9EOC: Integrator complex subunit 13

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

Structure of the Integrator arm module containing INTS10/13/14 subunits. Determined by electron microscopy at 3.3 Å resolution. Released 12 Jun 2024.

Method: Electron microscopy
Resolution: 3.3 Å
Organism: Homo sapiens
Chains: 3
Atoms: 11,437
Mol. weight: 220.24 kDa
Ligands: MG
Released: 12 Jun 2024

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

Secondary structure: helices and β-sheets

9EOC contains 83 α-helices and 55 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 A: 28 helices, 30 β-strands

Element	Residues	Length	Sheet
α-helix	6-8	3
β-strand	9-15	7	1
α-helix	18-21	4
β-strand	23	1	2
β-strand	28	1	3
α-helix	42-46	5
β-strand	47	1	3
β-strand	50	1	2
α-helix	51-69	19
β-strand	75-81	7	1
β-strand	86-87	2	1
α-helix	98-108	11
α-helix	111-112	2
α-helix	123-133	11
α-helix	138-146	9
β-strand	158-163	6	1
β-strand	164	1	4
α-helix	169-192	24
α-helix	197-199	3
β-strand	202-205	4	1
β-strand	208-210	3	4
β-strand	221-224	4	1
β-strand	230-234	5	1
β-strand	236-238	3	4
α-helix	241-254	14
β-strand	257-262	6	5
β-strand	263	1	6
β-strand	281-286	6	5
α-helix	287-290	4
β-strand	313-314	2	5
α-helix	316	1
β-strand	317-319	3	6
α-helix	320-322	3
β-strand	331-336	6	6
β-strand	339	1	5
α-helix	345-355	11
β-strand	360-364	5	6
β-strand	372-379	8	6
β-strand	384-389	6	6
α-helix	399-401	3
β-strand	413	1	7
α-helix	415-424	10
β-strand	426	1	8
β-strand	427-429	3	9
α-helix	433-434	2
β-strand	435	1	10
β-strand	441	1	10
α-helix	442-443	2
α-helix	444-455	12
β-strand	462	1	7
α-helix	463-465	3
α-helix	468-470	3
α-helix	472-474	3
α-helix	475-481	7
α-helix	488-507	20
α-helix	509-512	4
α-helix	525-541	17
α-helix	549-560	12

Chain B: 21 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	3-8	6	11
α-helix	11-14	4
β-strand	16-17	2	12
α-helix	23-24	2
β-strand	25-26	2	12
α-helix	27-44	18
β-strand	51-56	6	11
β-strand	60-67	8	11
α-helix	70-77	8
α-helix	89-102	14
β-strand	109-114	6	11
α-helix	126-132	7
β-strand	150-156	7	11
α-helix	161-166	6
α-helix	170-177	8
β-strand	183-187	5	11
α-helix	194-208	15
β-strand	212-218	7	8
β-strand	221-228	8	8
α-helix	230-233	4
β-strand	234	1	13
β-strand	245	1	13
α-helix	246-248	3
β-strand	250-258	9	8
α-helix	259-262	4
β-strand	269-275	7	8
α-helix	309-320	12
β-strand	322-329	8	8
β-strand	332-338	7	8
β-strand	348-352	5	8
α-helix	353-354	2
β-strand	369-371	3	9
α-helix	372-374	3
α-helix	389	1
α-helix	391-393	3
α-helix	409-424	16
α-helix	431-447	17
α-helix	450-465	16
α-helix	473-489	17

