8TQO: PDB entry 8TQO

Name: PDB 8TQO: Eukaryotic translation initiation factor 2B tetramer
Published: 2023-12-06
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: translation

Eukaryotic translation initiation factor 2B tetramer. Determined by electron microscopy at 3.1 Å resolution. Released 6 Dec 2023.

Method: Electron microscopy
Resolution: 3.1 Å
Organism: Homo sapiens
Chains: 4
Atoms: 11,122
Mol. weight: 229.41 kDa
Released: 6 Dec 2023

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

Secondary structure: helices and β-sheets

8TQO contains 57 α-helices and 102 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: 10 helices, 37 β-strands

Element	Residues	Length	Sheet
β-strand	44-48	5	1
α-helix	65-67	3
β-strand	69	1	2
β-strand	74	1	2
α-helix	75-86	12
β-strand	90-95	6	1
α-helix	99-107	9
β-strand	119-124	6	1
α-helix	131-140	10
β-strand	148-152	5	1
β-strand	155-157	3	3
α-helix	162-174	13
β-strand	179-187	9	1
β-strand	201-206	6	1
β-strand	211-217	7	1
β-strand	223-225	3	4
α-helix	229-233	5
β-strand	238-241	4	1
β-strand	244-252	9	1
α-helix	254-262	9
α-helix	269-278	10
β-strand	286-292	7	1
β-strand	297-299	3	3
α-helix	303-314	12
β-strand	337-338	2	5
β-strand	342-344	3	5
β-strand	350	1	6
α-helix	351	1
β-strand	355-356	2	7
β-strand	360-362	3	5
β-strand	367	1	8
β-strand	368	1	6
β-strand	373-375	3	7
β-strand	378-379	2	5
β-strand	384	1	8
β-strand	390-392	3	7
β-strand	395-396	2	5
β-strand	401-402	2	8
β-strand	407-409	3	7
β-strand	411-413	3	5
β-strand	418-419	2	8
β-strand	424-425	2	7
β-strand	429-431	3	5
β-strand	436	1	8
β-strand	442-443	2	7
β-strand	448-449	2	5
β-strand	457	1	5

Chain D: 19 helices, 16 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	129-145	17
α-helix	149-152	4
α-helix	155-158	4
β-strand	164-168	5	17
α-helix	172-181	10
β-strand	188-192	5	17
α-helix	193-194	2
α-helix	200-208	9
β-strand	214-217	4	17
α-helix	219-221	3
α-helix	222-225	4
β-strand	231-234	4	17
β-strand	239	1	18
β-strand	245	1	18
β-strand	248	1	19
α-helix	251-260	10
β-strand	265-268	4	17
α-helix	271-273	3
β-strand	274	1	18
β-strand	288	1	20
α-helix	297-299	3
α-helix	301-303	3
β-strand	306-308	3	21
β-strand	311	1	20
β-strand	313	1	19
β-strand	316	1	18
α-helix	318-320	3
β-strand	323-325	3	17
β-strand	331	1	17
α-helix	338-343	6
α-helix	346-348	3

Chain E: 20 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	168-171	4
α-helix	175-177	3
β-strand	185	1	22
α-helix	205-216	12
α-helix	222-239	18
α-helix	242-243	2
α-helix	248-266	19
α-helix	268-270	3
α-helix	271-285	15
α-helix	293-308	16
α-helix	309-313	5
α-helix	315-324	10
β-strand	332-336	5	21
α-helix	340-350	11
β-strand	357-362	6	21
α-helix	369-378	10
β-strand	383-387	5	21
α-helix	388-390	3
α-helix	391-394	4
α-helix	395-397	3
β-strand	400-404	5	21
β-strand	407-408	2	23
β-strand	414-417	4	23
α-helix	420-429	10
β-strand	434-437	4	21
α-helix	440-442	3
β-strand	443	1	23
β-strand	457	1	22
α-helix	460-462	3
β-strand	482-484	3	17
β-strand	489-492	4	23
β-strand	499-501	3	21
β-strand	502	1	24
β-strand	505	1	24
α-helix	512-516	5

