3erc

Crystal structure of the heterodimeric vaccinia virus mRNA polyadenylate polymerase with three fragments of RNA and 3'-deoxy ATP

Method: X-RAY DIFFRACTION

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

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

vaccinia virus WR

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 2 RNA 2	Poly(A) polymerase catalytic subunit × 1 （P23371） ;RNA/DNA chimera (5'-D(CP)R(UPUP)D(CPC)-3') ; × 1 ;RNA/DNA chimera (5'-D(CPCP)R(UPUP)D(C)-3') ; × 1 URIDINE-5'-MONOPHOSPHATE × 1 3'-DEOXYADENOSINE-5'-TRIPHOSPHATE × 1 CALCIUM ION × 2	Consistent with all polymers
2	Protein–RNA	Heteromer	Protein 2 RNA 2	Poly(A) polymerase catalytic subunit × 1 （P23371） ;RNA/DNA chimera (5'-D(CP)R(UPUP)D(CPC)-3') ; × 1 ;RNA/DNA chimera (5'-D(CP)R(UPUP*)-D(C)-3') ; × 1 URIDINE-5'-MONOPHOSPHATE × 1 3'-DEOXYADENOSINE-5'-TRIPHOSPHATE × 1 CALCIUM ION × 2 water × 1	Consistent with all polymers

Other States of the Same Protein in the Database

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–RNA	Heteromer	Protein 2 RNA 2	;Cap-specific mRNA (nucleoside-2'-O-)-methyltransferase ; × 1 （P07617） ;RNA/DNA chimera (5'-D(CP)R(UPUP)D(CPC)-3') ; × 1 ;RNA/DNA chimera (5'-D(CPCP)R(UPUP)D(C)-3') ; × 1 URIDINE-5'-MONOPHOSPHATE × 1 3'-DEOXYADENOSINE-5'-TRIPHOSPHATE × 1 CALCIUM ION × 2	Consistent with all polymers
2	Protein–RNA	Heteromer	Protein 2 RNA 2	;Cap-specific mRNA (nucleoside-2'-O-)-methyltransferase ; × 1 （P07617） ;RNA/DNA chimera (5'-D(CP)R(UPUP)D(CPC)-3') ; × 1 ;RNA/DNA chimera (5'-D(CP)R(UPUP*)-D(C)-3') ; × 1 URIDINE-5'-MONOPHOSPHATE × 1 3'-DEOXYADENOSINE-5'-TRIPHOSPHATE × 1 CALCIUM ION × 2 water × 1	Consistent with all polymers

Other States of the Same Protein in the Database

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	3erc
Deposition date deposition_date	2008-10-01
Structure title title	Crystal structure of the heterodimeric vaccinia virus mRNA polyadenylate polymerase with three fragments of RNA and 3'-deoxy ATP
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 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.

3erc__assembly_1__model_1

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

Download this curve (.dat)

3erc__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3erc__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	28.81 Å
Rg (electron density)	27.84 Å
Total Rg	28.63 Å
Atom count	6249
Residues	743
Excluded volume	111930 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3erc__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3erc__assembly_2__model_1`	tetrameric （4）	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 (9)

Entity 1 Entity 1 polymer

Description description	;Cap-specific mRNA (nucleoside-2'-O-)-methyltransferase ;
Molecular weight formula_weight	34589.0 kDa
EC 编号 ec_number	2.1.1.57
Mutation mutation	R140A,K142A,R143A
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	12480

MDVVSLDKPFMYFEEIDNELDYEPESANEVAKKLPYQGQLKLLLGELFFLSKLQRHGILDGATVVYIGSAPGTHIRYLRDHFYNLGVIIKWMLIDGRHHDPILNGLRDVTLVTRFVDEEYLRSIKKQLHPSKIILISDVASAAGGNEPSTADLLSNYALQNVMISILNPVASSLKWRCPFPDQWIKDFYIPHGNKMLQPFAPSYSAEMRLLSIYTGENMRLTRVTKSDAVNYEKKMYYLNKIVRNKVVVNFDYPNQEYDYFHMYFMLRTVYCNKTFPTTKAKVLFLQQSIFRFLNIP

