SAXSdb — 5n2v

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

mRNA-decapping enzyme subunit 1

Schizosaccharomyces pombe

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	mRNA decapping complex subunit 2 × 1 （O13828） Edc1 × 1 （Q10108） MAGNESIUM ION × 3 7N-METHYL-8-HYDROGUANOSINE-5'-DIPHOSPHATE × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	mRNA decapping complex subunit 2 × 1 （O13828） Edc1 × 1 （Q10108） MAGNESIUM ION × 3 7N-METHYL-8-HYDROGUANOSINE-5'-DIPHOSPHATE × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DCP1_SCHPO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–129； UniProt 1–127 Author chain D； PDBConstruct 3–129； UniProt 1–127

mRNA decapping complex subunit 2

Schizosaccharomyces pombe

UniProt O13828

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	mRNA-decapping enzyme subunit 1 × 1 （Q9P805） Edc1 × 1 （Q10108） MAGNESIUM ION × 3 7N-METHYL-8-HYDROGUANOSINE-5'-DIPHOSPHATE × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	mRNA-decapping enzyme subunit 1 × 1 （Q9P805） Edc1 × 1 （Q10108） MAGNESIUM ION × 3 7N-METHYL-8-HYDROGUANOSINE-5'-DIPHOSPHATE × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DCP2_SCHPO
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 3–245； UniProt 1–243 Author chain E； PDBConstruct 3–245； UniProt 1–243

Edc1

OrganismNot specified

UniProt Q10108

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	mRNA-decapping enzyme subunit 1 × 1 （Q9P805） mRNA decapping complex subunit 2 × 1 （O13828） MAGNESIUM ION × 3 7N-METHYL-8-HYDROGUANOSINE-5'-DIPHOSPHATE × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	mRNA-decapping enzyme subunit 1 × 1 （Q9P805） mRNA decapping complex subunit 2 × 1 （O13828） MAGNESIUM ION × 3 7N-METHYL-8-HYDROGUANOSINE-5'-DIPHOSPHATE × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	YAQ9_SCHPO
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–26； UniProt 155–180 Author chain F； PDBConstruct 1–26； UniProt 155–180

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	5n2v
Deposition date deposition_date	2017-02-08
Structure title title	Changes in conformational equilibria regulate the activity of the Dcp2 decapping enzyme
Keywords keywords	RNA binding protein; RNA BINDING PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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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.

5n2v__assembly_1__model_1

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

Download this curve (.dat)

5n2v__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5n2v__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	23.69 Å
Rg (electron density)	23.04 Å
Total Rg	24.03 Å
Atom count	3090
Residues	372
Excluded volume	55154 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5n2v__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5n2v__assembly_2__model_1`	trimeric （3）	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 (5)

Entity 1 Entity 1 polymer

Description description	mRNA-decapping enzyme subunit 1
Molecular weight formula_weight	15130.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,D
Atom count atom_count	6180

GAMEDENILRNAVNLQVLKFHYPEIESIIDIASHVAVYQFDVGSQKWLKTSIEGTFFLVKDQRARVGYVILNRNSPENLYLFINHPSNVHLVDRYLIHRTENQHVVGLWMFDPNDMSRIFNIVKESLLR

Source Source

Source organism organism	Schizosaccharomyces pombe
Common name common_name	Fission yeast
NCBI taxonomy ID ncbi_taxonomy_id	4896
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	mRNA decapping complex subunit 2
Molecular weight formula_weight	28689.1 kDa
EC 编号 ec_number	3.-.-.-
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,E

MGMSFTNATFSQVLDDLSARFILNLPAEEQSSVERLCFQIEQAHWFYEDFIRAQNDQLPSLGLRVFSAKLFAHCPLLWKWSKVHEEAFDDFLRYKTRIPVRGAIMLDMSMQQCVLVKGWKASSGWGFPKGKIDKDESDVDCAIREVYEETGFDCSSRINPNEFIDMTIRGQNVRLYIIPGISLDTRFESRTRKEISKIEWHNLMDLPTFKKNKPQTMKNKFYMVIPFLAPLKKWIKKRNIANNTT

Source Source

Source organism organism	Schizosaccharomyces pombe
Common name common_name	Fission yeast
NCBI taxonomy ID ncbi_taxonomy_id	4896
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Edc1
Molecular weight formula_weight	2742.1 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,F

SILYAGPTFTHSPAASNLPIPTFLHS

Entity 4 Entity 4 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 5 Entity 5 non-polymer

Description description	7N-METHYL-8-HYDROGUANOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	459.2 kDa
Source method src_method	syn
Copy count entity_count	2

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6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id	5n2vA00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	29 — PH-domain like
Homologous superfamily homologous superfamily	30 — Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)

Domain ID domain_id	5n2vB01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	1050 — Dcp2, box A domain

Domain ID domain_id	5n2vB02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	79 — Nucleoside Triphosphate Pyrophosphohydrolase
Homologous superfamily homologous superfamily	10 — Nucleoside Triphosphate Pyrophosphohydrolase

Domain ID domain_id	5n2vD00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	29 — PH-domain like
Homologous superfamily homologous superfamily	30 — Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)

Domain ID domain_id	5n2vE01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	1050 — Dcp2, box A domain

Domain ID domain_id	5n2vE02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	79 — Nucleoside Triphosphate Pyrophosphohydrolase
Homologous superfamily homologous superfamily	10 — Nucleoside Triphosphate Pyrophosphohydrolase

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Unit-cell length a length_a	63.841 Å
Unit-cell length b length_b	76.522 Å
Unit-cell length c length_c	89.526 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	102.83 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	3.100 Å
Low-resolution limit resolution_low	48.289 Å
R factor r_factor	0.2414
R_work r_work	0.2388
R_free r_free	0.2868

Changes in conformational equilibria regulate the activity of the Dcp2 decapping enzyme

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

mRNA-decapping enzyme subunit 1

State in the Current Structure

Other States of the Same Protein in the Database

mRNA decapping complex subunit 2

State in the Current Structure

Other States of the Same Protein in the Database

Edc1

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

5n2v__assembly_1__model_1

5n2v__assembly_1__model_1 | I(q)

5n2v__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (5)

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 non-polymer

Entity 5 Entity 5 non-polymer

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)

Changes in conformational equilibria regulate the activity of the Dcp2 decapping enzyme

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

mRNA-decapping enzyme 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

mRNA decapping complex subunit 2

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Edc1

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

5n2v__assembly_1__model_1

5n2v__assembly_1__model_1 | I(q)

5n2v__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (5)

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 non-polymer

Entity 5 Entity 5 non-polymer

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)