SAXSdb — 6hvo

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

Proliferating cell nuclear antigen

Homo sapiens

UniProt P12004

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 delta subunit 4 × 3 （Q9HCU8） SULFATE ION × 7 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PCNA_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–264； UniProt 1–261 Author chain B； PDBConstruct 4–264； UniProt 1–261 Author chain C； PDBConstruct 4–264； UniProt 1–261

DNA polymerase delta subunit 4

Homo sapiens

UniProt Q9HCU8

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Proliferating cell nuclear antigen × 3 （P12004） SULFATE ION × 7 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DPOD4_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain D； PDBConstruct 1–19； UniProt 1–19 Author chain E； PDBConstruct 1–19； UniProt 1–19 Author chain F； PDBConstruct 1–19； UniProt 1–19

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	6hvo
Deposition date deposition_date	2018-10-11
Structure title title	Crystal structure of human PCNA in complex with three peptides of p12 subunit of human polymerase delta
Keywords keywords	PCNA, POLD4, p12, replication, polymerase delta, crystal; REPLICATION
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.

6hvo__assembly_1__model_1

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

Download this curve (.dat)

6hvo__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6hvo__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	33.86 Å
Rg (electron density)	32.62 Å
Total Rg	33.35 Å
Atom count	6182
Residues	795
Excluded volume	110610 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6hvo__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 (4)

Entity 1 Entity 1 polymer

Description description	Proliferating cell nuclear antigen
Molecular weight formula_weight	29088.1 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	6521

GPHMFEARLVQGSILKKVLEALKDLINEACWDISSSGVNLQSMDSSHVSLVQLTLRSEGFDTYRCDRNLAMGVNLTSMSKILKCAGNEDIITLRAEDNADTLALVFEAPNQEKVSDYEMKLMDLDVEQLGIPEQEYSCVVKMPSGEFARICRDLSHIGDAVVISCAKDGVKFSASGELGNGNIKLSQTSNVDKEEEAVTIEMNEPVQLTFALRYLNFFTKATPLSSTVTLSMSADVPLVVEYKIADMGHLKYYLAPKIEDEEGS

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 BL21(DE3)

Entity 2 Entity 2 polymer

Description description	DNA polymerase delta subunit 4
Molecular weight formula_weight	2267.7 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

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

MGRKRLITDSYPVVKRREG

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 BL21(DE3)

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	243

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6. Fold Classification (SCOP + CATH) 11 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d6hvoa1
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.131.1.0 — automated matches

Domain ID domain_id	d6hvoa2
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.131.1.0 — automated matches

Domain ID domain_id	d6hvoa3
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	d6hvob1
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.131.1.0 — automated matches

Domain ID domain_id	d6hvob2
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.131.1.0 — automated matches

Domain ID domain_id	d6hvoc1
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.131.1.0 — automated matches

Domain ID domain_id	d6hvoc2
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.131.1.0 — automated matches

Domain ID domain_id	d6hvoc3
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 (3 domains)

Domain ID domain_id	6hvoA00
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	6hvoB00
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	6hvoC00
Class class	3 — Alpha Beta
Architecture architecture	70 — Box
Topology topology	10 — Proliferating Cell Nuclear Antigen
Homologous superfamily homologous superfamily	10 —

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Unit-cell length a length_a	71.965 Å
Unit-cell length b length_b	83.888 Å
Unit-cell length c length_c	154.982 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 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	73.880 Å
R factor r_factor	0.1975
R_work r_work	0.1949
R_free r_free	0.2444

Crystal structure of human PCNA in complex with three peptides of p12 subunit of human polymerase delta

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

Proliferating cell nuclear antigen

State in the Current Structure

Other States of the Same Protein in the Database

DNA polymerase delta subunit 4

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

6hvo__assembly_1__model_1

6hvo__assembly_1__model_1 | I(q)

6hvo__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 11 domains

SCOP 2.08 (8 domains)

CATH v4.4 (3 domains)

7. Citations (1)

Crystal structure of human PCNA in complex with three peptides of p12 subunit of human polymerase delta

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

Proliferating cell nuclear antigen

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

DNA polymerase delta subunit 4

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

6hvo__assembly_1__model_1

6hvo__assembly_1__model_1 | I(q)

6hvo__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 11 domains

SCOP 2.08 (8 domains)

CATH v4.4 (3 domains)

7. Citations (1)