← Back to search
9jpx

CryoEM structure of mouse RAG SEC-0

Method: ELECTRON MICROSCOPY Dmax: 135.7 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 × 4 DNA 4 PDB declaration: octameric（8） Consistent with all polymer counts Chain A； UniProt 1–1040 Chain C； UniProt 1–1040 Not recorded V(D)J recombination-activating protein 2 × 2 （P21784） ;DNA (5'-D(P*GP*GP*CP*TP*GP*TP*AP*TP*CP*AP*CP*TP*GP*TP*G)-3') ; × 1 ;DNA (5'-D(P*TP*TP*TP*GP*CP*AP*TP*CP*AP*CP*TP*GP*TP*G)-3') ; × 1 ;DNA (5'-D(*CP*AP*CP*AP*GP*TP*GP*AP*TP*AP*CP*AP*GP*CP*C)-3') ; × 1 ;DNA (5'-D(*CP*AP*CP*AP*GP*TP*GP*AP*TP*GP*CP*AP*AP*A)-3') ; × 1 CA CALCIUM ION × 2 ZN ZINC ION × 2 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 2.95 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 9JPX Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1RMD RAG1 DIMERIZATION DOMAIN Deposited 1997-01-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 265–380（116 aa） Fragment：ZINC-BINDING DIMERIZATION DOMAIN
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；5-10 % PEG 4K, 100MM HEPES, PH 7.5, 10% ETHYLENE GLYCOL
Resolution 2.10 Å R-free 0.257
21WB NZD domain of Mouse RAG1 Deposited 2025-12-31 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 89–223（135 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR mmCIF provides none of the parsed conditions Resolution not provided
3GNA Crystal structure of the RAG1 nonamer-binding domain with DNA Deposited 2009-03-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: hexameric
Chain A 389–464（76 aa） Fragment：Nonamer binding domain: UNP residues 389-456
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；30% PEG 400, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.40 Å R-free 0.271
3GNB Crystal structure of the RAG1 nonamer-binding domain with DNA Deposited 2009-03-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: hexameric
Chain A 389–464（76 aa） Fragment：Nonamer binding domain: UNP residues 389-456
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；20% PEG 400, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 3.00 Å R-free 0.267
4WWX Crystal structure of the core RAG1/2 recombinase Deposited 2014-11-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 392–1008（617 aa） Fragment：UNP Residues 391-1008
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；100 mM MES (pH 7.1), 10-15% PEG 3350, 200 mM tribasic ammonium citrate (pH 7.0), 100 mM KCl
Resolution 3.20 Å R-free 0.259
4WWX Crystal structure of the core RAG1/2 recombinase Deposited 2014-11-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 392–1008（617 aa） Fragment：UNP Residues 391-1008
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；100 mM MES (pH 7.1), 10-15% PEG 3350, 200 mM tribasic ammonium citrate (pH 7.0), 100 mM KCl
Resolution 3.20 Å R-free 0.259
5ZDZ Hairpin Forming Complex, RAG1/2-Nicked 12RSS/23RSS complex in Ca2+ Deposited 2018-02-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: hexameric
Chain A 384–1008（625 aa） Fragment：UNP residues 384-1008
Not recorded CA CALCIUM ION × 1 ZN ZINC ION × 1 EDO 1,2-ETHANEDIOL × 2 K POTASSIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；100mM MES (pH 6.8), 15% PEG 3350, 200mM Potassium formate
Resolution 2.80 Å R-free 0.242
5ZDZ Hairpin Forming Complex, RAG1/2-Nicked 12RSS/23RSS complex in Ca2+ Deposited 2018-02-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Heteromer；Protein × 2 PDB declaration: pentameric
Chain C 384–1008（625 aa） Fragment：UNP residues 384-1008
Not recorded CA CALCIUM ION × 1 ZN ZINC ION × 1 EDO 1,2-ETHANEDIOL × 1 K POTASSIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；100mM MES (pH 6.8), 15% PEG 3350, 200mM Potassium formate
Resolution 2.80 Å R-free 0.242
5ZE0 Hairpin Forming Complex, RAG1/2-Nicked(with Dideoxy) 12RSS/23RSS complex in Mg2+ Deposited 2018-02-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: hexameric
Chain A 384–1008（625 aa） Fragment：UNP residues 383-1008
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 1 EDO 1,2-ETHANEDIOL × 2 K POTASSIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；100mM MES (pH 6.8), 15% PEG 3350, 200 mM Potassium formate.
