7NZM: PDB entry 7NZM

Cryo-EM structure of pre-dephosphorylation complex of phosphorylated eIF2alpha with trapped holophosphatase (PP1A_D64A/PPP1R15A/G-actin/DNase I). Determined by electron microscopy at 3.96 Å resolution. Released 29 Sept 2021.

Method: Electron microscopy
Resolution: 3.96 Å
Organisms: Homo sapiens, Oryctolagus cuniculus, Bos taurus
Chains: 5
Atoms: 9,109
Mol. weight: 176.58 kDa
Ligands: ATP, MN
Released: 29 Sept 2021

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

Secondary structure: helices and β-sheets

7NZM contains 64 α-helices and 60 β-strands across 5 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: 24 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	8-11	4	7
β-strand	16-21	6	7
β-strand	22	1	8
β-strand	24	1	8
β-strand	29-32	4	7
β-strand	35-38	4	9
β-strand	42-44	3	10
α-helix	48-50	3
β-strand	53-54	2	9
α-helix	56-60	5
α-helix	62-64	3
β-strand	65-68	4	9
β-strand	71-72	2	11
β-strand	75-76	2	11
α-helix	79-87	9
α-helix	88-94	7
α-helix	98-100	3
β-strand	103-107	5	7
α-helix	113-125	13
β-strand	131-136	6	7
α-helix	137-145	9
β-strand	150-155	6	12
β-strand	160-166	7	12
β-strand	169-170	2	12
α-helix	172-174	3
β-strand	176-178	3	12
α-helix	182-196	15
α-helix	203-206	4
α-helix	208-216	9
α-helix	223-232	10
β-strand	238-241	4	13
β-strand	247-250	4	13
α-helix	253-262	10
α-helix	264-267	4
α-helix	272-273	2
α-helix	274-284	11
α-helix	290-294	5
β-strand	297-300	4	12
α-helix	302-304	3
α-helix	309-320	12
β-strand	329-330	2	12
α-helix	338-348	11
α-helix	351-354	4
β-strand	357-358	2	7
α-helix	359-365	7
α-helix	369-373	5

Chain B: 16 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	9-18	10
α-helix	23	1
α-helix	32-40	9
α-helix	43-48	6
β-strand	53	1	2
β-strand	59-62	4	3
β-strand	64	1	4
α-helix	69-79	11
β-strand	86-89	4	3
α-helix	100-113	14
β-strand	118-120	3	3
α-helix	121-123	3
α-helix	128-131	4
α-helix	136-143	8
α-helix	146-155	10
α-helix	156-158	3
β-strand	162-165	4	2
β-strand	169-172	4	2
α-helix	184-187	4
α-helix	194-196	3
α-helix	200-206	7
β-strand	208-209	2	5
β-strand	216-218	3	5
β-strand	225-227	3	5
α-helix	229-238	10
β-strand	244-246	3	6
β-strand	257	1	6
β-strand	263-265	3	6
β-strand	267	1	4
α-helix	272-274	3
β-strand	280-285	6	3
β-strand	291-296	6	3

Chain C: 3 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	562-565	4	3
α-helix	583-603	21
α-helix	604-606	3
α-helix	609-617	9

Chain D: 12 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	4-11	8	10
α-helix	13-17	5
α-helix	19-30	12
β-strand	34-40	7	10
α-helix	46-55	10
β-strand	64-67	4	10
α-helix	68-70	3
β-strand	71	1	14
β-strand	78	1	14
β-strand	79-84	6	10
β-strand	90-96	7	15
α-helix	112-113	2
β-strand	114-119	6	15
β-strand	127-134	8	15
α-helix	137-139	3
α-helix	140-158	19
β-strand	163-168	6	15
α-helix	178-183	6
α-helix	185-188	4
β-strand	193-194	2	15
β-strand	203	1	16
β-strand	213-217	5	15
α-helix	219-224	6
β-strand	231-232	2	10
α-helix	235-238	4
α-helix	243-249	7
β-strand	252	1	16
β-strand	255-256	2	10

Chain E: 9 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	13-14	2
β-strand	18-27	10	1
β-strand	30-35	6	1
β-strand	42-45	4	1
α-helix	56-60	5
α-helix	62-65	4
β-strand	69-76	8	1
β-strand	81-85	5	1
α-helix	91-117	27
α-helix	123-132	10
α-helix	134-141	8
α-helix	146-154	9
α-helix	159-162	4
α-helix	169-180	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Eukaryotic translation initiation factor 2 subunit 1	E	protein	186	Homo sapiens	P05198 (AlphaFold model)
Serine/threonine-protein phosphatase PP1-alpha catalytic subunit	B	protein	294	Oryctolagus cuniculus	P62139 (AlphaFold model)
Actin, alpha skeletal muscle, intermediate form	A	protein	375	Oryctolagus cuniculus	P68135 (AlphaFold model)
Deoxyribonuclease-1	D	protein	260	Bos taurus	P00639 (AlphaFold model)
Protein phosphatase 1 regulatory subunit 15A,Maltose/maltodextrin-binding periplasmic protein	C	protein	444	Homo sapiens, Escherichia coli (strain K12)	O75807, P0AEX9

