6xny

Structure of RAG1 (R848M/E649V)-RAG2-DNA Strand Transfer Complex (Paired-Form)

Method: ELECTRON MICROSCOPY D_max: 127.1 Å Quality: GOOD

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

V(D)J recombination-activating protein 1

Mus musculus

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 6 PDB declaration: decameric（10） Consistent with all polymer counts	Chain A； UniProt 261–1008 Chain C； UniProt 261–1008	Mutation：R848M, E649V	V(D)J recombination-activating protein 2 × 2 （P21784） 12RSS integration strand (55-mer) × 1 23RSS integration strand (66-mer) × 1 Flanking DNA top strand (16-mer) × 2 23RSS signal DNA top strand (45-mer) × 1 12RSS signal DNA top strand (34-mer) × 1 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

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 6XNY	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 mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions 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 construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions 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 construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions 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 construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions 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 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: 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 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: 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 construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions 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 construct Different mutation/modification Different ligand/ion Different experimental conditions 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 construct Different mutation/modification Different ligand/ion Different experimental conditions 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 experimental conditions 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 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
6XNZ Structure of RAG1 (R848M/E649V)-RAG2-DNA Target Capture Complex Deposited 2020-07-05	Different mutation/modification Different ligand/ion 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 construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions 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
9JPX CryoEM structure of mouse RAG SEC-0 Deposited 2024-09-26	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: octameric	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 2.95 Å
9JQN CryoEM structure of mouse RAG SEC-2DNA Deposited 2024-09-27	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: 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 construct Different mutation/modification Different ligand/ion Different experimental conditions 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 construct Different mutation/modification Different ligand/ion Different experimental conditions 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 3–750； UniProt 261–1008 Author chain C； PDBConstruct 3–750； UniProt 261–1008

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 6 PDB declaration: decameric（10） Consistent with all polymer counts	Chain B； UniProt 3–361 Chain D； UniProt 3–361	Not recorded	V(D)J recombination-activating protein 1 × 2 （P15919） 12RSS integration strand (55-mer) × 1 23RSS integration strand (66-mer) × 1 Flanking DNA top strand (16-mer) × 2 23RSS signal DNA top strand (45-mer) × 1 12RSS signal DNA top strand (34-mer) × 1 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

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 6XNY	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 ligand/ion Different experimental conditions 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 ligand/ion Different experimental conditions 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 construct Different oligomeric state Different ligand/ion Different experimental conditions 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 construct Different oligomeric state Different ligand/ion Different experimental conditions 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 construct Different oligomeric state Different ligand/ion Different experimental conditions 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 construct Different oligomeric state Different ligand/ion Different experimental conditions 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 construct Different oligomeric state Different ligand/ion Different experimental conditions 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 construct Different oligomeric state Different ligand/ion Different experimental conditions 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 construct Different ligand/ion Different experimental conditions 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 construct Different ligand/ion Different experimental conditions 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 experimental conditions 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 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
6XNZ Structure of RAG1 (R848M/E649V)-RAG2-DNA Target Capture Complex Deposited 2020-07-05	Different ligand/ion 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 experimental conditions 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
9JPX CryoEM structure of mouse RAG SEC-0 Deposited 2024-09-26	Different construct Different oligomeric state Different ligand/ion Different experimental conditions 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 × 2 ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.95 Å
9JQN CryoEM structure of mouse RAG SEC-2DNA Deposited 2024-09-27	Different construct Different oligomeric state Different ligand/ion Different experimental conditions 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 construct Different ligand/ion Different experimental conditions 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 construct Different ligand/ion Different experimental conditions 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 5–363； UniProt 3–361 Author chain D； PDBConstruct 5–363； UniProt 3–361

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

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	6xny
Deposition date deposition_date	2020-07-05
Structure title title	Structure of RAG1 (R848M/E649V)-RAG2-DNA Strand Transfer Complex (Paired-Form)
Keywords keywords	DNA Transposase, RECOMBINATION; RECOMBINATION
Experimental Method method	ELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier	37.92 Å
Radius of gyration Rg (electron density) rg_electron	37.84 Å
Forward intensity I(0) i0	1041790000.00
Molecular weight molecular_weight	239780.0 kDa
Excluded volume excluded_volume	288990 Å³
Envelope volume envelope_volume	341400 Å³
Hydration-shell volume shell_volume	71533 Å³
Envelope diameter envelope_diameter	143.8 Å
Shell Rg shell_rg	46.35 Å
Envelope Rg envelope_rg	38.03 Å
Shape Rg shape_rg	37.88 Å
Total Rg total_rg	38.13 Å
Total atoms total_atoms	16681
Residues n_residues	1909
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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

Maximum dimension Dmax dmax	127.1 Å
Rg (real space) rg_real	37.74 Å
Rg uncertainty (real space) rg_real_error	0.82 Å
I(0) (real space) i0_real	1.0420e+09
I(0) uncertainty (real space) i0_real_error	1.7860e+07
Rg (reciprocal space) rg_reciprocal	37.85 Å
I(0) (reciprocal space) i0_reciprocal	1042000000.0000
Solution quality estimate total_estimate	0.8747
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	48.4 Å
Skewness Skewness skewness	0.255
Kurtosis Kurtosis kurtosis	-0.270
Angular range angular_range	— – 0.2100 Å⁻¹
Current regularization parameter α current_alpha	0.0001
Highest regularization parameter α highest_alpha	167500000.0000
Real-space data points n_real_points	43
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.799; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.984; Smooth: 0.987

