9Y4B: PDB entry 9Y4B

Name: PDB 9Y4B: Eukaryotic translation initiation factor 2-B (eIF2B) with a truncation in the beta subunit (active-like-state) bound to the viral effector AcP10
Published: 2026-06-24
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: translation

Eukaryotic translation initiation factor 2-B (eIF2B) with a truncation in the beta subunit (active-like-state) bound to the viral effector AcP10. Determined by electron microscopy at 2.1 Å resolution. Released 24 Jun 2026.

Method: Electron microscopy
Resolution: 2.1 Å
Organisms: Homo sapiens, Beluga whale coronavirus SW1
Chains: 12
Atoms: 32,179
Mol. weight: 571.33 kDa
Ligands: PO4, ZN
Released: 24 Jun 2026

Explore 9Y4B in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9Y4B contains 229 α-helices and 248 β-strands across 12 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: 17 helices, 37 β-strands

Element	Residues	Length	Sheet
β-strand	44-48	5	1
α-helix	59-61	3
α-helix	65-67	3
β-strand	69-70	2	2
β-strand	73-74	2	2
α-helix	75-85	11
β-strand	90-95	6	1
α-helix	99-108	10
α-helix	110-112	3
β-strand	119-124	6	1
α-helix	131-140	10
β-strand	148-152	5	1
β-strand	155-157	3	3
α-helix	162-174	13
β-strand	179-187	9	1
α-helix	197-199	3
β-strand	201-206	6	1
β-strand	211-217	7	1
β-strand	223-227	5	4
α-helix	228-231	4
β-strand	238-241	4	1
β-strand	244-252	9	1
α-helix	254-262	9
α-helix	269-278	10
α-helix	280-283	4
β-strand	286-292	7	1
β-strand	297-299	3	3
α-helix	303-314	12
α-helix	323-325	3
β-strand	336-338	3	5
β-strand	342-344	3	5
β-strand	349-350	2	6
β-strand	355-356	2	7
β-strand	360-362	3	5
β-strand	367-368	2	6
β-strand	373-375	3	7
β-strand	377-379	3	5
β-strand	384-385	2	6
β-strand	390-392	3	7
β-strand	395-396	2	5
β-strand	401-402	2	6
β-strand	407-409	3	7
β-strand	412-413	2	5
β-strand	418-419	2	6
β-strand	424-425	2	7
β-strand	430-431	2	5
β-strand	436-437	2	6
β-strand	442-443	2	7
α-helix	444	1
β-strand	448-450	3	5
α-helix	485-488	4
β-strand	493	1	6
β-strand	495-497	3	5
α-helix	498	1

Chain B: 20 helices, 37 β-strands

Element	Residues	Length	Sheet
α-helix	40-43	4
β-strand	44-48	5	8
α-helix	59-62	4
α-helix	65-67	3
β-strand	69-70	2	9
β-strand	73-74	2	9
α-helix	75-85	11
β-strand	90-95	6	8
α-helix	99-107	9
α-helix	110-112	3
β-strand	119-124	6	8
α-helix	131-140	10
β-strand	148-152	5	8
β-strand	155-157	3	10
α-helix	162-174	13
β-strand	179-187	9	8
α-helix	197-199	3
β-strand	201-206	6	8
β-strand	211-217	7	8
β-strand	223-227	5	11
α-helix	228-231	4
β-strand	238-241	4	8
β-strand	244-252	9	8
α-helix	255-262	8
α-helix	269-278	10
α-helix	280-283	4
β-strand	286-292	7	8
β-strand	297-299	3	10
α-helix	303-314	12
α-helix	323-325	3
α-helix	331-333	3
β-strand	336-338	3	12
β-strand	342-344	3	12
β-strand	349-350	2	13
β-strand	355-356	2	14
β-strand	360-362	3	12
β-strand	367-368	2	13
β-strand	373-375	3	14
β-strand	378-379	2	12
β-strand	384-385	2	13
β-strand	390-392	3	14
β-strand	395-396	2	12
β-strand	401-402	2	13
β-strand	407-409	3	14
β-strand	412-413	2	12
β-strand	418-419	2	13
β-strand	424-425	2	14
β-strand	430-431	2	12
β-strand	436-437	2	13
β-strand	442-443	2	14
α-helix	444	1
β-strand	448-450	3	12
α-helix	482-484	3
α-helix	485-488	4
β-strand	493	1	13
β-strand	495-497	3	12
α-helix	498	1

Chain C: 20 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	9-24	16
α-helix	31-48	18
α-helix	54-71	18
α-helix	76-96	21
α-helix	101-104	4
α-helix	129-152	24
α-helix	155-157	3
β-strand	163-168	6	15
α-helix	172-181	10
β-strand	187-192	6	15
α-helix	199-209	11
β-strand	213-217	5	15
α-helix	219-221	3
α-helix	222-226	5
β-strand	231-234	4	15
β-strand	238-239	2	16
β-strand	245-248	4	16
α-helix	251-260	10
β-strand	265-268	4	15
α-helix	271-273	3
β-strand	274	1	16
α-helix	283-285	3
β-strand	288	1	17
α-helix	291-293	3
α-helix	297-304	8
β-strand	307-308	2	18
β-strand	311	1	17
β-strand	313-316	4	16
α-helix	318-320	3
β-strand	323-326	4	15
β-strand	329-331	3	15
α-helix	333-335	3
α-helix	336-343	8
α-helix	346-348	3

