7KMF: PDB entry 7KMF

Sugar phosphate activation of the stress sensor eIF2B. Determined by electron microscopy at 2.91 Å resolution. Released 14 Jul 2021.

Method: Electron microscopy
Resolution: 2.91 Å
Organism: Homo sapiens
Chains: 10
Atoms: 22,875
Mol. weight: 540.55 kDa
Ligands: F6P
Released: 14 Jul 2021

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

Secondary structure: helices and β-sheets

7KMF contains 140 α-helices and 170 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 B: 11 helices, 34 β-strands

Element	Residues	Length	Sheet
β-strand	44-48	5	17
α-helix	59-62	4
β-strand	69	1	18
β-strand	74	1	18
α-helix	75-86	12
β-strand	91-95	5	17
α-helix	99-106	8
α-helix	110-112	3
β-strand	122-124	3	17
α-helix	131-138	8
β-strand	148-151	4	17
β-strand	155-157	3	19
α-helix	163-173	11
β-strand	179-187	9	20
β-strand	202-206	5	20
β-strand	211-216	6	20
β-strand	223-227	5	21
β-strand	239-241	3	20
β-strand	244-245	2	20
β-strand	250	1	17
α-helix	254-261	8
α-helix	269-276	8
β-strand	286-292	7	20
β-strand	297-299	3	19
α-helix	303-314	12
α-helix	319-321	3
β-strand	337	1	22
β-strand	343-344	2	22
β-strand	355-356	2	23
β-strand	361-362	2	22
β-strand	368	1	24
β-strand	373-375	3	23
β-strand	378	1	22
β-strand	384-387	4	24
β-strand	390-392	3	23
β-strand	395	1	22
β-strand	396	1	25
β-strand	400-404	5	24
β-strand	407-408	2	23
β-strand	412-413	2	25
β-strand	417-421	5	24
α-helix	425-426	2
β-strand	430-431	2	25
β-strand	436-437	2	24
β-strand	448-449	2	25

Chain C: 18 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	10-23	14
α-helix	31-48	18
α-helix	54-71	18
α-helix	76-94	19
α-helix	129-141	13
α-helix	147-152	6
α-helix	155-158	4
β-strand	164-167	4	1
α-helix	172-182	11
β-strand	188-192	5	1
α-helix	201-209	9
β-strand	215-217	3	1
α-helix	225-228	4
β-strand	231-234	4	1
β-strand	238-239	2	2
β-strand	245-248	4	2
α-helix	251-260	10
β-strand	265-268	4	1
β-strand	274	1	2
β-strand	288	1	3
α-helix	291-293	3
α-helix	297-299	3
α-helix	301-304	4
β-strand	306-308	3	4
β-strand	311	1	3
β-strand	313-316	4	2
α-helix	318-320	3
β-strand	323-325	3	1
α-helix	333-335	3
α-helix	336-343	8
α-helix	346-348	3

Chain D: 16 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	10-24	15
α-helix	31-48	18
α-helix	54-71	18
α-helix	76-92	17
α-helix	129-141	13
α-helix	147-153	7
β-strand	164-167	4	5
α-helix	172-180	9
β-strand	188-192	5	5
α-helix	200-209	10
β-strand	213-217	5	5
β-strand	231-234	4	5
β-strand	238-239	2	6
β-strand	245-248	4	6
α-helix	251-260	10
β-strand	265-268	4	5
β-strand	274	1	6
β-strand	288	1	7
α-helix	291-293	3
α-helix	297-299	3
α-helix	301-304	4
β-strand	307-308	2	8
β-strand	311	1	7
β-strand	313-316	4	6
α-helix	318-320	3
β-strand	323-325	3	5
α-helix	333-335	3
α-helix	336-341	6
α-helix	346-348	3

