← Back to search
4lim

Crystal structure of the catalytic subunit of yeast primase

Method: X-RAY DIFFRACTION Dmax: 94.8 Å Quality: REASONABLE
▼

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

DNA primase small subunit

Saccharomyces cerevisiae

UniProt P10363

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 8–396 Fragment：UNP residues 8-396 ZN ZINC ION × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 1.63 Å R-free 0.189

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 4LIM Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
4MM2 Crystal structure of yeast primase catalytic subunit Deposited 2013-09-07 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–409（409 aa）
Not recorded CD CADMIUM ION × 5 CIT CITRIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 5.5；298 K；0.1M Na-Citrate, 0.2M NDSB, 5mM CdCl2, 30% PEG 600, 10mM ZnCl2 , pH 5.5, VAPOR DIFFUSION, temperature 298K
Resolution 1.60 Å R-free 0.293
4MM2 Crystal structure of yeast primase catalytic subunit Deposited 2013-09-07 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–409（409 aa）
Not recorded CD CADMIUM ION × 5 CIT CITRIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 5.5；298 K；0.1M Na-Citrate, 0.2M NDSB, 5mM CdCl2, 30% PEG 600, 10mM ZnCl2 , pH 5.5, VAPOR DIFFUSION, temperature 298K
Resolution 1.60 Å R-free 0.293
8B9A S. cerevisiae replisome + Ctf4, bound by pol alpha primase. Complex engaged with a fork DNA substrate containing a 60 nucleotide lagging strand. Deposited 2022-10-05 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 21 PDB declaration: 23-meric
Chain S 1–409（409 aa）
Not recorded ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 4 MG MAGNESIUM ION × 4 ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
8B9B S. cerevisiae replisome + Ctf4, bound by pol alpha. Complex engaged with a fork DNA substrate containing a 60 nucleotide lagging strand. Deposited 2022-10-05 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 21 PDB declaration: 23-meric
Chain S 1–409（409 aa）
Not recorded ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 4 MG MAGNESIUM ION × 4 ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
8B9C S. cerevisiae pol alpha - replisome complex Deposited 2022-10-05 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: eicosameric
Chain S 1–409（409 aa）
Not recorded ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 4 MG MAGNESIUM ION × 4 ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.60 Å

4 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PRI1_YEAST
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 3–391； UniProt 8–396

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.

SAXS scattering curve SAXS Profile

SAXS profile for 4lim

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4lim
Download Download
▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id4lim
Deposition date deposition_date2013-07-02
Structure title titleCrystal structure of the catalytic subunit of yeast primase
Keywords keywordsPrim fold, TRANSFERASE; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION
▼

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier24.66 Å
Radius of gyration Rg (electron density) rg_electron24.03 Å
Forward intensity I(0) i032684300.00
Molecular weight molecular_weight44392.0 kDa
Excluded volume excluded_volume55673 ų
Envelope volume envelope_volume65485 ų
Hydration-shell volume shell_volume23618 ų
Envelope diameter envelope_diameter85.2 Å
Shell Rg shell_rg30.23 Å
Envelope Rg envelope_rg24.40 Å
Shape Rg shape_rg24.01 Å
Total Rg total_rg24.80 Å
Total atoms total_atoms3125
Residues n_residues381
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax94.8 Å
Rg (real space) rg_real24.78 Å
Rg uncertainty (real space) rg_real_error1.16 Å
I(0) (real space) i0_real3.2680e+07
I(0) uncertainty (real space) i0_real_error5.3650e+05
Rg (reciprocal space) rg_reciprocal24.75 Å
I(0) (reciprocal space) i0_reciprocal32680000.0000
Solution quality estimate total_estimate0.5477
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary25.6 Å
Skewness Skewness skewness0.482
Kurtosis Kurtosis kurtosis-0.262
Angular range angular_range— – 0.3200 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha6163000.0000
Real-space data points n_real_points64
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.509; Stabil: 0.992; Sysdev: 0.338; Positv: 1.000; Valcen: 0.598; Smooth: 0.000
▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (3)

▼

7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id4limA00
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology920 — DNA primase, PRIM domain
Homologous superfamily homologous superfamily10 — DNA primase, PRIM domain
▶

8. Citations (1)

▶

9. Files and Curves (10)