7TRJ: PDB entry 7TRJ

Name: PDB 7TRJ: The eukaryotic translation initiation factor 2B from Homo sapiens with a H160D mutation in the beta subunit
Published: 2022-04-27
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: translation

The eukaryotic translation initiation factor 2B from Homo sapiens with a H160D mutation in the beta subunit. Determined by electron microscopy at 2.8 Å resolution. Released 27 Apr 2022.

Method: Electron microscopy
Resolution: 2.8 Å
Organism: Homo sapiens
Chains: 10
Atoms: 25,190
Mol. weight: 522.36 kDa
Released: 27 Apr 2022

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

Secondary structure: helices and β-sheets

7TRJ contains 152 α-helices and 180 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: 13 helices, 32 β-strands

Element	Residues	Length	Sheet
β-strand	44-48	5	1
α-helix	59-61	3
α-helix	65-67	3
α-helix	75-86	12
β-strand	90-95	6	1
α-helix	99-108	10
α-helix	110-112	3
β-strand	119-124	6	1
α-helix	131-141	11
β-strand	148-152	5	1
β-strand	155-157	3	2
α-helix	162-174	13
β-strand	181-186	6	1
β-strand	201-206	6	3
β-strand	212-217	6	3
β-strand	223-227	5	4
β-strand	238-241	4	3
β-strand	245-252	8	1
α-helix	254-262	9
α-helix	269-278	10
β-strand	287-292	6	1
β-strand	297-299	3	2
α-helix	303-314	12
β-strand	336-338	3	5
α-helix	339-341	3
β-strand	342-344	3	5
α-helix	350-351	2
β-strand	355-356	2	6
β-strand	361	1	5
β-strand	367	1	7
β-strand	373-375	3	6
β-strand	378-379	2	5
β-strand	384	1	7
β-strand	390-392	3	6
β-strand	395-396	2	5
β-strand	401-402	2	7
β-strand	407-409	3	6
β-strand	412-413	2	5
β-strand	418-419	2	7
β-strand	424-425	2	6
β-strand	430-431	2	5
β-strand	436-437	2	7
β-strand	442	1	6
α-helix	443-444	2
β-strand	448-449	2	5

Chain B: 13 helices, 32 β-strands

Element	Residues	Length	Sheet
β-strand	44-48	5	20
α-helix	59-61	3
α-helix	65-67	3
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	21
α-helix	162-174	13
β-strand	181-186	6	20
β-strand	201-206	6	22
β-strand	212-217	6	22
β-strand	223-226	4	23
β-strand	238-241	4	22
β-strand	245-252	8	20
α-helix	254-262	9
α-helix	269-278	10
β-strand	287-292	6	20
β-strand	297-299	3	21
α-helix	303-314	12
β-strand	336-338	3	24
α-helix	339-341	3
β-strand	342-344	3	24
α-helix	350-351	2
β-strand	355-356	2	25
β-strand	361	1	24
β-strand	367	1	26
β-strand	373-375	3	25
β-strand	378-379	2	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	412-413	2	24
β-strand	418-419	2	26
β-strand	424-425	2	25
β-strand	430-431	2	24
β-strand	436-437	2	26
β-strand	442	1	25
α-helix	443-444	2
β-strand	448-449	2	24

Chains C and 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	76-97	22
α-helix	109-112	4
α-helix	129-152	24
β-strand	163-168	6	27
α-helix	172-179	8
β-strand	187-192	6	27
α-helix	193-194	2
α-helix	200-208	9
β-strand	214-217	4	27
α-helix	222-225	4
β-strand	231-234	4	27
β-strand	238-239	2	28
β-strand	245-248	4	28
α-helix	251-261	11
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	301-304	4
β-strand	307-308	2	30
β-strand	311	1	29
β-strand	313-316	4	28
α-helix	318-320	3
β-strand	323-326	4	27
β-strand	329-331	3	27
α-helix	333-335	3
α-helix	336-343	8
α-helix	346-348	3

Chains E and F: 22 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	175-177	3
β-strand	185	1	12
α-helix	192-195	4
α-helix	205-216	12
α-helix	222-239	18
α-helix	248-266	19
α-helix	268-270	3
α-helix	271-285	15
α-helix	293-308	16
α-helix	309-314	6
α-helix	315-323	9
β-strand	332-336	5	11
α-helix	340-351	12
β-strand	357-362	6	11
α-helix	369-379	11
β-strand	383-387	5	11
α-helix	388-390	3
α-helix	391-394	4
α-helix	395-397	3
β-strand	400-404	5	11
β-strand	407-408	2	13
α-helix	413	1
β-strand	414-417	4	13
α-helix	421-429	9
β-strand	434-437	4	11
α-helix	440-442	3
β-strand	443	1	13
β-strand	457	1	12
α-helix	460-463	4
β-strand	467	1	14
β-strand	470	1	14
β-strand	483-484	2	8
β-strand	487	1	12
β-strand	489-492	4	13
α-helix	494-496	3
β-strand	499-501	3	11
β-strand	506-507	2	11
α-helix	509-511	3
α-helix	512-518	7