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (9)

Entity 1 Entity 1 polymer

Description description	V(D)J recombination-activating protein 1
Molecular weight formula_weight	85750.8 kDa
EC 编号 ec_number	3.1.-.-,2.3.2.27
Mutation mutation	R848M, E649V
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	16681

GPKKISNCSKIHLSTKLLAVDFPAHFVKSISCQICEHILADPVETSCKHLFCRICILRCLKVMGSYCPSCRYPCFPTDLESPVKSFLNILNSLMVKCPAQDCNEEVSLEKYNHHVSSHKESKETLVHINKGGRPRQHLLSLTRRAQKHRLRELKIQVKEFADKEEGGDVKAVCLTLFLLALRARNEHRQADELEAIMQGRGSGLQPAVCLAIRVNTFLSCSQYHKMYRTVKAITGRQIFQPLHALRNAEKVLLPGYHPFEWQPPLKNVSSRTDVGIIDGLSGLASSVDEYPVDTIAKRFRYDSALVSALMDMEEDILEGMRSQDLDDYLNGPFTVVVKESCDGMGDVSEKHGSGPAVPEKAVRFSFTVMRITIEHGSQNVKVFEEPKPNSVLCCKPLCLMLADESDHETLTAILSPLIAEREAMKSSELTLEMGGIPRTFKFIFRGTGYDEKLVREVEGLEASGSVYICTLCDTTRLEASQNLVFHSITRSHAENLQRYEVWRSNPYHESVEELRDRVKGVSAKPFIETVPSIDALHCDIGNAAEFYKIFQLEIGEVYKHPNASKEERKRWQATLDKHLRKRMNLKPIMMMNGNFARKLMTQETVDAVCELIPSEERHEALRELMDLYLKMKPVWRSSCPAKECPESLCQYSFNSQRFAELLSTKFKYRYEGKITNYFHKTLAHVPEIIERDGSIGAWASEGNESGNKLFRRFRKMNARQSKCYEMEDVLKHHWLYTSKYLQKFMNAHNA

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	Mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Homo sapiens

Entity 2 Entity 2 polymer

Description description	V(D)J recombination-activating protein 2
Molecular weight formula_weight	40417.0 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D

GPMALQMVTVGHNIALIQPGFSLMNFDGQVFFFGQKGWPKRSCPTGVFHFDIKQNHLKLKPAIFSKDSCYLPPLRYPATCSYKGSIDSDKHQYIIHGGKTPNNELSDKIYIMSVACKNNKKVTFRCTEKDLVGDVPEPRYGHSIDVVYSRGKSMGVLFGGRSYMPSTQRTTEKWNSVADCLPHVFLIDFEFGCATSYILPELQDGLSFHVSIARNDTVYILGGHSLASNIRPANLYRIRVDLPLGTPAVNCTVLPGGISVSSAILTQTNNDEFVIVGGYQLENQKRMVCSLVSLGDNTIEISEMETPDWTSDIKHSKIWFGSNMGNGTIFLGIPGDNKQAMSEAFYFYTLRCSEEDLSEDQKI

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	Mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Homo sapiens

Entity 3 Entity 3 polymer

Description description	12RSS integration strand (55-mer)
Molecular weight formula_weight	16901.8 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	x

GGTCGAGGTTTTTGTACAGCCTACTACCACTGTGCGCCGGTAGCCCTATCCTGAG

Entity 4 Entity 4 polymer

Description description	23RSS integration strand (66-mer)
Molecular weight formula_weight	20323.0 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	y

GGTCGAGGTTTTTGTACAGCCAGACAACAGCCTACTACCACTGTGCGGCGGTAGCCCTATCCTGAG

Entity 5 Entity 5 polymer

Description description	Flanking DNA top strand (16-mer)
Molecular weight formula_weight	4923.2 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	I,J

CTCAGGATAGGGCTAC

Entity 6 Entity 6 polymer

Description description	23RSS signal DNA top strand (45-mer)
Molecular weight formula_weight	13877.9 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	L

CACAGTGGTAGTAGGCTGTTGTCTGGCTGTACAAAAACCTCGACC

Entity 7 Entity 7 polymer

Description description	12RSS signal DNA top strand (34-mer)
Molecular weight formula_weight	10461.8 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	M

CACAGTGGTAGTAGGCTGTACAAAAACCTCGACC

Entity 8 Entity 8 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 9 Entity 9 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	2

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	2.90 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	44428

fit	/app/data/saxs_computation/xn/6xny/6xny.fit
pddf	/app/data/pr_computation/xn/6xny/6xny.pr.out
profile	/app/data/saxs_computation/xn/6xny/6xny.dat

Structure of RAG1 (R848M/E649V)-RAG2-DNA Strand Transfer Complex (Paired-Form)

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

V(D)J recombination-activating protein 1

State in the Current Structure

Other States of the Same Protein in the Database

V(D)J recombination-activating protein 2

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (9)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 polymer

Polymer Polymer

Entity 6 Entity 6 polymer

Polymer Polymer

Entity 7 Entity 7 polymer

Polymer Polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 non-polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)