Chain I: 8 helices, 34 β-strands

Element	Residues	Length	Sheet
β-strand	4-8	5	9
α-helix	25-27	3
β-strand	29-30	2	10
β-strand	33-34	2	10
α-helix	37-43	7
β-strand	51-53	3	9
β-strand	76-77	2	9
α-helix	86-92	7
β-strand	101-105	5	9
β-strand	109	1	11
α-helix	115-123	9
β-strand	128-133	6	9
β-strand	156-161	6	1
β-strand	166	1	9
β-strand	167-172	6	1
β-strand	181-183	3	4
α-helix	184-189	6
β-strand	192-196	5	1
β-strand	200-207	8	9
α-helix	209-217	9
α-helix	228-234	7
β-strand	300-305	6	9
β-strand	311	1	11
α-helix	316-333	18
β-strand	341	1	12
β-strand	353-354	2	13
β-strand	358	1	12
β-strand	369-371	3	13
β-strand	374	1	14
β-strand	375	1	12
β-strand	377	1	15
β-strand	386-388	3	13
β-strand	391-392	2	14
β-strand	394	1	15
β-strand	397	1	16
β-strand	403-405	3	13
β-strand	408-409	2	14
β-strand	414-415	2	16
β-strand	420-422	3	13
β-strand	425-426	2	14
β-strand	431-432	2	16
β-strand	436-437	2	13

Molecules and chains

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

Sequence of entity 1 (A), FASTA

>8TQO_1 Translation initiation factor eIF-2B subunit epsilon (chains A)
MAAPVVAPPGVVVSRANKRSGAGPGGSGGGGARGAEEEPPPPLQAVLVADSFDRRFFPIS
KDQPRVLLPLANVALIDYTLEFLTATGVQETFVFCCWKAAQIKEHLLKSKWCRPTSLNVV
RIITSELYRSLGDVLRDVDAKALVRSDFLLVYGDVISNINITRALEEHRLRRKLEKNVSV
MTMIFKESSPSHPTRCHEDNVVVAVDSTTNRVLHFQKTQGLRRFAFPLSLFQGSSDGVEV
RYDLLDCHISICSPQVAQLFTDNFDYQTRDDFVRGLLVNEEILGNQIHMHVTAKEYGARV
SNLHMYSAVCADVIRRWVYPLTPEANFTDSTTQSCTHSRHNIYRGPEVSLGHGSILEENV
LLGSGTVIGSNCFITNSVIGPGCHIGDNVVLDQTYLWQGVRVAAGAQIHQSLLCDNAEVK
ERVTLKPRSVLTSQVVVGPNITLPEGSVISLHPPDAEEDEDDGEFSDDSGADQEKDKVKM
KGYNPAEVGAAGKGYLWKAAGMNMEEEEELQQNLWGLKINMEEESESESEQSMDSEEPDS
RGGSPQMDDIKVFQNEVLGTLQRGKEENISCDNLVLEINSLKYAYNVSLKEVMQVLSHVV
LEFPLQQMDSPLDSSRYCALLLPLLKAWSPVFRNYIKRAADHLEALAAIEDFFLEHEALG
ISMAKVLMAFYQLEILAEETILSWFSQRDTTDKGQQLRKNQQLQRFIQWLKEAEEESSED
D