Resolution 2.75 Å R-free 0.234
5ZE0 Hairpin Forming Complex, RAG1/2-Nicked(with Dideoxy) 12RSS/23RSS complex in Mg2+ Deposited 2018-02-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Heteromer；Protein × 2 PDB declaration: pentameric
Chain C 384–1008（625 aa） Fragment：UNP residues 383-1008
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 1 EDO 1,2-ETHANEDIOL × 1 K POTASSIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；100mM MES (pH 6.8), 15% PEG 3350, 200 mM Potassium formate.
Resolution 2.75 Å R-free 0.234
5ZE1 Hairpin Forming Complex, RAG1/2-Nicked 12RSS/23RSS complex in 2mM Mn2+ for 10 min at 4'C Deposited 2018-02-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: hexameric
Chain A 384–1008（625 aa） Fragment：UNP residues 384-1008
Not recorded ZN ZINC ION × 1 MN MANGANESE (II) ION × 2 EDO 1,2-ETHANEDIOL × 1 K POTASSIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；100mM MES (pH 6.8), 15% PEG 3350, 200mM Potassium formate
Resolution 3.00 Å R-free 0.232
5ZE1 Hairpin Forming Complex, RAG1/2-Nicked 12RSS/23RSS complex in 2mM Mn2+ for 10 min at 4'C Deposited 2018-02-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Heteromer；Protein × 2 PDB declaration: pentameric
Chain C 384–1008（625 aa） Fragment：UNP residues 384-1008
Not recorded ZN ZINC ION × 1 MN MANGANESE (II) ION × 2 K POTASSIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；100mM MES (pH 6.8), 15% PEG 3350, 200mM Potassium formate
Resolution 3.00 Å R-free 0.232
5ZE2 Hairpin Complex, RAG1/2-hairpin 12RSS/23RSS complex in 5mM Mn2+ for 2 min at 4'C Deposited 2018-02-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: hexameric
Chain A 384–1008（625 aa） Fragment：UNP residues 384-1008
Not recorded ZN ZINC ION × 1 MN MANGANESE (II) ION × 2 EDO 1,2-ETHANEDIOL × 2 K POTASSIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；100mM MES (pH 6.8), 15% PEG 3350, 200mM Potassium formate
Resolution 3.30 Å R-free 0.237
5ZE2 Hairpin Complex, RAG1/2-hairpin 12RSS/23RSS complex in 5mM Mn2+ for 2 min at 4'C Deposited 2018-02-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Heteromer；Protein × 2 PDB declaration: pentameric
Chain C 384–1008（625 aa） Fragment：UNP residues 384-1008
Not recorded ZN ZINC ION × 1 MN MANGANESE (II) ION × 2 EDO 1,2-ETHANEDIOL × 1 K POTASSIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；100mM MES (pH 6.8), 15% PEG 3350, 200mM Potassium formate
Resolution 3.30 Å R-free 0.237
6CG0 Cryo-EM structure of mouse RAG1/2 HFC complex (3.17 A) Deposited 2018-02-19 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 5 PDB declaration: undecameric
Chain A 265–1039（775 aa）
Chain C 265–1039（775 aa）
Not recorded ZN ZINC ION × 2 CA CALCIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.17 Å
6CIJ Cryo-EM structure of mouse RAG1/2 HFC complex containing partial HMGB1 linker(3.9 A) Deposited 2018-02-24 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 5 PDB declaration: undecameric
Chain A 265–1040（776 aa）
Chain C 265–1040（776 aa）
Not recorded ZN ZINC ION × 2 CA CALCIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
6CIK Pre-Reaction Complex, RAG1(E962Q)/2-intact/nicked 12/23RSS complex in Mn2+ Deposited 2018-02-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 5 PDB declaration: decameric
Chain A 384–1008（625 aa）
Chain C 384–1008（625 aa）
Mutation：E962Q Mutation：E962Q ZN ZINC ION × 2 MN MANGANESE (II) ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.9；277 K；12-16% PEG 3350, 200 mM NaNO3, 50 mM HEPES, pH 6.9
Resolution 3.15 Å R-free 0.249
6CIL PRE-REACTION COMPLEX, RAG1(E962Q)/2-INTACT/INTACT 12/23RSS COMPLEX IN MN2+ Deposited 2018-02-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 5 PDB declaration: nonameric
