8TQZ: PDB entry 8TQZ

Name: PDB 8TQZ: Eukaryotic translation initiation factor 2B with a mutation (L516A) in the delta subunit
Published: 2023-12-06
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: translation

Eukaryotic translation initiation factor 2B with a mutation (L516A) in the delta subunit. Determined by electron microscopy at 2.9 Å resolution. Released 6 Dec 2023.

Method: Electron microscopy
Resolution: 2.9 Å
Organism: Homo sapiens
Chains: 10
Atoms: 22,334
Mol. weight: 530.17 kDa
Released: 6 Dec 2023

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

Secondary structure: helices and β-sheets

8TQZ contains 134 α-helices and 175 β-strands across 10 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: 10 helices, 36 β-strands

Element	Residues	Length	Sheet
β-strand	44-48	5	6
α-helix	65-67	3
β-strand	69	1	7
β-strand	74	1	7
α-helix	75-86	12
β-strand	90-95	6	6
α-helix	101-107	7
α-helix	110-112	3
β-strand	119-124	6	6
α-helix	131-141	11
β-strand	148-152	5	6
β-strand	155-157	3	8
α-helix	162-174	13
β-strand	179-187	9	6
β-strand	201-202	2	9
β-strand	203-206	4	6
β-strand	211-212	2	6
β-strand	216-217	2	9
β-strand	223-226	4	10
α-helix	229-232	4
β-strand	238-241	4	6
β-strand	244-252	9	6
α-helix	254-262	9
α-helix	269-275	7
β-strand	286-292	7	6
β-strand	297-299	3	8
α-helix	303-314	12
β-strand	336-338	3	11
β-strand	342-344	3	11
β-strand	355-356	2	12
β-strand	360-362	3	11
β-strand	367	1	13
β-strand	373-375	3	12
β-strand	377-379	3	11
β-strand	384-385	2	13
β-strand	390-392	3	12
β-strand	395-396	2	11
β-strand	401-402	2	13
β-strand	407-409	3	12
β-strand	411-413	3	11
β-strand	418-419	2	13
β-strand	424-425	2	12
β-strand	429-431	3	11
β-strand	436-437	2	13
β-strand	442-443	2	12
β-strand	448-449	2	11

Chain B: 12 helices, 34 β-strands

Element	Residues	Length	Sheet
β-strand	44-48	5	20
β-strand	69	1	21
β-strand	74	1	21
α-helix	75-86	12
β-strand	90-95	6	20
α-helix	99-108	10
α-helix	110-112	3
β-strand	119-124	6	20
α-helix	131-141	11
β-strand	148-152	5	20
β-strand	155-157	3	22
α-helix	164-174	11
β-strand	179-187	9	20
α-helix	197-199	3
β-strand	201-205	5	20
β-strand	212-217	6	20
β-strand	223-226	4	23
α-helix	229-233	5
β-strand	240-241	2	20
β-strand	244-252	9	20
α-helix	254-262	9
α-helix	269-276	8
β-strand	286-292	7	20
β-strand	297-299	3	22
α-helix	303-314	12
α-helix	331-333	3
β-strand	336-337	2	24
α-helix	339-341	3
β-strand	343-344	2	24
β-strand	355-356	2	25
β-strand	360-362	3	24
β-strand	367	1	26
β-strand	373-375	3	25
β-strand	377-379	3	24
β-strand	384	1	26
β-strand	390-392	3	25
β-strand	395-396	2	24
β-strand	401-402	2	26
β-strand	407-409	3	25
β-strand	411-413	3	24
β-strand	418-419	2	26
β-strand	424-425	2	25
β-strand	429-431	3	24
β-strand	442-443	2	25
β-strand	448-449	2	24
β-strand	456-457	2	24

Chain C: 17 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	9-23	15
α-helix	31-47	17
α-helix	54-71	18
α-helix	78-97	20
α-helix	129-152	24
β-strand	164-168	5	27
α-helix	172-181	10
β-strand	188-192	5	27
α-helix	200-208	9
β-strand	214-217	4	27
α-helix	220-222	3
β-strand	231-234	4	27
β-strand	238-239	2	28
β-strand	245-248	4	28
α-helix	251-260	10
β-strand	265-268	4	27
α-helix	271-273	3
β-strand	274	1	28
α-helix	287	1
β-strand	288	1	29
α-helix	297-299	3
α-helix	301-305	5
β-strand	306-308	3	30
β-strand	311	1	29
β-strand	313-316	4	28
α-helix	318-320	3
β-strand	323-325	3	27
β-strand	331	1	27
α-helix	333-335	3
α-helix	336-343	8
α-helix	346-348	3

