6oer

Cryo-EM structure of mouse RAG1/2 NFC complex (DNA2)

Method: ELECTRON MICROSCOPY Dmax: 156.3 Å Quality: GOOD

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

V(D)J recombination-activating protein 1

Mus musculus

UniProt P15919

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 4 PDB declaration: nonameric(9) Consistent with all polymer counts Chain A; UniProt 1–1040 Chain C; UniProt 1–1040 Mutation:E962Q V(D)J recombination-activating protein 2 × 2 (P21784) DNA (46-MER) × 1 DNA (46-MER) × 1 DNA (57-MER) × 1 DNA (57-MER) × 1 High mobility group protein B1 × 1 (Q08IE6) ZN ZINC ION × 2 CA CALCIUM ION × 4 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.29 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.

30 other PDB entries and 35 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RAG1_MOUSE
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–1040; UniProt 1–1040 Author chain C; PDBConstruct 1–1040; UniProt 1–1040

V(D)J recombination-activating protein 2

Mus musculus

UniProt P21784

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 4 PDB declaration: nonameric(9) Consistent with all polymer counts Chain B; UniProt 1–527 Chain D; UniProt 1–527 Not recorded V(D)J recombination-activating protein 1 × 2 (P15919) DNA (46-MER) × 1 DNA (46-MER) × 1 DNA (57-MER) × 1 DNA (57-MER) × 1 High mobility group protein B1 × 1 (Q08IE6) ZN ZINC ION × 2 CA CALCIUM ION × 4 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.29 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.

33 other PDB entries and 43 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RAG2_MOUSE
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 1–527; UniProt 1–527 Author chain D; PDBConstruct 1–527; UniProt 1–527

High mobility group protein B1

OrganismNot specified

UniProt Q08IE6

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 4 PDB declaration: nonameric(9) Consistent with all polymer counts Chain H; UniProt 1–163 Not recorded V(D)J recombination-activating protein 1 × 2 (P15919) V(D)J recombination-activating protein 2 × 2 (P21784) DNA (46-MER) × 1 DNA (46-MER) × 1 DNA (57-MER) × 1 DNA (57-MER) × 1 ZN ZINC ION × 2 CA CALCIUM ION × 4 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.29 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 HMGB1_HORSE
Isoform
PDB entities 7
Chains and sequence ranges Author chain H; PDBConstruct 1–163; UniProt 1–163

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 6oer

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6oer
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6oer
Deposition date deposition_date2019-03-27
Structure title titleCryo-EM structure of mouse RAG1/2 NFC complex (DNA2)
Keywords keywordsV(D)J recombination, DNA Transposition, RAG, SCID, RECOMBINATION, RECOMBINATION-DNA complex; RECOMBINATION/DNA
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier47.75
Radius of gyration Rg (electron density) rg_electron46.48
Forward intensity I(0) i01536800000.00
Molecular weight molecular_weight280960.0 kDa
Excluded volume excluded_volume332700 ų
Envelope volume envelope_volume490150 ų
Hydration-shell volume shell_volume86354 ų
Envelope diameter envelope_diameter161.9
Shell Rg shell_rg52.02
Envelope Rg envelope_rg46.18
Shape Rg shape_rg46.45
Total Rg total_rg46.75
Total atoms total_atoms19467
Residues n_residues2158
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 dmax156.3
Rg (real space) rg_real47.58
Rg uncertainty (real space) rg_real_error1.17
I(0) (real space) i0_real1.5370e+09
I(0) uncertainty (real space) i0_real_error2.8280e+07
Rg (reciprocal space) rg_reciprocal47.75
I(0) (reciprocal space) i0_reciprocal1537000000.0000
Solution quality estimate total_estimate0.8852
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary56.9
Skewness Skewness skewness0.242
Kurtosis Kurtosis kurtosis-0.369
Angular range angular_range— – 0.1650 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha87300000.0000
Real-space data points n_real_points34
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.882; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.984; Smooth: 0.872

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (9)

8. Citations (1)

9. Files and Curves (10)