Chain D: 20 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	9-24	16
α-helix	31-48	18
α-helix	54-71	18
α-helix	76-96	21
α-helix	101-104	4
α-helix	129-152	24
α-helix	155-157	3
β-strand	163-168	6	19
α-helix	172-182	11
β-strand	187-192	6	19
α-helix	200-209	10
β-strand	213-217	5	19
α-helix	219-221	3
α-helix	222-226	5
β-strand	231-234	4	19
β-strand	238-239	2	20
β-strand	245-248	4	20
α-helix	251-260	10
β-strand	265-268	4	19
α-helix	271-273	3
β-strand	274	1	20
α-helix	283-285	3
β-strand	288	1	21
α-helix	291-293	3
α-helix	297-304	8
β-strand	307-308	2	22
β-strand	311	1	21
β-strand	313-316	4	20
α-helix	318-320	3
β-strand	323-326	4	19
β-strand	329-331	3	19
α-helix	333-335	3
α-helix	336-343	8
α-helix	346-348	3

Chain E: 23 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	168-172	5
α-helix	178-180	3
β-strand	185	1	23
α-helix	192-195	4
α-helix	205-215	11
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	309-314	6
α-helix	315-324	10
β-strand	332-336	5	22
α-helix	340-351	12
β-strand	357-362	6	22
α-helix	369-379	11
β-strand	383-387	5	22
α-helix	388-390	3
α-helix	391-394	4
α-helix	395-397	3
β-strand	400-404	5	22
β-strand	407-409	3	24
β-strand	414-417	4	24
α-helix	420-429	10
β-strand	434-437	4	22
α-helix	440-442	3
β-strand	443-444	2	24
β-strand	457	1	23
α-helix	460-463	4
β-strand	466-467	2	25
β-strand	470-471	2	25
α-helix	476-478	3
β-strand	482-485	4	19
β-strand	487	1	23
β-strand	489-492	4	24
α-helix	494-496	3
β-strand	499-502	4	22
β-strand	505-507	3	22
α-helix	509-511	3
α-helix	512-520	9

Chain F: 24 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	168-172	5
α-helix	178-180	3
β-strand	185	1	26
α-helix	192-195	4
α-helix	205-215	11
α-helix	222-238	17
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	309-314	6
α-helix	315-324	10
β-strand	332-336	5	18
α-helix	340-351	12
β-strand	357-362	6	18
α-helix	369-378	10
β-strand	383-387	5	18
α-helix	388-390	3
α-helix	391-394	4
α-helix	395-397	3
β-strand	400-404	5	18
β-strand	407-409	3	27
β-strand	414-417	4	27
α-helix	420-429	10
β-strand	434-437	4	18
α-helix	440-442	3
β-strand	443-444	2	27
β-strand	457	1	26
α-helix	460-463	4
β-strand	466-467	2	28
β-strand	470-471	2	28
α-helix	476-478	3
β-strand	482-485	4	15
β-strand	487	1	26
β-strand	489-492	4	27
α-helix	494-496	3
β-strand	499-502	4	18
β-strand	505-507	3	18
α-helix	509-511	3
α-helix	512-520	9

Chain G: 18 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	3-15	13
α-helix	22-35	14
α-helix	42-59	18
α-helix	63-77	15
α-helix	78-81	4
α-helix	86-105	20
α-helix	107-115	9
α-helix	116-118	3
β-strand	124-128	5	29
α-helix	132-143	12
β-strand	149-153	5	29
α-helix	160-169	10
β-strand	175-178	4	29
α-helix	180-182	3
α-helix	183-186	4
α-helix	187-189	3
β-strand	192-196	5	29
β-strand	199-200	2	30
β-strand	206-209	4	30
α-helix	212-221	10
β-strand	226-229	4	29
α-helix	232-234	3
β-strand	235	1	30
α-helix	248-251	4
β-strand	267-268	2	31
β-strand	273-276	4	30
α-helix	278-280	3
β-strand	283-286	4	29
β-strand	289-291	3	29
α-helix	294-303	10

Chain H: 19 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	3-16	14
α-helix	22-35	14
α-helix	42-59	18
α-helix	63-77	15
α-helix	79-81	3
α-helix	86-104	19
α-helix	107-115	9
α-helix	116-118	3
β-strand	123-128	6	31
α-helix	132-143	12
β-strand	148-153	6	31
α-helix	160-170	11
β-strand	175-178	4	31
α-helix	180-182	3
α-helix	183-186	4
α-helix	187-189	3
β-strand	192-196	5	31
β-strand	199-200	2	32
β-strand	206-209	4	32
α-helix	212-221	10
β-strand	226-229	4	31
α-helix	232-234	3
β-strand	235	1	32
α-helix	243-245	3
α-helix	248-251	4
β-strand	267-269	3	29
β-strand	273-276	4	32
α-helix	278-280	3
β-strand	283-286	4	31
β-strand	289-291	3	31
α-helix	294-303	10

