9EP1: Integrator complex subunit 13

Name: PDB 9EP1: Structure of the Integrator arm module containing INTS10/13/14/15 subunits (state 2)
Published: 2024-06-12
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transcription

Structure of the Integrator arm module containing INTS10/13/14/15 subunits (state 2). Determined by electron microscopy at 4.0 Å resolution. Released 12 Jun 2024.

Method: Electron microscopy
Resolution: 4.0 Å
Organism: Homo sapiens
Chains: 4
Atoms: 14,333
Mol. weight: 247.69 kDa
Released: 12 Jun 2024

Explore 9EP1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9EP1 contains 106 α-helices and 58 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: 24 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	9-15	7	1
α-helix	18-21	4
β-strand	23	1	2
β-strand	28	1	3
β-strand	47	1	3
β-strand	50	1	2
α-helix	51-69	19
β-strand	75-81	7	1
β-strand	85-87	3	1
α-helix	93-95	3
α-helix	98-108	11
α-helix	111-112	2
α-helix	117-119	3
α-helix	123-133	11
α-helix	138-146	9
β-strand	158-164	7	1
α-helix	169-192	24
α-helix	197-199	3
β-strand	202-208	7	1
β-strand	224	1	1
β-strand	231-232	2	1
β-strand	236	1	1
α-helix	241-254	14
β-strand	257-260	4	4
β-strand	263	1	5
β-strand	283-286	4	4
α-helix	287-290	4
β-strand	317-318	2	5
β-strand	331-336	6	5
β-strand	337-339	3	4
α-helix	345-355	11
β-strand	360-364	5	5
β-strand	372-379	8	5
β-strand	384-389	6	5
α-helix	393-394	2
α-helix	399-401	3
β-strand	413	1	6
α-helix	415-423	9
β-strand	426	1	7
β-strand	427-429	3	8
β-strand	435	1	9
β-strand	441	1	9
α-helix	444-455	12
β-strand	462	1	6
α-helix	463-465	3
α-helix	472-474	3
α-helix	475-481	7
α-helix	488-507	20
α-helix	525-542	18
α-helix	544-546	3
α-helix	548-560	13

Chain B: 22 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-4	2	10
β-strand	7-8	2	10
α-helix	11-14	4
β-strand	16-17	2	11
β-strand	25-26	2	11
α-helix	27-44	18
β-strand	51-56	6	10
β-strand	61-67	7	10
α-helix	70-76	7
α-helix	88-102	15
β-strand	109-114	6	10
α-helix	126-136	11
β-strand	150-155	6	10
α-helix	161-165	5
α-helix	170-177	8
β-strand	183-186	4	10
α-helix	194-208	15
β-strand	213-218	6	12
β-strand	221-228	8	12
α-helix	230-233	4
β-strand	234	1	13
β-strand	245	1	13
β-strand	250-253	4	12
β-strand	256	1	7
β-strand	257-258	2	14
α-helix	259-262	4
β-strand	266	1	5
β-strand	271-275	5	12
α-helix	298-301	4
α-helix	310-320	11
β-strand	322-323	2	14
β-strand	326-327	2	12
β-strand	334-336	3	12
β-strand	348-352	5	12
α-helix	353-354	2
α-helix	361-363	3
α-helix	366-368	3
β-strand	369-371	3	8
α-helix	372-374	3
α-helix	389	1
α-helix	391-393	3
α-helix	409-424	16
α-helix	430-447	18
α-helix	450-465	16
α-helix	473-489	17

Chain C: 27 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	2-8	7
α-helix	13-34	22
α-helix	42-51	10
α-helix	68-84	17
α-helix	88-99	12
α-helix	107-124	18
α-helix	127-138	12
β-strand	141	1	15
α-helix	142-153	12
α-helix	154-158	5
α-helix	164-168	5
α-helix	170-173	4
α-helix	175-188	14
α-helix	194-196	3
α-helix	197-199	3
α-helix	200-212	13
α-helix	214-216	3
α-helix	219-223	5
α-helix	229-231	3
β-strand	234	1	15
α-helix	235-236	2
α-helix	240-257	18
α-helix	277-308	32
α-helix	319-321	3
α-helix	322-335	14
α-helix	342-362	21
α-helix	369-375	7
α-helix	380-381	2
α-helix	383-390	8

