5w1o

Crystal Structure of HPV16 L1 Pentamer Bound to Heparin Oligosaccharides

Method: X-RAY DIFFRACTION

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

Major capsid protein L1

Human papillomavirus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Homooligomer	Protein 5 其他Polymer 11	2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-alpha-D-glucopyranose × 10 ;2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-alpha-D-glucopyranose ; × 1 water × 5	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 391–427； UniProt 429–465 Author chain B； PDBConstruct 2–384； UniProt 12–394 Author chain B； PDBConstruct 391–427； UniProt 429–465 Author chain C； PDBConstruct 2–384； UniProt 12–394 Author chain C； PDBConstruct 391–427； UniProt 429–465 Author chain D； PDBConstruct 2–384； UniProt 12–394 Author chain D； PDBConstruct 391–427； UniProt 429–465 Author chain E； PDBConstruct 2–384； UniProt 12–394 Author chain E； PDBConstruct 391–427； UniProt 429–465

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	5w1o
Deposition date deposition_date	2017-06-04
Structure title title	Crystal Structure of HPV16 L1 Pentamer Bound to Heparin Oligosaccharides
Keywords keywords	human papillomavirus, jelly roll, capsid protein, receptor HSPG, virus capsid, 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.

5w1o__assembly_1__model_1

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

Download this curve (.dat)

5w1o__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5w1o__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	39.81 Å
Rg (electron density)	38.72 Å
Total Rg	39.28 Å
Atom count	17077
Residues	2131
Excluded volume	302190 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5w1o__assembly_1__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 (4)

Entity 1 Entity 1 polymer

Description description	Major capsid protein L1
Molecular weight formula_weight	47549.5 kDa
Source method src_method	man
Copy count entity_count	5

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E
Atom count atom_count	17224

AVVSTDEYVARTNIYYHAGTSRLLAVGHPYFPIKKPNNNKILVPKVSGLQYRVFRIHLPDPNKFGFPDTSFYNPDTQRLVWACVGVEVGRGQPLGVGISGHPLLNKLDDTENASAYAANAGVDNRECISMDYKQTQLCLIGCKPPIGEHWGKGSPCTNVAVNPGDCPPLELINTVIQDGDMVDTGFGAMDFTTLQANKSEVPLDICTSICKYPDYIKMVSEPYGDSLFFYLRREQMFVRHLFNRAGTVGENVPDDLYIKGSGSTANLASSNYFPTPSGSMVTSDAQIFNKPYWLQRAQGHNNGICWGNQLFVTVVDTTRSTNMSLCAAISTSETTYKNTNFKEYLRHGEEYDLQFIFQLCKITLTADVMTYIHSMNSTILEDWNGGGSGAEDPLKKYTFWEVNLKEKFSADLDQFPLGRKFLLQAGL

Source Source

Source organism organism	Human papillomavirus
NCBI taxonomy ID ncbi_taxonomy_id	10566
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 branched

Description description	2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-alpha-D-glucopyranose
Molecular weight formula_weight	500.4 kDa
Source method src_method	man
Copy count entity_count	10

Entity 3 Entity 3 branched

Description description	;2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-alpha-D-glucopyranose ;
Molecular weight formula_weight	1465.2 kDa
Source method src_method	man
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	147

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6. Fold Classification (SCOP + CATH) 15 domains

SCOP 2.08 (10 domains)

Domain ID domain_id	d5w1oa1
Class class	b — All beta proteins
Fold Fold fold	b.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamily	b.121.6 — Group I dsDNA viruses
Family Family family	b.121.6.1 — Papovaviridae-like VP

Domain ID domain_id	d5w1oa2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d5w1ob1
Class class	b — All beta proteins
Fold Fold fold	b.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamily	b.121.6 — Group I dsDNA viruses
Family Family family	b.121.6.1 — Papovaviridae-like VP

Domain ID domain_id	d5w1ob2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d5w1oc1
Class class	b — All beta proteins
Fold Fold fold	b.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamily	b.121.6 — Group I dsDNA viruses
Family Family family	b.121.6.1 — Papovaviridae-like VP

Domain ID domain_id	d5w1oc2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d5w1od1
Class class	b — All beta proteins
Fold Fold fold	b.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamily	b.121.6 — Group I dsDNA viruses
Family Family family	b.121.6.1 — Papovaviridae-like VP

Domain ID domain_id	d5w1od2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d5w1oe1
Class class	b — All beta proteins
Fold Fold fold	b.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamily	b.121.6 — Group I dsDNA viruses
Family Family family	b.121.6.1 — Papovaviridae-like VP

Domain ID domain_id	d5w1oe2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (5 domains)

Domain ID domain_id	5w1oA00
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	5w1oB00
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	5w1oC00
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	5w1oD00
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	5w1oE00
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	96.620 Å
Unit-cell length b length_b	101.252 Å
Unit-cell length c length_c	128.182 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.63 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	10

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

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	47.430 Å
R factor r_factor	0.2260
R_work r_work	0.2240
R_free r_free	0.2700

Crystal Structure of HPV16 L1 Pentamer Bound to Heparin Oligosaccharides

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

5w1o__assembly_1__model_1

5w1o__assembly_1__model_1 | I(q)

5w1o__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 branched

Entity 3 Entity 3 branched

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 15 domains

SCOP 2.08 (10 domains)

CATH v4.4 (5 domains)

7. Citations (1)

Crystal Structure of HPV16 L1 Pentamer Bound to Heparin Oligosaccharides

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

5w1o__assembly_1__model_1

5w1o__assembly_1__model_1 | I(q)

5w1o__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 branched

Entity 3 Entity 3 branched

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 15 domains

SCOP 2.08 (10 domains)

CATH v4.4 (5 domains)

7. Citations (1)