Chains G and H: 15 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	6-16	11
α-helix	22-34	13
α-helix	42-59	18
α-helix	63-80	18
α-helix	89-105	17
α-helix	107-115	9
α-helix	116-118	3
β-strand	124-127	4	15
α-helix	132-143	12
β-strand	149-153	5	15
α-helix	161-169	9
β-strand	175-178	4	15
α-helix	180-182	3
β-strand	192-196	5	15
β-strand	199-200	2	16
β-strand	206-208	3	16
α-helix	213-221	9
β-strand	226-229	4	15
α-helix	232-234	3
β-strand	235	1	16
α-helix	248-251	4
β-strand	274-276	3	16
α-helix	278-280	3
β-strand	283-286	4	15
β-strand	289-291	3	15
α-helix	295-303	9

Chain I: 8 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	3-8	6	17
β-strand	30	1	18
β-strand	33	1	18
α-helix	37-43	7
β-strand	51-55	5	17
β-strand	73-77	5	17
α-helix	86-92	7
β-strand	100-105	6	17
β-strand	109	1	19
α-helix	115-123	9
β-strand	128-133	6	17
β-strand	156-160	5	3
β-strand	166	1	17
β-strand	167-172	6	3
β-strand	179-183	5	4
α-helix	184-189	6
β-strand	192-196	5	3
β-strand	200-207	8	17
α-helix	210-217	8
α-helix	224-235	12
α-helix	263-265	3
β-strand	300-304	5	17
β-strand	311	1	19
α-helix	316-333	18

Chain J: 8 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	3-8	6	36
β-strand	30	1	37
β-strand	33	1	37
α-helix	37-43	7
β-strand	51-55	5	36
β-strand	73-77	5	36
α-helix	86-92	7
β-strand	100-105	6	36
β-strand	109	1	38
α-helix	115-123	9
β-strand	128-133	6	36
β-strand	156-160	5	22
β-strand	166	1	36
β-strand	167-172	6	22
β-strand	180-183	4	23
α-helix	184-189	6
β-strand	192-196	5	22
β-strand	200-207	8	36
α-helix	210-217	8
α-helix	224-235	12
α-helix	263-265	3
β-strand	300-304	5	36
β-strand	311	1	38
α-helix	316-333	18

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
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	351	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 alpha	G, H	protein	305	Homo sapiens	Q14232 (AlphaFold model)
Translation initiation factor eIF-2B subunit gamma	I, J	protein	452	Homo sapiens	Q9NR50

Sequence of entity 1 (A, B), FASTA

>7TRJ_1 Translation initiation factor eIF-2B subunit epsilon (chains A, B)
MAAPVVAPPGVVVSRANKRSGAGPGGSGGGGARGAEEEPPPPLQAVLVADSFDRRFFPIS
KDQPRVLLPLANVALIDYTLEFLTATGVQETFVFCCWKAAQIKEHLLKSKWCRPTSLNVV
RIITSELYRSLGDVLRDVDAKALVRSDFLLVYGDVISNINITRALEEHRLRRKLEKNVSV
MTMIFKESSPSHPTRCHEDNVVVAVDSTTNRVLHFQKTQGLRRFAFPLSLFQGSSDGVEV
RYDLLDCHISICSPQVAQLFTDNFDYQTRDDFVRGLLVNEEILGNQIHMHVTAKEYGARV
SNLHMYSAVCADVIRRWVYPLTPEANFTDSTTQSCTHSRHNIYRGPEVSLGHGSILEENV
LLGSGTVIGSNCFITNSVIGPGCHIGDNVVLDQTYLWQGVRVAAGAQIHQSLLCDNAEVK
ERVTLKPRSVLTSQVVVGPNITLPEGSVISLHPPDAEEDEDDGEFSDDSGADQEKDKVKM
KGYNPAEVGAAGKGYLWKAAGMNMEEEEELQQNLWGLKINMEEESESESEQSMDSEEPDS
RGGSPQMDDIKVFQNEVLGTLQRGKEENISCDNLVLEINSLKYAYNISLKEVMQVLSHVV
LEFPLQQMDSPLDSSRYCALLLPLLKAWSPVFRNYIKRAADHLEALAAIEDFFLEHEALG
ISMAKVLMAFYQLEILAEETILSWFSQRDTTDKGQQLRKNQQLQRFIQWLKEAEEESSED
D