Chain D: 33 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	3-17	15
α-helix	22-35	14
α-helix	40-53	14
α-helix	56-69	14
α-helix	74-87	14
α-helix	95-105	11
α-helix	108-121	14
α-helix	125-138	14
α-helix	140-142	3
α-helix	143-161	19
α-helix	169-173	5
α-helix	174-178	5
α-helix	179-184	6
α-helix	192-211	20
α-helix	255-270	16
α-helix	283-291	9
α-helix	292-296	5
α-helix	304-328	25
β-strand	345-347	3	16
β-strand	350	1	17
α-helix	406-425	20
α-helix	427-439	13
α-helix	447-459	13
α-helix	462-475	14
α-helix	494-505	12
α-helix	511-520	10
β-strand	549	1	17
β-strand	552-554	3	16
α-helix	557-576	20
α-helix	584-591	8
α-helix	601-614	14
β-strand	618	1	18
α-helix	622-624	3
α-helix	629-637	9
β-strand	649	1	18
α-helix	673-682	10
α-helix	683-685	3
α-helix	690-700	11
α-helix	704-707	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Integrator complex subunit 13	A	protein	564	Homo sapiens	Q9NVM9 (AlphaFold model)
Integrator complex subunit 14	B	protein	518	Homo sapiens	Q96SY0 (AlphaFold model)
Integrator complex subunit 15	C	protein	391	Homo sapiens	Q96N11 (AlphaFold model)
Integrator complex subunit 10	D	protein	710	Homo sapiens	Q9NVR2 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9EP1_1 Integrator complex subunit 13 (chains A)
MKIFSESHKTVFVVDHCPYMAESCRQHVEFDMLVKNRTQGIIPLAPISKSLWTCSVESSM
EYCRIMYDIFPFKKLVNFIVSDSGAHVLNSWTQEDQNLQELMAALAAVGPPNPRADPECC
SILHGLVAAVETLCKITEYQHEARTLLMENAERVGNRGRIICITNAKSDSHVRMLEDCVQ
ETIHEHNKLAANSDHLMQIQKCELVLIHTYPVGEDSLVSDRSKKELSPVLTSEVHSVRAG
RHLATKLNILVQQHFDLASTTITNIPMKEEQHANTSANYDVELLHHKDAHVDFLKSGDSH
LGGGSREGSFKETITLKWCTPRTNNIELHYCTGAYRISPVDVNSRPSSCLTNFLLNGRSV
LLEQPRKSGSKVISHMLSSHGGEIFLHVLSSSRSILEDPPSISEGCGGRVTDYRITDFGE
FMRENRLTPFLDPRYKIDGSLEVPLERAKDQLEKHTRYWPMIISQTTIFNMQAVVPLASV
IVKESLTEEDVLNCQKTIYNLVDMERKNDPLPISTVGTRGKGPKRDEQYRIMWNELETLV
RAHINNSEKHQRVLECLMACRSKP

Sequence of entity 2 (B), FASTA

>9EP1_2 Integrator complex subunit 14 (chains B)
MPTVVVMDVSLSMTRPVSIEGSEEYQRKHLAAHGLTMLFEHMATNYKLEFTALVVFSSLW
ELMVPFTRDYNTLQEALSNMDDYDKTCLESALVGVCNIVQQEWGGAIPCQVVLVTDGCLG
IGRGSLRHSLATQNQRSESNRFPLPFPFPSKLYIMCMANLEELQSTDSLECLERLIDLNN
GEGQIFTIDGPLCLKNVQSMFGKLIDLAYTPFHAVLKCGHLTADVQVFPRPEPFVVDEEI
DPIPKVINTDLEIVGFIDIADISSPPVLSRHLVLPIALNKEGDEVGTGITDDNEDENSAN
QIAGKIPNFCVLLHGSLKVEGMVAIVQLGPEWHGMLYSQADSKKKSNLMMSLFEPGPEPL
PWLGKMAQLGPISDAKENPYGEDDNKSPFPLQPKNKRSYAQNVTVWIKPSGLQTDVQKIL
RNARKLPEKTQTFYKELNRLRKAALAFGFLDLLKGVADMLERECTLLPETAHPDAAFQLT
HAAQQLKLASTGTSEYAAYDQNITPLHTDFSGSSTERI

