7jl8

Human PrimPol extending from the correct primer base C opposite the 8-oxoguanine lesion

Method: X-RAY DIFFRACTION

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

DNA-directed primase/polymerase protein

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Monomer	Protein 1 DNA 2	;DNA (5'-D(PAPTP(8OG)PCPCPTPAPCPCPAPCPA)-3') ; × 1 ;DNA (5'-D(PGPTPGPGPTPAPGPGP*C)-3') ; × 1 ;2'-DEOXYADENOSINE 5'-TRIPHOSPHATE ; × 1 CALCIUM ION × 1 GLYCEROL × 2 1,2-ETHANEDIOL × 1 DI(HYDROXYETHYL)ETHER × 2 water × 2	Consistent with all polymers
2	Protein–DNA	Monomer	Protein 1 DNA 2	;DNA (5'-D(PAPTP(8OG)PCPCPTPAPCPCPAPCPA)-3') ; × 1 ;DNA (5'-D(PGPTPGPGPTPAPGPGP*C)-3') ; × 1 ;2'-DEOXYADENOSINE 5'-TRIPHOSPHATE ; × 1 CALCIUM ION × 2 GLYCEROL × 3 DI(HYDROXYETHYL)ETHER × 1 water × 3	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PRIPO_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–354； UniProt 1–354 Author chain B； PDBConstruct 1–354； UniProt 1–354

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	7jl8
Deposition date deposition_date	2020-07-29
Structure title title	Human PrimPol extending from the correct primer base C opposite the 8-oxoguanine lesion
Keywords keywords	Translesion, DNA synthesis, DNA Replication, DNA damage, TRANSFERASE, TRANSFERASE-DNA complex; TRANSFERASE/DNA
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.

7jl8__assembly_1__model_1

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

Download this curve (.dat)

7jl8__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7jl8__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	21.33 Å
Rg (electron density)	20.12 Å
Total Rg	21.05 Å
Atom count	4785
Residues	290
Excluded volume	44207 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7jl8__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`7jl8__assembly_2__model_1`	trimeric （3）	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 (9)

Entity 1 Entity 1 polymer

Description description	DNA-directed primase/polymerase protein
Molecular weight formula_weight	41038.5 kDa
EC 编号 ec_number	2.7.7.-
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	9581

MNRKWEAKLKQIEERASHYERKPLSSVYRPRLSKPEEPPSIWRLFHRQAQAFNFVKSCKEDVHVFALECKVGDGQRIYLVTTYAEFWFYYKSRKNLLHCYEVIPENAVCKLYFDLEFNKPANPGADGKKMVALLIEYVCKALQELYGVNCSAEDVLNLDSSTDEKFSRHLIFQLHDVAFKDNIHVGNFLRKILQPALDLLGSEDDDSAPETTGHGFPHFSEAPARQGFSFNKMFTEKATEESWTSNSKKLERLGSAEQSSPDLSFLVVKNNMGEKHLFVDLGVYTRNRNFRLYKSSKIGKRVALEVTEDNKFFPIQSKDVSDEYQYFLSSLVSNVRFSDTLRILTCEPSQNKQK

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Saccharomyces cerevisiae

Entity 2 Entity 2 polymer

Description description	;DNA (5'-D(PAPTP(8OG)PCPCPTPAPCPCPAPCPA)-3') ;
Molecular weight formula_weight	5053.3 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	C,G

CATGCCTACCACACCCC

Entity 3 Entity 3 polymer

Description description	;DNA (5'-D(PGPTPGPGPTPAPGPGP*C)-3') ;
Molecular weight formula_weight	4103.7 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	D,H

GGGTGTGGTAGGC

Entity 4 Entity 4 non-polymer

Description description	;2'-DEOXYADENOSINE 5'-TRIPHOSPHATE ;
Molecular weight formula_weight	491.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 6 Entity 6 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 7 Entity 7 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 8 Entity 8 non-polymer

Description description	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 9 Entity 9 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	161

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Unit-cell length a length_a	50.689 Å
Unit-cell length b length_b	65.330 Å
Unit-cell length c length_c	72.001 Å
Unit-cell angle α angle_alpha	68.47 °
Unit-cell angle β angle_beta	85.67 °
Unit-cell angle γ angle_gamma	86.92 °
Molecules per unit cell Z z_pdb	2

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

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	28.160 Å
R factor r_factor	0.1883
R_work r_work	0.1871
R_free r_free	0.2133

Human PrimPol extending from the correct primer base C opposite the 8-oxoguanine lesion

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

DNA-directed primase/polymerase 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

7jl8__assembly_1__model_1

7jl8__assembly_1__model_1 | I(q)

7jl8__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 (9)

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

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 water

7. Citations (1)

Human PrimPol extending from the correct primer base C opposite the 8-oxoguanine lesion

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

DNA-directed primase/polymerase 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

7jl8__assembly_1__model_1

7jl8__assembly_1__model_1 | I(q)

7jl8__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 (9)

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

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 water

7. Citations (1)