7BFP: Integrator cleavage module with INTS4/9/11

Structure of the Integrator cleavage module with INTS4/9/11. Determined by electron microscopy at 3.56 Å resolution. Released 24 Mar 2021.

Method: Electron microscopy
Resolution: 3.56 Å
Organism: Homo sapiens
Chains: 4
Atoms: 10,071
Mol. weight: 259.83 kDa
Released: 24 Mar 2021

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

Secondary structure: helices and β-sheets

7BFP contains 59 α-helices and 61 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: 23 helices, 33 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

Chain B: 17 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	3-8	6	11
β-strand	20-23	4	11
β-strand	29-30	2	11
α-helix	57-60	4
β-strand	63-65	3	11
α-helix	71-74	4
α-helix	79-81	3
β-strand	90-92	3	11
α-helix	94-113	20
α-helix	120-122	3
α-helix	123-130	8
β-strand	133-135	3	11
β-strand	141-143	3	12
β-strand	149-151	3	12
β-strand	154	1	13
β-strand	162	1	13
β-strand	165-167	3	12
β-strand	172-176	5	12
β-strand	199-203	5	12
α-helix	213-229	17
β-strand	235-238	4	14
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	14
α-helix	332-340	9
β-strand	347-350	4	14
α-helix	358-365	8
β-strand	369-371	3	15
β-strand	377-379	3	15
β-strand	383-386	4	14
α-helix	395-405	11
β-strand	409-413	5	12
α-helix	417-430	14
β-strand	434-436	3	12
β-strand	444-447	4	11
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

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	10
β-strand	277-278	2	10
α-helix	279-291	13
α-helix	298-308	11
α-helix	314-318	5
α-helix	329-343	15

Chain U: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	351-359	9
α-helix	366-368	3
α-helix	369-380	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	36	Homo sapiens

Sequence of entity 1 (A), FASTA

>7BFP_1 Integrator complex subunit 9 (chains A)
MKLYCLSGHPTLPCNVLKFKSTTIMLDCGLDMTSTLNFLPLPLVQSPRLSNLPGWSLKDG
NAFLDKELKECSGHVFVDSVPEFCLPETELIDLSTVDVILISNYHCMMALPYITEHTGFT
GTVYATEPTVQIGRLLMEELVNFIERVPKAQSASLWKNKDIQRLLPSPLKDAVEVSTWRR
CYTMQEVNSALSKIQLVGYSQKIELFGAVQVTPLSSGYALGSSNWIIQSHYEKVSYVSGS
SLLTTHPQPMDQASLKNSDVLVLTGLTQIPTANPDGMVGEFCSNLALTVRNGGNVLVPCY
PSGVIYDLLECLYQYIDSAGLSSVPLYFISPVANSSLEFSQIFAEWLCHNKQSKVYLPEP
PFPHAELIQTNKLKHYPSIHGDFSNDFRQPCVVFTGHPSLRFGDVVHFMELWGKSSLNTV
IFTEPDFSYLEALAPYQPLAMKCIYCPIDTRLNFIQVSKLLKEVQPLHVVCPEQYTQPPP
AQSHRMDLMIDCQPPAMSYRRAEVLALPFKRRYEKIEIMPELADSLVPMEIKPGISLATV
SAVLHTKDNKHLLQPPPRPAQPTSGKKRKRVSDDVPDCKVLKPLLSGSIPVEQFVQTLEK
HGFSDIKVEDTAKGHIVLLQEAETLIQIEEDSTHIICDNDEMLRVRLRDLVLKFLQKF

Sequence of entity 2 (C), FASTA

>7BFP_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

>7BFP_3 Integrator complex subunit 11 (chains B)
MDEKTTGWRGGHVVEGLAGELEQLRARLEHHPQGQREPPPSGADPMPEIRVTPLGAGQDV
GRSCILVSIAGKNVMLDCGMHMGFNDDRRFPDFSYITQNGRLTDFLDCVIISHFHLDHCG
ALPYFSEMVGYDGPIYMTHPTQAICPILLEDYRKIAVDKKGEANFFTSQMIKDCMKKVVA
VHLHQTVQVDDELEIKAYYAGHVLGAAMFQIKVGSESVVYTGDYNMTPDRHLGAAWIDKC
RPNLLITESTYATTIRDSKRCRERDFLKKVHETVERGGKVLIPVFALGRAQELCILLETF
WERMNLKVPIYFSTGLTEKANHYYKLFIPWTNQKIRKTFVQRNMFEFKHIKAFDRAFADN
PGPMVVFATPGMLHAGQSLQIFRKWAGNEKNMVIMPGYCVQGTVGHKILSGQRKLEMEGR
QVLEVKMQVEYMSFSAHADAKGIMQLVGQAEPESVLLVHGEAKKMEFLKQKIEQELRVNC
YMPANGETVTLLTSPSIPVGISLGLLKREMAQGLLPEAKKPRLLHGTLIMKDSNFRLVSS
EQALKELGLAEHQLRFTCRVHLHDTRKEQETALRVYSHLKSVLKDHCVQHLPDGSVTVES
VLLQAAAPSEDPGTKVLLVSWTYQDEELGSFLTSLLKKGLPQAPS

Sequence of entity 4 (U), FASTA

>7BFP_4 Unknown (chains U)
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

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
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…

Browse structure collections

About this viewer

MolViewer shows 7BFP directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.