SAXSdb — 9lgj

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

Capsid protein VP1

Adeno-associated virus 2 Srivastava/1982

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	CAPSD_AAV2S
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–743； UniProt 1–735 Author chain AA； PDBConstruct 1–743； UniProt 1–735 Author chain AB； PDBConstruct 1–743； UniProt 1–735 Author chain B； PDBConstruct 1–743； UniProt 1–735 Author chain BA； PDBConstruct 1–743； UniProt 1–735 Author chain BB； PDBConstruct 1–743； UniProt 1–735 Author chain C； PDBConstruct 1–743； UniProt 1–735 Author chain CA； PDBConstruct 1–743； UniProt 1–735 Author chain CB； PDBConstruct 1–743； UniProt 1–735 Author chain D； PDBConstruct 1–743； UniProt 1–735 Author chain DA； PDBConstruct 1–743； UniProt 1–735 Author chain DB； PDBConstruct 1–743； UniProt 1–735 Author chain E； PDBConstruct 1–743； UniProt 1–735 Author chain EA； PDBConstruct 1–743； UniProt 1–735 Author chain EB； PDBConstruct 1–743； UniProt 1–735 Author chain F； PDBConstruct 1–743； UniProt 1–735 Author chain FA； PDBConstruct 1–743； UniProt 1–735 Author chain FB； PDBConstruct 1–743； UniProt 1–735 Author chain G； PDBConstruct 1–743； UniProt 1–735 Author chain GA； PDBConstruct 1–743； UniProt 1–735 Author chain GB； PDBConstruct 1–743； UniProt 1–735 Author chain H； PDBConstruct 1–743； UniProt 1–735 Author chain HA； PDBConstruct 1–743； UniProt 1–735 Author chain HB； PDBConstruct 1–743； UniProt 1–735 Author chain I； PDBConstruct 1–743； UniProt 1–735 Author chain IA； PDBConstruct 1–743； UniProt 1–735 Author chain IB； PDBConstruct 1–743； UniProt 1–735 Author chain J； PDBConstruct 1–743； UniProt 1–735 Author chain JA； PDBConstruct 1–743； UniProt 1–735 Author chain K； PDBConstruct 1–743； UniProt 1–735 Author chain KA； PDBConstruct 1–743； UniProt 1–735 Author chain L； PDBConstruct 1–743； UniProt 1–735 Author chain LA； PDBConstruct 1–743； UniProt 1–735 Author chain M； PDBConstruct 1–743； UniProt 1–735 Author chain MA； PDBConstruct 1–743； UniProt 1–735 Author chain N； PDBConstruct 1–743； UniProt 1–735 Author chain NA； PDBConstruct 1–743； UniProt 1–735 Author chain O； PDBConstruct 1–743； UniProt 1–735 Author chain OA； PDBConstruct 1–743； UniProt 1–735 Author chain P； PDBConstruct 1–743； UniProt 1–735 Author chain PA； PDBConstruct 1–743； UniProt 1–735 Author chain Q； PDBConstruct 1–743； UniProt 1–735 Author chain QA； PDBConstruct 1–743； UniProt 1–735 Author chain R； PDBConstruct 1–743； UniProt 1–735 Author chain RA； PDBConstruct 1–743； UniProt 1–735 Author chain S； PDBConstruct 1–743； UniProt 1–735 Author chain SA； PDBConstruct 1–743； UniProt 1–735 Author chain T； PDBConstruct 1–743； UniProt 1–735 Author chain TA； PDBConstruct 1–743； UniProt 1–735 Author chain UA； PDBConstruct 1–743； UniProt 1–735 Author chain V； PDBConstruct 1–743； UniProt 1–735 Author chain VA； PDBConstruct 1–743； UniProt 1–735 Author chain W； PDBConstruct 1–743； UniProt 1–735 Author chain WA； PDBConstruct 1–743； UniProt 1–735 Author chain X； PDBConstruct 1–743； UniProt 1–735 Author chain XA； PDBConstruct 1–743； UniProt 1–735 Author chain Y； PDBConstruct 1–743； UniProt 1–735 Author chain YA； PDBConstruct 1–743； UniProt 1–735 Author chain Z； PDBConstruct 1–743； UniProt 1–735 Author chain ZA； PDBConstruct 1–743； UniProt 1–735

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	9lgj
Deposition date deposition_date	2025-01-10
Structure title title	Cryo-EM structure of a designed AAV2-based vector
Keywords keywords	Virus, AAV2, Adeno-associated Virus Serotype 2 mutant; 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.

9lgj__assembly_1__model_1

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

Download this curve (.dat)

9lgj__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9lgj__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)	109.20 Å
Total Rg	109.40 Å
Atom count	249660
Residues	31200
Excluded volume	4358600 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9lgj__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)

Entity 1 Entity 1 polymer

Description description	Capsid protein VP1
Molecular weight formula_weight	82852.2 kDa
Mutation mutation	I204T, V716I
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,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA,KA,LA,MA,NA,OA,PA,QA,RA,SA,TA,UA,VA,WA,XA,YA,ZA,AB,BB,CB,DB,EB,FB,GB,HB,IB ;
Atom count atom_count	249660

MAADGYLPDWLEDTLSEGIRQWWKLKPGPPPPKPAERHKDDSRGLVLPGYKYLGPFNGLDKGEPVNEADAAALEHDKAYDRQLDSGDNPYLKYNHADAEFQERLKEDTSFGGNLGRAVFQAKKRVLEPLGLVEEPVKTAPGKKRPVEHSPVEPDSSSGTGKAGQQPARKRLNFGQTGDADSVPDPQPLGQPPAAPSGLGTNTMATGSGAPMADNNEGADGVGNSSGNWHCDSTWMGDRVTTTSTRTWALPTYNNHLYKQISSQSGASNDNHYFGYSTPWGYFDFNRFHCHFSPRDWQRLINNNWGFRPKRLNFKLFNIQVKEVTQNDGTTTIANNLTSTVQVFTDSEYQLPYVLGSAHQGCLPPFPADVFMVPQYGYLTLNNGSQAVGRSSFYCLEYFPSQMLRTGNNFTFSYTFEDVPFHSSYAHSQSLDRLMNPLIDQYLYYLSRTNTPSGTTTQSRLQFSQAGASDIRDQSRNWLPGPCYRQQRVSKTSADNNNSEYSWTGATKYHLNGRDSLVNPGPAMASHKDDEEKFFPQSGVLIFGKQGSEKTNVDIEKVMITDEEEIRTTNPVATEQYGSVSTNLQRGNIADSSRTSRQAATADVNTQGVLPGMVWQDRDVYLQGPIWAKIPHTDGHFHPSPLMGGFGLKHPPPQILIKNTPVPANPSTTFSAAKFASFITQYSTGQVSVEIEWELQKENSKRWNPEIQYTSNYNKSINVDFTVDTNGVYSEPRPIGTRYLTRNL

Source Source

Source organism organism	Adeno-associated virus 2 Srivastava/1982
NCBI taxonomy ID ncbi_taxonomy_id	648242
Host organism host_organism	Homo sapiens

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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	triclinic

Resolution resolution	2.58 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	19555

Cryo-EM structure of a designed AAV2-based vector

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

Capsid protein VP1

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

9lgj__assembly_1__model_1

9lgj__assembly_1__model_1 | I(q)

9lgj__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 (1)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

7. Citations (1)

Cryo-EM structure of a designed AAV2-based vector

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

Capsid protein VP1

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

9lgj__assembly_1__model_1

9lgj__assembly_1__model_1 | I(q)

9lgj__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 (1)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

7. Citations (1)