7jps

ORC-DNA: Human Origin Recognition Complex (ORC) with DNA bound in the core

Method: ELECTRON MICROSCOPY Dmax: 150.8 Å Quality: GOOD

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

Origin recognition complex subunit 1

Homo sapiens

UniProt Q13415

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 × 5 DNA 2 PDB declaration: heptameric(7) Consistent with all polymer counts Chain A; UniProt 471–861 Not recorded Origin recognition complex subunit 2 × 1 (Q13416) Origin recognition complex subunit 3 × 1 (Q9UBD5) Origin recognition complex subunit 4 × 1 (O43929) Origin recognition complex subunit 5 × 1 (O43913) ;DNA (5'-D(*AP*TP*AP*TP*AP*TP*AP*TP*AP*TP*AP*AP*T)-3') ; × 1 ;DNA (5'-D(*AP*TP*TP*AP*TP*AP*TP*AP*TP*AP*TP*AP*T)-3') ; × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 3 MG MAGNESIUM ION × 3 K POTASSIUM ION × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 4.40 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.

12 other PDB entries and 13 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ORC1_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 2–392; UniProt 471–861

Origin recognition complex subunit 2

Homo sapiens

UniProt Q13416

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 × 5 DNA 2 PDB declaration: heptameric(7) Consistent with all polymer counts Chain B; UniProt 1–577 Not recorded Origin recognition complex subunit 1 × 1 (Q13415) Origin recognition complex subunit 3 × 1 (Q9UBD5) Origin recognition complex subunit 4 × 1 (O43929) Origin recognition complex subunit 5 × 1 (O43913) ;DNA (5'-D(*AP*TP*AP*TP*AP*TP*AP*TP*AP*TP*AP*AP*T)-3') ; × 1 ;DNA (5'-D(*AP*TP*TP*AP*TP*AP*TP*AP*TP*AP*TP*AP*T)-3') ; × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 3 MG MAGNESIUM ION × 3 K POTASSIUM ION × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 4.40 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.

15 other PDB entries and 20 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ORC2_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 1–577; UniProt 1–577

Origin recognition complex subunit 3

Homo sapiens

UniProt Q9UBD5

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 × 5 DNA 2 PDB declaration: heptameric(7) Consistent with all polymer counts Chain C; UniProt 1–712 Not recorded Origin recognition complex subunit 1 × 1 (Q13415) Origin recognition complex subunit 2 × 1 (Q13416) Origin recognition complex subunit 4 × 1 (O43929) Origin recognition complex subunit 5 × 1 (O43913) ;DNA (5'-D(*AP*TP*AP*TP*AP*TP*AP*TP*AP*TP*AP*AP*T)-3') ; × 1 ;DNA (5'-D(*AP*TP*TP*AP*TP*AP*TP*AP*TP*AP*TP*AP*T)-3') ; × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 3 MG MAGNESIUM ION × 3 K POTASSIUM ION × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 4.40 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.

14 other PDB entries and 19 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ORC3_HUMAN
Isoform Q9UBD5-2
PDB entities 3
Chains and sequence ranges Author chain C; PDBConstruct 1–712; UniProt 1–712

Origin recognition complex subunit 4

Homo sapiens

UniProt O43929

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 × 5 DNA 2 PDB declaration: heptameric(7) Consistent with all polymer counts Chain D; UniProt 1–436 Not recorded Origin recognition complex subunit 1 × 1 (Q13415) Origin recognition complex subunit 2 × 1 (Q13416) Origin recognition complex subunit 3 × 1 (Q9UBD5) Origin recognition complex subunit 5 × 1 (O43913) ;DNA (5'-D(*AP*TP*AP*TP*AP*TP*AP*TP*AP*TP*AP*AP*T)-3') ; × 1 ;DNA (5'-D(*AP*TP*TP*AP*TP*AP*TP*AP*TP*AP*TP*AP*T)-3') ; × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 3 MG MAGNESIUM ION × 3 K POTASSIUM ION × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 4.40 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.

14 other PDB entries and 15 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ORC4_HUMAN
Isoform
PDB entities 4
Chains and sequence ranges Author chain D; PDBConstruct 1–436; UniProt 1–436

Origin recognition complex subunit 5

Homo sapiens

UniProt O43913

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 × 5 DNA 2 PDB declaration: heptameric(7) Consistent with all polymer counts Chain E; UniProt 1–435 Not recorded Origin recognition complex subunit 1 × 1 (Q13415) Origin recognition complex subunit 2 × 1 (Q13416) Origin recognition complex subunit 3 × 1 (Q9UBD5) Origin recognition complex subunit 4 × 1 (O43929) ;DNA (5'-D(*AP*TP*AP*TP*AP*TP*AP*TP*AP*TP*AP*AP*T)-3') ; × 1 ;DNA (5'-D(*AP*TP*TP*AP*TP*AP*TP*AP*TP*AP*TP*AP*T)-3') ; × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 3 MG MAGNESIUM ION × 3 K POTASSIUM ION × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 4.40 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.

14 other PDB entries and 15 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ORC5_HUMAN
Isoform
PDB entities 5
Chains and sequence ranges Author chain E; PDBConstruct 1–435; UniProt 1–435

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 7jps

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id7jps
Deposition date deposition_date2020-08-09
Structure title titleORC-DNA: Human Origin Recognition Complex (ORC) with DNA bound in the core
Keywords keywordsreplication, AAA+, ORC, DNA-binding, cryoEM, replication-DNA complex; replication/DNA
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier44.50
Radius of gyration Rg (electron density) rg_electron44.51
Forward intensity I(0) i0791592000.00
Molecular weight molecular_weight232870.0 kDa
Excluded volume excluded_volume291850 ų
Envelope volume envelope_volume407810 ų
Hydration-shell volume shell_volume76314 ų
Envelope diameter envelope_diameter158.2
Shell Rg shell_rg49.25
Envelope Rg envelope_rg43.90
Shape Rg shape_rg44.53
Total Rg total_rg44.67
Total atoms total_atoms16352
Residues n_residues1958
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −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 dmax150.8
Rg (real space) rg_real44.53
Rg uncertainty (real space) rg_real_error1.73
I(0) (real space) i0_real7.9160e+08
I(0) uncertainty (real space) i0_real_error1.5140e+07
Rg (reciprocal space) rg_reciprocal44.50
I(0) (reciprocal space) i0_reciprocal791600000.0000
Solution quality estimate total_estimate0.8674
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary51.7
Skewness Skewness skewness0.394
Kurtosis Kurtosis kurtosis-0.231
Angular range angular_range— – 0.1750 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha118900000.0000
Real-space data points n_real_points36
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.832; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.782

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (10)

8. Citations (1)

9. Files and Curves (10)