1ksx

Crystal Structures of Two Intermediates in the Assembly of the Papillomavirus Replication Initiation Complex

Method: X-RAY DIFFRACTION

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

REPLICATION PROTEIN E1

Bovine papillomavirus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Homooligomer	Protein 4 DNA 2	E1 Recognition Sequence × 2 water × 4	Consistent with all polymers
2	Protein–DNA	Homooligomer	Protein 4 DNA 2	E1 Recognition Sequence × 2 water × 5	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 4–148； UniProt 159–303 Author chain B； PDBConstruct 4–148； UniProt 159–303 Author chain E； PDBConstruct 4–148； UniProt 159–303 Author chain F； PDBConstruct 4–148； UniProt 159–303 Author chain I； PDBConstruct 4–148； UniProt 159–303 Author chain J； PDBConstruct 4–148； UniProt 159–303 Author chain M； PDBConstruct 4–148； UniProt 159–303 Author chain N； PDBConstruct 4–148； UniProt 159–303

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	1ksx
Deposition date deposition_date	2002-01-14
Structure title title	Crystal Structures of Two Intermediates in the Assembly of the Papillomavirus Replication Initiation Complex
Keywords keywords	PAPILLOMAVIRUS, DNA-BINDING DOMAIN, REPLICATION, INITIATOR PROTEIN, HELICASE, 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.

1ksx__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

1ksx__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1ksx__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	29.16 Å
Rg (electron density)	28.97 Å
Total Rg	29.59 Å
Atom count	5512
Residues	622
Excluded volume	96841 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1ksx__assembly_1__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1ksx__assembly_2__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 (3)

Entity 1 Entity 1 polymer

Description description	E1 Recognition Sequence
Molecular weight formula_weight	6444.2 kDa
Source method src_method	syn
Copy count entity_count	4

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	C,G,K,O
Atom count atom_count	11044

ATAATTGTTGTTAACAACAAT

Entity 2 Entity 2 polymer

Description description	REPLICATION PROTEIN E1
Molecular weight formula_weight	16877.8 kDa
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,E,F,I,J,M,N

GSRATVFKLGLFKSLFLCSFHDITRLFKNDKTTNQQWVLAVFGLAEVFFEASFELLKKQCSFLQMQKRSHEGGTCAVYLICFNTAKSRETVRNLMANMLNVREECLMLQPPKIRGLSAALFWFKSSLSPATLKHGALPEWIRAQTTLN

Source Source

Source organism organism	Bovine papillomavirus
NCBI taxonomy ID ncbi_taxonomy_id	10571
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	20

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6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d1ksxa_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.89 — Origin of replication-binding domain, RBD-like
Superfamily Superfamily superfamily	d.89.1 — Origin of replication-binding domain, RBD-like
Family Family family	d.89.1.2 — Replication initiation protein E1

Domain ID domain_id	d1ksxb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.89 — Origin of replication-binding domain, RBD-like
Superfamily Superfamily superfamily	d.89.1 — Origin of replication-binding domain, RBD-like
Family Family family	d.89.1.2 — Replication initiation protein E1

Domain ID domain_id	d1ksxe_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.89 — Origin of replication-binding domain, RBD-like
Superfamily Superfamily superfamily	d.89.1 — Origin of replication-binding domain, RBD-like
Family Family family	d.89.1.2 — Replication initiation protein E1

Domain ID domain_id	d1ksxf_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.89 — Origin of replication-binding domain, RBD-like
Superfamily Superfamily superfamily	d.89.1 — Origin of replication-binding domain, RBD-like
Family Family family	d.89.1.2 — Replication initiation protein E1

Domain ID domain_id	d1ksxi_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.89 — Origin of replication-binding domain, RBD-like
Superfamily Superfamily superfamily	d.89.1 — Origin of replication-binding domain, RBD-like
Family Family family	d.89.1.2 — Replication initiation protein E1

Domain ID domain_id	d1ksxj_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.89 — Origin of replication-binding domain, RBD-like
Superfamily Superfamily superfamily	d.89.1 — Origin of replication-binding domain, RBD-like
Family Family family	d.89.1.2 — Replication initiation protein E1

Domain ID domain_id	d1ksxm_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.89 — Origin of replication-binding domain, RBD-like
Superfamily Superfamily superfamily	d.89.1 — Origin of replication-binding domain, RBD-like
Family Family family	d.89.1.2 — Replication initiation protein E1

Domain ID domain_id	d1ksxn_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.89 — Origin of replication-binding domain, RBD-like
Superfamily Superfamily superfamily	d.89.1 — Origin of replication-binding domain, RBD-like
Family Family family	d.89.1.2 — Replication initiation protein E1

CATH v4.4 (8 domains)

Domain ID domain_id	1ksxA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1310 — Replication Protein E1; Chain: A,
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1ksxB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1310 — Replication Protein E1; Chain: A,
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1ksxE00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1310 — Replication Protein E1; Chain: A,
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1ksxF00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1310 — Replication Protein E1; Chain: A,
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1ksxI00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1310 — Replication Protein E1; Chain: A,
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1ksxJ00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1310 — Replication Protein E1; Chain: A,
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1ksxM00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1310 — Replication Protein E1; Chain: A,
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1ksxN00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1310 — Replication Protein E1; Chain: A,
Homologous superfamily homologous superfamily	10 —

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Unit-cell length a length_a	84.246 Å
Unit-cell length b length_b	103.650 Å
Unit-cell length c length_c	124.996 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	99.53 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	3.200 Å
Low-resolution limit resolution_low	42.620 Å
R factor r_factor	—
R_work r_work	0.2630
R_free r_free	0.2850

Crystal Structures of Two Intermediates in the Assembly of the Papillomavirus Replication Initiation Complex

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

1ksx__assembly_2__model_1

1ksx__assembly_2__model_1 | I(q)

1ksx__assembly_2__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)

Crystal Structures of Two Intermediates in the Assembly of the Papillomavirus Replication Initiation Complex

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

1ksx__assembly_2__model_1

1ksx__assembly_2__model_1 | I(q)

1ksx__assembly_2__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)