2r5j

Pentamer Structure of Major Capsid protein L1 of Human Papilloma Virus Type 35

Method: X-RAY DIFFRACTION

▼

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

Major capsid protein L1

Human papillomavirus type 35

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 5	No other associated polymer	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 5	No other associated polymer	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 5	No other associated polymer	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VL1_HPV35
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–382； UniProt 21–401 Author chain A； PDBConstruct 388–423； UniProt 437–472 Author chain B； PDBConstruct 2–382； UniProt 21–401 Author chain B； PDBConstruct 388–423； UniProt 437–472 Author chain C； PDBConstruct 2–382； UniProt 21–401 Author chain C； PDBConstruct 388–423； UniProt 437–472 Author chain D； PDBConstruct 2–382； UniProt 21–401 Author chain D； PDBConstruct 388–423； UniProt 437–472 Author chain E； PDBConstruct 2–382； UniProt 21–401 Author chain E； PDBConstruct 388–423； UniProt 437–472 Author chain F； PDBConstruct 2–382； UniProt 21–401 Author chain F； PDBConstruct 388–423； UniProt 437–472 Author chain G； PDBConstruct 2–382； UniProt 21–401 Author chain G； PDBConstruct 388–423； UniProt 437–472 Author chain H； PDBConstruct 2–382； UniProt 21–401 Author chain H； PDBConstruct 388–423； UniProt 437–472 Author chain I； PDBConstruct 2–382； UniProt 21–401 Author chain I； PDBConstruct 388–423； UniProt 437–472 Author chain J； PDBConstruct 2–382； UniProt 21–401 Author chain J； PDBConstruct 388–423； UniProt 437–472 Author chain K； PDBConstruct 2–382； UniProt 21–401 Author chain K； PDBConstruct 388–423； UniProt 437–472 Author chain L； PDBConstruct 2–382； UniProt 21–401 Author chain L； PDBConstruct 388–423； UniProt 437–472 Author chain M； PDBConstruct 2–382； UniProt 21–401 Author chain M； PDBConstruct 388–423； UniProt 437–472 Author chain N； PDBConstruct 2–382； UniProt 21–401 Author chain N； PDBConstruct 388–423； UniProt 437–472 Author chain O； PDBConstruct 2–382； UniProt 21–401 Author chain O； PDBConstruct 388–423； UniProt 437–472

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	2r5j
Deposition date deposition_date	2007-09-03
Structure title title	Pentamer Structure of Major Capsid protein L1 of Human Papilloma Virus Type 35
Keywords keywords	HPV35, Capsid, Pentamer, Type specific epitope, Capsid protein, Late protein, Virion, VIRAL PROTEIN; VIRAL PROTEIN
Experimental Method method	X-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.

2r5j__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2r5j__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2r5j__assembly_3__model_1 | P(r) · Pending

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

Rg（Guinier）	39.09 Å
Rg (electron density)	38.21 Å
Total Rg	38.69 Å
Atom count	16450
Residues	2085
Excluded volume	291780 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2r5j__assembly_1__model_1`	pentameric （5）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2r5j__assembly_2__model_1`	pentameric （5）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2r5j__assembly_3__model_1`	pentameric （5）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (1)

▼

6. Fold Classification (SCOP + CATH) 15 domains

CATH v4.4 (15 domains)

Domain ID domain_id	2r5jA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	175 — Polyomavirus Vp1; Chain A
Homologous superfamily homologous superfamily	20 — Major capsid L1 (late) superfamily, Papillomavirus

Domain ID domain_id	2r5jB00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	175 — Polyomavirus Vp1; Chain A
Homologous superfamily homologous superfamily	20 — Major capsid L1 (late) superfamily, Papillomavirus

Domain ID domain_id	2r5jC00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	175 — Polyomavirus Vp1; Chain A
Homologous superfamily homologous superfamily	20 — Major capsid L1 (late) superfamily, Papillomavirus

Domain ID domain_id	2r5jD00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	175 — Polyomavirus Vp1; Chain A
Homologous superfamily homologous superfamily	20 — Major capsid L1 (late) superfamily, Papillomavirus

Domain ID domain_id	2r5jE00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	175 — Polyomavirus Vp1; Chain A
Homologous superfamily homologous superfamily	20 — Major capsid L1 (late) superfamily, Papillomavirus

Domain ID domain_id	2r5jF00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	175 — Polyomavirus Vp1; Chain A
Homologous superfamily homologous superfamily	20 — Major capsid L1 (late) superfamily, Papillomavirus

Domain ID domain_id	2r5jG00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	175 — Polyomavirus Vp1; Chain A
Homologous superfamily homologous superfamily	20 — Major capsid L1 (late) superfamily, Papillomavirus

Domain ID domain_id	2r5jH00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	175 — Polyomavirus Vp1; Chain A
Homologous superfamily homologous superfamily	20 — Major capsid L1 (late) superfamily, Papillomavirus

Domain ID domain_id	2r5jI00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	175 — Polyomavirus Vp1; Chain A
Homologous superfamily homologous superfamily	20 — Major capsid L1 (late) superfamily, Papillomavirus

Domain ID domain_id	2r5jJ00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	175 — Polyomavirus Vp1; Chain A
Homologous superfamily homologous superfamily	20 — Major capsid L1 (late) superfamily, Papillomavirus

Domain ID domain_id	2r5jK00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	175 — Polyomavirus Vp1; Chain A
Homologous superfamily homologous superfamily	20 — Major capsid L1 (late) superfamily, Papillomavirus

Domain ID domain_id	2r5jL00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	175 — Polyomavirus Vp1; Chain A
Homologous superfamily homologous superfamily	20 — Major capsid L1 (late) superfamily, Papillomavirus

Domain ID domain_id	2r5jM00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	175 — Polyomavirus Vp1; Chain A
Homologous superfamily homologous superfamily	20 — Major capsid L1 (late) superfamily, Papillomavirus

Domain ID domain_id	2r5jN00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	175 — Polyomavirus Vp1; Chain A
Homologous superfamily homologous superfamily	20 — Major capsid L1 (late) superfamily, Papillomavirus

Domain ID domain_id	2r5jO00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	175 — Polyomavirus Vp1; Chain A
Homologous superfamily homologous superfamily	20 — Major capsid L1 (late) superfamily, Papillomavirus

▶

Unit-cell length a length_a	150.410 Å
Unit-cell length b length_b	176.606 Å
Unit-cell length c length_c	197.073 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	92.11 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	30

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

Resolution resolution	3.300 Å
Low-resolution limit resolution_low	15.000 Å
R factor r_factor	0.3171
R_work r_work	0.3155
R_free r_free	0.3482

Description description	Major capsid protein L1
Molecular weight formula_weight	47231.1 kDa
Source method src_method	man
Copy count entity_count	15

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J,K,L,M,N,O
Atom count atom_count	49350

Pentamer Structure of Major Capsid protein L1 of Human Papilloma Virus Type 35

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

Major capsid protein L1

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

2r5j__assembly_3__model_1

2r5j__assembly_3__model_1 | I(q)

2r5j__assembly_3__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 15 domains

CATH v4.4 (15 domains)

7. Citations (1)

Source organism organism	Human papillomavirus type 35
NCBI taxonomy ID ncbi_taxonomy_id	10587
Host organism host_organism	Escherichia coli

Pentamer Structure of Major Capsid protein L1 of Human Papilloma Virus Type 35

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

Major capsid protein L1

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

2r5j__assembly_3__model_1

2r5j__assembly_3__model_1 | I(q)

2r5j__assembly_3__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 15 domains

CATH v4.4 (15 domains)

7. Citations (1)