SAXSdb — 9bu7

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

Protein Rep68

adeno-associated virus 2

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Homooligomer	Protein 7 DNA 2	DNA (21-MER) × 1 DNA (21-MER) × 1 PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 3 MAGNESIUM ION × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	REP68_AAV2S
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–491； UniProt 2–490 Author chain B； PDBConstruct 3–491； UniProt 2–490 Author chain C； PDBConstruct 3–491； UniProt 2–490 Author chain D； PDBConstruct 3–491； UniProt 2–490 Author chain E； PDBConstruct 3–491； UniProt 2–490 Author chain F； PDBConstruct 3–491； UniProt 2–490 Author chain G； PDBConstruct 3–491； UniProt 2–490

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	9bu7
Deposition date deposition_date	2024-05-16
Last revision last_revision	2025-02-12
Structure title title	Cryo-EM Structure of AAV2 Rep68 bound to integration site AAVS1: Insights into the mechanism of DNA melting.
Keywords keywords	AAV, Protein-DNA complex, Replication, Helicase, AAA+, SF3, DNA BINDING PROTEIN, VIRAL PROTEIN-DNA complex; VIRAL PROTEIN/DNA
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.

9bu7__assembly_1__model_1

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

Download this curve (.dat)

9bu7__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9bu7__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	42.02 Å
Rg (electron density)	41.59 Å
Total Rg	41.55 Å
Atom count	12831
Residues	1961
Excluded volume	218040 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9bu7__assembly_1__model_1`	nonameric （9）	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 (5)

Entity 1 Entity 1 polymer

Description description	Protein Rep68
Molecular weight formula_weight	55896.2 kDa
EC 编号 ec_number	3.6.4.12
Source method src_method	man
Copy count entity_count	7

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G
Atom count atom_count	12831

GPPGFYEIVIKVPSDLDGHLPGISDSFVNWVAEKEWELPPDSDMDLNLIEQAPLTVAEKLQRDFLTEWRRVSKAPEALFFVQFEKGESYFHMHVLVETTGVKSMVLGRFLSQIREKLIQRIYRGIEPTLPNWFAVTKTRNGAGGGNKVVDESYIPNYLLPKTQPELQWAWTNMEQYLSACLNLTERKRLVAQHLTHVSQTQEQNKENQNPNSDAPVIRSKTSARYMELVGWLVDKGITSEKQWIQEDQASYISFNAASNSRSQIKAALDNAGKIMSLTKTAPDYLVGQQPVEDISSNRIYKILELNGYDPQYAASVFLGWATKKFGKRNTIWLFGPATTGKTNIAEAIAHTVPFYGCVNWTNENFPFNDCVDKMVIWWEEGKMTAKVVESAKAILGGSKVRVDQKCKSSAQIDPTPVIVTSNTNMCAVIDGNSTTFEHQQPLQDRMFKFELTRRLDHDFGKVTKQEVKDFFRWAKDHVVEVEHEFYVKKGG

Source Source

Source organism organism	adeno-associated virus 2
NCBI taxonomy ID ncbi_taxonomy_id	10804
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	DNA (21-MER)
Molecular weight formula_weight	6463.1 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	H

GTTGGGGCTCGGCGCTCGCTC

Entity 3 Entity 3 polymer

Description description	DNA (21-MER)
Molecular weight formula_weight	6428.2 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	I

GAGCGAGCGCCGAGCCCCAAC

Entity 4 Entity 4 non-polymer

Description description	PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
Molecular weight formula_weight	523.2 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 5 Entity 5 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	2

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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	3.640 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

Resolution resolution	3.64 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	268936

Cryo-EM Structure of AAV2 Rep68 bound to integration site AAVS1: Insights into the mechanism of DNA melting.

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

Protein Rep68

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

9bu7__assembly_1__model_1

9bu7__assembly_1__model_1 | I(q)

9bu7__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

7. Citations (1)

Cryo-EM Structure of AAV2 Rep68 bound to integration site AAVS1: Insights into the mechanism of DNA melting.

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

Protein Rep68

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

9bu7__assembly_1__model_1

9bu7__assembly_1__model_1 | I(q)

9bu7__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

7. Citations (1)