Chain D: 18 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	9-24	16
α-helix	31-47	17
α-helix	54-71	18
α-helix	77-97	21
α-helix	129-144	16
α-helix	147-152	6
α-helix	155-158	4
β-strand	164-168	5	14
α-helix	172-180	9
β-strand	188-192	5	14
α-helix	200-208	9
β-strand	214-217	4	14
α-helix	219-221	3
β-strand	231-234	4	14
β-strand	238-239	2	15
β-strand	245-248	4	15
α-helix	251-260	10
β-strand	265-268	4	14
α-helix	271-273	3
β-strand	274	1	15
β-strand	288	1	16
α-helix	297-299	3
α-helix	301-304	4
β-strand	307-308	2	17
β-strand	311	1	16
β-strand	313-316	4	15
α-helix	318-320	3
β-strand	323-325	3	14
β-strand	331	1	14
α-helix	333-335	3
α-helix	336-343	8
α-helix	346-348	3

Chain E: 15 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	223-237	15
α-helix	272-282	11
α-helix	294-308	15
α-helix	309-313	5
α-helix	314-324	11
β-strand	332-336	5	17
α-helix	340-352	13
β-strand	357-362	6	17
α-helix	369-379	11
β-strand	384-387	4	17
α-helix	388-390	3
α-helix	391-394	4
α-helix	395-397	3
β-strand	400-403	4	17
β-strand	407-408	2	18
β-strand	414-417	4	18
α-helix	418-429	12
β-strand	434-437	4	17
β-strand	443	1	18
α-helix	460-462	3
β-strand	482-484	3	14
β-strand	489-491	3	18
α-helix	494-496	3
β-strand	499-502	4	17
β-strand	505-507	3	17
α-helix	509-511	3
α-helix	512-515	4

Chain F: 21 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	185	1	31
α-helix	192-195	4
α-helix	205-216	12
α-helix	222-238	17
α-helix	242-243	2
α-helix	248-266	19
α-helix	271-285	15
α-helix	293-308	16
α-helix	309-313	5
α-helix	314-324	11
β-strand	332-336	5	30
α-helix	340-352	13
β-strand	357-362	6	30
α-helix	369-378	10
β-strand	383-387	5	30
α-helix	388-390	3
α-helix	391-394	4
α-helix	395-397	3
β-strand	400-404	5	30
β-strand	407-408	2	32
β-strand	414-417	4	32
α-helix	421-429	9
β-strand	434-437	4	30
α-helix	440-442	3
β-strand	443	1	32
β-strand	457	1	31
α-helix	460-463	4
β-strand	467	1	33
β-strand	470	1	33
α-helix	476-478	3
β-strand	482-484	3	27
β-strand	487	1	31
β-strand	489-492	4	32
α-helix	494-496	3
β-strand	499-501	3	30
β-strand	506-508	3	30
α-helix	509-511	3
α-helix	512-516	5

Chain G: 15 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	11-14	4
α-helix	22-34	13
α-helix	45-59	15
α-helix	63-73	11
α-helix	74-76	3
α-helix	91-115	25
α-helix	116-118	3
β-strand	123-127	5	1
α-helix	132-143	12
β-strand	148-153	6	1
α-helix	161-169	9
β-strand	175-178	4	1
β-strand	192-196	5	1
β-strand	199-200	2	2
β-strand	206-207	2	2
α-helix	210-212	3
α-helix	213-221	9
β-strand	226-229	4	1
α-helix	232-234	3
β-strand	235	1	2
α-helix	248-251	4
β-strand	276	1	2
α-helix	278-280	3
β-strand	283-286	4	1
β-strand	289-291	3	1
α-helix	296-302	7

Chain H: 16 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	7-16	10
α-helix	22-34	13
α-helix	46-59	14
α-helix	63-75	13
α-helix	97-115	19
α-helix	116-118	3
β-strand	124-126	3	3
α-helix	132-143	12
β-strand	149-153	5	3
α-helix	161-169	9
β-strand	175-178	4	3
α-helix	180-182	3
α-helix	187-189	3
β-strand	192-196	5	3
β-strand	200	1	4
β-strand	206	1	4
β-strand	209	1	5
α-helix	212-221	10
β-strand	226-229	4	3
β-strand	235	1	4
α-helix	243-245	3
α-helix	248-251	4
β-strand	273	1	5
β-strand	276	1	4
α-helix	278-280	3
β-strand	283-286	4	3
β-strand	289-291	3	3
α-helix	293-295	3
α-helix	296-303	8

