3bsu

Hybrid-binding domain of human RNase H1 in complex with 12-mer RNA/DNA

Method: X-RAY DIFFRACTION

▼

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

Ribonuclease H1

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Homooligomer	Protein 3 DNA 1 RNA 1	;RNA (5'-R(GPAPCPAPCPCPUPGPAPUPUPC)-3') ; × 1 ;DNA (5'-D(DGPDAPDAPDTPDCPDAPDGPDGP(5IU)PDGPDTPDC)-3') ; × 1 MAGNESIUM ION × 2 water × 5	Consistent with all polymers
2	Other combination	Homooligomer	Protein 3 DNA 1 RNA 1	;RNA (5'-R(GPAPCPAPCPCPUPGPAPUPUPC)-3') ; × 1 ;DNA (5'-D(DGPDAPDAPDTPDCPDAPDGPDGP(5IU)PDGPDTPDC)-3') ; × 1 water × 5	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RNH1_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain A； PDBConstruct 1–53； UniProt 24–76 Author chain B； PDBConstruct 1–53； UniProt 24–76 Author chain C； PDBConstruct 1–53； UniProt 24–76 Author chain F； PDBConstruct 1–53； UniProt 24–76 Author chain G； PDBConstruct 1–53； UniProt 24–76 Author chain H； PDBConstruct 1–53； UniProt 24–76

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	3bsu
Deposition date deposition_date	2007-12-26
Structure title title	Hybrid-binding domain of human RNase H1 in complex with 12-mer RNA/DNA
Keywords keywords	RNase H, RNA/DNA hybrid, dsRNA, HYDROLASE-RNA-DNA COMPLEX; HYDROLASE/RNA/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.

3bsu__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3bsu__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3bsu__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	18.37 Å
Rg (electron density)	18.72 Å
Total Rg	19.23 Å
Atom count	1726
Residues	169
Excluded volume	28918 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3bsu__assembly_1__model_1`	pentameric （5）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3bsu__assembly_2__model_1`	pentameric （5）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	;RNA (5'-R(GPAPCPAPCPCPUPGPAPUPUPC)-3') ;
Molecular weight formula_weight	3772.3 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	D,I
Atom count atom_count	3743

GACACCUGAUUC

Entity 2 Entity 2 polymer

Description description	;DNA (5'-D(DGPDAPDAPDTPDCPDAPDGPDGP(5IU)PDGPDTPDC)-3') ;
Molecular weight formula_weight	3814.3 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	E,J

GAATCAGGUGTC

Entity 3 Entity 3 polymer

Description description	Ribonuclease H1
Molecular weight formula_weight	6197.1 kDa
EC 编号 ec_number	3.1.26.4
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,F,G,H

GSHMFYAVRRGRKTGVFLTWNECRAQVDRFPAARFKKFATEDEAWAFVRKSAS

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 non-polymer

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

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	252

▼

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (10 domains)

Domain ID domain_id	d3bsua1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.100 — MbtH/L9 domain-like
Superfamily Superfamily superfamily	d.100.1 — L9 N-domain-like
Family Family family	d.100.1.0 — automated matches

Domain ID domain_id	d3bsua2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d3bsub1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.100 — MbtH/L9 domain-like
Superfamily Superfamily superfamily	d.100.1 — L9 N-domain-like
Family Family family	d.100.1.0 — automated matches

Domain ID domain_id	d3bsub2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d3bsuc_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.100 — MbtH/L9 domain-like
Superfamily Superfamily superfamily	d.100.1 — L9 N-domain-like
Family Family family	d.100.1.0 — automated matches

Domain ID domain_id	d3bsuf1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.100 — MbtH/L9 domain-like
Superfamily Superfamily superfamily	d.100.1 — L9 N-domain-like
Family Family family	d.100.1.0 — automated matches

Domain ID domain_id	d3bsuf2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d3bsug_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.100 — MbtH/L9 domain-like
Superfamily Superfamily superfamily	d.100.1 — L9 N-domain-like
Family Family family	d.100.1.0 — automated matches

Domain ID domain_id	d3bsuh1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.100 — MbtH/L9 domain-like
Superfamily Superfamily superfamily	d.100.1 — L9 N-domain-like
Family Family family	d.100.1.0 — automated matches

Domain ID domain_id	d3bsuh2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (6 domains)

Domain ID domain_id	3bsuA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	970 — Ribonuclease HI; Chain A
Homologous superfamily homologous superfamily	10 — Ribonuclease H1, N-terminal domain

Domain ID domain_id	3bsuB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	970 — Ribonuclease HI; Chain A
Homologous superfamily homologous superfamily	10 — Ribonuclease H1, N-terminal domain

Domain ID domain_id	3bsuC00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	970 — Ribonuclease HI; Chain A
Homologous superfamily homologous superfamily	10 — Ribonuclease H1, N-terminal domain

Domain ID domain_id	3bsuF00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	970 — Ribonuclease HI; Chain A
Homologous superfamily homologous superfamily	10 — Ribonuclease H1, N-terminal domain

Domain ID domain_id	3bsuG00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	970 — Ribonuclease HI; Chain A
Homologous superfamily homologous superfamily	10 — Ribonuclease H1, N-terminal domain

Domain ID domain_id	3bsuH00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	970 — Ribonuclease HI; Chain A
Homologous superfamily homologous superfamily	10 — Ribonuclease H1, N-terminal domain

▶

Unit-cell length a length_a	45.492 Å
Unit-cell length b length_b	64.262 Å
Unit-cell length c length_c	140.322 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	24

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	—
R_work r_work	0.2200
R_free r_free	0.2900

Hybrid-binding domain of human RNase H1 in complex with 12-mer RNA/DNA

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

Ribonuclease H1

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

3bsu__assembly_2__model_1

3bsu__assembly_2__model_1 | I(q)

3bsu__assembly_2__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (10 domains)

CATH v4.4 (6 domains)

7. Citations (1)

Hybrid-binding domain of human RNase H1 in complex with 12-mer RNA/DNA

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

Ribonuclease H1

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

3bsu__assembly_2__model_1

3bsu__assembly_2__model_1 | I(q)

3bsu__assembly_2__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (10 domains)

CATH v4.4 (6 domains)

7. Citations (1)