6cim

Pre-Reaction Complex, RAG1(E962Q)/2-nicked/intact 12/23RSS complex in Mn2+

Method: X-RAY DIFFRACTION D_max: 147.9 Å Quality: REASONABLE

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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 × 5 DNA 5 PDB declaration: decameric（10） Consistent with all polymer counts	Chain A； UniProt 384–1008 Chain C； UniProt 384–1008	Mutation：E962Q	V(D)J recombination-activating protein 2 × 2 （P21784） High mobility group protein B1 × 1 （P09429） Nicked 12RSS intermediate reverse strand × 1 ;DNA (5'-D(GPCPCPTPGPTPCPTPTPA)-3') ; × 1 Nicked 12RSS intermediate forward strand × 1 Intact 23RSS substrate reverse strand × 1 Intact 23RSS substrate forward strand × 1 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

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 6CIM	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 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 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 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 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 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 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 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 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 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 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 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 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 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 method 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 method 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 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 oligomeric state 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
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 method 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 oligomeric state Different ligand/ion Different experimental method 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 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 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 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 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 method 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 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 × 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 method 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 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 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 method 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 method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 1–625； UniProt 384–1008 Author chain C； PDBConstruct 1–625； UniProt 384–1008

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 × 5 DNA 5 PDB declaration: decameric（10） Consistent with all polymer counts	Chain B； UniProt 1–359 Chain D； UniProt 1–359	Not recorded	V(D)J recombination-activating protein 1 × 2 （P15919） High mobility group protein B1 × 1 （P09429） Nicked 12RSS intermediate reverse strand × 1 ;DNA (5'-D(GPCPCPTPGPTPCPTPTPA)-3') ; × 1 Nicked 12RSS intermediate forward strand × 1 Intact 23RSS substrate reverse strand × 1 Intact 23RSS substrate forward strand × 1 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

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 6CIM	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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 method 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 method 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 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 oligomeric state 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
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 method 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 method 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 method 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 method 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 method 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 method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 method 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 construct Different oligomeric state Different ligand/ion Different experimental method 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 method 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 method 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 experimental method 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 method 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 method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 1–359； UniProt 1–359 Author chain D； PDBConstruct 1–359； UniProt 1–359

High mobility group protein B1

Homo sapiens

UniProt P09429

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein–DNA Heteromer Protein × 5 DNA 5 PDB declaration: decameric（10） Consistent with all polymer counts	Chain N； UniProt 1–163	Not recorded	V(D)J recombination-activating protein 1 × 2 （P15919） V(D)J recombination-activating protein 2 × 2 （P21784） Nicked 12RSS intermediate reverse strand × 1 ;DNA (5'-D(GPCPCPTPGPTPCPTPTPA)-3') ; × 1 Nicked 12RSS intermediate forward strand × 1 Intact 23RSS substrate reverse strand × 1 Intact 23RSS substrate forward strand × 1 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

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 6CIM	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2LY4 HMGB1-facilitated p53 DNA binding occurs via HMG-box/p53 transactivation domain interaction and is regulated by the acidic tail Deposited 2012-09-12	Different construct 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 2–84（83 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 0.01；Pressure ambient NMR sample composition 10 mM sodium phosphate, 1 mM EDTA, 1 mM DTT, 0.5 mM PMSF, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2RTU Solution structure of oxidized human HMGB1 A box Deposited 2013-09-12	Different construct 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 1–84（84 aa） Fragment：HMG box 1, UNP residues 1-84	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.4；293 K；Ionic strength (raw mmCIF value) 200；Pressure ambient NMR sample composition 0.5-0.6 mM [U-13C; U-15N] protein-1, 50 mM potassium phosphate-2, 10 % [U-2H] D2O-3, 150 mM potassium chloride-4, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.5-0.6 mM [U-13C; U-15N] protein-5, 5 % C12E5/n-hexanol-6, 10 % U-2H D2O-7, 150 mM potassium chloride-8, 50 mM potassium phosphate-9, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2YRQ Solution structure of the tandem HMG box domain from Human High mobility group protein B1 Deposited 2007-04-02	Different construct 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 1–166（166 aa） Fragment：HMG box domain	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；296 K；Ionic strength (raw mmCIF value) 120mM；Pressure ambient NMR sample composition 1.09mM HMG box domain U-15N,13C; 20mM d-Tris-HCl (pH 7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 90% H2O, 10% D2O \| 90% H2O/10% D2O	Resolution not provided
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 method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 5 PDB declaration: undecameric	Chain N 15–140（126 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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 5 PDB declaration: undecameric	Chain N 1–163（163 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 experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 5 PDB declaration: decameric	Chain N 1–163（163 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 oligomeric state Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 5 PDB declaration: nonameric	Chain N 1–163（163 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
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 method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: decameric	Chain H 15–155（141 aa） Chain N 15–155（141 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: decameric	Chain H 1–163（163 aa） Chain N 1–163（163 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 experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 5 PDB declaration: nonameric	Chain N 1–163（163 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
8I9M The RAGE and HMGB1 complex Deposited 2023-02-07	Different construct 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 89–163（75 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen NITROGEN	Resolution 5.19 Å
9CG9 Cryo-EM structure of an HMGB1 box bound to nucleosome at SHL-2 Deposited 2024-06-28	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric	Chain K 1–215（215 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE；3 uL of sample was applied to grid.	Resolution 2.94 Å