4 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 epsilon	A, B	protein	721	Homo sapiens	Q13144 (AlphaFold model)
Translation initiation factor eIF2B subunit beta	C, D	protein	355	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
Uridine kinase P10	K, L	protein	210	Beluga whale coronavirus SW1	B2BW43

Sequence of entity 1 (A, B), FASTA

>9Y4B_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

>9Y4B_2 Translation initiation factor eIF2B subunit beta (chains C, D)
MHHHHHHGGGSENLYFQSPGSAAKGSELSERIESFVETLKRGGGPRSSEEMARETLGLLR
QIITDHRWSNAGELMELIRREGRRMTAAQPSETTVGNMVRRVLKIIREEYGRLHGRGSGS
GLNEDFSFHYAQLQSNIIEAINELLVELEGTMENIAAQALEHIHSNEVIMTIGFSRTVEA
FLKEAARKRKFHVIVAECAPFCQGHEMAVNLSKAGIETTVMTDAAIFAVMSRVNKVIIGT
KTILANGALRAVTGTHTLALAAKHHSTPLIVCAPMFKLSPQFPNEEDSFHKFVAPEEVLP
FTEGDILEKVSVHCPVFDYVPPELITLFISNIGGNAPSYIYRLMSELYHPDDHVL

Sequence of entity 3 (E, F), FASTA

>9Y4B_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

>9Y4B_4 Translation initiation factor eIF-2B subunit alpha (chains G, H)
MDDKELIEYFKSQMKEDPDMASAVAAIRTLLEFLKRDKGETIQGLRANLTSAIETLCGVD
SSVAVSSGGELFLRFISLASLEYSDYSKCKKIMIERGELFLRRISLSRNKIADLCHTFIK
DGATILTHAYSRVVLRVLEAAVAAKKRFSVYVTESQPDLSGKKMAKALCHLNVPVTVVLD
AAVGYIMEKADLVIVGAEGVVENGGIINKIGTNQMAVCAKAQNKPFYVVAESFKFVRLFP
LNQQDVPDKFKYKADTLKVAQTGQDLKEEHPWVDYTAPSLITLLFTDLGVLTPSAVSDEL
IKLYL

Sequence of entity 5 (I, J), FASTA

>9Y4B_5 Translation initiation factor eIF-2B subunit gamma (chains I, J)
MEFQAVVMAVGGGSRMTDLTSSIPKPLLPVGNKPLIWYPLNLLERVGFEEVIVVTTRDVQ
KALCAEFKMKMKPDIVCIPDDADMGTADSLRYIYPKLKTDVLVLSCDLITDVALHEVVDL
FRAYDASLAMLMRKGQDSIEPVPGQKGKKKAVEQRDFIGVDSTGKRLLFMANEADLDEEL
VIKGSILQKHPRIRFHTGLVDAHLYCLKKYIVDFLMENGSITSIRSELIPYLVRKQFSSA
SSQQGQEEKEEDLKKKELKSLDIYSFIKEANTLNLAPYDACWNACRGDRWEDLSRSQVRC
YVHIMKEGLCSRVSTLGLYMEANRQVPKLLSALCPEEPPVHSSAQIVSKHLVGVDSLIGP
ETQIGEKSSIKRSVIGSSCLIKDRVTITNCLLMNSVTVEEGSNIQGSVICNNAVIEKGAD
IKDCLIGSGQRIEAKAKRVNEVIVGNDQLMEI

Sequence of entity 6 (K, L), FASTA

>9Y4B_6 Uridine kinase P10 (chains K, L)
MKPYIIGISGISGSGKSTFAANLKTKCGDFYAGDVVIINLDGFYRSINEDDMCLVKAGEY
NFDHPYAIDLDHARRCISAIADGHLVAVPIYDFEKKKCVGHYEVNNPRVVIVEGIHALHP
KLFPLYDITAFLEVPMSVALSRRAVRDNKERGRTPEDTAEMFRKFVLPMYKLHVEPNVKK
AAILVNGLNTGVHINMLYEHIKPLLIYPRF

Ligands and cofactors

ID	Name	Formula	Copies
PO4	Phosphate ion	O4 P	4
ZN	Zinc ion	Zn	2

Water and common crystallization additives (CL) are not listed.

Primary citation

Allosteric disordering of eIF2B regulates the integrated stress response. Dalwadi, U., Subramanian, A., Deal, A. et al. Nat Chem Biol (2026). DOI 10.1038/s41589-026-02256-4 · 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…
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…
7L70 2.8 Å, The eukaryotic translation initiation factor 2B from Homo sapiens in its apo form

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