Sequence of entity 1 (E), FASTA

>7NZM_1 Eukaryotic translation initiation factor 2 subunit 1 (chains E)
PGLSCRFYQHKFPEVEDVVMVNVRSIAEMGAYVSLLEYNNIEGMILLSELSRRRIRSINK
LIRIGRNECVVVIRVDKEKGYIDLSKRRVSPEEAIKCEDKFTKSKTVYSILRHVAEVLEY
TKDEQLESLFQRTAWVFDDKYKRPGYGAYDAFKHAVSDPSILDSLDLNEDEREVLINNIN
RRLTPQ

Sequence of entity 2 (B), FASTA

>7NZM_2 Serine/threonine-protein phosphatase PP1-alpha catalytic subunit (chains B)
LNLDSIIGRLLEVQGSRPGKNVQLTENEIRGLCLKSREIFLSQPILLELEAPLKICGAIH
GQYYDLLRLFEYGGFPPESNYLFLGDYVDRGKQSLETICLLLAYKIKYPENFFLLRGNHE
CASINRIYGFYDECKRRYNIKLWKTFTDCFNCLPIAAIVDEKIFCCHGGLSPDLQSMEQI
RRIMRPTDVPDQGLLCDLLWSDPDKDVQGWGENDRGVSFTFGAEVVAKFLHKHDLDLICR
AHQVVEDGYEFFAKRQLVTLFSAPNYCGEFDNAGAMMSVDETLMCSFQILKPAD

Sequence of entity 3 (A), FASTA

>7NZM_3 Actin, alpha skeletal muscle, intermediate form (chains A)
DEDETTALVCDNGSGLVKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQS
KRGILTLKYPIEHGIITNWDDMEKIWHHTFYNELRVAPEEHPTLLTEAPLNPKANREKMT
QIMFETFNVPAMYVAIQAVLSLYASGRTTGIVLDSGDGVTHNVPIYEGYALPHAIMRLDL
AGRDLTDYLMKILTERGYSFVTTAEREIVRDIKEKLCYVALDFENEMATAASSSSLEKSY
ELPDGQVITIGNERFRCPETLFQPSFIGMESAGIHETTYNSIMKCDIDIRKDLYANNVMS
GGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWITKQ
EYDEAGPSIVHRKCF

Sequence of entity 4 (D), FASTA

>7NZM_4 Deoxyribonuclease-1 (chains D)
LKIAAFNIRTFGETKMSNATLASYIVRIVRRYDIVLIQEVRDSHLVAVGKLLDYLNQDDP
NTYHYVVSEPLGRNSYKERYLFLFRPNKVSVLDTYQYDDGCESCGNDSFSREPAVVKFSS
HSTKVKEFAIVALHSAPSDAVAEINSLYDVYLDVQQKWHLNDVMLMGDFNADCSYVTSSQ
WSSIRLRTSSTFQWLIPDSADTTATSTNCAYDRIVVAGSLLQSSVVPGSAAPFDFQAAYG
LSNEMALAISDHYPVEVTLT

Sequence of entity 5 (C), FASTA

>7NZM_5 Protein phosphatase 1 regulatory subunit 15A,Maltose/maltodextrin-binding periplasmic protein (chains C)
ARKVRFSEKVTVHFLAVWAGPAQAARQGPWEQLARDRSRFARRITQAQEELSPCLTPAAR
ARAWARLRNPPLQAKIEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEK
FPQVAATGDGPDIIFWAHDRFGGYAQSGLLAEITPDKAFQDKLYPFTWDAVRYNGKLIAY
PIAVEALSLIYNKDLLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGG
YAFKYENGKYDIKDVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKGETAMTI
NGPWAWSNIDTSKVNYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEFLENYLLT
DEGLEAVNKDKPLGAVALKSYEEELAKDPRIAATMENAQKGEIMPNIPQMSAFWYAVRTA
VINAASGRQTVDEALKDAQTRITK

Ligands and cofactors

ID	Name	Formula	Copies
ATP	Adenosine-5'-triphosphate	C10 H16 N5 O13 P3	1
MN	Manganese (II) ion	Mn	1

Primary citation

Higher-order phosphatase-substrate contacts terminate the integrated stress response. Yan, Y., Harding, H.P., Ron, D. Nat Struct Mol Biol (2021) 28:835-846. DOI 10.1038/s41594-021-00666-7 · PubMed

Other PDB entries of the same protein (UniProt P05198 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1KL9 1.9 Å, Crystal structure of the N-terminal segment of Human eukaryotic initiation factor 2alpha
8PPL 2.65 Å, MERS-CoV Nsp1 bound to the human 43S pre-initiation complex
9HVE 2.7 Å, Native human eIF2-eIF2B complex
7F66 2.76 Å, eIF2B-SFSV NSs-1-eIF2
28ZX 2.8 Å, human 48S PIC with mRNA (Kozak_1)
9QC6 2.83 Å, Structure of eIF2B decamer bound to (P)eIF2 alpha and Compound A-(S)
28ZV 2.9 Å, human 48S PIC with mRNA (non-Kozak)
6ZP4 2.9 Å, SARS-CoV-2 Nsp1 bound to a human 43S preinitiation ribosome complex - state 2
28ZY 3.0 Å, human 48S PIC with mRNA (Kozak_2)
9Y5R 3.01 Å, Eukaryotic translation initiation factor 2-B (eIF2B) bound to phosphorylated eIF2alpha…
6O85 3.03 Å, Electron cryo-microscopy of the eukaryotic translation initiation factor 2B bound to…
6O9Z 3.03 Å, Electron cryo-microscopy of the eukaryotic translation initiation factor 2B bound to…

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