SAXSdb — 5kq1

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

mRNA-decapping enzyme subunit 1

Schizosaccharomyces pombe (strain 972 / ATCC 24843)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Proline-rich nuclear receptor coactivator 2 × 2 （Q9NPJ4） mRNA decapping complex subunit 2 × 2 （O13828）	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 Author chain D； PDBConstruct 4–130； UniProt 1–127

Proline-rich nuclear receptor coactivator 2

Homo sapiens

UniProt Q9NPJ4

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	mRNA-decapping enzyme subunit 1 × 2 （Q9P805） mRNA decapping complex subunit 2 × 2 （O13828）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PNRC2_HUMAN
Isoform	Q9NPJ4-2
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–31； UniProt 72–102 Author chain F； PDBConstruct 1–31； UniProt 72–102

mRNA decapping complex subunit 2

Schizosaccharomyces pombe (strain 972 / ATCC 24843)

UniProt O13828

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	mRNA-decapping enzyme subunit 1 × 2 （Q9P805） Proline-rich nuclear receptor coactivator 2 × 2 （Q9NPJ4）	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	3
Chains and sequence ranges	Author chain B； PDBConstruct 6–249； UniProt 1–244 Author chain E； PDBConstruct 6–249； UniProt 1–244

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	5kq1
Deposition date deposition_date	2016-07-05
Structure title title	Crystal structure of S. pombe Dcp1/Dcp2 in complex with H. sapiens PNRC2
Keywords keywords	decapping mRNA decay Nudix cap analog, HYDROLASE; 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.

5kq1__assembly_1__model_1

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

Download this curve (.dat)

5kq1__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5kq1__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	33.27 Å
Rg (electron density)	32.47 Å
Total Rg	33.25 Å
Atom count	6274
Residues	762
Excluded volume	112280 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5kq1__assembly_1__model_1`	hexameric （6）	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 (3)

Entity 1 Entity 1 polymer

Description description	mRNA-decapping enzyme subunit 1
Molecular weight formula_weight	15335.5 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	6274

GEFMEDENILRNAVNLQVLKFHYPEIESIIDIASHVAVYQFDVGSQKWLKTSIEGTFFLVKDQRARVGYVILNRNSPENLYLFINHPSNVHLVDRYLIHRTENQHVVGLWMFDPNDMSRIFNIVKESLLR

Source Source

Source organism organism	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
Common name common_name	Fission yeast
NCBI taxonomy ID ncbi_taxonomy_id	284812
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Proline-rich nuclear receptor coactivator 2
Molecular weight formula_weight	3365.8 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

QNYAGAKFSEPPSPSVLPKPPSHWVPVSFNP

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 3 Entity 3 polymer

Description description	mRNA decapping complex subunit 2
Molecular weight formula_weight	28945.4 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

GGGGSMSFTNATFSQVLDDLSARFILNLPAEEQSSVERLCFQIEQAHWFYEDFIRAQNDQLPSLGLRVFSAKLFAHCPLLWKWSKVHEEAFDDFLRYKTRIPVRGAIMLDMSMQQCVLVKGWKASSGWGFPKGKIDKDESDVDCAIREVYEETGFDCSSRINPNEFIDMTIRGQNVRLYIIPGISLDTRFESRTRKEISKIEWHNLMDLPTFKKNKPQTMKNKFYMVIPFLAPLKKWIKKRNIANNTTK

Source Source

Source organism organism	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
Common name common_name	Fission yeast
NCBI taxonomy ID ncbi_taxonomy_id	284812
Host organism host_organism	Escherichia coli

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d5kq1b1
Class class	a — All alpha proteins
Fold Fold fold	a.242 — Dcp2 domain-like
Superfamily Superfamily superfamily	a.242.1 — Dcp2 domain-like
Family Family family	a.242.1.0 — automated matches

Domain ID domain_id	d5kq1b2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.113 — Nudix
Superfamily Superfamily superfamily	d.113.1 — Nudix
Family Family family	d.113.1.7 — mRNA decapping enzyme-like

Domain ID domain_id	d5kq1b3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d5kq1e1
Class class	a — All alpha proteins
Fold Fold fold	a.242 — Dcp2 domain-like
Superfamily Superfamily superfamily	a.242.1 — Dcp2 domain-like
Family Family family	a.242.1.0 — automated matches

Domain ID domain_id	d5kq1e2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.113 — Nudix
Superfamily Superfamily superfamily	d.113.1 — Nudix
Family Family family	d.113.1.7 — mRNA decapping enzyme-like

Domain ID domain_id	d5kq1e3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (6 domains)

Domain ID domain_id	5kq1A00
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	5kq1B01
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	5kq1B02
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	5kq1D00
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	5kq1E01
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	5kq1E02
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	45.622 Å
Unit-cell length b length_b	118.727 Å
Unit-cell length c length_c	93.174 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	102.77 °
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	3.002 Å
Low-resolution limit resolution_low	44.494 Å
R factor r_factor	0.2120
R_work r_work	0.2101
R_free r_free	0.2474

Crystal structure of S. pombe Dcp1/Dcp2 in complex with H. sapiens PNRC2

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

Proline-rich nuclear receptor coactivator 2

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

5kq1__assembly_1__model_1

5kq1__assembly_1__model_1 | I(q)

5kq1__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 (3)

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

Source Source

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)

Crystal structure of S. pombe Dcp1/Dcp2 in complex with H. sapiens PNRC2

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

Proline-rich nuclear receptor coactivator 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

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

5kq1__assembly_1__model_1

5kq1__assembly_1__model_1 | I(q)

5kq1__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 (3)

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

Source Source

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)