← Back to search
3er8

Crystal structure of the heterodimeric vaccinia virus mRNA polyadenylate polymerase complex with two fragments of RNA

Method: X-RAY DIFFRACTION
▼

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

;Cap-specific mRNA (nucleoside-2'-O-)-methyltransferase ;

vaccinia virus WR

UniProt P07617

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–DNA Heteromer Protein 2 DNA 2 Poly(A) polymerase catalytic subunit × 1 （P23371） ;RNA/DNA chimera 5'-D(CP*CP*)R(UP*UP*)D(C)-3' ; × 1 ;RNA/DNA chimera 5'-D(P*CP*)R(UP*U)-3' ; × 1 Consistent with all polymers
2 Protein–DNA Heteromer Protein 2 DNA 2 Poly(A) polymerase catalytic subunit × 1 （P23371） ;RNA/DNA chimera 5'-R(P*UP*UP*)D(C)-3' ; × 1 ;RNA/DNA chimera 5'-D(P*CP*)R(UP*U)-3' ; × 1 Consistent with all polymers

Other States of the Same Protein in the Database

Monomer
1eam 1jsz 1jte 1jtf 4dcg

5 assemblies

Homodimer
1b42 1bky 1eqa 1p39 1v39 1vp3 1vp9 1vpt 2vp3 3mag 3mct

11 assemblies

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
1av6 2ga9 2gaf 3er8 3er8 3er9 3erc 3erc

8 assemblies

View Construct and Data Evidence
UniProt name PAP2_VACCV
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–297； UniProt 1–297 Author chain B； PDBConstruct 1–297； UniProt 1–297

Poly(A) polymerase catalytic subunit

vaccinia virus WR

UniProt P23371

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–DNA Heteromer Protein 2 DNA 2 ;Cap-specific mRNA (nucleoside-2'-O-)-methyltransferase ; × 1 （P07617） ;RNA/DNA chimera 5'-D(CP*CP*)R(UP*UP*)D(C)-3' ; × 1 ;RNA/DNA chimera 5'-D(P*CP*)R(UP*U)-3' ; × 1 Consistent with all polymers
2 Protein–DNA Heteromer Protein 2 DNA 2 ;Cap-specific mRNA (nucleoside-2'-O-)-methyltransferase ; × 1 （P07617） ;RNA/DNA chimera 5'-R(P*UP*UP*)D(C)-3' ; × 1 ;RNA/DNA chimera 5'-D(P*CP*)R(UP*U)-3' ; × 1 Consistent with all polymers

Other States of the Same Protein in the Database

Monomer
3owg 3owg

2 assemblies

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
2ga9 2gaf 3er8 3er8 3er9 3erc 3erc

7 assemblies

View Construct and Data Evidence
UniProt name PAP1_VACCV
Isoform —
PDB entities 2
Chains and sequence ranges Author chain C； PDBConstruct 1–479； UniProt 1–479 Author chain D； PDBConstruct 1–479； UniProt 1–479

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id3er8
Deposition date deposition_date2008-10-01
Structure title titleCrystal structure of the heterodimeric vaccinia virus mRNA polyadenylate polymerase complex with two fragments of RNA
Keywords keywords;Polyadenylate polymerase, translocation, single tranded RNA poly(A) polymerase, RNA protein complex, processivity, heterodimer, nucleotidyltransferase, poxvirus; Methyltransferase, mRNA capping, mRNA processing, S-adenosyl-L-methionine, Transcription, Transferase, Transferase/DNA, RNA COMPLEX, Transferase-DNA ;; Transcription, Transferase/DNA, RNA
Experimental Method methodX-RAY DIFFRACTION
▼

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.

3er8__assembly_1__model_1

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

Download this curve (.dat)

3er8__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.

3er8__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）29.27 Å
Rg (electron density)28.16 Å
Total Rg28.98 Å
Atom count6162
Residues741
Excluded volume110610 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 3er8__assembly_1__model_1 tetrameric （4） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 3er8__assembly_2__model_1 tetrameric （4） Success 4.1.3-1-20251215 (887e7ef) View Download
▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (5)

▼

6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd3er8a_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.66 — S-adenosyl-L-methionine-dependent methyltransferases
Superfamily Superfamily superfamilyc.66.1 — S-adenosyl-L-methionine-dependent methyltransferases
Family Family familyc.66.1.25 — mRNA cap methylase
Domain ID domain_idd3er8b_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.66 — S-adenosyl-L-methionine-dependent methyltransferases
Superfamily Superfamily superfamilyc.66.1 — S-adenosyl-L-methionine-dependent methyltransferases
Family Family familyc.66.1.25 — mRNA cap methylase
Domain ID domain_idd3er8c_
Class classe — Multi-domain proteins (alpha and beta)
Fold Fold folde.69 — Poly(A) polymerase catalytic subunit-like
Superfamily Superfamily superfamilye.69.1 — Poly(A) polymerase catalytic subunit-like
Family Family familye.69.1.1 — Poxvirus poly(A) polymerase catalytic subunit-like
Domain ID domain_idd3er8d_
Class classe — Multi-domain proteins (alpha and beta)
Fold Fold folde.69 — Poly(A) polymerase catalytic subunit-like
Superfamily Superfamily superfamilye.69.1 — Poly(A) polymerase catalytic subunit-like
Family Family familye.69.1.1 — Poxvirus poly(A) polymerase catalytic subunit-like

CATH v4.4 (6 domains)

Domain ID domain_id3er8A00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily150 — Vaccinia Virus protein VP39
Domain ID domain_id3er8B00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily150 — Vaccinia Virus protein VP39
Domain ID domain_id3er8C01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1270 — Substrate Binding Domain Of Dnak; Chain:A; Domain 2
Homologous superfamily homologous superfamily320 — Poxvirus poly(A) polymerase, N domain
Domain ID domain_id3er8C03
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology460 — Beta Polymerase; domain 2
Homologous superfamily homologous superfamily60 — Poxvirus poly(A) polymerase, nucleotidyltransferase domain
Domain ID domain_id3er8D01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1270 — Substrate Binding Domain Of Dnak; Chain:A; Domain 2
Homologous superfamily homologous superfamily320 — Poxvirus poly(A) polymerase, N domain
Domain ID domain_id3er8D03
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology460 — Beta Polymerase; domain 2
Homologous superfamily homologous superfamily60 — Poxvirus poly(A) polymerase, nucleotidyltransferase domain
▶

7. Citations (2)