SAXSdb — 9dcb

▼

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–DNA	Homooligomer	Protein 60 DNA 60	;DNA (5'-D(PAPA)-3') ; × 60	Consistent with all polymers

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	9dcb
Deposition date deposition_date	2024-08-25
Structure title title	The Structure of AAV5 at 4 Degrees
Keywords keywords	temperature, genome, vector, icosahedron, VIRUS; VIRUS
Experimental Method method	ELECTRON MICROSCOPY

▼

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.

9dcb__assembly_1__model_1

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

Download this curve (.dat)

9dcb__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9dcb__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)	108.90 Å
Total Rg	109.10 Å
Atom count	249480
Residues	31140
Excluded volume	4358800 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9dcb__assembly_1__model_1`	120-meric （120）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	Capsid protein
Molecular weight formula_weight	80497.4 kDa
Source method src_method	man
Copy count entity_count	60

Polymer Polymer

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	249480

MSFVDHPPDWLEEVGEGLREFLGLEAGPPKPKPNQQHQDQARGLVLPGYNYLGPGNGLDRGEPVNRADEVAREHDISYNEQLEAGDNPYLKYNHADAEFQEKLADDTSFGGNLGKAVFQAKKRVLEPFGLVEEGAKTAPTGKRIDDHFPKRKKARTEEDSKPSTSSDAEAGPSGSQQLQIPAQPASSLGADTMSAGGGGPLGDNNQGADGVGNASGDWHCDSTWMGDRVVTKSTRTWVLPSYNNHQYREIKSGSVDGSNANAYFGYSTPWGYFDFNRFHSHWSPRDWQRLINNYWGFRPRSLRVKIFNIQVKEVTVQDSTTTIANNLTSTVQVFTDDDYQLPYVVGNGTEGCLPAFPPQVFTLPQYGYATLNRDNTENPTERSSFFCLEYFPSKMLRTGNNFEFTYNFEEVPFHSSFAPSQNLFKLANPLVDQYLYRFVSTNNTGGVQFNKNLAGRYANTYKNWFPGPMGRTQGWNLGSGVNRASVSAFATTNRMELEGASYQVPPQPNGMTNNLQGSNTYALENTMIFNSQPANPGTTATYLEGNMLITSESETQPVNRVAYNVGGQMATNNQSSTTAPATGTYNLQEIVPGSVWMERDVYLQGPIWAKIPETGAHFHPSPAMGGFGLKHPPPMMLIKNTPVPGNITSFSDVPVSSFITQYSTGQVTVEMEWELKKENSKRWNPEIQYTNNYNDPQFVDFAPDSTGEYRTTRPIGTRYLTRPL

Source Source

Source organism organism	adeno-associated virus 5
NCBI taxonomy ID ncbi_taxonomy_id	82300
Host organism host_organism	Spodoptera frugiperda

Entity 2 Entity 2 polymer

Description description	;DNA (5'-D(PAPA)-3') ;
Molecular weight formula_weight	581.5 kDa
Source method src_method	man
Copy count entity_count	60

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	;0,JA,UA,fA,qA,1A,3A,4A,5A,9,AA,BA,CA,DA,EA,FA,GA,HA,IA,KA,LA,MA,NA,OA,PA,QA,RA,SA,TA,VA,WA,XA,YA,ZA,aA,bA,cA,dA,eA,gA,hA,iA,jA,kA,lA,mA,nA,oA,pA,rA,sA,tA,uA,vA,wA,xA,yA,zA,0A,2A ;

AA

Source Source

Source organism organism	adeno-associated virus 5
NCBI taxonomy ID ncbi_taxonomy_id	82300
Host organism host_organism	Spodoptera frugiperda

▶

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	2.89 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	23000

The Structure of AAV5 at 4 Degrees

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

9dcb__assembly_1__model_1

9dcb__assembly_1__model_1 | I(q)

9dcb__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

7. Citations (1)

The Structure of AAV5 at 4 Degrees

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

9dcb__assembly_1__model_1

9dcb__assembly_1__model_1 | I(q)

9dcb__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

7. Citations (1)