQHLPDGSVTVES
VLLQAAAPSEDPGTKVLLVSWTYQDEELGSFLTSLLKKGLPQAPS

Sequence of entity 4 (U), FASTA

>7BFQ_4 Unknown (chains U)
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

Primary citation

Structure of the catalytic core of the Integrator complex. Pfleiderer, M.M., Galej, W.P. Mol Cell (2021) 81:1246. DOI 10.1016/j.molcel.2021.01.005 · 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
8UIB 3.21 Å, Structure of the human 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

Browse structure collections

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