Sequence of entity 3 (C), FASTA

>9EP1_3 Integrator complex subunit 15 (chains C)
MSDIRHSLLRRDALSAAKEVLYHLDIYFSSQLQSAPLPIVDKGPVELLEEFVFQVPKERS
AQPKRLNSLQELQLLEIMCNYFQEQTKDSVRQIIFSSLFSPQGNKADDSRMSLLGKLVSM
AVAVCRIPVLECAASWLQRTPVVYCVRLAKALVDDYCCLVPGSIQTLKQIFSASPRFCCQ
FITSVTALYDLSSDDLIPPMDLLEMIVTWIFEDPRLILITFLNTPIAANLPIGFLELTPL
VGLIRWCVKAPLAYKRKKKPPLSNGHVSNKVTKDPGVGMDRDSHLLYSKLHLSVLQVLMT
LQLHLTEKNLYGRLGLILFDHMVPLVEEINRLADELNPLNASQEIELSLDRLAQALQVAM
ASGALLCTRDDLRTLCSRLPHNNLLQLVISG

Sequence of entity 4 (D), FASTA

>9EP1_4 Integrator complex subunit 10 (chains D)
MSAQGDCEFLVQRARELVPQDLWAAKAWLITARSLYPADFNIQYEMYTIERNAERTATAG
RLLYDMFVNFPDQPVVWREISIITSALRNDSQDKQTQFLRSLFETLPGRVQCEMLLKVTE
QCFNTLERSEMLLLLLRRFPETVVQHGVGLGEALLEAETIEEQESPVNCFRKLFVCDVLP
LIINNHDVRLPANLLYKYLNKAAEFYINYVTRSTQIENQHQGAQDTSDLMSPSKRSSQKY
IIEGLTEKSSQIVDPWERLFKILNVVGMRCEWQMDKGRRSYGDILHRMKDLCRYMNNFDS
EAHAKYKNQVVYSTMLVFFKNAFQYVNSIQPSLFQGPNAPSQVPLVLLEDVSNVYGDVEI
DRNKHIHKKRKLAEGREKTMSSDDEDCSAKGRNRHIVVNKAELANSTEVLESFKLARESW
ELLYSLEFLDKEFTRICLAWKTDTWLWLRIFLTDMIIYQGQYKKAIASLHHLAALQGSIS
QPQITGQGTLEHQRALIQLATCHFALGEYRMTCEKVLDLMCYMVLPIQDGGKSQEEPSKV
KPKFRKGSDLKLLPCTSKAIMPYCLHLMLACFKLRAFTDNRDDMALGHVIVLLQQEWPRG
ENLFLKAVNKICQQGNFQYENFFNYVTNIDMLEEFAYLRTQEGGKIHLELLPNQGMLIKH
HTVTRGITKGVKEDFRLAMERQVSRCGENLMVVLHRFCINEKILLLQTLT

Primary citation

Structural basis of the Integrator complex assembly and association with transcription factors. Razew, M., Fraudeau, A., Pfleiderer, M.M. et al. Mol Cell (2024) 84:2542. DOI 10.1016/j.molcel.2024.05.009 · PubMed

Other PDB entries of the same protein (UniProt Q9NVM9 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8PK5 2.5 Å, INTS13-INTS14 complex with ZNF609
6SN1 2.54 Å, Crystal structure of the human INTS13-INTS14 complex
8RC4 3.1 Å, Structure of Integrator-PP2A complex
8PK6 3.21 Å, INTS13 complex with ZNF655
9EOC 3.3 Å, Structure of the Integrator arm module containing INTS10/13/14 subunits
8RBZ 3.7 Å, Structure of Integrator-PP2A-SOSS-CTD post-termination complex
9FA4 4.0 Å, Structure of the Integrator arm module containing subunits INTS10/13/14/15 (state 1)
9FA7 4.0 Å, Structure of the Integrator arm module containing subunits INTS10/13/14/15 (state 3)
8RBX 4.1 Å, Structure of Integrator-PP2A bound to a paused RNA polymerase II-DSIF-NELF-nucleosome…

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