Chain E: 18 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	185	1	11
α-helix	205-216	12
α-helix	222-232	11
α-helix	234-239	6
α-helix	249-266	18
α-helix	268-270	3
α-helix	271-286	16
α-helix	293-302	10
α-helix	305-308	4
α-helix	309-313	5
α-helix	314-324	11
β-strand	332-336	5	8
β-strand	357-362	6	8
α-helix	371-377	7
β-strand	384-387	4	8
α-helix	388-391	4
α-helix	395-397	3
β-strand	400-404	5	8
β-strand	407-408	2	12
β-strand	414-416	3	12
α-helix	419-429	11
β-strand	434-437	4	8
β-strand	443	1	12
β-strand	457	1	11
α-helix	460-463	4
α-helix	476-478	3
β-strand	482-484	3	5
β-strand	487	1	11
β-strand	490-492	3	12
α-helix	494-496	3
β-strand	500-501	2	8
β-strand	506-507	2	8
α-helix	512-518	7

Chain F: 17 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	184	1
β-strand	185	1	9
α-helix	205-216	12
α-helix	222-238	17
α-helix	249-266	18
α-helix	268-270	3
α-helix	271-286	16
α-helix	295-308	14
α-helix	309-313	5
α-helix	314-325	12
β-strand	332-336	5	4
α-helix	342-351	10
β-strand	357-362	6	4
α-helix	369-379	11
β-strand	383-387	5	4
α-helix	388-390	3
α-helix	391-394	4
β-strand	400-404	5	4
β-strand	407-408	2	10
β-strand	414-417	4	10
α-helix	420-429	10
β-strand	434-437	4	4
α-helix	440-442	3
β-strand	443	1	10
β-strand	457	1	9
α-helix	460-462	3
β-strand	483-485	3	1
β-strand	487	1	9
β-strand	489-492	4	10
β-strand	499-501	3	4
β-strand	506-507	2	4
α-helix	512-518	7

Chain G: 19 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	5-15	11
α-helix	22-34	13
α-helix	44-60	17
α-helix	63-75	13
α-helix	77-82	6
α-helix	88-102	15
α-helix	107-115	9
α-helix	116-118	3
α-helix	120	1
β-strand	123-127	5	15
α-helix	134-142	9
β-strand	148-153	6	15
α-helix	160-168	9
α-helix	169-171	3
β-strand	175-178	4	15
α-helix	183-186	4
α-helix	187-189	3
β-strand	192-195	4	15
β-strand	199-200	2	16
β-strand	206-209	4	16
α-helix	212-222	11
β-strand	226-228	3	15
α-helix	232-234	3
β-strand	235	1	16
α-helix	248-251	4
β-strand	267-268	2	13
β-strand	273-276	4	16
α-helix	278-280	3
β-strand	283-286	4	15
β-strand	289-291	3	15
α-helix	293-303	11

Chain H: 17 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	5-15	11
α-helix	22-34	13
α-helix	45-59	15
α-helix	63-75	13
α-helix	77-79	3
α-helix	89-102	14
α-helix	107-115	9
α-helix	116-118	3
β-strand	123-127	5	13
α-helix	132-143	12
β-strand	148-153	6	13
α-helix	160-168	9
α-helix	169-171	3
β-strand	175-178	4	13
α-helix	183-186	4
β-strand	192-195	4	13
β-strand	199-200	2	14
β-strand	206-209	4	14
α-helix	212-221	10
β-strand	226-228	3	13
α-helix	232-234	3
β-strand	235	1	14
α-helix	248-251	4
β-strand	267	1	15
β-strand	273-276	4	14
β-strand	283-286	4	13
β-strand	289-291	3	13
α-helix	293-295	3
α-helix	296-301	6

