1rmd

RAG1 DIMERIZATION DOMAIN

Method: X-RAY DIFFRACTION D_max: 65.1 Å Quality: GOOD

▼

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

RAG1

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 265–380	Fragment：ZINC-BINDING DIMERIZATION DOMAIN	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

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 1RMD	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
21WB NZD domain of Mouse RAG1 Deposited 2025-12-31	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 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 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 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 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 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 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 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 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 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 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 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 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 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 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: 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 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 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 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 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 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 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 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）	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 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 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）	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 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）	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 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 1–116； UniProt 265–380

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

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	1rmd
Deposition date deposition_date	1997-01-10
Structure title title	RAG1 DIMERIZATION DOMAIN
Keywords keywords	;RAG1, V(D)J RECOMBINATION, ANTIBODY, MAD, RING FINGER, ZINC BINUCLEAR CLUSTER, ZINC FINGER, DNA-BINDING PROTEIN, DNA BINDING PROTEIN ;; DNA BINDING PROTEIN
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	16.80 Å
Radius of gyration Rg (electron density) rg_electron	15.91 Å
Forward intensity I(0) i0	3871110.00
Molecular weight molecular_weight	13378.0 kDa
Excluded volume excluded_volume	16506 Å³
Envelope volume envelope_volume	20092 Å³
Hydration-shell volume shell_volume	11418 Å³
Envelope diameter envelope_diameter	61.8 Å
Shell Rg shell_rg	20.76 Å
Envelope Rg envelope_rg	16.56 Å
Shape Rg shape_rg	15.96 Å
Total Rg total_rg	16.77 Å
Total atoms total_atoms	915
Residues n_residues	116
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

▼

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

Maximum dimension Dmax dmax	65.1 Å
Rg (real space) rg_real	16.88 Å
Rg uncertainty (real space) rg_real_error	0.68 Å
I(0) (real space) i0_real	3.8710e+06
I(0) uncertainty (real space) i0_real_error	5.3090e+04
Rg (reciprocal space) rg_reciprocal	16.87 Å
I(0) (reciprocal space) i0_reciprocal	3871000.0000
Solution quality estimate total_estimate	0.7865
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	17.8 Å
Skewness Skewness skewness	0.475
Kurtosis Kurtosis kurtosis	-0.100
Angular range angular_range	— – 0.4750 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	372100.0000
Real-space data points n_real_points	78
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.512; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.685; Smooth: 1.000

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	RAG1
Molecular weight formula_weight	13151.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	967

NCSKIHLSTKLLAVDFPAHFVKSISCQICEHILADPVETSCKHLFCRICILRCLKVMGSYCPSCRYPCFPTDLESPVKSFLNILNSLMVKCPAQDCNEEVSLEKYNHHVSSHKESK

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	house mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	52

▼

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1rmda1
Class class	g — Small proteins
Fold Fold fold	g.37 — beta-beta-alpha zinc fingers
Superfamily Superfamily superfamily	g.37.1 — beta-beta-alpha zinc fingers
Family Family family	g.37.1.1 — Classic zinc finger, C2H2

Domain ID domain_id	d1rmda2
Class class	g — Small proteins
Fold Fold fold	g.44 — RING/U-box
Superfamily Superfamily superfamily	g.44.1 — RING/U-box
Family Family family	g.44.1.1 — RING finger domain, C3HC4

CATH v4.4 (2 domains)

Domain ID domain_id	1rmdA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	40 — Herpes Virus-1
Homologous superfamily homologous superfamily	10 — Zinc/RING finger domain, C3HC4 (zinc finger)

Domain ID domain_id	1rmdA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	160 — Double Stranded RNA Binding Domain
Homologous superfamily homologous superfamily	60 — Classic Zinc Finger

▶

8. Citations (1)

▶

Unit-cell length a length_a	57.580 Å
Unit-cell length b length_b	57.580 Å
Unit-cell length c length_c	98.430 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 32 2 1
Space-group number int_tables_number	154
Crystal system crystal_system	—

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2090
R_work r_work	0.2090
R_free r_free	0.2570

fit	/app/data/saxs_computation/rm/1rmd/1rmd.fit
pddf	/app/data/pr_computation/rm/1rmd/1rmd.pr.out
profile	/app/data/saxs_computation/rm/1rmd/1rmd.dat