7nzm

Cryo-EM structure of pre-dephosphorylation complex of phosphorylated eIF2alpha with trapped holophosphatase (PP1A_D64A/PPP1R15A/G-actin/DNase I)

Method: ELECTRON MICROSCOPY

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Eukaryotic translation initiation factor 2 subunit 1

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 5 其他Polymer 1	Serine/threonine-protein phosphatase PP1-alpha catalytic subunit × 1 （P62139） Actin, alpha skeletal muscle, intermediate form × 1 （P68135） Deoxyribonuclease-1 × 1 （P00639） Protein phosphatase 1 regulatory subunit 15A,Maltose/maltodextrin-binding periplasmic protein × 1 （O75807,P0AEX9） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 MANGANESE (II) ION × 1 ADENOSINE-5'-TRIPHOSPHATE × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	IF2A_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain E； PDBConstruct 1–186； UniProt 2–187

Serine/threonine-protein phosphatase PP1-alpha catalytic subunit

Oryctolagus cuniculus

UniProt P62139

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 5 其他Polymer 1	Eukaryotic translation initiation factor 2 subunit 1 × 1 （P05198） Actin, alpha skeletal muscle, intermediate form × 1 （P68135） Deoxyribonuclease-1 × 1 （P00639） Protein phosphatase 1 regulatory subunit 15A,Maltose/maltodextrin-binding periplasmic protein × 1 （O75807,P0AEX9） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 MANGANESE (II) ION × 1 ADENOSINE-5'-TRIPHOSPHATE × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PP1A_RABIT
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–294； UniProt 7–300

Actin, alpha skeletal muscle, intermediate form

OrganismNot specified

UniProt P68135

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 5 其他Polymer 1	Eukaryotic translation initiation factor 2 subunit 1 × 1 （P05198） Serine/threonine-protein phosphatase PP1-alpha catalytic subunit × 1 （P62139） Deoxyribonuclease-1 × 1 （P00639） Protein phosphatase 1 regulatory subunit 15A,Maltose/maltodextrin-binding periplasmic protein × 1 （O75807,P0AEX9） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 MANGANESE (II) ION × 1 ADENOSINE-5'-TRIPHOSPHATE × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ACTS_RABIT
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain A； PDBConstruct 1–375； UniProt 3–377

Deoxyribonuclease-1

OrganismNot specified

UniProt P00639

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 5 其他Polymer 1	Eukaryotic translation initiation factor 2 subunit 1 × 1 （P05198） Serine/threonine-protein phosphatase PP1-alpha catalytic subunit × 1 （P62139） Actin, alpha skeletal muscle, intermediate form × 1 （P68135） Protein phosphatase 1 regulatory subunit 15A,Maltose/maltodextrin-binding periplasmic protein × 1 （O75807,P0AEX9） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 MANGANESE (II) ION × 1 ADENOSINE-5'-TRIPHOSPHATE × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DNAS1_BOVIN
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 1–260； UniProt 23–282

Protein phosphatase 1 regulatory subunit 15A,Maltose/maltodextrin-binding periplasmic protein

Escherichia coli (strain K12)

UniProt O75807

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 5 其他Polymer 1	Eukaryotic translation initiation factor 2 subunit 1 × 1 （P05198） Serine/threonine-protein phosphatase PP1-alpha catalytic subunit × 1 （P62139） Actin, alpha skeletal muscle, intermediate form × 1 （P68135） Deoxyribonuclease-1 × 1 （P00639） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 MANGANESE (II) ION × 1 ADENOSINE-5'-TRIPHOSPHATE × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PR15A_HUMAN
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain C； PDBConstruct 1–72； UniProt 553–624

Protein phosphatase 1 regulatory subunit 15A,Maltose/maltodextrin-binding periplasmic protein

Escherichia coli (strain K12)

UniProt P0AEX9

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 5 其他Polymer 1	Eukaryotic translation initiation factor 2 subunit 1 × 1 （P05198） Serine/threonine-protein phosphatase PP1-alpha catalytic subunit × 1 （P62139） Actin, alpha skeletal muscle, intermediate form × 1 （P68135） Deoxyribonuclease-1 × 1 （P00639） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 MANGANESE (II) ION × 1 ADENOSINE-5'-TRIPHOSPHATE × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MALE_ECOLI
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain C； PDBConstruct 74–444； UniProt 26–396

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	7nzm
Deposition date deposition_date	2021-03-24
Structure title title	Cryo-EM structure of pre-dephosphorylation complex of phosphorylated eIF2alpha with trapped holophosphatase (PP1A_D64A/PPP1R15A/G-actin/DNase I)
Keywords keywords	holophosphatase, PP1, PPP1R15A, phosphorylated eIF2alpha, HYDROLASE; HYDROLASE
Experimental Method method	ELECTRON MICROSCOPY

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

7nzm__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

7nzm__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7nzm__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	36.76 Å
Rg (electron density)	36.16 Å
Total Rg	36.62 Å
Atom count	9109
Residues	1156
Excluded volume	161830 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7nzm__assembly_1__model_1`	pentameric （5）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Description description	Eukaryotic translation initiation factor 2 subunit 1
Molecular weight formula_weight	21817.9 kDa
Mutation mutation	phosphorylated Ser51
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E
Atom count atom_count	9109

