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7kc0

Structure of the Saccharomyces cerevisiae replicative polymerase delta in complex with a primer/template and the PCNA clamp

Method: ELECTRON MICROSCOPY Dmax: 159.6 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Proliferating cell nuclear antigen

Saccharomyces cerevisiae

UniProt A0A6B7JGY6

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–DNA Heteromer Protein × 6 DNA 2 PDB declaration: octameric（8） Consistent with all polymer counts Chain E； UniProt 1–258 Chain F； UniProt 1–258 Chain G； UniProt 1–258 Not recorded ;DNA (5'-D(P*AP*TP*GP*AP*CP*CP*AP*TP*GP*AP*TP*TP*AP*CP*GP*AP*AP*TP*TP*GP*C)-3') ; × 1 DNA (25-MER) × 1 DNA polymerase × 1 （A0A6A5Q0V0） POL31 isoform 1 × 1 （A0A6A5PTG9） POL32 isoform 1 × 1 （A0A6A5PT00） MG MAGNESIUM ION × 2 SF4 IRON/SULFUR CLUSTER × 1 D3T 2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.20 Å

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 7KC0 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
8DR0 Closed state of RFC:PCNA bound to a 3' ss/dsDNA junction Deposited 2022-07-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain F 1–258（258 aa）
Chain G 1–258（258 aa）
Chain H 1–258（258 aa）
Not recorded AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 4 MG MAGNESIUM ION × 4 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.42 Å
8DR5 Open state of RFC:PCNA bound to a 3' ss/dsDNA junction (DNA2) with NTD Deposited 2022-07-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: dodecameric
Chain F 1–258（258 aa）
Chain G 1–258（258 aa）
Chain H 1–258（258 aa）
Not recorded MG MAGNESIUM ION × 4 AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 4 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.76 Å
8DR7 Open state of RFC:PCNA bound to a nicked dsDNA Deposited 2022-07-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: undecameric
Chain F 1–258（258 aa）
Chain G 1–258（258 aa）
Chain H 1–258（258 aa）
Not recorded AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 4 MG MAGNESIUM ION × 4 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
8THC Structure of the Saccharomyces cerevisiae clamp unloader Elg1-RFC bound to a cracked PCNA Deposited 2023-07-14 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain F 1–258（258 aa）
Chain G 1–258（258 aa）
Chain H 1–258（258 aa）
Not recorded AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 4 MG MAGNESIUM ION × 3 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.67 Å
8THD Structure of the Saccharomyces cerevisiae clamp unloader Elg1-RFC bound to PCNA Deposited 2023-07-14 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain F 1–258（258 aa）
Chain G 1–258（258 aa）
Chain H 1–258（258 aa）
Not recorded AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 4 MG MAGNESIUM ION × 3 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.25 Å

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

View Construct and Data Evidence
UniProt name A0A6B7JGY6_YEASX
Isoform —
PDB entities 3
Chains and sequence ranges Author chain E； PDBConstruct 1–258； UniProt 1–258 Author chain F； PDBConstruct 1–258； UniProt 1–258 Author chain G； PDBConstruct 1–258； UniProt 1–258

DNA polymerase

Saccharomyces cerevisiae

UniProt A0A6A5Q0V0

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–DNA Heteromer Protein × 6 DNA 2 PDB declaration: octameric（8） Consistent with all polymer counts Chain A； UniProt 1–1097 Not recorded ;DNA (5'-D(P*AP*TP*GP*AP*CP*CP*AP*TP*GP*AP*TP*TP*AP*CP*GP*AP*AP*TP*TP*GP*C)-3') ; × 1 DNA (25-MER) × 1 Proliferating cell nuclear antigen × 3 （A0A6B7JGY6） POL31 isoform 1 × 1 （A0A6A5PTG9） POL32 isoform 1 × 1 （A0A6A5PT00） MG MAGNESIUM ION × 2 SF4 IRON/SULFUR CLUSTER × 1 D3T 2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.20 Å

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence
UniProt name A0A6A5Q0V0_YEASX
Isoform —
PDB entities 4
Chains and sequence ranges Author chain A； PDBConstruct 1–1097； UniProt 1–1097