Chain I: 13 helices, 32 β-strands

Element	Residues	Length	Sheet
β-strand	44-48	5	26
α-helix	65-67	3
α-helix	75-86	12
β-strand	90-95	6	26
α-helix	99-107	9
α-helix	110-112	3
β-strand	119	1	26
β-strand	122-124	3	26
α-helix	131-136	6
β-strand	150-151	2	26
β-strand	155-157	3	27
α-helix	163-173	11
β-strand	179-187	9	28
β-strand	201-205	5	29
β-strand	211	1	28
β-strand	212-217	6	29
β-strand	223-227	5	30
β-strand	239-241	3	29
β-strand	244-245	2	28
α-helix	254-262	9
α-helix	269-276	8
β-strand	286-292	7	28
β-strand	297-299	3	27
α-helix	303-314	12
α-helix	319-321	3
α-helix	323-325	3
β-strand	336-337	2	31
α-helix	339-341	3
β-strand	343-344	2	31
β-strand	361-362	2	31
β-strand	368	1	32
β-strand	373-375	3	33
β-strand	378	1	31
β-strand	384-387	4	32
β-strand	390-392	3	33
β-strand	395	1	31
β-strand	396	1	34
β-strand	400-404	5	32
β-strand	407-408	2	33
β-strand	411-413	3	34
β-strand	417-419	3	32
α-helix	425-426	2
β-strand	429-431	3	34
β-strand	436-437	2	32
β-strand	448-449	2	34

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 beta	C, D	protein	367	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	377	Homo sapiens	Q14232 (AlphaFold model)
Translation initiation factor eIF-2B subunit epsilon	B, I	protein	721	Homo sapiens	Q13144 (AlphaFold model)
Translation initiation factor eIF-2B subunit gamma	J, K	protein	452	Homo sapiens	Q9NR50

Sequence of entity 1 (C, D), FASTA

>7KMF_1 Translation initiation factor eIF-2B subunit beta (chains C, D)
MDYKDDDDKENLYFQSMPGSAAKGSELSERIESFVETLKRGGGPRSSEEMARETLGLLRQ
IITDHRWSNAGELMELIRREGRRMTAAQPSETTVGNMVRRVLKIIREEYGRLHGRSDESD
QQESLHKLLTSGGLNEDFSFHYAQLQSNIIEAINELLVELEGTMENIAAQALEHIHSNEV
IMTIGFSRTVEAFLKEAARKRKFHVIVAECAPFCQGHEMAVNLSKAGIETTVMTDAAIFA
VMSRVNKVIIGTKTILANGALRAVTGTHTLALAAKHHSTPLIVCAPMFKLSPQFPNEEDS
FHKFVAPEEVLPFTEGDILEKVSVHCPVFDYVPPELITLFISNIGGNAPSYIYRLMSELY
HPDDHVL

Sequence of entity 2 (E, F), FASTA

>7KMF_2 Translation initiation factor eIF-2B subunit delta (chains E, F)
MAAVAVAVREDSGSGMKAELPPGPGAVGREMTKEEKLQLRKEKKQQKKKRKEEKGAEPET
GSAVSAAQCQVGPTRELPESGIQLGTPREKVPAGRSKAELRAERRAKQEAERALKQARKG
EQGGPPPKASPSTAGETPSGVKRLPEYPQVDDLLLRRLVKKPERQQVPTRKDYGSKVSLF
SHLPQYSRQNSLTQFMSIPSSVIHPAMVRLGLQYSQGLVSGSNARCIALLRALQQVIQDY
TTPPNEELSRDLVNKLKPYMSFLTQCRPLSASMHNAIKFLNKEITSVGSSKREEEAKSEL
RAAIDRYVQEKIVLAAQAISRFAYQKISNGDVILVYGCSSLVSRILQEAWTEGRRFRVVV
VDSRPWLEGRHTLRSLVHAGVPASYLLIPAASYVLPEVSKVLLGAHALLANGSVMSRVGT
AQLALVARAHNVPVLVCCETYKFCERVQTDAFVSNELDDPDDLQCKRGEHVALANWQNHA
SLRLLNLVYDVTPPELVDLVITELGMIPCSSVPVVLRVKSSDQ

Sequence of entity 3 (G, H), FASTA

>7KMF_3 Translation initiation factor eIF-2B subunit alpha (chains G, H)
MDDKELIEYFKSQMKEDPDMASAVAAIRTLLEFLKRDKGETIQGLRANLTSAIETLCGVD
SSVAVSSGGELFLRFISLASLEYSDYSKCKKIMIERGELFLRRISLSRNKIADLCHTFIK
DGATILTHAYSRVVLRVLEAAVAAKKRFSVYVTESQPDLSGKKMAKALCHLNVPVTVVLD
AAVGYIMEKADLVIVGAEGVVENGGIINKIGTNQMAVCAKAQNKPFYVVAESFKFVRLFP
LNQQDVPDKFKYKADTLKVAQTGQDLKEEHPWVDYTAPSLITLLFTDLGVLTPSAVSDEL
IKLYLGGENLYFQAEDKGGGSGGGGSGGGGSASQGGLNDIFEAQKIEWHEGGGGSGGGGS
GGGGSGRDQDYKDDDDK

