2r5i

Pentamer Structure of Major Capsid Protein L1 of Human Papilloma Virus type 18

Method: X-RAY DIFFRACTION

▼

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

L1 protein

Human papillomavirus type 18

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	Q80B70_HPV18
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–385； UniProt 82–465 Author chain A； PDBConstruct 391–428； UniProt 499–536 Author chain B； PDBConstruct 2–385； UniProt 82–465 Author chain B； PDBConstruct 391–428； UniProt 499–536 Author chain C； PDBConstruct 2–385； UniProt 82–465 Author chain C； PDBConstruct 391–428； UniProt 499–536 Author chain D； PDBConstruct 2–385； UniProt 82–465 Author chain D； PDBConstruct 391–428； UniProt 499–536 Author chain E； PDBConstruct 2–385； UniProt 82–465 Author chain E； PDBConstruct 391–428； UniProt 499–536 Author chain F； PDBConstruct 2–385； UniProt 82–465 Author chain F； PDBConstruct 391–428； UniProt 499–536 Author chain G； PDBConstruct 2–385； UniProt 82–465 Author chain G； PDBConstruct 391–428； UniProt 499–536 Author chain H； PDBConstruct 2–385； UniProt 82–465 Author chain H； PDBConstruct 391–428； UniProt 499–536 Author chain I； PDBConstruct 2–385； UniProt 82–465 Author chain I； PDBConstruct 391–428； UniProt 499–536 Author chain J； PDBConstruct 2–385； UniProt 82–465 Author chain J； PDBConstruct 391–428； UniProt 499–536 Author chain K； PDBConstruct 2–385； UniProt 82–465 Author chain K； PDBConstruct 391–428； UniProt 499–536 Author chain L； PDBConstruct 2–385； UniProt 82–465 Author chain L； PDBConstruct 391–428； UniProt 499–536 Author chain M； PDBConstruct 2–385； UniProt 82–465 Author chain M； PDBConstruct 391–428； UniProt 499–536 Author chain N； PDBConstruct 2–385； UniProt 82–465 Author chain N； PDBConstruct 391–428； UniProt 499–536 Author chain O； PDBConstruct 2–385； UniProt 82–465 Author chain O； PDBConstruct 391–428； UniProt 499–536

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	2r5i
Deposition date deposition_date	2007-09-03
Structure title title	Pentamer Structure of Major Capsid Protein L1 of Human Papilloma Virus type 18
Keywords keywords	HPV18, pentamer, type specific epitope, capsid, Capsid 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.

2r5i__assembly_3__model_1

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

Download this curve (.dat)

2r5i__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2r5i__assembly_3__model_1 | P(r) · Pending

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

Rg（Guinier）	39.19 Å
Rg (electron density)	38.31 Å
Total Rg	38.87 Å
Atom count	16615
Residues	2115
Excluded volume	293300 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2r5i__assembly_1__model_1`	pentameric （5）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2r5i__assembly_2__model_1`	pentameric （5）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2r5i__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	2r5iA00
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	2r5iB00
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	2r5iC00
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	2r5iD00
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	2r5iE00
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	2r5iF00
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	2r5iG00
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	2r5iH00
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	2r5iI00
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	2r5iJ00
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	2r5iK00
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	2r5iL00
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	2r5iM00
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	2r5iN00
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	2r5iO00
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	81.161 Å
Unit-cell length b length_b	105.039 Å
Unit-cell length c length_c	235.749 Å
Unit-cell angle α angle_alpha	87.56 °
Unit-cell angle β angle_beta	85.66 °
Unit-cell angle γ angle_gamma	68.16 °
Molecules per unit cell Z z_pdb	15

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

Resolution resolution	3.400 Å
Low-resolution limit resolution_low	40.000 Å
R factor r_factor	0.2162
R_work r_work	0.2138
R_free r_free	0.2602

Description description	L1 protein
Molecular weight formula_weight	47591.2 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	49845

Pentamer Structure of Major Capsid Protein L1 of Human Papilloma Virus type 18

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

L1 protein

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

2r5i__assembly_3__model_1

2r5i__assembly_3__model_1 | I(q)

2r5i__assembly_3__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 (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 18
NCBI taxonomy ID ncbi_taxonomy_id	333761
Host organism host_organism	Escherichia coli

Pentamer Structure of Major Capsid Protein L1 of Human Papilloma Virus type 18

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

L1 protein

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

2r5i__assembly_3__model_1

2r5i__assembly_3__model_1 | I(q)

2r5i__assembly_3__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 (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)