POL31 isoform 1

Saccharomyces cerevisiae

UniProt A0A6A5PTG9

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–DNA Heteromer Protein × 6 DNA 2 PDB declaration: octameric（8） Consistent with all polymer counts Chain B； UniProt 1–487 Not recorded ;DNA (5'-D(P*AP*TP*GP*AP*CP*CP*AP*TP*GP*AP*TP*TP*AP*CP*GP*AP*AP*TP*TP*GP*C)-3') ; × 1 DNA (25-MER) × 1 Proliferating cell nuclear antigen × 3 （A0A6B7JGY6） DNA polymerase × 1 （A0A6A5Q0V0） POL32 isoform 1 × 1 （A0A6A5PT00） MG MAGNESIUM ION × 2 SF4 IRON/SULFUR CLUSTER × 1 D3T 2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.20 Å

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 7KC0 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
7S0T Structure of DNA polymerase zeta with mismatched DNA Deposited 2021-08-31 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 5 PDB declaration: heptameric
Chain F 1–487（487 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 CA CALCIUM ION × 1 DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.05 Å
8TLQ Cryo-EM structure of the Rev1-Polzeta-DNA-dCTP complex Deposited 2023-07-27 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: octameric
Chain F 1–487（487 aa）
Not recorded CA CALCIUM ION × 1 DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.53 Å
8TLT Cryo-EM structure of Rev1(deltaN)-Polzeta-DNA-dCTP complex Deposited 2023-07-27 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: octameric
Chain F 1–487（487 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 CA CALCIUM ION × 1 DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.85 Å

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name A0A6A5PTG9_YEASX
Isoform —
PDB entities 5
Chains and sequence ranges Author chain B； PDBConstruct 1–487； UniProt 1–487

POL32 isoform 1

Saccharomyces cerevisiae

UniProt A0A6A5PT00

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–DNA Heteromer Protein × 6 DNA 2 PDB declaration: octameric（8） Consistent with all polymer counts Chain C； UniProt 8–350 Not recorded ;DNA (5'-D(P*AP*TP*GP*AP*CP*CP*AP*TP*GP*AP*TP*TP*AP*CP*GP*AP*AP*TP*TP*GP*C)-3') ; × 1 DNA (25-MER) × 1 Proliferating cell nuclear antigen × 3 （A0A6B7JGY6） DNA polymerase × 1 （A0A6A5Q0V0） POL31 isoform 1 × 1 （A0A6A5PTG9） MG MAGNESIUM ION × 2 SF4 IRON/SULFUR CLUSTER × 1 D3T 2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.20 Å

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence
UniProt name A0A6A5PT00_YEASX
Isoform —
PDB entities 6
Chains and sequence ranges Author chain C； PDBConstruct 8–350； UniProt 8–350

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 7kc0

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7kc0
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7kc0
Deposition date deposition_date2020-10-04
Structure title titleStructure of the Saccharomyces cerevisiae replicative polymerase delta in complex with a primer/template and the PCNA clamp
Keywords keywordsPolymerase delta, PCNA, primed DNA, complex, REPLICATION; REPLICATION
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier48.05 Å
Radius of gyration Rg (electron density) rg_electron48.22 Å
Forward intensity I(0) i01154180000.00
Molecular weight molecular_weight279150.0 kDa
Excluded volume excluded_volume347960 ų
Envelope volume envelope_volume493630 ų
Hydration-shell volume shell_volume85138 ų
Envelope diameter envelope_diameter161.5 Å
Shell Rg shell_rg52.59 Å
Envelope Rg envelope_rg47.38 Å
Shape Rg shape_rg48.26 Å
Total Rg total_rg48.22 Å
Total atoms total_atoms19553
Residues n_residues2380
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
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax159.6 Å
Rg (real space) rg_real47.92 Å
Rg uncertainty (real space) rg_real_error1.29 Å
I(0) (real space) i0_real1.1540e+09
I(0) uncertainty (real space) i0_real_error2.0490e+07
Rg (reciprocal space) rg_reciprocal48.05 Å
I(0) (reciprocal space) i0_reciprocal1154000000.0000
Solution quality estimate total_estimate0.8902
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary62.9 Å
Skewness Skewness skewness0.218
Kurtosis Kurtosis kurtosis-0.479
Angular range angular_range— – 0.1650 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha144400000.0000
Real-space data points n_real_points34
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.894; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.890
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (10)

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id7kc0B01
Class class3 — Alpha Beta
Architecture architecture60 — 4-Layer Sandwich
Topology topology21 — Purple Acid Phosphatase; chain A, domain 2
Homologous superfamily homologous superfamily50 —
Domain ID domain_id7kc0B02
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily430 —
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8. Citations (1)

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9. Files and Curves (10)