SAXSdb — 5of3

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

DNA primase small subunit PriS

Sulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	DNA primase large subunit PriL × 2 （Q9UWW1） Uncharacterized protein × 2 （Q97ZS7） DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER × 4 MANGANESE (II) ION × 4 ZINC ION × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PRIS_SULSO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–330； UniProt 1–330 Author chain D； PDBConstruct 1–330； UniProt 1–330

DNA primase large subunit PriL

Sulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)

UniProt Q9UWW1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	DNA primase small subunit PriS × 2 （Q97Z83） Uncharacterized protein × 2 （Q97ZS7） DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER × 4 MANGANESE (II) ION × 4 ZINC ION × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PRIL_SULSO
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–307； UniProt 1–307 Author chain E； PDBConstruct 1–307； UniProt 1–307

Uncharacterized protein

Sulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)

UniProt Q97ZS7

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	DNA primase small subunit PriS × 2 （Q97Z83） DNA primase large subunit PriL × 2 （Q9UWW1） DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER × 4 MANGANESE (II) ION × 4 ZINC ION × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q97ZS7_SULSO
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–154； UniProt 1–154 Author chain F； PDBConstruct 1–154； UniProt 1–154

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	5of3
Deposition date deposition_date	2017-07-10
Structure title title	Crystal structure of the heterotrimeric PriSLX primase from S. solfataricus.
Keywords keywords	Primase, DNA-dependent RNA polymerase, DNA replication, REPLICATION; 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.

5of3__assembly_1__model_1

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

Download this curve (.dat)

5of3__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5of3__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	39.86 Å
Rg (electron density)	39.68 Å
Total Rg	40.10 Å
Atom count	11526
Residues	1395
Excluded volume	207560 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5of3__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 (6)

Entity 1 Entity 1 polymer

Description description	DNA primase small subunit PriS
Molecular weight formula_weight	37643.9 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,D
Atom count atom_count	11540

MGTFTLHQGQTNLIKSFFRNYYLNAELELPKDMELREFALQPFGSDTYVRHLSFSSSEELRDYLVNRNLPLHLFYSSARYQLPSARNMEEKAWMGSDLLFDIDADHLCKLRSIRFCPVCGNAVVSEKCERDNVETLEYVEMTSECIKRGLEQTRNLVEILEDDFGLKPKVYFSGNRGFHVQVDCYGNCALLDSDERKEIAEYVMGIGVPGYPGGSENAPGWVGRKNRGINGVTIDEQVTIDVKRLIRIPNSLHGKSGLIVKRVPNLDDFEFNETLSPFTGYTIFLPYITIETEVLGSIIKLNRGIPIKIKSSIGIYLHLRNLGEVKAYVR

Source Source

Source organism organism	Sulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)
NCBI taxonomy ID ncbi_taxonomy_id	273057
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	DNA primase large subunit PriL
Molecular weight formula_weight	35789.0 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MALDVKKYPFIKSLDDELKKYGGGITLTDLLLNSTTLIDQAKDRIQKTKSGDELPHYVSYNEPVLVFYTTLLSLAILNDVKLIRRYAYAEAKQFRSLLHTENEENLLEISKLLDLKINRCDPIKFYLEKKRRIIQKEFCVHFIDYLKYTKDLKEDWKLSGQILHKGYVYLDKNQLIGLIAESIKSKIVEMIRPLNLKEIPEKLKSLIERRGIIPPCIENILAKEKLNEEEIRTLITFYIDIGKGLSGIVSIMKKYNVSNVEDLYRKYRGDKGTRYIVYSCAKMKQLGLCVSSCNVKNPLQLYFLSNE

Source Source

Source organism organism	Sulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)
NCBI taxonomy ID ncbi_taxonomy_id	273057
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 polymer

Description description	Uncharacterized protein
Molecular weight formula_weight	18056.7 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,F

MSQEKKAKKIILHYPDDTPAGYIEYAEGSSSIYDNEGNFLFKVEGKFPPQPKKSSDYSWIEKVLEMGLQDSRKRFILYVASRYLVNVKGVNEDEALQTLKEFYYKLQSGKVYESWLKSVINGVKKKGLLPWSLKRIEERDKEMYNEIIRVLKNS

Source Source

Source organism organism	Sulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)
NCBI taxonomy ID ncbi_taxonomy_id	273057
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 4 Entity 4 non-polymer

Description description	DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER
Molecular weight formula_weight	505.2 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 non-polymer

Description description	MANGANESE (II) ION
Molecular weight formula_weight	54.9 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 6 Entity 6 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	2

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d5of3a_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.264 — Prim-pol domain
Superfamily Superfamily superfamily	d.264.1 — Prim-pol domain
Family Family family	d.264.1.1 — PriA-like

Domain ID domain_id	d5of3d_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.264 — Prim-pol domain
Superfamily Superfamily superfamily	d.264.1 — Prim-pol domain
Family Family family	d.264.1.1 — PriA-like

CATH v4.4 (2 domains)

Domain ID domain_id	5of3A00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	920 — DNA primase, PRIM domain
Homologous superfamily homologous superfamily	10 — DNA primase, PRIM domain

Domain ID domain_id	5of3D00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	920 — DNA primase, PRIM domain
Homologous superfamily homologous superfamily	10 — DNA primase, PRIM domain

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Unit-cell length a length_a	104.889 Å
Unit-cell length b length_b	104.889 Å
Unit-cell length c length_c	229.758 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	8

Space group space_group	P 41
Space-group number int_tables_number	76
Crystal system crystal_system	—

Resolution resolution	2.906 Å
Low-resolution limit resolution_low	46.910 Å
R factor r_factor	0.2305
R_work r_work	0.2283
R_free r_free	0.2713

Crystal structure of the heterotrimeric PriSLX primase from S. solfataricus.

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

DNA primase small subunit PriS

State in the Current Structure

Other States of the Same Protein in the Database

DNA primase large subunit PriL

State in the Current Structure

Other States of the Same Protein in the Database

Uncharacterized 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

5of3__assembly_1__model_1

5of3__assembly_1__model_1 | I(q)

5of3__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of the heterotrimeric PriSLX primase from S. solfataricus.

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

DNA primase small subunit PriS

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 primase large subunit PriL

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Uncharacterized 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

5of3__assembly_1__model_1

5of3__assembly_1__model_1 | I(q)

5of3__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)