SAXSdb — 5j3t

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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） FORMIC ACID × 5 MAGNESIUM ION × 1 water × 3	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 4–130； 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） FORMIC ACID × 5 MAGNESIUM ION × 1 water × 3	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 1–242； UniProt 1–242

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） FORMIC ACID × 5 MAGNESIUM ION × 1 water × 3	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

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	5j3t
Deposition date deposition_date	2016-03-31
Structure title title	Crystal structure of S. pombe Dcp2:Dcp1:Edc1 mRNA decapping complex
Keywords keywords	hydrolase, decapping, mRNA decay, EVH1, Nudix; HYDROLASE
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.

5j3t__assembly_1__model_1

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

Download this curve (.dat)

5j3t__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5j3t__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	24.55 Å
Rg (electron density)	23.44 Å
Total Rg	24.38 Å
Atom count	3150
Residues	381
Excluded volume	56202 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5j3t__assembly_1__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 (6)

Entity 1 Entity 1 polymer

Description description	mRNA-decapping enzyme subunit 1
Molecular weight formula_weight	15294.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3470

GPHMEDENILRNAVNLQVLKFHYPEIESIIDIASHVAVYQFDVGSQKWLKTSIEGTFFLVKDQRARVGYVILNRNSPENLYLFINHPSNVHLVDRYLIHRTENQHVVGLWMFDPNDMSRIFNIVKESLLR

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 BL21(DE3)

Entity 2 Entity 2 polymer

Description description	mRNA decapping complex subunit 2
Molecular weight formula_weight	28399.8 kDa
EC 编号 ec_number	3.6.1.62
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MSFTNATFSQVLDDLSARFILNLPAEEQSSVERLCFQIEQAHWFYEDFIRAQNDQLPSLGLRVFSAKLFAHCPLLWKWSKVHEEAFDDFLRYKTRIPVRGAIMLDMSMQQCVLVKGWKASSGWGFPKGKIDKDESDVDCAIREVYEETGFDCSSRINPNEFIDMTIRGQNVRLYIIPGISLDTRFESRTRKEISKIEWHNLMDLPTFKKNKPQTMKNKFYMVIPFLAPLKKWIKKRNIANNT

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 BL21(DE3)

Entity 3 Entity 3 polymer

Description description	Edc1
Molecular weight formula_weight	2742.1 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

SILYAGPTFTHSPAASNLPIPTFLHS

Entity 4 Entity 4 non-polymer

Description description	FORMIC ACID
Molecular weight formula_weight	46.0 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 5 Entity 5 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	215

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6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	5j3tA00
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)

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Unit-cell length a length_a	98.809 Å
Unit-cell length b length_b	41.371 Å
Unit-cell length c length_c	93.718 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	114.04 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.600 Å
Low-resolution limit resolution_low	23.430 Å
R factor r_factor	0.1876
R_work r_work	0.1860
R_free r_free	0.2191

Crystal structure of S. pombe Dcp2:Dcp1:Edc1 mRNA decapping complex

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

5j3t__assembly_1__model_1

5j3t__assembly_1__model_1 | I(q)

5j3t__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 (6)

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

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)

Crystal structure of S. pombe Dcp2:Dcp1:Edc1 mRNA decapping complex

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

5j3t__assembly_1__model_1

5j3t__assembly_1__model_1 | I(q)

5j3t__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 (6)

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

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)