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

View Construct and Data Evidence

UniProt name	HMGB1_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain N； PDBConstruct 1–163； UniProt 1–163

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

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	6cim
Deposition date deposition_date	2018-02-24
Structure title title	Pre-Reaction Complex, RAG1(E962Q)/2-nicked/intact 12/23RSS complex in Mn2+
Keywords keywords	VDJ recombination, RSS, RAG1/2, RECOMBINATION, RECOMBINATION-DNA complex; RECOMBINATION/DNA
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	46.28 Å
Radius of gyration Rg (electron density) rg_electron	45.60 Å
Forward intensity I(0) i0	1394350000.00
Molecular weight molecular_weight	270520.0 kDa
Excluded volume excluded_volume	321820 Å³
Envelope volume envelope_volume	481810 Å³
Hydration-shell volume shell_volume	85842 Å³
Envelope diameter envelope_diameter	159.2 Å
Shell Rg shell_rg	51.88 Å
Envelope Rg envelope_rg	45.26 Å
Shape Rg shape_rg	45.62 Å
Total Rg total_rg	45.76 Å
Total atoms total_atoms	18784
Residues n_residues	2156
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	147.9 Å
Rg (real space) rg_real	46.07 Å
Rg uncertainty (real space) rg_real_error	0.81 Å
I(0) (real space) i0_real	1.3940e+09
I(0) uncertainty (real space) i0_real_error	2.4230e+07
Rg (reciprocal space) rg_reciprocal	46.28 Å
I(0) (reciprocal space) i0_reciprocal	1395000000.0000
Solution quality estimate total_estimate	0.6865
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	56.6 Å
Skewness Skewness skewness	0.186
Kurtosis Kurtosis kurtosis	-0.446
Angular range angular_range	— – 0.1700 Å⁻¹
Current regularization parameter α current_alpha	0.0002
Highest regularization parameter α highest_alpha	99520000.0000
Real-space data points n_real_points	35
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.912; Stabil: 1.000; Sysdev: 0.115; Positv: 1.000; Valcen: 0.974; Smooth: 0.866

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (11)

Entity 1 Entity 1 polymer

Description description	V(D)J recombination-activating protein 1
Molecular weight formula_weight	71716.1 kDa
EC 编号 ec_number	3.1.-.-,2.3.2.27
Mutation mutation	E962Q
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	18804

