3ng9

Structure to Function Correlations for Adeno-associated Virus Serotype 1

Method: X-RAY DIFFRACTION

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

Capsid protein

Adeno-associated virus - 1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 60	ADENINE × 60 6-AMINOPYRIMIDIN-2(1H)-ONE × 60 water × 60	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 10	ADENINE × 10 6-AMINOPYRIMIDIN-2(1H)-ONE × 10 water × 10	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 10	ADENINE × 10 6-AMINOPYRIMIDIN-2(1H)-ONE × 10 water × 10	Consistent with protein count
4	Protein homooligomer	Homooligomer	Protein 10	ADENINE × 10 6-AMINOPYRIMIDIN-2(1H)-ONE × 10 water × 10	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9WBP8_9VIRU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–736； UniProt 1–736 Author chain B； PDBConstruct 1–736； UniProt 1–736 Author chain C； PDBConstruct 1–736； UniProt 1–736 Author chain D； PDBConstruct 1–736； UniProt 1–736 Author chain E； PDBConstruct 1–736； UniProt 1–736 Author chain F； PDBConstruct 1–736； UniProt 1–736 Author chain G； PDBConstruct 1–736； UniProt 1–736 Author chain H； PDBConstruct 1–736； UniProt 1–736 Author chain I； PDBConstruct 1–736； UniProt 1–736 Author chain J； PDBConstruct 1–736； UniProt 1–736

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	3ng9
Deposition date deposition_date	2010-06-11
Structure title title	Structure to Function Correlations for Adeno-associated Virus Serotype 1
Keywords keywords	Adeno-Associated Virus 1, beta barrel, single-stranded DNA virus, parvovirus, icosahedral virus, Virus; VIRUS
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.

3ng9__assembly_1__model_1

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

Download this curve (.dat)

3ng9__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3ng9__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	0.00 Å
Rg (electron density)	108.80 Å
Total Rg	109.10 Å
Atom count	248280
Residues	31200
Excluded volume	4345300 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3ng9__assembly_1__model_1`	60-MERIC （60）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3ng9__assembly_2__model_1`	decameric （10）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
3	1	`3ng9__assembly_3__model_1`	decameric （10）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
4	1	`3ng9__assembly_4__model_1`	decameric （10）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.

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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	Capsid protein
Molecular weight formula_weight	81454.9 kDa
Source method src_method	man
Copy count entity_count	10

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J
Atom count atom_count	42680

MAADGYLPDWLEDNLSEGIREWWDLKPGAPKPKANQQKQDDGRGLVLPGYKYLGPFNGLDKGEPVNAADAAALEHDKAYDQQLKAGDNPYLRYNHADAEFQERLQEDTSFGGNLGRAVFQAKKRVLEPLGLVEEGAKTAPGKKRPVEQSPQEPDSSSGIGKTGQQPAKKRLNFGQTGDSESVPDPQPLGEPPATPAAVGPTTMASGGGAPMADNNEGADGVGNASGNWHCDSTWLGDRVITTSTRTWALPTYNNHLYKQISSASTGASNDNHYFGYSTPWGYFDFNRFHCHFSPRDWQRLINNNWGFRPKRLNFKLFNIQVKEVTTNDGVTTIANNLTSTVQVFSDSEYQLPYVLGSAHQGCLPPFPADVFMIPQYGYLTLNNGSQAVGRSSFYCLEYFPSQMLRTGNNFTFSYTFEEVPFHSSYAHSQSLDRLMNPLIDQYLYYLNRTQNQSGSAQNKDLLFSRGSPAGMSVQPKNWLPGPCYRQQRVSKTKTDNNNSNFTWTGASKYNLNGRESIINPGTAMASHKDDEDKFFPMSGVMIFGKESAGASNTALDNVMITDEEEIKATNPVATERFGTVAVNFQSSSTDPATGDVHAMGALPGMVWQDRDVYLQGPIWAKIPHTDGHFHPSPLMGGFGLKNPPPQILIKNTPVPANPPAEFSATKFASFITQYSTGQVSVEIEWELQKENSKRWNPEVQYTSNYAKSANVDFTVDNNGLYTEPRPIGTRYLTRPL

Source Source

Source organism organism	Adeno-associated virus - 1
NCBI taxonomy ID ncbi_taxonomy_id	85106

Entity 2 Entity 2 non-polymer

Description description	ADENINE
Molecular weight formula_weight	135.1 kDa
Source method src_method	syn
Copy count entity_count	10

Entity 3 Entity 3 non-polymer

Description description	6-AMINOPYRIMIDIN-2(1H)-ONE
Molecular weight formula_weight	111.1 kDa
Source method src_method	syn
Copy count entity_count	10

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1300

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6. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (10 domains)

Domain ID domain_id	d3ng9a_
Class class	b — All beta proteins
Fold Fold fold	b.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamily	b.121.5 — ssDNA viruses
Family Family family	b.121.5.2 — Parvoviridae-like VP

Domain ID domain_id	d3ng9b_
Class class	b — All beta proteins
Fold Fold fold	b.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamily	b.121.5 — ssDNA viruses
Family Family family	b.121.5.2 — Parvoviridae-like VP

Domain ID domain_id	d3ng9c_
Class class	b — All beta proteins
Fold Fold fold	b.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamily	b.121.5 — ssDNA viruses
Family Family family	b.121.5.2 — Parvoviridae-like VP