2 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Translation initiation factor eIF-2B subunit alpha	G, H	protein	322	Homo sapiens	Q14232 (AlphaFold model)
Translation initiation factor eIF-2B subunit epsilon	A, B	protein	721	Homo sapiens	Q13144 (AlphaFold model)
Translation initiation factor eIF-2B subunit beta	C, D	protein	368	Homo sapiens	P49770 (AlphaFold model)
Translation initiation factor eIF-2B subunit delta	E, F	protein	523	Homo sapiens	Q9UI10 (AlphaFold model)
Translation initiation factor eIF-2B subunit gamma	I, J	protein	452	Homo sapiens	Q9NR50

Sequence of entity 1 (G, H), FASTA

>8TQZ_1 Translation initiation factor eIF-2B subunit alpha (chains G, H)
MHHHHHHGGGSENLYFQSDDKELIEYFKSQMKEDPDMASAVAAIRTLLEFLKRDKGETIQ
GLRANLTSAIETLCGVDSSVAVSSGGELFLRFISLASLEYSDYSKCKKIMIERGELFLRR
ISLSRNKIADLCHTFIKDGATILTHAYSRVVLRVLEAAVAAKKRFSVYVTESQPDLSGKK
MAKALCHLNVPVTVVLDAAVGYIMEKADLVIVGAEGVVENGGIINKIGTNQMAVCAKAQN
KPFYVVAESFKFVRLFPLNQQDVPDKFKYKADTLKVAQTGQDLKEEHPWVDYTAPSLITL
LFTDLGVLTPSAVSDELIKLYL

Sequence of entity 2 (A, B), FASTA

>8TQZ_2 Translation initiation factor eIF-2B subunit epsilon (chains A, B)
MAAPVVAPPGVVVSRANKRSGAGPGGSGGGGARGAEEEPPPPLQAVLVADSFDRRFFPIS
KDQPRVLLPLANVALIDYTLEFLTATGVQETFVFCCWKAAQIKEHLLKSKWCRPTSLNVV
RIITSELYRSLGDVLRDVDAKALVRSDFLLVYGDVISNINITRALEEHRLRRKLEKNVSV
MTMIFKESSPSHPTRCHEDNVVVAVDSTTNRVLHFQKTQGLRRFAFPLSLFQGSSDGVEV
RYDLLDCHISICSPQVAQLFTDNFDYQTRDDFVRGLLVNEEILGNQIHMHVTAKEYGARV
SNLHMYSAVCADVIRRWVYPLTPEANFTDSTTQSCTHSRHNIYRGPEVSLGHGSILEENV
LLGSGTVIGSNCFITNSVIGPGCHIGDNVVLDQTYLWQGVRVAAGAQIHQSLLCDNAEVK
ERVTLKPRSVLTSQVVVGPNITLPEGSVISLHPPDAEEDEDDGEFSDDSGADQEKDKVKM
KGYNPAEVGAAGKGYLWKAAGMNMEEEEELQQNLWGLKINMEEESESESEQSMDSEEPDS
RGGSPQMDDIKVFQNEVLGTLQRGKEENISCDNLVLEINSLKYAYNVSLKEVMQVLSHVV
LEFPLQQMDSPLDSSRYCALLLPLLKAWSPVFRNYIKRAADHLEALAAIEDFFLEHEALG
ISMAKVLMAFYQLEILAEETILSWFSQRDTTDKGQQLRKNQQLQRFIQWLKEAEEESSED
D

Sequence of entity 3 (C, D), FASTA

>8TQZ_3 Translation initiation factor eIF-2B subunit beta (chains C, D)
MHHHHHHGGGSENLYFQSPGSAAKGSELSERIESFVETLKRGGGPRSSEEMARETLGLLR
QIITDHRWSNAGELMELIRREGRRMTAAQPSETTVGNMVRRVLKIIREEYGRLHGRSDES
DQQESLHKLLTSGGLNEDFSFHYAQLQSNIIEAINELLVELEGTMENIAAQALEHIHSNE
VIMTIGFSRTVEAFLKEAARKRKFHVIVAECAPFCQGHEMAVNLSKAGIETTVMTDAAIF
AVMSRVNKVIIGTKTILANGALRAVTGTHTLALAAKHHSTPLIVCAPMFKLSPQFPNEED
SFHKFVAPEEVLPFTEGDILEKVSVHCPVFDYVPPELITLFISNIGGNAPSYIYRLMSEL
YHPDDHVL