Chain A 384–1008（625 aa）
Chain C 384–1008（625 aa）
Mutation：E962Q Mutation：E962Q ZN ZINC ION × 2 MN MANGANESE (II) ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.9；277 K；18% PEG3350, 200 mM KNO3, 50 mM HEPES pH 6.9
Resolution 4.15 Å R-free 0.231
6CIM Pre-Reaction Complex, RAG1(E962Q)/2-nicked/intact 12/23RSS complex in Mn2+ Deposited 2018-02-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 5 PDB declaration: decameric
Chain A 384–1008（625 aa）
Chain C 384–1008（625 aa）
Mutation：E962Q Mutation：E962Q ZN ZINC ION × 2 MN MANGANESE (II) ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.9；277 K；18% PEG3350, 200 mM KNO3, 50 mM HEPES pH 6.9
Resolution 3.60 Å R-free 0.254
6OEM Cryo-EM structure of mouse RAG1/2 PRC complex (DNA0) Deposited 2019-03-27 Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: decameric
Chain A 1–1040（1040 aa）
Chain C 1–1040（1040 aa）
Mutation：E962Q Mutation：E962Q MG MAGNESIUM ION × 2 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
6OEN Cryo-EM structure of mouse RAG1/2 PRC complex (DNA1) Deposited 2019-03-27 Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: decameric
Chain A 1–1040（1040 aa）
Chain C 1–1040（1040 aa）
Mutation：E962Q Mutation：E962Q ZN ZINC ION × 2 CA CALCIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
6OEO Cryo-EM structure of mouse RAG1/2 NFC complex (DNA1) Deposited 2019-03-27 Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 5 PDB declaration: nonameric
Chain A 1–1040（1040 aa）
Chain C 1–1040（1040 aa）
Mutation：E962Q Mutation：E962Q CA CALCIUM ION × 4 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.69 Å
6OEP Cryo-EM structure of mouse RAG1/2 12RSS-NFC/23RSS-PRC complex (DNA1) Deposited 2019-03-27 Different mutation/modification Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: octameric
Chain A 1–1040（1040 aa）
Chain C 1–1040（1040 aa）
Mutation：E962Q Mutation：E962Q CA CALCIUM ION × 3 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
6OEQ Cryo-EM structure of mouse RAG1/2 12RSS-PRC/23RSS-NFC complex (DNA1) Deposited 2019-03-27 Different mutation/modification Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: octameric
Chain A 1–1040（1040 aa）
Chain C 1–1040（1040 aa）
Mutation：E962Q Mutation：E962Q ZN ZINC ION × 2 CA CALCIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
6OER Cryo-EM structure of mouse RAG1/2 NFC complex (DNA2) Deposited 2019-03-27 Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 5 PDB declaration: nonameric
Chain A 1–1040（1040 aa）
Chain C 1–1040（1040 aa）
Mutation：E962Q Mutation：E962Q 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
6OES Cryo-EM structure of mouse RAG1/2 STC complex (without NBD domain) Deposited 2019-03-27 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: decameric
Chain A 1–1040（1040 aa）
Chain C 1–1040（1040 aa）
Not recorded CA CALCIUM ION × 2 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.06 Å
6OET Cryo-EM structure of mouse RAG1/2 STC complex Deposited 2019-03-27 Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: decameric
Chain A 1–1040（1040 aa）
Chain C 1–1040（1040 aa）
Mutation：E962Q Mutation：E962Q CA CALCIUM ION × 2 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
6V0V Cryo-EM structure of mouse WT RAG1/2 NFC complex (DNA0) Deposited 2019-11-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric
Chain A 265–1039（775 aa）
Not recorded CA CALCIUM ION × 2 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.61 Å
6XNX Structure of RAG1 (R848M/E649V)-RAG2-DNA Strand Transfer Complex (Dynamic-Form) Deposited 2020-07-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: decameric
Chain A 261–1008（748 aa）
Chain C 261–1008（748 aa）
