7KMA: Eif2Balpha with a ligand

Crystal structure of eif2Balpha with a ligand. Determined by X-ray diffraction at 2.7 Å resolution. Released 21 Jul 2021.

Method: X-ray diffraction
Resolution: 2.7 Å
Organism: Homo sapiens
Chains: 8
Atoms: 17,172
Mol. weight: 279.44 kDa
Ligands: M6P
Released: 21 Jul 2021

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

Secondary structure: helices and β-sheets

7KMA contains 151 α-helices and 95 β-strands across 8 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: 19 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	3-16	14
α-helix	22-36	15
α-helix	42-59	18
α-helix	63-75	13
α-helix	86-103	18
α-helix	107-115	9
α-helix	116-118	3
β-strand	123-128	6	1
α-helix	132-143	12
β-strand	148-153	6	1
α-helix	160-169	10
β-strand	175-178	4	1
α-helix	180-182	3
α-helix	183-186	4
α-helix	187-189	3
β-strand	192-195	4	1
β-strand	199-200	2	2
β-strand	206-209	4	2
α-helix	212-221	10
β-strand	226-229	4	1
α-helix	232-234	3
β-strand	235	1	2
α-helix	243-245	3
α-helix	248-251	4
β-strand	266-267	2	3
β-strand	273-276	4	2
α-helix	278-280	3
β-strand	283-286	4	1
β-strand	289-291	3	1
α-helix	293-295	3
α-helix	296-305	10

Chain B: 19 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	7-16	10
α-helix	22-35	14
α-helix	48-56	9
α-helix	63-75	13
α-helix	93-105	13
α-helix	107-114	8
α-helix	115-118	4
β-strand	124-128	5	4
α-helix	132-143	12
β-strand	149-153	5	4
α-helix	160-169	10
β-strand	175-178	4	4
α-helix	180-182	3
α-helix	183-186	4
α-helix	187-189	3
β-strand	192-195	4	4
β-strand	199-200	2	5
β-strand	206-209	4	5
α-helix	212-221	10
β-strand	226-229	4	4
α-helix	232-234	3
β-strand	235	1	5
α-helix	243-245	3
α-helix	248-251	4
β-strand	267-268	2	6
β-strand	273-276	4	5
α-helix	278-280	3
β-strand	283-286	4	4
β-strand	289-291	3	4
α-helix	293-295	3
α-helix	296-304	9

Chain C: 18 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	3-16	14
α-helix	22-36	15
α-helix	42-57	16
α-helix	63-76	14
α-helix	86-104	19
α-helix	107-115	9
α-helix	116-118	3
β-strand	123-128	6	3
α-helix	132-143	12
β-strand	148-153	6	3
α-helix	160-170	11
β-strand	175-178	4	3
α-helix	180-182	3
α-helix	183-186	4
α-helix	187-189	3
β-strand	192-195	4	3
β-strand	199-200	2	7
β-strand	206-209	4	7
α-helix	212-221	10
β-strand	226-229	4	3
α-helix	232-234	3
β-strand	235	1	7
α-helix	248-251	4
β-strand	268-269	2	1
β-strand	273-276	4	7
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

Chain D: 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	63-75	13
α-helix	87-105	19
α-helix	107-115	9
α-helix	116-118	3
β-strand	124-128	5	8
α-helix	132-143	12
β-strand	149-153	5	8
α-helix	160-170	11
β-strand	175-178	4	8
α-helix	180-182	3
α-helix	183-186	4
α-helix	187-189	3
β-strand	192-195	4	8
β-strand	199-200	2	9
β-strand	206-209	4	9
α-helix	212-221	10
β-strand	226-229	4	8
α-helix	232-234	3
β-strand	235	1	9
α-helix	243-245	3
α-helix	248-251	4
β-strand	267-268	2	10
β-strand	273-276	4	9
α-helix	278-280	3
β-strand	283-286	4	8
β-strand	289-291	3	8
α-helix	293-295	3
α-helix	296-305	10

