3p83

Structure of the PCNA:RNase HII complex from Archaeoglobus fulgidus.

Method: X-RAY DIFFRACTION

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

DNA polymerase sliding clamp

Archaeoglobus fulgidus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Ribonuclease HII × 3 （O29634）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PCNA_ARCFU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–245； UniProt 1–245 Author chain B； PDBConstruct 1–245； UniProt 1–245 Author chain C； PDBConstruct 1–245； UniProt 1–245

Ribonuclease HII

Archaeoglobus fulgidus

UniProt O29634

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	DNA polymerase sliding clamp × 3 （O29912）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RNH2_ARCFU
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain D； PDBConstruct 13–217； UniProt 1–205 Author chain E； PDBConstruct 13–217； UniProt 1–205 Author chain F； PDBConstruct 13–217； UniProt 1–205

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	3p83
Deposition date deposition_date	2010-10-13
Structure title title	Structure of the PCNA:RNase HII complex from Archaeoglobus fulgidus.
Keywords keywords	DNA clamp, RNase H fold, cleaves RNA/DNA hybrids, nucleus, HYDROLASE-DNA BINDING PROTEIN complex; HYDROLASE/DNA BINDING PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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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.

3p83__assembly_1__model_1

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

Download this curve (.dat)

3p83__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3p83__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	36.04 Å
Rg (electron density)	35.06 Å
Total Rg	35.63 Å
Atom count	10465
Residues	1351
Excluded volume	188040 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3p83__assembly_1__model_1`	hexameric （6）	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 (2)

Entity 1 Entity 1 polymer

Description description	DNA polymerase sliding clamp
Molecular weight formula_weight	27301.5 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	10465

MIDVIMTGELLKTVTRAIVALVSEARIHFLEKGLHSRAVDPANVAMVIVDIPKDSFEVYNIDEEKTIGVDMDRIFDISKSISTKDLVELIVEDESTLKVKFGSVEYKVALIDPSAIRKEPRIPELELPAKIVMDAGEFKKAIAAADKISDQVIFRSDKEGFRIEAKGDVDSIVFHMTETELIEFNGGEARSMFSVDYLKEFCKVAGSGDLLTIHLGTNYPVRLVFELVGGRAKVEYILAPRIESE

Source Source

Source organism organism	Archaeoglobus fulgidus
NCBI taxonomy ID ncbi_taxonomy_id	2234
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Ribonuclease HII
Molecular weight formula_weight	24431.2 kDa
EC 编号 ec_number	3.1.26.4
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,E,F

GPLGSPEFPGRLMKAGIDEAGKGCVIGPLVVAGVACSDEDRLRKLGVKDSKKLSQGRREELAEEIRKICRTEVLKVSPENLDERMAAKTINEILKECYAEIILRLKPEIAYVDSPDVIPERLSRELEEITGLRVVAEHKADEKYPLVAAASIIAKVEREREIERLKEKFGDFGSGYASDPRTREVLKEWIASGRIPSCVRMRWKTVSNLRQKTLDDF

Source Source

Source organism organism	Archaeoglobus fulgidus
NCBI taxonomy ID ncbi_taxonomy_id	2234
Host organism host_organism	Escherichia coli

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6. Fold Classification (SCOP + CATH) 19 domains

SCOP 2.08 (11 domains)

Domain ID domain_id	d3p83a1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.131 — DNA clamp
Superfamily Superfamily superfamily	d.131.1 — DNA clamp
Family Family family	d.131.1.2 — DNA polymerase processivity factor

Domain ID domain_id	d3p83a2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.131 — DNA clamp
Superfamily Superfamily superfamily	d.131.1 — DNA clamp
Family Family family	d.131.1.2 — DNA polymerase processivity factor

Domain ID domain_id	d3p83b1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.131 — DNA clamp
Superfamily Superfamily superfamily	d.131.1 — DNA clamp
Family Family family	d.131.1.2 — DNA polymerase processivity factor

Domain ID domain_id	d3p83b2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.131 — DNA clamp
Superfamily Superfamily superfamily	d.131.1 — DNA clamp
Family Family family	d.131.1.2 — DNA polymerase processivity factor

Domain ID domain_id	d3p83c1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.131 — DNA clamp
Superfamily Superfamily superfamily	d.131.1 — DNA clamp
Family Family family	d.131.1.2 — DNA polymerase processivity factor

Domain ID domain_id	d3p83c2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.131 — DNA clamp
Superfamily Superfamily superfamily	d.131.1 — DNA clamp
Family Family family	d.131.1.2 — DNA polymerase processivity factor

Domain ID domain_id	d3p83d1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamily	c.55.3 — Ribonuclease H-like
Family Family family	c.55.3.0 — automated matches

Domain ID domain_id	d3p83d2
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	d3p83e1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamily	c.55.3 — Ribonuclease H-like
Family Family family	c.55.3.0 — automated matches

Domain ID domain_id	d3p83e2
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	d3p83f_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamily	c.55.3 — Ribonuclease H-like
Family Family family	c.55.3.0 — automated matches

CATH v4.4 (8 domains)

Domain ID domain_id	3p83A00
Class class	3 — Alpha Beta
Architecture architecture	70 — Box
Topology topology	10 — Proliferating Cell Nuclear Antigen
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	3p83B00
Class class	3 — Alpha Beta
Architecture architecture	70 — Box
Topology topology	10 — Proliferating Cell Nuclear Antigen
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	3p83C00
Class class	3 — Alpha Beta
Architecture architecture	70 — Box
Topology topology	10 — Proliferating Cell Nuclear Antigen
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	3p83D00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily	10 — Ribonuclease H-like superfamily/Ribonuclease H

Domain ID domain_id	3p83E01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily	10 — Ribonuclease H-like superfamily/Ribonuclease H

Domain ID domain_id	3p83E02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	460 — Ribonuclease hii. Domain 2

Domain ID domain_id	3p83F01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily	10 — Ribonuclease H-like superfamily/Ribonuclease H

Domain ID domain_id	3p83F02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	460 — Ribonuclease hii. Domain 2

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Unit-cell length a length_a	149.670 Å
Unit-cell length b length_b	152.030 Å
Unit-cell length c length_c	90.160 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	12

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	3.050 Å
Low-resolution limit resolution_low	44.540 Å
R factor r_factor	0.1882
R_work r_work	0.1868
R_free r_free	0.2159

Structure of the PCNA:RNase HII complex from Archaeoglobus fulgidus.

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

DNA polymerase sliding clamp

State in the Current Structure

Other States of the Same Protein in the Database

Ribonuclease HII

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

3p83__assembly_1__model_1

3p83__assembly_1__model_1 | I(q)

3p83__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 19 domains

SCOP 2.08 (11 domains)

CATH v4.4 (8 domains)

7. Citations (1)

Structure of the PCNA:RNase HII complex from Archaeoglobus fulgidus.

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

DNA polymerase sliding clamp

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Ribonuclease HII

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

3p83__assembly_1__model_1

3p83__assembly_1__model_1 | I(q)

3p83__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 19 domains

SCOP 2.08 (11 domains)

CATH v4.4 (8 domains)

7. Citations (1)