Mutation：R848M, E649V Mutation：R848M, E649V MG MAGNESIUM ION × 4 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；20 mM HEPES pH7.6, 0.5 mM TCEP, 5 mM MgCl2 and 150 mM KCl
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
6XNY Structure of RAG1 (R848M/E649V)-RAG2-DNA Strand Transfer Complex (Paired-Form) Deposited 2020-07-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: decameric
Chain A 261–1008（748 aa）
Chain C 261–1008（748 aa）
Mutation：R848M, E649V Mutation：R848M, E649V MG MAGNESIUM ION × 4 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；20 mM HEPES pH7.6, 0.5 mM TCEP, 5 mM MgCl2 and 150 mM KCl
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
6XNZ Structure of RAG1 (R848M/E649V)-RAG2-DNA Target Capture Complex Deposited 2020-07-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: decameric
Chain A 261–1008（748 aa）
Chain C 261–1008（748 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；20 mM HEPES pH7.6, 0.5 mM TCEP, 5 mM MgCl2 and 150 mM KCl
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
9JPU CryoEM structure of mouse RAG SEC-PHD Deposited 2024-09-26 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 5 PDB declaration: nonameric
Chain A 1–1040（1040 aa）
Chain C 1–1040（1040 aa）
Not recorded CA CALCIUM ION × 2 ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.25 Å
9JQN CryoEM structure of mouse RAG SEC-2DNA Deposited 2024-09-27 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: dodecameric
Chain A 1–1040（1040 aa）
Chain C 1–1040（1040 aa）
Not recorded CA CALCIUM ION × 2 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.03 Å
9JTS CryoEM structure of mouse RAG SEC-1DNA (12RSS side) Deposited 2024-10-07 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: decameric
Chain A 1–1040（1040 aa）
Chain C 1–1040（1040 aa）
Not recorded CA CALCIUM ION × 2 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.36 Å
9JTU CryoEM structure of mouse RAG SEC-1DNA (23RSS side) Deposited 2024-10-07 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: decameric
Chain A 1–1040（1040 aa）
Chain C 1–1040（1040 aa）
Not recorded CA CALCIUM ION × 2 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.43 Å

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 × 4 DNA 4 PDB declaration: octameric（8） 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 (5'-D(P*GP*GP*CP*TP*GP*TP*AP*TP*CP*AP*CP*TP*GP*TP*G)-3') ; × 1 ;DNA (5'-D(P*TP*TP*TP*GP*CP*AP*TP*CP*AP*CP*TP*GP*TP*G)-3') ; × 1 ;DNA (5'-D(*CP*AP*CP*AP*GP*TP*GP*AP*TP*AP*CP*AP*GP*CP*C)-3') ; × 1 ;DNA (5'-D(*CP*AP*CP*AP*GP*TP*GP*AP*TP*GP*CP*AP*AP*A)-3') ; × 1 CA CALCIUM ION × 2 ZN ZINC ION × 2 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 2.95 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 9JPX Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2JWO A PHD finger motif in the C-terminus of RAG2 modulates recombination activity Deposited 2007-10-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 414–487（74 aa） Fragment：PHD finger motif: Residues 414-487
Not recorded ZN ZINC ION × 2 SOLUTION NMR
NMR measurement conditions pH 7.2；298 K；Ionic strength (raw mmCIF value) 0；Pressure ambient
NMR sample composition 0.5 mM [U-99% 13C; U-99% 15N] RAG2 PHD domain, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
2V83 Crystal structure of RAG2-PHD finger in complex with H3K4me3 peptide Deposited 2007-08-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 414–487（74 aa） Fragment：RESIDUES 414-487
Chain B 414–487（74 aa） Fragment：RESIDUES 414-487
Chain C 414–487（74 aa） Fragment：RESIDUES 414-487
Not recorded ZN ZINC ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；10% PEG 5000 MONOMETHYL ETHER, 0.1 M BIS-TRIS PH 6.5 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K.