Sequence of entity 2 (I), FASTA

>8TQO_2 Translation initiation factor eIF-2B subunit gamma (chains I)
MEFQAVVMAVGGGSRMTDLTSSIPKPLLPVGNKPLIWYPLNLLERVGFEEVIVVTTRDVQ
KALCAEFKMKMKPDIVCIPDDADMGTADSLRYIYPKLKTDVLVLSCDLITDVALHEVVDL
FRAYDASLAMLMRKGQDSIEPVPGQKGKKKAVEQRDFIGVDSTGKRLLFMANEADLDEEL
VIKGSILQKHPRIRFHTGLVDAHLYCLKKYIVDFLMENGSITSIRSELIPYLVRKQFSSA
SSQQGQEEKEEDLKKKELKSLDIYSFIKEANTLNLAPYDACWNACRGDRWEDLSRSQVRC
YVHIMKEGLCSRVSTLGLYMEANRQVPKLLSALCPEEPPVHSSAQIVSKHLVGVDSLIGP
ETQIGEKSSIKRSVIGSSCLIKDRVTITNCLLMNSVTVEEGSNIQGSVICNNAVIEKGAD
IKDCLIGSGQRIEAKAKRVNEVIVGNDQLMEI

Sequence of entity 3 (D), FASTA

>8TQO_3 Translation initiation factor eIF-2B subunit beta (chains D)
MHHHHHHGGGSENLYFQSPGSAAKGSELSERIESFVETLKRGGGPRSSEEMARETLGLLR
QIITDHRWSNAGELMELIRREGRRMTAAQPSETTVGNMVRRVLKIIREEYGRLHGRSDES
DQQESLHKLLTSGGLNEDFSFHYAQLQSNIIEAINELLVELEGTMENIAAQALEHIHSNE
VIMTIGFSRTVEAFLKEAARKRKFHVIVAECAPFCQGHEMAVNLSKAGIETTVMTDAAIF
AVMSRVNKVIIGTKTILANGALRAVTGTHTLALAAKHHSTPLIVCAPMFKLSPQFPNEED
SFHKFVAPEEVLPFTEGDILEKVSVHCPVFDYVPPELITLFISNIGGNAPSYIYRLMSEL
YHPDDHVL

Sequence of entity 4 (E), FASTA

>8TQO_4 Translation initiation factor eIF-2B subunit delta (chains E)
MAAVAVAVREDSGSGMKAELPPGPGAVGREMTKEEKLQLRKEKKQQKKKRKEEKGAEPET
GSAVSAAQCQVGPTRELPESGIQLGTPREKVPAGRSKAELRAERRAKQEAERALKQARKG
EQGGPPPKASPSTAGETPSGVKRLPEYPQVDDLLLRRLVKKPERQQVPTRKDYGSKVSLF
SHLPQYSRQNSLTQFMSIPSSVIHPAMVRLGLQYSQGLVSGSNARCIALLRALQQVIQDY
TTPPNEELSRDLVNKLKPYMSFLTQCRPLSASMHNAIKFLNKEITSVGSSKREEEAKSEL
RAAIDRYVQEKIVLAAQAISRFAYQKISNGDVILVYGCSSLVSRILQEAWTEGRRFRVVV
VDSRPWLEGRHTLRSLVHAGVPASYLLIPAASYVLPEVSKVLLGAHALLANGSVMSRVGT
AQLALVARAHNVPVLVCCETYKFCERVQTDAFVSNELDDPDDLQCKRGEHVALANWQNHA
SLRLLNLVYDVTPPELVDLVITELGMIPCSSVPVVLRVKSSDQ

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 Q13144 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3JUI 2.0 Å, Crystal Structure of the C-terminal Domain of Human Translation Initiation Factor eIF2B…
9Y4B 2.1 Å, Eukaryotic translation initiation factor 2-B (eIF2B) with a truncation in the beta…
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…
9HVE 2.7 Å, Native human eIF2-eIF2B complex
7F66 2.76 Å, eIF2B-SFSV NSs-1-eIF2
9Y5T 2.78 Å, eIF2B lacking the latch helix bound to ISRACT-02 (Active state)
6CAJ 2.8 Å, Electron cryo-microscopy of the eukaryotic translation initiation factor 2B from Homo…

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