Source Source

Source organism organism	vaccinia virus WR
NCBI taxonomy ID ncbi_taxonomy_id	10254
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Poly(A) polymerase catalytic subunit
Molecular weight formula_weight	55574.1 kDa
EC 编号 ec_number	2.7.7.19
Mutation mutation	L36S
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MNRNPDQNTLPNITLKIIETYLGRVPSVNEYHMLKSQARNIQKITVFNKDIFVSLVKKNKKRFFSDVNTSASEIKDRILSYFSKQTQTYNIGKLFTIIELQSVLVTTYTDILGVLTIKAPNVISSKISYNVTSMEELARDMLNSMNVAVIDKAKVMGRHNVSSLVKNVNKLMEEYLRRHNKSCICYGSYSLYLINPNIRYGDIDILQTNSRTFLIDLAFLIKFITGNNIILSKIPYLRNYMVIKDENDNHIIDSFNIRQDTMNVVPKIFIDNIYIVDPTFQLLNMIKMFSQIDRLEDLSKDPEKFNARMATMLEYVRYTHGIVFDGKRNNMPMKCIIDENNRIVTVTTKDYFSFKKCLVYLDENVLSSDILDLNADTSCDFESVTNSVYLIHDNIMYTYFSNTILLSDKGKVHEISARGLCAHILLYQMLTSGEYKQCLSDLLNSMMNRDKIPIYSHTERDKKPGRHGFINIEKDIIVF

Source Source

Source organism organism	vaccinia virus WR
NCBI taxonomy ID ncbi_taxonomy_id	10254
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	;RNA/DNA chimera (5'-D(CP)R(UPUP)D(CPC)-3') ;
Molecular weight formula_weight	1434.9 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	E,F

CUUCC

Entity 4 Entity 4 polymer

Description description	;RNA/DNA chimera (5'-D(CP)R(UPUP*)-D(C)-3') ;
Molecular weight formula_weight	1145.7 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	G

CUUC

Entity 5 Entity 5 polymer

Description description	;RNA/DNA chimera (5'-D(CPCP)R(UPUP)D(C)-3') ;
Molecular weight formula_weight	1434.9 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	I

CCUUC

Entity 6 Entity 6 non-polymer

Description description	URIDINE-5'-MONOPHOSPHATE
Molecular weight formula_weight	324.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 non-polymer

Description description	3'-DEOXYADENOSINE-5'-TRIPHOSPHATE
Molecular weight formula_weight	491.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 8 Entity 8 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 9 Entity 9 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1

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6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id	3ercA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	150 — Vaccinia Virus protein VP39

Domain ID domain_id	3ercB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	150 — Vaccinia Virus protein VP39

Domain ID domain_id	3ercC01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1270 — Substrate Binding Domain Of Dnak; Chain:A; Domain 2
Homologous superfamily homologous superfamily	320 — Poxvirus poly(A) polymerase, N domain

Domain ID domain_id	3ercC03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	460 — Beta Polymerase; domain 2
Homologous superfamily homologous superfamily	60 — Poxvirus poly(A) polymerase, nucleotidyltransferase domain

Domain ID domain_id	3ercD01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1270 — Substrate Binding Domain Of Dnak; Chain:A; Domain 2
Homologous superfamily homologous superfamily	320 — Poxvirus poly(A) polymerase, N domain

Domain ID domain_id	3ercD03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	460 — Beta Polymerase; domain 2
Homologous superfamily homologous superfamily	60 — Poxvirus poly(A) polymerase, nucleotidyltransferase domain

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Unit-cell length a length_a	69.925 Å
Unit-cell length b length_b	77.153 Å
Unit-cell length c length_c	108.030 Å
Unit-cell angle α angle_alpha	89.52 °
Unit-cell angle β angle_beta	73.45 °
Unit-cell angle γ angle_gamma	63.76 °
Molecules per unit cell Z z_pdb	2

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

Resolution resolution	3.210 Å
Low-resolution limit resolution_low	38.550 Å
R factor r_factor	0.2451
R_work r_work	0.2450
R_free r_free	0.3090

Crystal structure of the heterodimeric vaccinia virus mRNA polyadenylate polymerase with three fragments of RNA and 3'-deoxy ATP

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

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

State in the Current Structure

Other States of the Same Protein in the Database

Poly(A) polymerase catalytic subunit

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

3erc__assembly_1__model_1

3erc__assembly_1__model_1 | I(q)

3erc__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 (9)

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 polymer

Polymer Polymer

Entity 5 Entity 5 polymer

Polymer Polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 water

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (2)

Crystal structure of the heterodimeric vaccinia virus mRNA polyadenylate polymerase with three fragments of RNA and 3'-deoxy ATP

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

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

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Poly(A) polymerase catalytic subunit

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

3erc__assembly_1__model_1

3erc__assembly_1__model_1 | I(q)

3erc__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 (9)

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 polymer

Polymer Polymer

Entity 5 Entity 5 polymer

Polymer Polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 water

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (2)