Resolution 2.40 Å R-free 0.230
2V85 Crystal structure of RAG2-PHD finger in complex with H3R2me1K4me3 peptide Deposited 2007-08-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 414–487（74 aa） Fragment：RESIDUES 414-487
Not recorded ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION. HANGING DROP. 20% PEG 3350, 0.2 M POTASSIUM THIOCYANATE
Resolution 2.00 Å R-free 0.197
2V85 Crystal structure of RAG2-PHD finger in complex with H3R2me1K4me3 peptide Deposited 2007-08-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 414–487（74 aa） Fragment：RESIDUES 414-487
Not recorded ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION. HANGING DROP. 20% PEG 3350, 0.2 M POTASSIUM THIOCYANATE
Resolution 2.00 Å R-free 0.197
2V86 Crystal structure of RAG2-PHD finger in complex with H3R2me2aK4me3 peptide Deposited 2007-08-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 414–487（74 aa） Fragment：RESIDUES 414-487
Not recorded ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；VAPOR DIFFUSION. HANGING DROP. 28% PEG 20,000, 0.1M MES PH 6.5, 3% ISOPROPANOL TEMPERATURE 293K
Resolution 2.05 Å R-free 0.211
2V86 Crystal structure of RAG2-PHD finger in complex with H3R2me2aK4me3 peptide Deposited 2007-08-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 414–487（74 aa） Fragment：RESIDUES 414-487
Not recorded ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；VAPOR DIFFUSION. HANGING DROP. 28% PEG 20,000, 0.1M MES PH 6.5, 3% ISOPROPANOL TEMPERATURE 293K
Resolution 2.05 Å R-free 0.211
2V87 Crystal structure of RAG2-PHD finger in complex with H3R2me2sK4me3 peptide Deposited 2007-08-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 414–487（74 aa） Fragment：RESIDUES 414-487
Not recorded ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；VAPOR DIFFUSION. HANGING DROP. 22% PEG 3350, 120-240 MM OF POTASSIUM FORMATE. TEMPERATURE 293K
Resolution 1.80 Å R-free 0.208
2V87 Crystal structure of RAG2-PHD finger in complex with H3R2me2sK4me3 peptide Deposited 2007-08-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 414–487（74 aa） Fragment：RESIDUES 414-487
Not recorded ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；VAPOR DIFFUSION. HANGING DROP. 22% PEG 3350, 120-240 MM OF POTASSIUM FORMATE. TEMPERATURE 293K
Resolution 1.80 Å R-free 0.208
2V88 Crystal structure of RAG2-PHD finger in complex with H3R2me2sK4me2 peptide Deposited 2007-08-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 414–487（74 aa） Fragment：RESIDUES 414-487
Not recorded ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；VAPOR DIFFUSION. HANGING DROP. 22% PEG 3350, 120-240 MM POTASSIUM FLUORIDE. TEMPERATURE 293K
Resolution 2.00 Å R-free 0.232
2V88 Crystal structure of RAG2-PHD finger in complex with H3R2me2sK4me2 peptide Deposited 2007-08-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 414–487（74 aa） Fragment：RESIDUES 414-487
Not recorded ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；VAPOR DIFFUSION. HANGING DROP. 22% PEG 3350, 120-240 MM POTASSIUM FLUORIDE. TEMPERATURE 293K
Resolution 2.00 Å R-free 0.232
2V89 Crystal structure of RAG2-PHD finger in complex with H3K4me3 peptide at 1.1A resolution Deposited 2007-08-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 414–487（74 aa） Fragment：RESIDUES 414-487
Not recorded ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；CRYSTALS OF COMPLEX WERE OBTAINED AT 3 MG/ML PROTEIN CONCENTRATION AND 1:1.5 MOLAR RATIO OF PROTEIN TO PEPTIDE USING HANGING DROP AND VAPOR DIFFUSION TECHNIQUE AT 293K. PRECIPITANT SOLUTION: 26% PEG 3350, 0.18M POTASSIUM THIOCYANATE.
Resolution 1.10 Å R-free 0.155
2V89 Crystal structure of RAG2-PHD finger in complex with H3K4me3 peptide at 1.1A resolution Deposited 2007-08-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 414–487（74 aa） Fragment：RESIDUES 414-487
Not recorded ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；CRYSTALS OF COMPLEX WERE OBTAINED AT 3 MG/ML PROTEIN CONCENTRATION AND 1:1.5 MOLAR RATIO OF PROTEIN TO PEPTIDE USING HANGING DROP AND VAPOR DIFFUSION TECHNIQUE AT 293K. PRECIPITANT SOLUTION: 26% PEG 3350, 0.18M POTASSIUM THIOCYANATE.
