SAXSdb — 9f26

▼

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

DNA primase small subunit PriS

Pyrococcus abyssi

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	DNA primase large subunit PriL × 1 （Q9V291） RPA32 subunit of the hetero-oligomeric complex involved in homologous recombination × 1 （Q9V1Z1） ZINC ION × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PRIS_PYRAB
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–346； UniProt 1–345

DNA primase large subunit PriL

Pyrococcus abyssi

UniProt Q9V291

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	DNA primase small subunit PriS × 1 （Q9V292） RPA32 subunit of the hetero-oligomeric complex involved in homologous recombination × 1 （Q9V1Z1） ZINC ION × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PRIL_PYRAB
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–393； UniProt 1–393

RPA32 subunit of the hetero-oligomeric complex involved in homologous recombination

Pyrococcus abyssi

UniProt Q9V1Z1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	DNA primase small subunit PriS × 1 （Q9V292） DNA primase large subunit PriL × 1 （Q9V291） ZINC ION × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9V1Z1_PYRAB
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–272； UniProt 1–272

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	9f26
Deposition date deposition_date	2024-04-22
Structure title title	Crystal structure of the PriS_PriL-Rpa2WH ternary complex from P. abyssi
Keywords keywords	Replication protein A, ssDNA-Binding protein, DNA BINDING PROTEIN; DNA BINDING PROTEIN
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.

9f26__assembly_1__model_1

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

Download this curve (.dat)

9f26__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9f26__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	31.16 Å
Rg (electron density)	30.63 Å
Total Rg	31.32 Å
Atom count	5290
Residues	637
Excluded volume	94940 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9f26__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	DNA primase small subunit PriS
Molecular weight formula_weight	40662.6 kDa
EC 编号 ec_number	2.7.7.-
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	5290

SMLLREVTKEERKEFYSNEWNAKQIPDFILQNLDKREFGFDHTGEGPSDRKNSYTDVRDLEDYIKATAPYAVYSSVAFYEKPQEMEGWLGAELVFDIDAKDLPLRRCNHEPGKVCPICLNDAKEIARDTLIVLKEELGFEDVHVVYSGRGYHIRVMDGWALSLDSKSRERILSFISASEIEDHSEFRKMLLERRGWFVLNHGYPRVFRLRFGYFILRVKVEHLINFGIRKNIAKRILDNKETIYEEFVRKGILAAFPDGVGIESLAKLFALSTRFSKAYFDGRVTVDLKRILRLPSTLHSKVGLIAKYIGNNERDVMRFNPFKHAVPKFRRKEVKEEYKRFLEENF

Source Source

Source organism organism	Pyrococcus abyssi
NCBI taxonomy ID ncbi_taxonomy_id	29292
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	DNA primase large subunit PriL
Molecular weight formula_weight	45548.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MLDPFSEKAKELLKEFGSINDFLNSIPRIVDVEEVIERVKIASDRKLLEGFVDIEDIKDLAQFYALLGALSYSPYGLELELVKKANILLYSERIRREKEIRPEEISLRINKAIEFPIDDLKKIERVFGKLPEYTIHLAEFLDLIPGERLSEYYIYNGNVYLRKEDLIKVWMKAFERNIEKSVNMLYEIRDELPGFFREVLGGIKEVAEQEFGKSGEVKAGTLRPDLFPPCVKNALKGVPQGLRNYAITVLLTSFLSYARICPNPPRRNVRVKDCIDDIRIITDEILPLIIEAANRCSPPLFEDQPNEIKNIWYHLGFGYTANPKLEDSGNSTWYFPPNCDKIRANAPQLCTPDKHCKYVRNPLTYYLRRLYLEGRKNASKGGNERGEKRVLQQ

Source Source

Source organism organism	Pyrococcus abyssi
NCBI taxonomy ID ncbi_taxonomy_id	29292
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 polymer

Description description	RPA32 subunit of the hetero-oligomeric complex involved in homologous recombination
Molecular weight formula_weight	31874.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MVIEMKKRMPATRLYIKDILEGYFVKSEGDFEPNYLITKYARKVYRAKIVGTVVREPLIAEDETYGKFQVDDGTGVIWVLGFRDDTKFAKLVRKGDLVQVIGKIAEWRDDKQILVEGVSKVHPNMWILHRYETLKEKIEHIKKAKIALEIYNQYGITAKSKVIAKNKGIEEELLEVIDELYGIMMEERSIEEPMEELLEEEIPEEKEENELLEKAKEDILNILRQKRTAISRKYILKKLGDKYDEETIDDAITELLAQGEIYEPETGYYKLL

Source Source

Source organism organism	Pyrococcus abyssi
NCBI taxonomy ID ncbi_taxonomy_id	29292
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 4 Entity 4 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	1

▶

Unit-cell length a length_a	63.815 Å
Unit-cell length b length_b	101.505 Å
Unit-cell length c length_c	177.805 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	4

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

Resolution resolution	3.501 Å
Low-resolution limit resolution_low	48.800 Å
R factor r_factor	0.2356
R_work r_work	0.2345
R_free r_free	0.2555

Crystal structure of the PriS_PriL-Rpa2WH ternary complex from P. abyssi

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

RPA32 subunit of the hetero-oligomeric complex involved in homologous recombination

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

9f26__assembly_1__model_1

9f26__assembly_1__model_1 | I(q)

9f26__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 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

7. Citations (1)

Crystal structure of the PriS_PriL-Rpa2WH ternary complex from P. abyssi

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

RPA32 subunit of the hetero-oligomeric complex involved in homologous recombination

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

9f26__assembly_1__model_1

9f26__assembly_1__model_1 | I(q)

9f26__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 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

7. Citations (1)