Domain ID domain_id	d3ng9d_
Class class	b — All beta proteins
Fold Fold fold	b.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamily	b.121.5 — ssDNA viruses
Family Family family	b.121.5.2 — Parvoviridae-like VP

Domain ID domain_id	d3ng9e_
Class class	b — All beta proteins
Fold Fold fold	b.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamily	b.121.5 — ssDNA viruses
Family Family family	b.121.5.2 — Parvoviridae-like VP

Domain ID domain_id	d3ng9f_
Class class	b — All beta proteins
Fold Fold fold	b.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamily	b.121.5 — ssDNA viruses
Family Family family	b.121.5.2 — Parvoviridae-like VP

Domain ID domain_id	d3ng9g_
Class class	b — All beta proteins
Fold Fold fold	b.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamily	b.121.5 — ssDNA viruses
Family Family family	b.121.5.2 — Parvoviridae-like VP

Domain ID domain_id	d3ng9h_
Class class	b — All beta proteins
Fold Fold fold	b.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamily	b.121.5 — ssDNA viruses
Family Family family	b.121.5.2 — Parvoviridae-like VP

Domain ID domain_id	d3ng9i_
Class class	b — All beta proteins
Fold Fold fold	b.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamily	b.121.5 — ssDNA viruses
Family Family family	b.121.5.2 — Parvoviridae-like VP

Domain ID domain_id	d3ng9j_
Class class	b — All beta proteins
Fold Fold fold	b.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamily	b.121.5 — ssDNA viruses
Family Family family	b.121.5.2 — Parvoviridae-like VP

CATH v4.4 (10 domains)

Domain ID domain_id	3ng9A00
Class class	2 — Mainly Beta
Architecture architecture	170 — Beta Complex
Topology topology	30 — Empty Capsid Viral Protein 2
Homologous superfamily homologous superfamily	10 — Parvovirus coat protein VP1/VP2

Domain ID domain_id	3ng9B00
Class class	2 — Mainly Beta
Architecture architecture	170 — Beta Complex
Topology topology	30 — Empty Capsid Viral Protein 2
Homologous superfamily homologous superfamily	10 — Parvovirus coat protein VP1/VP2

Domain ID domain_id	3ng9C00
Class class	2 — Mainly Beta
Architecture architecture	170 — Beta Complex
Topology topology	30 — Empty Capsid Viral Protein 2
Homologous superfamily homologous superfamily	10 — Parvovirus coat protein VP1/VP2

Domain ID domain_id	3ng9D00
Class class	2 — Mainly Beta
Architecture architecture	170 — Beta Complex
Topology topology	30 — Empty Capsid Viral Protein 2
Homologous superfamily homologous superfamily	10 — Parvovirus coat protein VP1/VP2

Domain ID domain_id	3ng9E00
Class class	2 — Mainly Beta
Architecture architecture	170 — Beta Complex
Topology topology	30 — Empty Capsid Viral Protein 2
Homologous superfamily homologous superfamily	10 — Parvovirus coat protein VP1/VP2

Domain ID domain_id	3ng9F00
Class class	2 — Mainly Beta
Architecture architecture	170 — Beta Complex
Topology topology	30 — Empty Capsid Viral Protein 2
Homologous superfamily homologous superfamily	10 — Parvovirus coat protein VP1/VP2

Domain ID domain_id	3ng9G00
Class class	2 — Mainly Beta
Architecture architecture	170 — Beta Complex
Topology topology	30 — Empty Capsid Viral Protein 2
Homologous superfamily homologous superfamily	10 — Parvovirus coat protein VP1/VP2

Domain ID domain_id	3ng9H00
Class class	2 — Mainly Beta
Architecture architecture	170 — Beta Complex
Topology topology	30 — Empty Capsid Viral Protein 2
Homologous superfamily homologous superfamily	10 — Parvovirus coat protein VP1/VP2

Domain ID domain_id	3ng9I00
Class class	2 — Mainly Beta
Architecture architecture	170 — Beta Complex
Topology topology	30 — Empty Capsid Viral Protein 2
Homologous superfamily homologous superfamily	10 — Parvovirus coat protein VP1/VP2

Domain ID domain_id	3ng9J00
Class class	2 — Mainly Beta
Architecture architecture	170 — Beta Complex
Topology topology	30 — Empty Capsid Viral Protein 2
Homologous superfamily homologous superfamily	10 — Parvovirus coat protein VP1/VP2

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Unit-cell length a length_a	262.700 Å
Unit-cell length b length_b	262.700 Å
Unit-cell length c length_c	612.300 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	180

Space group space_group	H 3 2
Space-group number int_tables_number	155
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.2300
R_work r_work	0.2300
R_free r_free	0.2500

Structure to Function Correlations for Adeno-associated Virus Serotype 1

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

Capsid 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

3ng9__assembly_1__model_1

3ng9__assembly_1__model_1 | I(q)

3ng9__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 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (10 domains)

CATH v4.4 (10 domains)

7. Citations (1)

Structure to Function Correlations for Adeno-associated Virus Serotype 1

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

Capsid 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

3ng9__assembly_1__model_1

3ng9__assembly_1__model_1 | I(q)

3ng9__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 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (10 domains)

CATH v4.4 (10 domains)

7. Citations (1)