Resolution 1.10 Å R-free 0.155
4WWX Crystal structure of the core RAG1/2 recombinase Deposited 2014-11-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain X 2–350（349 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；100 mM MES (pH 7.1), 10-15% PEG 3350, 200 mM tribasic ammonium citrate (pH 7.0), 100 mM KCl
Resolution 3.20 Å R-free 0.259
4WWX Crystal structure of the core RAG1/2 recombinase Deposited 2014-11-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain Y 2–350（349 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；100 mM MES (pH 7.1), 10-15% PEG 3350, 200 mM tribasic ammonium citrate (pH 7.0), 100 mM KCl
Resolution 3.20 Å R-free 0.259
5ZDZ Hairpin Forming Complex, RAG1/2-Nicked 12RSS/23RSS complex in Ca2+ Deposited 2018-02-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: hexameric
Chain B 1–387（387 aa） Fragment：UNP residues 1-387
Mutation：M1V CA CALCIUM ION × 1 ZN ZINC ION × 1 EDO 1,2-ETHANEDIOL × 2 K POTASSIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；100mM MES (pH 6.8), 15% PEG 3350, 200mM Potassium formate
Resolution 2.80 Å R-free 0.242
5ZDZ Hairpin Forming Complex, RAG1/2-Nicked 12RSS/23RSS complex in Ca2+ Deposited 2018-02-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Heteromer；Protein × 2 PDB declaration: pentameric
Chain D 1–387（387 aa） Fragment：UNP residues 1-387
Mutation：M1V CA CALCIUM ION × 1 ZN ZINC ION × 1 EDO 1,2-ETHANEDIOL × 1 K POTASSIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；100mM MES (pH 6.8), 15% PEG 3350, 200mM Potassium formate
Resolution 2.80 Å R-free 0.242
5ZE0 Hairpin Forming Complex, RAG1/2-Nicked(with Dideoxy) 12RSS/23RSS complex in Mg2+ Deposited 2018-02-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: hexameric
Chain B 1–387（387 aa） Fragment：UNP residues 1-387
Mutation：M1V MG MAGNESIUM ION × 1 ZN ZINC ION × 1 EDO 1,2-ETHANEDIOL × 2 K POTASSIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；100mM MES (pH 6.8), 15% PEG 3350, 200 mM Potassium formate.
Resolution 2.75 Å R-free 0.234
5ZE0 Hairpin Forming Complex, RAG1/2-Nicked(with Dideoxy) 12RSS/23RSS complex in Mg2+ Deposited 2018-02-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Heteromer；Protein × 2 PDB declaration: pentameric
Chain D 1–387（387 aa） Fragment：UNP residues 1-387
Mutation：M1V MG MAGNESIUM ION × 1 ZN ZINC ION × 1 EDO 1,2-ETHANEDIOL × 1 K POTASSIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；100mM MES (pH 6.8), 15% PEG 3350, 200 mM Potassium formate.
Resolution 2.75 Å R-free 0.234
5ZE1 Hairpin Forming Complex, RAG1/2-Nicked 12RSS/23RSS complex in 2mM Mn2+ for 10 min at 4'C Deposited 2018-02-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: hexameric
Chain B 1–387（387 aa） Fragment：UNP residues 1-387
Mutation：M1V ZN ZINC ION × 1 MN MANGANESE (II) ION × 2 EDO 1,2-ETHANEDIOL × 1 K POTASSIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；100mM MES (pH 6.8), 15% PEG 3350, 200mM Potassium formate
Resolution 3.00 Å R-free 0.232
5ZE1 Hairpin Forming Complex, RAG1/2-Nicked 12RSS/23RSS complex in 2mM Mn2+ for 10 min at 4'C Deposited 2018-02-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Heteromer；Protein × 2 PDB declaration: pentameric
Chain D 1–387（387 aa） Fragment：UNP residues 1-387
Mutation：M1V ZN ZINC ION × 1 MN MANGANESE (II) ION × 2 K POTASSIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；100mM MES (pH 6.8), 15% PEG 3350, 200mM Potassium formate
Resolution 3.00 Å R-free 0.232
5ZE2 Hairpin Complex, RAG1/2-hairpin 12RSS/23RSS complex in 5mM Mn2+ for 2 min at 4'C Deposited 2018-02-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: hexameric
Chain B 1–387（387 aa） Fragment：UNP residues 1-387
Mutation：M1V ZN ZINC ION × 1 MN MANGANESE (II) ION × 2 EDO 1,2-ETHANEDIOL × 2 K POTASSIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；100mM MES (pH 6.8), 15% PEG 3350, 200mM Potassium formate
Resolution 3.30 Å R-free 0.237
5ZE2 Hairpin Complex, RAG1/2-hairpin 12RSS/23RSS complex in 5mM Mn2+ for 2 min at 4'C Deposited 2018-02-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Heteromer；Protein × 2 PDB declaration: pentameric
Chain D 1–387（387 aa） Fragment：UNP residues 1-387
Mutation：M1V ZN ZINC ION × 1 MN MANGANESE (II) ION × 2 EDO 1,2-ETHANEDIOL × 1 K POTASSIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；100mM MES (pH 6.8), 15% PEG 3350, 200mM Potassium formate
Resolution 3.30 Å R-free 0.237
