2r5h

Pentamer structure of Major Capsid Protein L1 of Human Papilloma Virus type 16

Method: X-RAY DIFFRACTION

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

Late major capsid protein L1

Human papillomavirus

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	Q81007_9PAPI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–384； UniProt 12–394 Author chain A； PDBConstruct 390–423； UniProt 429–462 Author chain B； PDBConstruct 2–384； UniProt 12–394 Author chain B； PDBConstruct 390–423； UniProt 429–462 Author chain C； PDBConstruct 2–384； UniProt 12–394 Author chain C； PDBConstruct 390–423； UniProt 429–462 Author chain D； PDBConstruct 2–384； UniProt 12–394 Author chain D； PDBConstruct 390–423； UniProt 429–462 Author chain E； PDBConstruct 2–384； UniProt 12–394 Author chain E； PDBConstruct 390–423； UniProt 429–462 Author chain F； PDBConstruct 2–384； UniProt 12–394 Author chain F； PDBConstruct 390–423； UniProt 429–462 Author chain G； PDBConstruct 2–384； UniProt 12–394 Author chain G； PDBConstruct 390–423； UniProt 429–462 Author chain H； PDBConstruct 2–384； UniProt 12–394 Author chain H； PDBConstruct 390–423； UniProt 429–462 Author chain I； PDBConstruct 2–384； UniProt 12–394 Author chain I； PDBConstruct 390–423； UniProt 429–462 Author chain J； PDBConstruct 2–384； UniProt 12–394 Author chain J； PDBConstruct 390–423； UniProt 429–462 Author chain K； PDBConstruct 2–384； UniProt 12–394 Author chain K； PDBConstruct 390–423； UniProt 429–462 Author chain L； PDBConstruct 2–384； UniProt 12–394 Author chain L； PDBConstruct 390–423； UniProt 429–462 Author chain M； PDBConstruct 2–384； UniProt 12–394 Author chain M； PDBConstruct 390–423； UniProt 429–462 Author chain N； PDBConstruct 2–384； UniProt 12–394 Author chain N； PDBConstruct 390–423； UniProt 429–462 Author chain O； PDBConstruct 2–384； UniProt 12–394 Author chain O； PDBConstruct 390–423； UniProt 429–462

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	2r5h
Deposition date deposition_date	2007-09-03
Structure title title	Pentamer structure of Major Capsid Protein L1 of Human Papilloma Virus type 16
Keywords keywords	Capsid, Pentamer, Protein, Type specific epitope, Capsid protein, Virion, VIRAL PROTEIN; VIRAL PROTEIN
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.

2r5h__assembly_2__model_1

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

Download this curve (.dat)

2r5h__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2r5h__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	38.94 Å
Rg (electron density)	38.08 Å
Total Rg	38.57 Å
Atom count	16550
Residues	2095
Excluded volume	293900 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2r5h__assembly_1__model_1`	pentameric （5）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2r5h__assembly_2__model_1`	pentameric （5）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2r5h__assembly_3__model_1`	pentameric （5）	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 (1)

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6. Fold Classification (SCOP + CATH) 15 domains

CATH v4.4 (15 domains)

Domain ID domain_id	2r5hA00
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	2r5hB00
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	2r5hC00
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	2r5hD00
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	2r5hE00
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	2r5hF00
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	2r5hG00
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	2r5hH00
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	2r5hI00
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	2r5hJ00
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	2r5hK00
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	2r5hL00
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	2r5hM00
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	2r5hN00
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	2r5hO00
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

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Unit-cell length a length_a	105.000 Å
Unit-cell length b length_b	159.052 Å
Unit-cell length c length_c	413.738 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	60

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	3.700 Å
Low-resolution limit resolution_low	15.000 Å
R factor r_factor	0.2501
R_work r_work	0.2473
R_free r_free	0.3052

Description description	Late major capsid protein L1
Molecular weight formula_weight	47378.4 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	49650

Pentamer structure of Major Capsid Protein L1 of Human Papilloma Virus type 16

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

Late 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

2r5h__assembly_2__model_1

2r5h__assembly_2__model_1 | I(q)

2r5h__assembly_2__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
NCBI taxonomy ID ncbi_taxonomy_id	10566
Host organism host_organism	Escherichia coli

Pentamer structure of Major Capsid Protein L1 of Human Papilloma Virus type 16

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

Late 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

2r5h__assembly_2__model_1

2r5h__assembly_2__model_1 | I(q)

2r5h__assembly_2__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)