VHINKGGRPRQHLLSLTRRAQKHRLRELKIQVKEFADKEEGGDVKAVCLTLFLLALRARNEHRQADELEAIMQGRGSGLQPAVCLAIRVNTFLSCSQYHKMYRTVKAITGRQIFQPLHALRNAEKVLLPGYHPFEWQPPLKNVSSRTDVGIIDGLSGLASSVDEYPVDTIAKRFRYDSALVSALMDMEEDILEGMRSQDLDDYLNGPFTVVVKESCDGMGDVSEKHGSGPAVPEKAVRFSFTVMRITIEHGSQNVKVFEEPKPNSELCCKPLCLMLADESDHETLTAILSPLIAEREAMKSSELTLEMGGIPRTFKFIFRGTGYDEKLVREVEGLEASGSVYICTLCDTTRLEASQNLVFHSITRSHAENLQRYEVWRSNPYHESVEELRDRVKGVSAKPFIETVPSIDALHCDIGNAAEFYKIFQLEIGEVYKHPNASKEERKRWQATLDKHLRKRMNLKPIMRMNGNFARKLMTQETVDAVCELIPSEERHEALRELMDLYLKMKPVWRSSCPAKECPESLCQYSFNSQRFAELLSTKFKYRYEGKITNYFHKTLAHVPEIIERDGSIGAWASEGNQSGNKLFRRFRKMNARQSKCYEMEDVLKHHWLYTSKYLQKFMNAHNA

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	40036.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MSLQMVTVGHNIALIQPGFSLMNFDGQVFFFGQKGWPKRSCPTGVFHFDIKQNHLKLKPAIFSKDSCYLPPLRYPATCSYKGSIDSDKHQYIIHGGKTPNNELSDKIYIMSVACKNNKKVTFRCTEKDLVGDVPEPRYGHSIDVVYSRGKSMGVLFGGRSYMPSTQRTTEKWNSVADCLPHVFLIDFEFGCATSYILPELQDGLSFHVSIARNDTVYILGGHSLASNIRPANLYRIRVDLPLGTPAVNCTVLPGGISVSSAILTQTNNDEFVIVGGYQLENQKRMVCSLVSLGDNTIEISEMETPDWTSDIKHSKIWFGSNMGNGTIFLGIPGDNKQAMSEAFYFYTLRCSEEDLSEDQ

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	High mobility group protein B1
Molecular weight formula_weight	18897.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	N

MGKGDPKKPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTYIPPKGETKKKFKDPNAPKRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKDIAAYR

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 4 Entity 4 polymer

Description description	Nicked 12RSS intermediate reverse strand
Molecular weight formula_weight	12430.0 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	F

CGGGTTTTTGTTAAGGGCTGTATCACTGTGTAAGACAGGC

Entity 5 Entity 5 polymer

Description description	;DNA (5'-D(GPCPCPTPGPTPCPTPTPA)-3') ;
Molecular weight formula_weight	3011.0 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	I

GCCTGTCTTA

Entity 6 Entity 6 polymer

Description description	Nicked 12RSS intermediate forward strand
Molecular weight formula_weight	9138.9 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	L

CACAGTGATACAGCCCTTAACAAAAACCCG

Entity 7 Entity 7 polymer

Description description	Intact 23RSS substrate reverse strand
Molecular weight formula_weight	17259.0 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	G

CGGGTTTTTGTCTGGCTTCACACTTGATTTGCATCACTGTGTAAGACAGGCCAGAT

Entity 8 Entity 8 polymer

Description description	Intact 23RSS substrate forward strand
Molecular weight formula_weight	17251.1 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	J

ATCTGGCCTGTCTTACACAGTGATGCAAATCAAGTGTGAAGCCAGACAAAAACCCG

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

Entity 10 Entity 10 non-polymer

Description description	MANGANESE (II) ION
Molecular weight formula_weight	54.9 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 11 Entity 11 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	3

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8. Citations (1)

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Unit-cell length a length_a	156.678 Å
Unit-cell length b length_b	123.562 Å
Unit-cell length c length_c	186.286 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	105.60 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	3.600 Å
Low-resolution limit resolution_low	38.693 Å
R factor r_factor	0.2160
R_work r_work	0.2140
R_free r_free	0.2537

fit	/app/data/saxs_computation/ci/6cim/6cim.fit
pddf	/app/data/pr_computation/ci/6cim/6cim.pr.out
profile	/app/data/saxs_computation/ci/6cim/6cim.dat

Pre-Reaction Complex, RAG1(E962Q)/2-nicked/intact 12/23RSS complex in Mn2+

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

High mobility group protein B1

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

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (11)

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

来源 Source

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 polymer

Polymer Polymer

Entity 9 Entity 9 non-polymer

Entity 10 Entity 10 non-polymer

Entity 11 Entity 11 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)