6CG0 Cryo-EM structure of mouse RAG1/2 HFC complex (3.17 A) Deposited 2018-02-19 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 5 PDB declaration: undecameric
Chain B 1–520（520 aa）
Chain D 1–520（520 aa）
Not recorded ZN ZINC ION × 2 CA CALCIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.17 Å
6CIJ Cryo-EM structure of mouse RAG1/2 HFC complex containing partial HMGB1 linker(3.9 A) Deposited 2018-02-24 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 5 PDB declaration: undecameric
Chain B 1–520（520 aa）
Chain D 1–520（520 aa）
Not recorded ZN ZINC ION × 2 CA CALCIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
6CIK Pre-Reaction Complex, RAG1(E962Q)/2-intact/nicked 12/23RSS complex in Mn2+ Deposited 2018-02-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 5 PDB declaration: decameric
Chain B 1–359（359 aa）
Chain D 1–359（359 aa）
Not recorded ZN ZINC ION × 2 MN MANGANESE (II) ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.9；277 K；12-16% PEG 3350, 200 mM NaNO3, 50 mM HEPES, pH 6.9
Resolution 3.15 Å R-free 0.249
6CIL PRE-REACTION COMPLEX, RAG1(E962Q)/2-INTACT/INTACT 12/23RSS COMPLEX IN MN2+ Deposited 2018-02-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 5 PDB declaration: nonameric
Chain B 1–359（359 aa）
Chain D 1–359（359 aa）
Not recorded ZN ZINC ION × 2 MN MANGANESE (II) ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.9；277 K；18% PEG3350, 200 mM KNO3, 50 mM HEPES pH 6.9
Resolution 4.15 Å R-free 0.231
6CIM Pre-Reaction Complex, RAG1(E962Q)/2-nicked/intact 12/23RSS complex in Mn2+ Deposited 2018-02-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 5 PDB declaration: decameric
Chain B 1–359（359 aa）
Chain D 1–359（359 aa）
Not recorded ZN ZINC ION × 2 MN MANGANESE (II) ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.9；277 K；18% PEG3350, 200 mM KNO3, 50 mM HEPES pH 6.9
Resolution 3.60 Å R-free 0.254
6OEM Cryo-EM structure of mouse RAG1/2 PRC complex (DNA0) Deposited 2019-03-27 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: decameric
Chain B 1–527（527 aa）
Chain D 1–527（527 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
6OEN Cryo-EM structure of mouse RAG1/2 PRC complex (DNA1) Deposited 2019-03-27 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: decameric
Chain B 1–527（527 aa）
Chain D 1–527（527 aa）
Not recorded ZN ZINC ION × 2 CA CALCIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
6OEO Cryo-EM structure of mouse RAG1/2 NFC complex (DNA1) Deposited 2019-03-27 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 5 PDB declaration: nonameric
Chain B 1–527（527 aa）
Chain D 1–527（527 aa）
Not recorded CA CALCIUM ION × 4 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.69 Å
6OEP Cryo-EM structure of mouse RAG1/2 12RSS-NFC/23RSS-PRC complex (DNA1) Deposited 2019-03-27 Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: octameric
Chain B 1–527（527 aa）
Chain D 1–527（527 aa）
Not recorded CA CALCIUM ION × 3 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
6OEQ Cryo-EM structure of mouse RAG1/2 12RSS-PRC/23RSS-NFC complex (DNA1) Deposited 2019-03-27 Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: octameric
Chain B 1–527（527 aa）
Chain D 1–527（527 aa）
Not recorded ZN ZINC ION × 2 CA CALCIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
6OER Cryo-EM structure of mouse RAG1/2 NFC complex (DNA2) Deposited 2019-03-27 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 5 PDB declaration: nonameric
Chain B 1–527（527 aa）
Chain D 1–527（527 aa）
Not recorded 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
6OES Cryo-EM structure of mouse RAG1/2 STC complex (without NBD domain) Deposited 2019-03-27 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: decameric
Chain B 1–527（527 aa）
Chain D 1–527（527 aa）
Not recorded CA CALCIUM ION × 2 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.06 Å
6OET Cryo-EM structure of mouse RAG1/2 STC complex Deposited 2019-03-27 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: decameric
Chain B 1–527（527 aa）
Chain D 1–527（527 aa）
Not recorded CA CALCIUM ION × 2 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
6V0V Cryo-EM structure of mouse WT RAG1/2 NFC complex (DNA0) Deposited 2019-11-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric
Chain B 1–520（520 aa）
Not recorded CA CALCIUM ION × 2 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.61 Å
