SAXSdb — 1rz9

▼

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

Rep 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 5 DNA 2	26-MER × 1 26-MER × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9YJC1_9VIRU
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain A； PDBConstruct 1–197； UniProt 1–197 Author chain B； PDBConstruct 1–197； UniProt 1–197 Author chain C； PDBConstruct 1–197； UniProt 1–197 Author chain D； PDBConstruct 1–197； UniProt 1–197 Author chain E； PDBConstruct 1–197； UniProt 1–197

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	1rz9
Deposition date deposition_date	2003-12-24
Structure title title	Crystal Structure of AAV Rep complexed with the Rep-binding sequence
Keywords keywords	Protein-DNA complex, Viral protein-DNA COMPLEX; Viral protein/DNA
Experimental Method method	X-RAY DIFFRACTION

▼

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.

1rz9__assembly_1__model_1

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

Download this curve (.dat)

1rz9__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1rz9__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	36.50 Å
Rg (electron density)	36.60 Å
Total Rg	36.87 Å
Atom count	8960
Residues	1017
Excluded volume	157420 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1rz9__assembly_1__model_1`	heptameric （7）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	26-MER
Molecular weight formula_weight	7939.1 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	F
Atom count atom_count	8960

CGCGTTCGCTCGCTCGCTGGCTCGTG

Entity 2 Entity 2 polymer

Description description	26-MER
Molecular weight formula_weight	8042.2 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	G

CACGAGCCAGCGAGCGAGCGAACGCG

Entity 3 Entity 3 polymer

Description description	Rep protein
Molecular weight formula_weight	22777.0 kDa
Source method src_method	man
Copy count entity_count	5

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E

MATFYEVIVRVPFDVEEHLPGISDSFVDWVTGQIWELPPESDLNLTLVEQPQLTVADRIRRVFLYEWNKFSKQESKFFVQFEKGSEYFHLHTLVETSGISSMVLGRYVSQIRAQLVKVVFQGIEPQINDWVAITKVKKGGANKVVDSGYIPAYLLPKVQPELQWAWTNLDEYKLAALNLEERKRLVAQFLAESSQRS

Source Source

Source organism organism	Adeno-associated virus - 5
NCBI taxonomy ID ncbi_taxonomy_id	82300
Host organism host_organism	Escherichia coli BL21(DE3)

▼

6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (5 domains)

Domain ID domain_id	d1rz9a_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.89 — Origin of replication-binding domain, RBD-like
Superfamily Superfamily superfamily	d.89.1 — Origin of replication-binding domain, RBD-like
Family Family family	d.89.1.3 — Replication protein Rep, nuclease domain

Domain ID domain_id	d1rz9b_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.89 — Origin of replication-binding domain, RBD-like
Superfamily Superfamily superfamily	d.89.1 — Origin of replication-binding domain, RBD-like
Family Family family	d.89.1.3 — Replication protein Rep, nuclease domain

Domain ID domain_id	d1rz9c_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.89 — Origin of replication-binding domain, RBD-like
Superfamily Superfamily superfamily	d.89.1 — Origin of replication-binding domain, RBD-like
Family Family family	d.89.1.3 — Replication protein Rep, nuclease domain

Domain ID domain_id	d1rz9d_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.89 — Origin of replication-binding domain, RBD-like
Superfamily Superfamily superfamily	d.89.1 — Origin of replication-binding domain, RBD-like
Family Family family	d.89.1.3 — Replication protein Rep, nuclease domain

Domain ID domain_id	d1rz9e_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.89 — Origin of replication-binding domain, RBD-like
Superfamily Superfamily superfamily	d.89.1 — Origin of replication-binding domain, RBD-like
Family Family family	d.89.1.3 — Replication protein Rep, nuclease domain

CATH v4.4 (5 domains)

Domain ID domain_id	1rz9A00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1310 — Replication Protein E1; Chain: A,
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	1rz9B00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1310 — Replication Protein E1; Chain: A,
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	1rz9C00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1310 — Replication Protein E1; Chain: A,
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	1rz9D00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1310 — Replication Protein E1; Chain: A,
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	1rz9E00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1310 — Replication Protein E1; Chain: A,
Homologous superfamily homologous superfamily	20 —

▶

Unit-cell length a length_a	78.671 Å
Unit-cell length b length_b	131.706 Å
Unit-cell length c length_c	82.164 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	112.68 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	10

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	3.100 Å
Low-resolution limit resolution_low	19.880 Å
R factor r_factor	0.2860
R_work r_work	0.2860
R_free r_free	0.3150

Crystal Structure of AAV Rep complexed with the Rep-binding sequence

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

Rep 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

1rz9__assembly_1__model_1

1rz9__assembly_1__model_1 | I(q)

1rz9__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

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (5 domains)

CATH v4.4 (5 domains)

7. Citations (2)

Crystal Structure of AAV Rep complexed with the Rep-binding sequence

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

Rep 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

1rz9__assembly_1__model_1

1rz9__assembly_1__model_1 | I(q)

1rz9__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

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (5 domains)

CATH v4.4 (5 domains)

7. Citations (2)