Chain D: 34 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	3-17	15
α-helix	22-35	14
α-helix	40-52	13
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	140-144	5
α-helix	147-161	15
α-helix	169-173	5
α-helix	174-178	5
α-helix	179-184	6
α-helix	192-211	20
α-helix	255-269	15
α-helix	283-295	13
α-helix	304-328	25
β-strand	345-350	6	14
β-strand	396-397	2	14
α-helix	406-425	20
α-helix	427-439	13
α-helix	447-459	13
α-helix	463-475	13
α-helix	495-505	11
α-helix	511-519	9
α-helix	520-522	3
β-strand	549-554	6	14
α-helix	557-576	20
α-helix	584-591	8
α-helix	592-594	3
α-helix	601-614	14
β-strand	618	1	15
α-helix	622-625	4
α-helix	629-637	9
β-strand	649	1	15
α-helix	673-682	10
α-helix	683-685	3
β-strand	686	1	16
β-strand	688	1	16
α-helix	690-700	11
α-helix	704-708	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Integrator complex subunit 13	A	protein	706	Homo sapiens	Q9NVM9 (AlphaFold model)
Integrator complex subunit 14	B	protein	518	Homo sapiens	Q96SY0 (AlphaFold model)
Integrator complex subunit 10	D	protein	710	Homo sapiens	Q9NVR2 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9EOC_1 Integrator complex subunit 13 (chains A)
MKIFSESHKTVFVVDHCPYMAESCRQHVEFDMLVKNRTQGIIPLAPISKSLWTCSVESSM
EYCRIMYDIFPFKKLVNFIVSDSGAHVLNSWTQEDQNLQELMAALAAVGPPNPRADPECC
SILHGLVAAVETLCKITEYQHEARTLLMENAERVGNRGRIICITNAKSDSHVRMLEDCVQ
ETIHEHNKLAANSDHLMQIQKCELVLIHTYPVGEDSLVSDRSKKELSPVLTSEVHSVRAG
RHLATKLNILVQQHFDLASTTITNIPMKEEQHANTSANYDVELLHHKDAHVDFLKSGDSH
LGGGSREGSFKETITLKWCTPRTNNIELHYCTGAYRISPVDVNSRPSSCLTNFLLNGRSV
LLEQPRKSGSKVISHMLSSHGGEIFLHVLSSSRSILEDPPSISEGCGGRVTDYRITDFGE
FMRENRLTPFLDPRYKIDGSLEVPLERAKDQLEKHTRYWPMIISQTTIFNMQAVVPLASV
IVKESLTEEDVLNCQKTIYNLVDMERKNDPLPISTVGTRGKGPKRDEQYRIMWNELETLV
RAHINNSEKHQRVLECLMACRSKPPEEEERKKRGRKREDKEDKSEKAVKDYEQEKSWQDS
ERLKGILERGKEELAEAEIIKDSPDSPEPPNKKPLVEMDETPQVEKSKGPVSLLSLWSNR
INTANSRKHQEFAGRLNSVNNRAELYQHLKEENGMETTENGKASRQ

Sequence of entity 2 (B), FASTA

>9EOC_2 Integrator complex subunit 14 (chains B)
MPTVVVMDVSLSMTRPVSIEGSEEYQRKHLAAHGLTMLFEHMATNYKLEFTALVVFSSLW
ELMVPFTRDYNTLQEALSNMDDYDKTCLESALVGVCNIVQQEWGGAIPCQVVLVTDGCLG
IGRGSLRHSLATQNQRSESNRFPLPFPFPSKLYIMCMANLEELQSTDSLECLERLIDLNN
GEGQIFTIDGPLCLKNVQSMFGKLIDLAYTPFHAVLKCGHLTADVQVFPRPEPFVVDEEI
DPIPKVINTDLEIVGFIDIADISSPPVLSRHLVLPIALNKEGDEVGTGITDDNEDENSAN
QIAGKIPNFCVLLHGSLKVEGMVAIVQLGPEWHGMLYSQADSKKKSNLMMSLFEPGPEPL
PWLGKMAQLGPISDAKENPYGEDDNKSPFPLQPKNKRSYAQNVTVWIKPSGLQTDVQKIL
RNARKLPEKTQTFYKELNRLRKAALAFGFLDLLKGVADMLERECTLLPETAHPDAAFQLT
HAAQQLKLASTGTSEYAAYDQNITPLHTDFSGSSTERI

Sequence of entity 3 (D), FASTA

>9EOC_3 Integrator complex subunit 10 (chains D)
MSAQGDCEFLVQRARELVPQDLWAAKAWLITARSLYPADFNIQYEMYTIERNAERTATAG
RLLYDMFVNFPDQPVVWREISIITSALRNDSQDKQTQFLRSLFETLPGRVQCEMLLKVTE
QCFNTLERSEMLLLLLRRFPETVVQHGVGLGEALLEAETIEEQESPVNCFRKLFVCDVLP
LIINNHDVRLPANLLYKYLNKAAEFYINYVTRSTQIENQHQGAQDTSDLMSPSKRSSQKY
IIEGLTEKSSQIVDPWERLFKILNVVGMRCEWQMDKGRRSYGDILHRMKDLCRYMNNFDS
EAHAKYKNQVVYSTMLVFFKNAFQYVNSIQPSLFQGPNAPSQVPLVLLEDVSNVYGDVEI
DRNKHIHKKRKLAEGREKTMSSDDEDCSAKGRNRHIVVNKAELANSTEVLESFKLARESW
ELLYSLEFLDKEFTRICLAWKTDTWLWLRIFLTDMIIYQGQYKKAIASLHHLAALQGSIS
QPQITGQGTLEHQRALIQLATCHFALGEYRMTCEKVLDLMCYMVLPIQDGGKSQEEPSKV
KPKFRKGSDLKLLPCTSKAIMPYCLHLMLACFKLRAFTDNRDDMALGHVIVLLQQEWPRG
ENLFLKAVNKICQQGNFQYENFFNYVTNIDMLEEFAYLRTQEGGKIHLELLPNQGMLIKH
HTVTRGITKGVKEDFRLAMERQVSRCGENLMVVLHRFCINEKILLLQTLT

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	1

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
8RBZ 3.7 Å, Structure of Integrator-PP2A-SOSS-CTD post-termination complex
9EP1 4.0 Å, Structure of the Integrator arm module containing INTS10/13/14/15 subunits (state 2)
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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