PGLSCRFYQHKFPEVEDVVMVNVRSIAEMGAYVSLLEYNNIEGMILLSELSRRRIRSINKLIRIGRNECVVVIRVDKEKGYIDLSKRRVSPEEAIKCEDKFTKSKTVYSILRHVAEVLEYTKDEQLESLFQRTAWVFDDKYKRPGYGAYDAFKHAVSDPSILDSLDLNEDEREVLINNINRRLTPQ

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
Molecular weight formula_weight	33647.6 kDa
EC 编号 ec_number	3.1.3.16
Mutation mutation	D64A
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

LNLDSIIGRLLEVQGSRPGKNVQLTENEIRGLCLKSREIFLSQPILLELEAPLKICGAIHGQYYDLLRLFEYGGFPPESNYLFLGDYVDRGKQSLETICLLLAYKIKYPENFFLLRGNHECASINRIYGFYDECKRRYNIKLWKTFTDCFNCLPIAAIVDEKIFCCHGGLSPDLQSMEQIRRIMRPTDVPDQGLLCDLLWSDPDKDVQGWGENDRGVSFTFGAEVVAKFLHKHDLDLICRAHQVVEDGYEFFAKRQLVTLFSAPNYCGEFDNAGAMMSVDETLMCSFQILKPAD

Source Source

Source organism organism	Oryctolagus cuniculus
Common name common_name	Rabbit
NCBI taxonomy ID ncbi_taxonomy_id	9986
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Actin, alpha skeletal muscle, intermediate form
Molecular weight formula_weight	41862.6 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A

DEDETTALVCDNGSGLVKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLKYPIEHGIITNWDDMEKIWHHTFYNELRVAPEEHPTLLTEAPLNPKANREKMTQIMFETFNVPAMYVAIQAVLSLYASGRTTGIVLDSGDGVTHNVPIYEGYALPHAIMRLDLAGRDLTDYLMKILTERGYSFVTTAEREIVRDIKEKLCYVALDFENEMATAASSSSLEKSYELPDGQVITIGNERFRCPETLFQPSFIGMESAGIHETTYNSIMKCDIDIRKDLYANNVMSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWITKQEYDEAGPSIVHRKCF

Entity 4 Entity 4 polymer

Description description	Deoxyribonuclease-1
Molecular weight formula_weight	29092.6 kDa
EC 编号 ec_number	3.1.21.1
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

LKIAAFNIRTFGETKMSNATLASYIVRIVRRYDIVLIQEVRDSHLVAVGKLLDYLNQDDPNTYHYVVSEPLGRNSYKERYLFLFRPNKVSVLDTYQYDDGCESCGNDSFSREPAVVKFSSHSTKVKEFAIVALHSAPSDAVAEINSLYDVYLDVQQKWHLNDVMLMGDFNADCSYVTSSQWSSIRLRTSSTFQWLIPDSADTTATSTNCAYDRIVVAGSLLQSSVVPGSAAPFDFQAAYGLSNEMALAISDHYPVEVTLT

Entity 5 Entity 5 polymer

Description description	Protein phosphatase 1 regulatory subunit 15A,Maltose/maltodextrin-binding periplasmic protein
Molecular weight formula_weight	49169.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

ARKVRFSEKVTVHFLAVWAGPAQAARQGPWEQLARDRSRFARRITQAQEELSPCLTPAARARAWARLRNPPLQAKIEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQVAATGDGPDIIFWAHDRFGGYAQSGLLAEITPDKAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLIYNKDLLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFKYENGKYDIKDVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKGETAMTINGPWAWSNIDTSKVNYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEFLENYLLTDEGLEAVNKDKPLGAVALKSYEEELAKDPRIAATMENAQKGEIMPNIPQMSAFWYAVRTAVINAASGRQTVDEALKDAQTRITK

Source Source

Source organism organism	Escherichia coli (strain K12)
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	Escherichia coli

Entity 6 Entity 6 branched

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	424.4 kDa
Source method src_method	man
Copy count entity_count	1

Entity 7 Entity 7 non-polymer

Description description	MANGANESE (II) ION
Molecular weight formula_weight	54.9 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 8 Entity 8 non-polymer

Description description	ADENOSINE-5'-TRIPHOSPHATE
Molecular weight formula_weight	507.2 kDa
Source method src_method	syn
Copy count entity_count	1

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	7nzmA01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	640 — Actin; Chain A, domain 4
Homologous superfamily homologous superfamily	10 — ATPase, substrate binding domain, subdomain 4

Domain ID domain_id	7nzmB01
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	21 — Purple Acid Phosphatase; chain A, domain 2
Homologous superfamily homologous superfamily	10 — Metallo-dependent phosphatases

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	3.96 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	60413

Cryo-EM structure of pre-dephosphorylation complex of phosphorylated eIF2alpha with trapped holophosphatase (PP1A_D64A/PPP1R15A/G-actin/DNase I)

1. Protein Identity and Related Structures Protein Identity & Related Structures

Eukaryotic translation initiation factor 2 subunit 1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Serine/threonine-protein phosphatase PP1-alpha catalytic subunit

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Actin, alpha skeletal muscle, intermediate form

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Deoxyribonuclease-1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Protein phosphatase 1 regulatory subunit 15A,Maltose/maltodextrin-binding periplasmic protein

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Protein phosphatase 1 regulatory subunit 15A,Maltose/maltodextrin-binding periplasmic protein

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

7nzm__assembly_1__model_1

7nzm__assembly_1__model_1 | I(q)

7nzm__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 polymer

Polymer Polymer

Source Source

Entity 6 Entity 6 branched

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)