2gxa

Crystal structure of papillomavirus E1 hexameric helicase with ssDNA and MgADP

Method: X-RAY DIFFRACTION

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

Replication protein E1

Bovine papillomavirus type 1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Homooligomer	Protein 6 DNA 1	5'-D(TPTPTPTPTPTPTPTPTPTPTPTP*T)-3' × 1 MAGNESIUM ION × 5 CHLORIDE ION × 2 ADENOSINE-5'-DIPHOSPHATE × 6 water × 4	Consistent with all polymers
2	Protein–DNA	Homooligomer	Protein 6 DNA 1	5'-D(TPTPTPTPTPTPTPTPTPTPTPTP*T)-3' × 1 MAGNESIUM ION × 5 CHLORIDE ION × 1 ADENOSINE-5'-DIPHOSPHATE × 5 water × 3	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VE1_BPV1
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain A； PDBConstruct 2–274； UniProt 305–577 Author chain B； PDBConstruct 2–274； UniProt 305–577 Author chain C； PDBConstruct 2–274； UniProt 305–577 Author chain D； PDBConstruct 2–274； UniProt 305–577 Author chain E； PDBConstruct 2–274； UniProt 305–577 Author chain F； PDBConstruct 2–274； UniProt 305–577 Author chain G； PDBConstruct 2–274； UniProt 305–577 Author chain H； PDBConstruct 2–274； UniProt 305–577 Author chain I； PDBConstruct 2–274； UniProt 305–577 Author chain J； PDBConstruct 2–274； UniProt 305–577 Author chain K； PDBConstruct 2–274； UniProt 305–577 Author chain L； PDBConstruct 2–274； UniProt 305–577

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	2gxa
Deposition date deposition_date	2006-05-08
Structure title title	Crystal structure of papillomavirus E1 hexameric helicase with ssDNA and MgADP
Keywords keywords	DNA helicase, AAA+, ATPase, replication, virus, initiator protein, replication-DNA COMPLEX; replication/DNA
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.

2gxa__assembly_1__model_1

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

Download this curve (.dat)

2gxa__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2gxa__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	36.61 Å
Rg (electron density)	35.97 Å
Total Rg	36.49 Å
Atom count	13167
Residues	1630
Excluded volume	233450 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2gxa__assembly_1__model_1`	heptameric （7）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2gxa__assembly_2__model_1`	heptameric （7）	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 (6)

Entity 1 Entity 1 polymer

Description description	5'-D(TPTPTPTPTPTPTPTPTPTPTPTP*T)-3'
Molecular weight formula_weight	3909.5 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	M,N
Atom count atom_count	26374

TTTTTTTTTTTTT

Entity 2 Entity 2 polymer

Description description	Replication protein E1
Molecular weight formula_weight	31123.4 kDa
Source method src_method	man
Copy count entity_count	12

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J,K,L

GSLQTEKFDFGTMVQWAYDHKYAEESKIAYEYALAAGSDSNARAFLATNSQAKHVKDCATMVRHYLRAETQALSMPAYIKARCKLATGEGSWKSILTFFNYQNIELITFINALKLWLKGIPKKNCLAFIGPPNTGKSMLCNSLIHFLGGSVLSFANHKSHFWLASLADTRAALVDDATHACWRYFDTYLRNALDGYPVSIDRKHKAAVQIKAPPLLVTSNIDVQAEDRYLYLHSRVQTFRFEQPCTDESGEQPFNITDADWKSFFVRLWGRLDL

Source Source

Source organism organism	Bovine papillomavirus type 1
NCBI taxonomy ID ncbi_taxonomy_id	10559
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	10

Entity 4 Entity 4 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 5 Entity 5 non-polymer

Description description	ADENOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	427.2 kDa
Source method src_method	syn
Copy count entity_count	11

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	15

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6. Fold Classification (SCOP + CATH) 24 domains

CATH v4.4 (24 domains)

Domain ID domain_id	2gxaA01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	510 — Zinc finger, large T-antigen D1 domain

Domain ID domain_id	2gxaA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	2gxaB01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	510 — Zinc finger, large T-antigen D1 domain

Domain ID domain_id	2gxaB02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	2gxaC01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	510 — Zinc finger, large T-antigen D1 domain

Domain ID domain_id	2gxaC02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	2gxaD01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	510 — Zinc finger, large T-antigen D1 domain

Domain ID domain_id	2gxaD02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	2gxaE01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	510 — Zinc finger, large T-antigen D1 domain

Domain ID domain_id	2gxaE02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	2gxaF01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	510 — Zinc finger, large T-antigen D1 domain

Domain ID domain_id	2gxaF02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	2gxaG01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	510 — Zinc finger, large T-antigen D1 domain

Domain ID domain_id	2gxaG02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	2gxaH01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	510 — Zinc finger, large T-antigen D1 domain

Domain ID domain_id	2gxaH02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	2gxaI01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	510 — Zinc finger, large T-antigen D1 domain

Domain ID domain_id	2gxaI02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	2gxaJ01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	510 — Zinc finger, large T-antigen D1 domain

Domain ID domain_id	2gxaJ02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	2gxaK01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	510 — Zinc finger, large T-antigen D1 domain

Domain ID domain_id	2gxaK02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	2gxaL01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	510 — Zinc finger, large T-antigen D1 domain

Domain ID domain_id	2gxaL02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

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Unit-cell length a length_a	100.510 Å
Unit-cell length b length_b	100.881 Å
Unit-cell length c length_c	125.023 Å
Unit-cell angle α angle_alpha	92.60 °
Unit-cell angle β angle_beta	111.46 °
Unit-cell angle γ angle_gamma	106.01 °
Molecules per unit cell Z z_pdb	12

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

Resolution resolution	3.150 Å
Low-resolution limit resolution_low	44.650 Å
R factor r_factor	0.2390
R_work r_work	0.2390
R_free r_free	0.2980

Crystal structure of papillomavirus E1 hexameric helicase with ssDNA and MgADP

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

Replication protein E1

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

2gxa__assembly_1__model_1

2gxa__assembly_1__model_1 | I(q)

2gxa__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 24 domains

CATH v4.4 (24 domains)

7. Citations (1)

Crystal structure of papillomavirus E1 hexameric helicase with ssDNA and MgADP

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

Replication protein E1

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

2gxa__assembly_1__model_1

2gxa__assembly_1__model_1 | I(q)

2gxa__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 24 domains

CATH v4.4 (24 domains)

7. Citations (1)