SAXSdb — 9umb

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

Capsid protein

adeno-associated virus 5

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 60	No other associated polymer	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9YIJ1_9VIRU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain 1； PDBConstruct 1–724； UniProt 1–724 Author chain 2； PDBConstruct 1–724； UniProt 1–724 Author chain 3； PDBConstruct 1–724； UniProt 1–724 Author chain 4； PDBConstruct 1–724； UniProt 1–724 Author chain 5； PDBConstruct 1–724； UniProt 1–724 Author chain 6； PDBConstruct 1–724； UniProt 1–724 Author chain 7； PDBConstruct 1–724； UniProt 1–724 Author chain 8； PDBConstruct 1–724； UniProt 1–724 Author chain A； PDBConstruct 1–724； UniProt 1–724 Author chain B； PDBConstruct 1–724； UniProt 1–724 Author chain C； PDBConstruct 1–724； UniProt 1–724 Author chain D； PDBConstruct 1–724； UniProt 1–724 Author chain E； PDBConstruct 1–724； UniProt 1–724 Author chain F； PDBConstruct 1–724； UniProt 1–724 Author chain G； PDBConstruct 1–724； UniProt 1–724 Author chain H； PDBConstruct 1–724； UniProt 1–724 Author chain I； PDBConstruct 1–724； UniProt 1–724 Author chain J； PDBConstruct 1–724； UniProt 1–724 Author chain K； PDBConstruct 1–724； UniProt 1–724 Author chain L； PDBConstruct 1–724； UniProt 1–724 Author chain M； PDBConstruct 1–724； UniProt 1–724 Author chain N； PDBConstruct 1–724； UniProt 1–724 Author chain O； PDBConstruct 1–724； UniProt 1–724 Author chain P； PDBConstruct 1–724； UniProt 1–724 Author chain Q； PDBConstruct 1–724； UniProt 1–724 Author chain R； PDBConstruct 1–724； UniProt 1–724 Author chain S； PDBConstruct 1–724； UniProt 1–724 Author chain T； PDBConstruct 1–724； UniProt 1–724 Author chain U； PDBConstruct 1–724； UniProt 1–724 Author chain V； PDBConstruct 1–724； UniProt 1–724 Author chain W； PDBConstruct 1–724； UniProt 1–724 Author chain X； PDBConstruct 1–724； UniProt 1–724 Author chain Y； PDBConstruct 1–724； UniProt 1–724 Author chain Z； PDBConstruct 1–724； UniProt 1–724 Author chain a； PDBConstruct 1–724； UniProt 1–724 Author chain b； PDBConstruct 1–724； UniProt 1–724 Author chain c； PDBConstruct 1–724； UniProt 1–724 Author chain d； PDBConstruct 1–724； UniProt 1–724 Author chain e； PDBConstruct 1–724； UniProt 1–724 Author chain f； PDBConstruct 1–724； UniProt 1–724 Author chain g； PDBConstruct 1–724； UniProt 1–724 Author chain h； PDBConstruct 1–724； UniProt 1–724 Author chain i； PDBConstruct 1–724； UniProt 1–724 Author chain j； PDBConstruct 1–724； UniProt 1–724 Author chain k； PDBConstruct 1–724； UniProt 1–724 Author chain l； PDBConstruct 1–724； UniProt 1–724 Author chain m； PDBConstruct 1–724； UniProt 1–724 Author chain n； PDBConstruct 1–724； UniProt 1–724 Author chain o； PDBConstruct 1–724； UniProt 1–724 Author chain p； PDBConstruct 1–724； UniProt 1–724 Author chain q； PDBConstruct 1–724； UniProt 1–724 Author chain r； PDBConstruct 1–724； UniProt 1–724 Author chain s； PDBConstruct 1–724； UniProt 1–724 Author chain t； PDBConstruct 1–724； UniProt 1–724 Author chain u； PDBConstruct 1–724； UniProt 1–724 Author chain v； PDBConstruct 1–724； UniProt 1–724 Author chain w； PDBConstruct 1–724； UniProt 1–724 Author chain x； PDBConstruct 1–724； UniProt 1–724 Author chain y； PDBConstruct 1–724； UniProt 1–724 Author chain z； PDBConstruct 1–724； UniProt 1–724

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	9umb
Deposition date deposition_date	2025-04-21
Structure title title	Structure of Modified adeno-associated viral vector, AAV5-BCD
Keywords keywords	adeno-associated virus, AAV5, VIRUS; VIRUS
Experimental Method method	ELECTRON MICROSCOPY

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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.

9umb__assembly_1__model_1

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

Download this curve (.dat)

9umb__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9umb__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)	111.60 Å
Total Rg	111.80 Å
Atom count	246600
Residues	30960
Excluded volume	4316500 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9umb__assembly_1__model_1`	60-meric （60）	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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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	—

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

Resolution resolution	2.550 Å
Low-resolution limit resolution_low	2.550 Å
R factor r_factor	0.3988
R_work r_work	0.3988
R_free r_free	—

Resolution resolution	2.55 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	285362

Description description	Capsid protein
Molecular weight formula_weight	80467.4 kDa
Source method src_method	man
Copy count entity_count	60

Structure of Modified adeno-associated viral vector, AAV5-BCD

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

9umb__assembly_1__model_1

9umb__assembly_1__model_1 | I(q)

9umb__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

7. Citations (1)

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,a,b,c,d,e,f,g,h,i,j,k,l,m,n,o,p,q,r,s,t,u,v,w,x,y,z,1,2,3,4,5,6,7,8
Atom count atom_count	246600

Source organism organism	adeno-associated virus 5
NCBI taxonomy ID ncbi_taxonomy_id	82300
Host organism host_organism	Homo sapiens

Structure of Modified adeno-associated viral vector, AAV5-BCD

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

9umb__assembly_1__model_1

9umb__assembly_1__model_1 | I(q)

9umb__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

7. Citations (1)