Sequence of entity 4 (B, I), FASTA

>7KMF_4 Translation initiation factor eIF-2B subunit epsilon (chains B, I)
MAAPVVAPPGVVVSRANKRSGAGPGGSGGGGARGAEEEPPPPLQAVLVADSFDRRFFPIS
KDQPRVLLPLANVALIDYTLEFLTATGVQETFVFCCWKAAQIKEHLLKSKWCRPTSLNVV
RIITSELYRSLGDVLRDVDAKALVRSDFLLVYGDVISNINITRALEEHRLRRKLEKNVSV
MTMIFKESSPSHPTRCHEDNVVVAVDSTTNRVLHFQKTQGLRRFAFPLSLFQGSSDGVEV
RYDLLDCHISICSPQVAQLFTDNFDYQTRDDFVRGLLVNEEILGNQIHMHVTAKEYGARV
SNLHMYSAVCADVIRRWVYPLTPEANFTDSTTQSCTHSRHNIYRGPEVSLGHGSILEENV
LLGSGTVIGSNCFITNSVIGPGCHIGDNVVLDQTYLWQGVRVAAGAQIHQSLLCDNAEVK
ERVTLKPRSVLTSQVVVGPNITLPEGSVISLHPPDAEEDEDDGEFSDDSGADQEKDKVKM
KGYNPAEVGAAGKGYLWKAAGMNMEEEEELQQNLWGLKINMEEESESESEQSMDSEEPDS
RGGSPQMDDIKVFQNEVLGTLQRGKEENISCDNLVLEINSLKYAYNISLKEVMQVLSHVV
LEFPLQQMDSPLDSSRYCALLLPLLKAWSPVFRNYIKRAADHLEALAAIEDFFLEHEALG
ISMAKVLMAFYQLEILAEETILSWFSQRDTTDKGQQLRKNQQLQRFIQWLKEAEEESSED
D

Sequence of entity 5 (J, K), FASTA

>7KMF_5 Translation initiation factor eIF-2B subunit gamma (chains J, K)
MEFQAVVMAVGGGSRMTDLTSSIPKPLLPVGNKPLIWYPLNLLERVGFEEVIVVTTRDVQ
KALCAEFKMKMKPDIVCIPDDADMGTADSLRYIYPKLKTDVLVLSCDLITDVALHEVVDL
FRAYDASLAMLMRKGQDSIEPVPGQKGKKKAVEQRDFIGVDSTGKRLLFMANEADLDEEL
VIKGSILQKHPRIRFHTGLVDAHLYCLKKYIVDFLMENGSITSIRSELIPYLVRKQFSSA
SSQQGQEEKEEDLKKKELKSLDIYSFIKEANTLNLAPYDACWNACRGDRWEDLSRSQVRC
YVHIMKEGLCSRVSTLGLYMEANRQVPKLLSALCPEEPPVHSSAQIVSKHLVGVDSLIGP
ETQIGEKSSIKRSVIGSSCLIKDRVTITNCLLMNSVTVEEGSNIQGSVICNNAVIEKGAD
IKDCLIGSGQRIEAKAKRVNEVIVGNDQLMEI

Ligands and cofactors

ID	Name	Formula	Copies
F6P	6-O-phosphono-beta-D-fructofuranose	C6 H13 O9 P	2

Primary citation

Sugar phosphate activation of the stress sensor eIF2B. Hao, Q., Heo, J.M., Nocek, B.P. et al. Nat Commun (2021) 12:3440-3440. DOI 10.1038/s41467-021-23836-z · PubMed

Other PDB entries of the same protein (UniProt P49770 (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…
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…

Browse structure collections

About this viewer

MolViewer shows 7KMF directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.