Sequence of entity 2 (C, D), FASTA

>7TRJ_2 Translation initiation factor eIF-2B subunit beta (chains C, D)
MPGSAAKGSELSERIESFVETLKRGGGPRSSEEMARETLGLLRQIITDHRWSNAGELMEL
IRREGRRMTAAQPSETTVGNMVRRVLKIIREEYGRLHGRSDESDQQESLHKLLTSGGLNE
DFSFHYAQLQSNIIEAINELLVELEGTMENIAAQALEHIDSNEVIMTIGFSRTVEAFLKE
AARKRKFHVIVAECAPFCQGHEMAVNLSKAGIETTVMTDAAIFAVMSRVNKVIIGTKTIL
ANGALRAVTGTHTLALAAKHHSTPLIVCAPMFKLSPQFPNEEDSFHKFVAPEEVLPFTEG
DILEKVSVHCPVFDYVPPELITLFISNIGGNAPSYIYRLMSELYHPDDHVL

Sequence of entity 3 (E, F), FASTA

>7TRJ_3 Translation initiation factor eIF-2B subunit delta (chains E, F)
MAAVAVAVREDSGSGMKAELPPGPGAVGREMTKEEKLQLRKEKKQQKKKRKEEKGAEPET
GSAVSAAQCQVGPTRELPESGIQLGTPREKVPAGRSKAELRAERRAKQEAERALKQARKG
EQGGPPPKASPSTAGETPSGVKRLPEYPQVDDLLLRRLVKKPERQQVPTRKDYGSKVSLF
SHLPQYSRQNSLTQFMSIPSSVIHPAMVRLGLQYSQGLVSGSNARCIALLRALQQVIQDY
TTPPNEELSRDLVNKLKPYMSFLTQCRPLSASMHNAIKFLNKEITSVGSSKREEEAKSEL
RAAIDRYVQEKIVLAAQAISRFAYQKISNGDVILVYGCSSLVSRILQEAWTEGRRFRVVV
VDSRPWLEGRHTLRSLVHAGVPASYLLIPAASYVLPEVSKVLLGAHALLANGSVMSRVGT
AQLALVARAHNVPVLVCCETYKFCERVQTDAFVSNELDDPDDLQCKRGEHVALANWQNHA
SLRLLNLVYDVTPPELVDLVITELGMIPCSSVPVVLRVKSSDQ

Sequence of entity 4 (G, H), FASTA

>7TRJ_4 Translation initiation factor eIF-2B subunit alpha (chains G, H)
MDDKELIEYFKSQMKEDPDMASAVAAIRTLLEFLKRDKGETIQGLRANLTSAIETLCGVD
SSVAVSSGGELFLRFISLASLEYSDYSKCKKIMIERGELFLRRISLSRNKIADLCHTFIK
DGATILTHAYSRVVLRVLEAAVAAKKRFSVYVTESQPDLSGKKMAKALCHLNVPVTVVLD
AAVGYIMEKADLVIVGAEGVVENGGIINKIGTNQMAVCAKAQNKPFYVVAESFKFVRLFP
LNQQDVPDKFKYKADTLKVAQTGQDLKEEHPWVDYTAPSLITLLFTDLGVLTPSAVSDEL
IKLYL

Sequence of entity 5 (I, J), FASTA

>7TRJ_5 Translation initiation factor eIF-2B subunit gamma (chains I, J)
MEFQAVVMAVGGGSRMTDLTSSIPKPLLPVGNKPLIWYPLNLLERVGFEEVIVVTTRDVQ
KALCAEFKMKMKPDIVCIPDDADMGTADSLRYIYPKLKTDVLVLSCDLITDVALHEVVDL
FRAYDASLAMLMRKGQDSIEPVPGQKGKKKAVEQRDFIGVDSTGKRLLFMANEADLDEEL
VIKGSILQKHPRIRFHTGLVDAHLYCLKKYIVDFLMENGSITSIRSELIPYLVRKQFSSA
SSQQGQEEKEEDLKKKELKSLDIYSFIKEANTLNLAPYDACWNACRGDRWEDLSRSQVRC
YVHIMKEGLCSRVSTLGLYMEANRQVPKLLSALCPEEPPVHSSAQIVSKHLVGVDSLIGP
ETQIGEKSSIKRSVIGSSCLIKDRVTITNCLLMNSVTVEEGSNIQGSVICNNAVIEKGAD
IKDCLIGSGQRIEAKAKRVNEVIVGNDQLMEI

Primary citation

A point mutation in the nucleotide exchange factor eIF2B constitutively activates the integrated stress response by allosteric modulation. Boone, M., Wang, L., Lawrence, R. et al. Elife (2022) 11. DOI 10.7554/eLife.76171 · 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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