Sequence of entity 4 (E, F), FASTA

>8TQZ_4 Translation initiation factor eIF-2B subunit delta (chains E, F)
MAAVAVAVREDSGSGMKAELPPGPGAVGREMTKEEKLQLRKEKKQQKKKRKEEKGAEPET
GSAVSAAQCQVGPTRELPESGIQLGTPREKVPAGRSKAELRAERRAKQEAERALKQARKG
EQGGPPPKASPSTAGETPSGVKRLPEYPQVDDLLLRRLVKKPERQQVPTRKDYGSKVSLF
SHLPQYSRQNSLTQFMSIPSSVIHPAMVRLGLQYSQGLVSGSNARCIALLRALQQVIQDY
TTPPNEELSRDLVNKLKPYMSFLTQCRPLSASMHNAIKFLNKEITSVGSSKREEEAKSEL
RAAIDRYVQEKIVLAAQAISRFAYQKISNGDVILVYGCSSLVSRILQEAWTEGRRFRVVV
VDSRPWLEGRHTLRSLVHAGVPASYLLIPAASYVLPEVSKVLLGAHALLANGSVMSRVGT
AQLALVARAHNVPVLVCCETYKFCERVQTDAFVSNELDDPDDLQCKRGEHVALANWQNHA
SLRLLNLVYDVTPPELVDLVITELGMIPCSSVPVVARVKSSDQ

Sequence of entity 5 (I, J), FASTA

>8TQZ_5 Translation initiation factor eIF-2B subunit gamma (chains I, J)
MEFQAVVMAVGGGSRMTDLTSSIPKPLLPVGNKPLIWYPLNLLERVGFEEVIVVTTRDVQ
KALCAEFKMKMKPDIVCIPDDADMGTADSLRYIYPKLKTDVLVLSCDLITDVALHEVVDL
FRAYDASLAMLMRKGQDSIEPVPGQKGKKKAVEQRDFIGVDSTGKRLLFMANEADLDEEL
VIKGSILQKHPRIRFHTGLVDAHLYCLKKYIVDFLMENGSITSIRSELIPYLVRKQFSSA
SSQQGQEEKEEDLKKKELKSLDIYSFIKEANTLNLAPYDACWNACRGDRWEDLSRSQVRC
YVHIMKEGLCSRVSTLGLYMEANRQVPKLLSALCPEEPPVHSSAQIVSKHLVGVDSLIGP
ETQIGEKSSIKRSVIGSSCLIKDRVTITNCLLMNSVTVEEGSNIQGSVICNNAVIEKGAD
IKDCLIGSGQRIEAKAKRVNEVIVGNDQLMEI

Primary citation

A helical fulcrum in eIF2B coordinates allosteric regulation of stress signaling. Lawrence, R.E., Shoemaker, S.R., Deal, A. et al. Nat Chem Biol (2024) 20:422-431. DOI 10.1038/s41589-023-01453-9 · PubMed

Other PDB entries of the same protein (UniProt Q14232 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9Y4B 2.1 Å, Eukaryotic translation initiation factor 2-B (eIF2B) with a truncation in the beta…
9ZUZ 2.25 Å, Translation Initiation Factor eIF-2B complex with the Isohexide Diamine GSK735
7VLK 2.27 Å, eIF2B-SFSV NSs C2-imposed
9Y3U 2.4 Å, Eukaryotic translation initiation factor 2-B (eIF2B) with a truncation in the beta…
9Y4W 2.4 Å, Eukaryotic translation initiation factor 2-B (eIF2B) with a truncation in the beta…
7F64 2.42 Å, eIF2B-SFSV NSs
9Y3T 2.5 Å, Eukaryotic translation initiation factor 2-B (eIF2B) with a truncation in the beta…
7RLO 2.6 Å, Structure of the human eukaryotic translation initiation factor 2B (eIF2B) in complex…
3ECS 2.65 Å, Crystal structure of human eIF2B alpha
7KMA 2.7 Å, Crystal structure of eif2Balpha with a ligand.
9HVE 2.7 Å, Native human eIF2-eIF2B complex
7F66 2.76 Å, eIF2B-SFSV NSs-1-eIF2

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