6XNX Structure of RAG1 (R848M/E649V)-RAG2-DNA Strand Transfer Complex (Dynamic-Form) Deposited 2020-07-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: decameric
Chain B 3–361（359 aa）
Chain D 3–361（359 aa）
Not recorded MG MAGNESIUM ION × 4 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；20 mM HEPES pH7.6, 0.5 mM TCEP, 5 mM MgCl2 and 150 mM KCl
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
6XNY Structure of RAG1 (R848M/E649V)-RAG2-DNA Strand Transfer Complex (Paired-Form) Deposited 2020-07-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: decameric
Chain B 3–361（359 aa）
Chain D 3–361（359 aa）
Not recorded MG MAGNESIUM ION × 4 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；20 mM HEPES pH7.6, 0.5 mM TCEP, 5 mM MgCl2 and 150 mM KCl
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
6XNZ Structure of RAG1 (R848M/E649V)-RAG2-DNA Target Capture Complex Deposited 2020-07-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: decameric
Chain B 3–361（359 aa）
Chain D 3–361（359 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；20 mM HEPES pH7.6, 0.5 mM TCEP, 5 mM MgCl2 and 150 mM KCl
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
9JPU CryoEM structure of mouse RAG SEC-PHD Deposited 2024-09-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 5 PDB declaration: nonameric
Chain B 1–527（527 aa）
Chain D 1–527（527 aa）
Chain E 1–527（527 aa）
Not recorded CA CALCIUM ION × 2 ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.25 Å
9JQN CryoEM structure of mouse RAG SEC-2DNA Deposited 2024-09-27 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: dodecameric
Chain B 1–527（527 aa）
Chain D 1–527（527 aa）
Not recorded CA CALCIUM ION × 2 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.03 Å
9JTS CryoEM structure of mouse RAG SEC-1DNA (12RSS side) Deposited 2024-10-07 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: decameric
Chain B 1–527（527 aa）
Chain D 1–527（527 aa）
Not recorded CA CALCIUM ION × 2 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.36 Å
9JTU CryoEM structure of mouse RAG SEC-1DNA (23RSS side) Deposited 2024-10-07 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: decameric
Chain B 1–527（527 aa）
Chain D 1–527（527 aa）
Not recorded CA CALCIUM ION × 2 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.43 Å

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

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 9jpx

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9jpx
Download Download
▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id9jpx
Deposition date deposition_date2024-09-26
Structure title titleCryoEM structure of mouse RAG SEC-0
Keywords keywordsV(D)J recombination, RAG, Transposition, DNA BINDING PROTEIN, DNA BINDING PROTEIN-DNA complex; DNA BINDING PROTEIN/DNA
Experimental Method methodELECTRON MICROSCOPY
▼

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

Radius of gyration Rg (Guinier) rg_guinier40.49 Å
Radius of gyration Rg (electron density) rg_electron40.27 Å
Forward intensity I(0) i0801566000.00
Molecular weight molecular_weight219850.0 kDa
Excluded volume excluded_volume269590 ų
Envelope volume envelope_volume357630 ų
Hydration-shell volume shell_volume71498 ų
Envelope diameter envelope_diameter147.9 Å
Shell Rg shell_rg47.99 Å
Envelope Rg envelope_rg39.85 Å
Shape Rg shape_rg40.29 Å
Total Rg total_rg40.55 Å
Total atoms total_atoms15360
Residues n_residues1842
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 dmax135.7 Å
Rg (real space) rg_real40.37 Å
Rg uncertainty (real space) rg_real_error1.00 Å
I(0) (real space) i0_real8.0160e+08
I(0) uncertainty (real space) i0_real_error1.5110e+07
Rg (reciprocal space) rg_reciprocal40.49 Å
I(0) (reciprocal space) i0_reciprocal801700000.0000
Solution quality estimate total_estimate0.8830
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary52.2 Å
Skewness Skewness skewness0.228
Kurtosis Kurtosis kurtosis-0.339
Angular range angular_range— – 0.1950 Å−1
Current regularization parameter α current_alpha0.0001
Highest regularization parameter α highest_alpha109700000.0000
Real-space data points n_real_points40
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.834; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.972
▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (9)

▶

8. Citations (1)

▶

9. Files and Curves (10)