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5kq4

Crystal structure of S. pombe Dcp1/Dcp2 in complex with H. sapiens PNRC2 and synthetic cap analog

Method: X-RAY DIFFRACTION
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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)

UniProt Q9P805

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） ;[[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-7-methyl-6-oxidanylidene-3~{H}-purin-7-ium-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-sulfanyl-phosphoryl] [[[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-7-methyl-6-oxidanylidene-3~{H}-purin-7-ium-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-sulfanyl-phosphoryl]oxy-oxidanyl-phosphoryl] hydrogen phosphate ; × 2 water × 5 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
2qkl 2qkm 2qkm 2qkm 2qkm 5j3q 5j3q 5j3t 5j3y 5j3y 5jp4 5kq1

15 assemblies; showing the first 12

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） ;[[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-7-methyl-6-oxidanylidene-3~{H}-purin-7-ium-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-sulfanyl-phosphoryl] [[[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-7-methyl-6-oxidanylidene-3~{H}-purin-7-ium-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-sulfanyl-phosphoryl]oxy-oxidanyl-phosphoryl] hydrogen phosphate ; × 2 water × 5 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
4b6h 4b6h 5kq1 5kq4

4 assemblies

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） ;[[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-7-methyl-6-oxidanylidene-3~{H}-purin-7-ium-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-sulfanyl-phosphoryl] [[[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-7-methyl-6-oxidanylidene-3~{H}-purin-7-ium-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-sulfanyl-phosphoryl]oxy-oxidanyl-phosphoryl] hydrogen phosphate ; × 2 water × 5 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
2a6t 2a6t

2 assemblies

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
2qkl 2qkm 2qkm 2qkm 2qkm 4a54 5j3t 5j3y 5j3y 5kq1 5kq4 5n2v

13 assemblies; showing the first 12

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_id5kq4
Deposition date deposition_date2016-07-05
Structure title titleCrystal structure of S. pombe Dcp1/Dcp2 in complex with H. sapiens PNRC2 and synthetic cap analog
Keywords keywordsdecapping mRNA decay Nudix cap analog, HYDROLASE; HYDROLASE
Experimental Method methodX-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.

5kq4__assembly_1__model_1

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

Download this curve (.dat)

5kq4__assembly_1__model_1 | I(q)

10-2 10-1 106 107 108 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

5kq4__assembly_1__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg（Guinier）34.21 Å
Rg (electron density)33.66 Å
Total Rg34.32 Å
Atom count6461
Residues772
Excluded volume115070 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 5kq4__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 (5)

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_idd5kq4b1
Class classa — All alpha proteins
Fold Fold folda.242 — Dcp2 domain-like
Superfamily Superfamily superfamilya.242.1 — Dcp2 domain-like
Family Family familya.242.1.0 — automated matches
Domain ID domain_idd5kq4b2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.113 — Nudix
Superfamily Superfamily superfamilyd.113.1 — Nudix
Family Family familyd.113.1.7 — mRNA decapping enzyme-like
Domain ID domain_idd5kq4b3
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd5kq4e1
Class classa — All alpha proteins
Fold Fold folda.242 — Dcp2 domain-like
Superfamily Superfamily superfamilya.242.1 — Dcp2 domain-like
Family Family familya.242.1.0 — automated matches
Domain ID domain_idd5kq4e2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.113 — Nudix
Superfamily Superfamily superfamilyd.113.1 — Nudix
Family Family familyd.113.1.7 — mRNA decapping enzyme-like
Domain ID domain_idd5kq4e3
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (6 domains)

Domain ID domain_id5kq4A00
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology29 — PH-domain like
Homologous superfamily homologous superfamily30 — Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)
Domain ID domain_id5kq4B01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily1050 — Dcp2, box A domain
Domain ID domain_id5kq4B02
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology79 — Nucleoside Triphosphate Pyrophosphohydrolase
Homologous superfamily homologous superfamily10 — Nucleoside Triphosphate Pyrophosphohydrolase
Domain ID domain_id5kq4D00
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology29 — PH-domain like
Homologous superfamily homologous superfamily30 — Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)
Domain ID domain_id5kq4E01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily1050 — Dcp2, box A domain
Domain ID domain_id5kq4E02
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology79 — Nucleoside Triphosphate Pyrophosphohydrolase
Homologous superfamily homologous superfamily10 — Nucleoside Triphosphate Pyrophosphohydrolase
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7. Citations (1)