SAXSdb — 8q3r

▼

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

Uracil-DNA glycosylase

Vaccinia virus Copenhagen

UniProt P20536

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	DNA polymerase processivity factor component OPG148 × 1 （P20995） DNA polymerase × 1 （P20509）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	UNG_VACCC
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain D； PDBConstruct 25–242； UniProt 1–218

DNA polymerase processivity factor component OPG148

Vaccinia virus Copenhagen

UniProt P20995

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Uracil-DNA glycosylase × 1 （P20536） DNA polymerase × 1 （P20509）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PG148_VACCC
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain A； PDBConstruct 1–426； UniProt 1–426

DNA polymerase

Vaccinia virus Copenhagen

UniProt P20509

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Uracil-DNA glycosylase × 1 （P20536） DNA polymerase processivity factor component OPG148 × 1 （P20995）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DPOL_VACCC
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain E； PDBConstruct 29–1033； UniProt 2–1006

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_id	8q3r
Deposition date deposition_date	2023-08-04
Structure title title	Cryo-EM structure of the DNA polymerase holoenzyme E9-A20-D4 of vaccinia virus
Keywords keywords	DNA polymerase, holoenzyme, processivity factor, uracil-DNA glycosylase, VIRAL PROTEIN; VIRAL PROTEIN
Experimental Method method	ELECTRON MICROSCOPY

▼

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.

8q3r__assembly_1__model_1

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

Download this curve (.dat)

8q3r__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8q3r__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	41.80 Å
Rg (electron density)	41.38 Å
Total Rg	41.79 Å
Atom count	11921
Residues	1465
Excluded volume	213730 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8q3r__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Uracil-DNA glycosylase
Molecular weight formula_weight	27468.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D
Atom count atom_count	11921

MASWSHPQFEKSGGGGGLVPRGSAMNSVTVSHAPYTITYHDDWEPVMSQLVEFYNEVASWLLRDETSPIPDKFFIQLKQPLRNKRVCVCGIDPYPKDGTGVPFESPNFTKKSIKEIASSISRLTGVIDYKGYNLNIIDGVIPWNYYLSCKLGETKSHAIYWDKISKLLLQHITKHVSVLYCLGKTDFSNIRAKLESPVTTIVGYHPAARDRQFEKDRSFEIINVLLELDNKAPINWAQGFIY

Source Source

Source organism organism	Vaccinia virus Copenhagen
NCBI taxonomy ID ncbi_taxonomy_id	10249
Host organism host_organism	Trichoplusia ni

Entity 2 Entity 2 polymer

Description description	DNA polymerase processivity factor component OPG148
Molecular weight formula_weight	49247.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A

MTSSADLTNLKELLSLYKSLRFSDSAAIEKYNSLVEWGTSTYWKIGVQKVANVETSISDYYDEVKNKPFNIDPGYYIFLPVYFGSVFIYSKGKNMVELGSGNSFQIPDDMRSACNKVLDSDNGIDFLRFVLLNNRWIMEDAISKYQSPVNIFKLASEYGLNIPKYLEIEIEEDTLFDDELYSIIERSFDDKFPKISISYIKLGELRRQVVDFFKFSFMYIESIKVDRIGDNIFIPSVITKSGKKILVKDVDHLIRSKVREHTFVKVKKKNTFSILYDYDGNGTETRGEVIKRIIDTIGRDYYVNGKYFSKVGSAGLKQLTNKLDINECATVDELVDEINKSGTVKRKIKNQSAFDLSRECLGYPEADFITLVNNMRFKIENCKVVNFNIENTNCLNNPSIETIYRNFNQFVSIFNVVTDVKKRLFE

Source Source

Source organism organism	Vaccinia virus Copenhagen
NCBI taxonomy ID ncbi_taxonomy_id	10249
Host organism host_organism	Trichoplusia ni

Entity 3 Entity 3 polymer

Description description	DNA polymerase
Molecular weight formula_weight	120361.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E

MSYYHHHHHHDYDIPTTENLYFQGAMDPDVRCINWFESHGENRFLYLKSRCRNGETVFIRFPHYFYYVVTDEIYQSLSPPPFNARPLGKMRTIDIDETISYNLDIKDRKCSVADMWLIEEPKKRSIQNATMDEFLNISWFYISNGISPDGCYSLDEQYLTKINNGCYHCDDPRNCFAKKIPRFDIPRSYLFLDIECHFDKKFPSVFINPISHTSYCYIDLSGKRLLFTLINEEMLTEQEIQEAVDRGCLRIQSLMEMDYERELVLCSEIVLLRIAKQLLELTFDYVVTFNGHNFDLRYITNRLELLTGEKIIFRSPDKKEAVHLCIYERNQSSHKGVGGMANTTFHVNNNNGTIFFDLYSFIQKSEKLDSYKLDSISKNAFSCMGKVLNRGVREMTFIGDDTTDAKGKAAAFAKVLTTGNYVTVDEDIICKVIRKDIWENGFKVVLLCPTLPNDTYKLSFGKDDVDLAQMYKDYNLNIALDMARYCIHDACLCQYLWEYYGVETKTDAGASTYVLPQSMVFEYRASTVIKGPLLKLLLETKTILVRSETKQKFPYEGGKVFAPKQKMFSNNVLIFDYNSLYPNVCIFGNLSPETLVGVVVSTNRLEEEINNQLLLQKYPPPRYITVHCEPRLPNLISEIAIFDRSIEGTIPRLLRTFLAERARYKKMLKQATSSTEKAIYDSMQYTYKIVANSVYGLMGFRNSALYSYASAKSCTSIGRRMILYLESVLNGAELSNGMLRFANPLSNPFYMDDRDINPIVKTSLPIDYRFRFRSVYGDTDSVFTEIDSQDVDKSIEIAKELERLINNRVLFNNFKIEFEAVYKNLIMQSKKKYTTMKYSASSNSKSVPERINKGTSETRRDVSKFHKNMIKTYKTRLSEMLSEGRMNSNQVCIDILRSLETDLRSEFDSRSSPLELFMLSRMHHSNYKSADNPNMYLVTEYNKNNPETIELGERYYFAYICPANVPWTKKLVNIKTYETIIDRSFKLGSDQRIFYEVYFKRLTSEIVNLLDNKVLCISFFERMFGSKPTFYEA

Source Source

Source organism organism	Vaccinia virus Copenhagen
NCBI taxonomy ID ncbi_taxonomy_id	10249
Host organism host_organism	Trichoplusia ni

▶

Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	—

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

Resolution resolution	3.80 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	104239

Cryo-EM structure of the DNA polymerase holoenzyme E9-A20-D4 of vaccinia virus

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

Uracil-DNA glycosylase

State in the Current Structure

Other States of the Same Protein in the Database

DNA polymerase processivity factor component OPG148

State in the Current Structure

Other States of the Same Protein in the Database

DNA polymerase

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

8q3r__assembly_1__model_1

8q3r__assembly_1__model_1 | I(q)

8q3r__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

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

7. Citations (1)

Cryo-EM structure of the DNA polymerase holoenzyme E9-A20-D4 of vaccinia virus

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

Uracil-DNA glycosylase

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

DNA polymerase processivity factor component OPG148

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

DNA polymerase

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

8q3r__assembly_1__model_1

8q3r__assembly_1__model_1 | I(q)

8q3r__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

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

7. Citations (1)