SAXSdb — 3ra9

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

Capsid protein

Adeno-associated virus - 8

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Homooligomer	Protein 60 DNA 60	;DNA (5'-D(PCPA)-3') ; × 60 water × 60	Consistent with all polymers
2	Protein–DNA	Monomer	Protein 1 DNA 1	;DNA (5'-D(PCPA)-3') ; × 1 water × 1	Consistent with all polymers
3	Protein–DNA	Homooligomer	Protein 5 DNA 5	;DNA (5'-D(PCPA)-3') ; × 5 water × 5	Consistent with all polymers
4	Protein–DNA	Homooligomer	Protein 6 DNA 6	;DNA (5'-D(PCPA)-3') ; × 6 water × 6	Consistent with all polymers
5	Protein–DNA	Monomer	Protein 1 DNA 1	;DNA (5'-D(PCPA)-3') ; × 1 water × 1	Consistent with all polymers
6	Protein–DNA	Homooligomer	Protein 10 DNA 10	;DNA (5'-D(PCPA)-3') ; × 10 water × 10	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q8JQF8_9VIRU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–519； UniProt 220–738

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	3ra9
Deposition date deposition_date	2011-03-27
Structure title title	Structural studies of AAV8 capsid transitions associated with endosomal trafficking
Keywords keywords	Beta Barrel, Viral Capsid, 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.

3ra9__assembly_1__model_1

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

Download this curve (.dat)

3ra9__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3ra9__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)	109.50 Å
Total Rg	109.70 Å
Atom count	250620
Residues	31260
Excluded volume	4376000 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3ra9__assembly_1__model_1`	120-meric （120）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3ra9__assembly_2__model_1`	dimeric （2）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
3	1	`3ra9__assembly_3__model_1`	decameric （10）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
4	1	`3ra9__assembly_4__model_1`	dodecameric （12）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
5	1	`3ra9__assembly_5__model_1`	dimeric （2）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
6	1	`3ra9__assembly_6__model_1`	eicosameric （20）	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 (3)

Entity 1 Entity 1 polymer

Description description	Capsid protein
Molecular weight formula_weight	58528.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	4231

DGVGSSSGNWHCDSTWLGDRVITTSTRTWALPTYNNHLYKQISNGTSGGATNDNTYFGYSTPWGYFDFNRFHCHFSPRDWQRLINNNWGFRPKRLSFKLFNIQVKEVTQNEGTKTIANNLTSTIQVFTDSEYQLPYVLGSAHQGCLPPFPADVFMIPQYGYLTLNNGSQAVGRSSFYCLEYFPSQMLRTGNNFQFTYTFEDVPFHSSYAHSQSLDRLMNPLIDQYLYYLSRTQTTGGTANTQTLGFSQGGPNTMANQAKNWLPGPCYRQQRVSTTTGQNNNSNFAWTAGTKYHLNGRNSLANPGIAMATHKDDEERFFPSNGILIFGKQNAARDNADYSDVMLTSEEEIKTTNPVATEEYGIVADNLQQQNTAPQIGTVNSQGALPGMVWQNRDVYLQGPIWAKIPHTDGNFHPSPLMGGFGLKHPPPQILIKNTPVPADPPTTFNQSKLNSFITQYSTGQVSVEIEWELQKENSKRWNPEIQYTSNYYKSTSVDFAVNTEGVYSEPRPIGTRYLTRNL

Source Source

Source organism organism	Adeno-associated virus - 8
NCBI taxonomy ID ncbi_taxonomy_id	202813
Host organism host_organism	Homo sapiens

Entity 2 Entity 2 polymer

Description description	;DNA (5'-D(PCPA)-3') ;
Molecular weight formula_weight	557.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	D

CA

Source Source

Source organism organism	Aequorea victoria
NCBI taxonomy ID ncbi_taxonomy_id	6100
Host organism host_organism	Homo sapiens

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	54

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6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d3ra9a_
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 (1 domains)

Domain ID domain_id	3ra9A00
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	257.940 Å
Unit-cell length b length_b	257.940 Å
Unit-cell length c length_c	448.690 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	120

Space group space_group	P 63 2 2
Space-group number int_tables_number	182
Crystal system crystal_system	—

Resolution resolution	2.700 Å
Low-resolution limit resolution_low	40.000 Å
R factor r_factor	0.2440
R_work r_work	0.2430
R_free r_free	0.2480

Structural studies of AAV8 capsid transitions associated with endosomal trafficking

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

3ra9__assembly_1__model_1

3ra9__assembly_1__model_1 | I(q)

3ra9__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)

Structural studies of AAV8 capsid transitions associated with endosomal trafficking

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

3ra9__assembly_1__model_1

3ra9__assembly_1__model_1 | I(q)

3ra9__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)