Chain E: 18 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	4-16	13
α-helix	22-35	14
α-helix	45-59	15
α-helix	63-75	13
α-helix	86-105	20
α-helix	107-114	8
α-helix	120	1
β-strand	123-128	6	10
α-helix	132-143	12
β-strand	148-153	6	10
α-helix	160-169	10
β-strand	175-178	4	10
α-helix	180-182	3
α-helix	183-186	4
α-helix	187-189	3
β-strand	192-195	4	10
β-strand	199-200	2	11
β-strand	206-209	4	11
α-helix	212-221	10
β-strand	226-229	4	10
α-helix	232-234	3
β-strand	235	1	11
α-helix	248-251	4
β-strand	268	1	8
β-strand	273-276	4	11
α-helix	278-280	3
β-strand	283-286	4	10
β-strand	289-291	3	10
α-helix	293-295	3
α-helix	296-303	8

Chain F: 18 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	63-75	13
α-helix	86-104	19
α-helix	107-115	9
α-helix	116-118	3
β-strand	123-128	6	12
α-helix	132-143	12
β-strand	148-153	6	12
α-helix	160-170	11
β-strand	175-178	4	12
α-helix	180-182	3
α-helix	183-186	4
α-helix	187-189	3
β-strand	192-195	4	12
β-strand	199-200	2	13
β-strand	206-209	4	13
α-helix	212-221	10
β-strand	226-229	4	12
α-helix	232-234	3
β-strand	235	1	13
α-helix	243-245	3
β-strand	267-268	2	14
β-strand	273-276	4	13
α-helix	278-280	3
β-strand	283-286	4	12
β-strand	289-291	3	12
α-helix	293-295	3
α-helix	296-304	9

Chain G: 21 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	3-15	13
α-helix	22-35	14
α-helix	46-48	3
α-helix	49-59	11
α-helix	63-76	14
α-helix	79-82	4
α-helix	86-104	19
α-helix	107-115	9
α-helix	120	1
β-strand	123-128	6	14
α-helix	132-143	12
β-strand	148-153	6	14
α-helix	160-170	11
β-strand	175-178	4	14
α-helix	180-182	3
α-helix	183-186	4
α-helix	187-189	3
β-strand	192-195	4	14
β-strand	199-200	2	15
β-strand	206-209	4	15
α-helix	212-221	10
β-strand	226-229	4	14
α-helix	232-234	3
β-strand	235	1	15
α-helix	243-245	3
α-helix	248-251	4
β-strand	268	1	12
β-strand	273-276	4	15
α-helix	278-280	3
β-strand	283-286	4	14
β-strand	289-291	3	14
α-helix	293-295	3
α-helix	296-304	9

Chain H: 19 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	5-16	12
α-helix	22-35	14
α-helix	42-56	15
α-helix	63-76	14
α-helix	79-82	4
α-helix	86-104	19
α-helix	107-114	8
α-helix	120	1
β-strand	123-128	6	6
α-helix	132-143	12
β-strand	148-153	6	6
α-helix	160-170	11
β-strand	175-178	4	6
α-helix	180-182	3
α-helix	183-187	5
β-strand	192-195	4	6
β-strand	199-200	2	16
β-strand	206-209	4	16
α-helix	212-221	10
β-strand	226-229	4	6
α-helix	232-234	3
β-strand	235	1	16
α-helix	243-245	3
α-helix	248-251	4
β-strand	273-276	4	16
α-helix	278-280	3
β-strand	283-286	4	6
β-strand	289-291	3	6
α-helix	293-295	3
α-helix	296-304	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Translation initiation factor eIF-2B subunit alpha	A, B, C, D, E, F, G, H	protein	313	Homo sapiens	Q14232 (AlphaFold model)

Sequence of entity 1 (A, B, C, D, E, F, G, H), FASTA

>7KMA_1 Translation initiation factor eIF-2B subunit alpha (chains A, B, C, D, E, F, G, H)
MDDKELIEYFKSQMKEDPDMASAVAAIRTLLEFLKRDKGETIQGLRANLTSAIETLCGVD
SSVAVSSGGELFLRFISLASLEYSDYSKCKKIMIERGELFLRRISLSRNKIADLCHTFIK
DGATILTHAYSRVVLRVLEAAVAAKKRFSVYVTESQPDLSGKKMAKALCHLNVPVTVVLD
AAVGYIMEKADLVIVGAEGVVENGGIINKIGTNQMAVCAKAQNKPFYVVAESFKFVRLFP
LNQQDVPDKFKYKADTLKVAQTGQDLKEEHPWVDYTAPSLITLLFTDLGVLTPSAVSDEL
IKLYLGGENLYFQ

Ligands and cofactors

ID	Name	Formula	Copies
M6P	6-O-phosphono-alpha-D-mannopyranose	C6 H13 O9 P	8

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

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 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
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)

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