2v87

Crystal structure of RAG2-PHD finger in complex with H3R2me2sK4me3 peptide

Method: X-RAY DIFFRACTION D_max: 62.7 Å Quality: GOOD

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

VDJ RECOMBINATION-ACTIVATING PROTEIN 2

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 414–487	Fragment：RESIDUES 414-487	HISTONE H3.2 × 1 （P84228） 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
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 414–487	Fragment：RESIDUES 414-487	HISTONE H3.2 × 1 （P84228） 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

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 2V87	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 oligomeric state 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 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 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 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 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
2V88 Crystal structure of RAG2-PHD finger in complex with H3R2me2sK4me2 peptide Deposited 2007-08-03	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 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 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 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 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 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 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 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 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 B 1–520（520 aa） Chain D 1–520（520 aa）	Not recorded	ZN ZINC ION × 2 CA CALCIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.90 Å
6CIK Pre-Reaction Complex, RAG1(E962Q)/2-intact/nicked 12/23RSS complex in Mn2+ Deposited 2018-02-24	Different construct Different 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 B 1–359（359 aa） Chain D 1–359（359 aa）	Not recorded	ZN ZINC ION × 2 MN MANGANESE (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.9；277 K；12-16% PEG 3350, 200 mM NaNO3, 50 mM HEPES, pH 6.9	Resolution 3.15 Å R-free 0.249
6CIL PRE-REACTION COMPLEX, RAG1(E962Q)/2-INTACT/INTACT 12/23RSS COMPLEX IN MN2+ Deposited 2018-02-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 5 PDB declaration: nonameric	Chain B 1–359（359 aa） Chain D 1–359（359 aa）	Not recorded	ZN ZINC ION × 2 MN MANGANESE (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.9；277 K；18% PEG3350, 200 mM KNO3, 50 mM HEPES pH 6.9	Resolution 4.15 Å R-free 0.231
6CIM Pre-Reaction Complex, RAG1(E962Q)/2-nicked/intact 12/23RSS complex in Mn2+ Deposited 2018-02-24	Different construct Different 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 B 1–359（359 aa） Chain D 1–359（359 aa）	Not recorded	ZN ZINC ION × 2 MN MANGANESE (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.9；277 K；18% PEG3350, 200 mM KNO3, 50 mM HEPES pH 6.9	Resolution 3.60 Å R-free 0.254
6OEM Cryo-EM structure of mouse RAG1/2 PRC complex (DNA0) Deposited 2019-03-27	Different construct Different 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 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 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 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 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）	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 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 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 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 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 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）	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 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 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 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 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 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 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 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 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 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 mutation/modification Different oligomeric state 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 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 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 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 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 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 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 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 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 42 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RAG2_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 9–82； UniProt 414–487 Author chain B； PDBConstruct 9–82； UniProt 414–487

HISTONE H3.2

OrganismNot specified

UniProt P84228

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain D； UniProt 2–14	Fragment：H3 (1-21), BIOTINYLATED AT C-TERMINUS, UNP RESIDUES 2-14 Non-standard monomer：Yes (specific site not provided by mmCIF)	VDJ RECOMBINATION-ACTIVATING PROTEIN 2 × 1 （P21784） 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
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain E； UniProt 2–14	Fragment：H3 (1-21), BIOTINYLATED AT C-TERMINUS, UNP RESIDUES 2-14 Non-standard monomer：Yes (specific site not provided by mmCIF)	VDJ RECOMBINATION-ACTIVATING PROTEIN 2 × 1 （P21784） 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

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 2V87	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2V86 Crystal structure of RAG2-PHD finger in complex with H3R2me2aK4me3 peptide Deposited 2007-08-02	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 2–10（9 aa） Fragment：H3 (1-21), BIOTINILATED AT C-TERMINUS	Non-standard monomer：Yes (specific site not provided by mmCIF)	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 experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 2–10（9 aa） Fragment：H3 (1-21), BIOTINILATED AT C-TERMINUS	Non-standard monomer：Yes (specific site not provided by mmCIF)	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
4QWN Histone demethylase KDM2A-H3K36ME1-alpha-KG complex structure Deposited 2014-07-16	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain E 30–44（15 aa） Fragment：UNP residues 30-44	Non-standard monomer：Yes (specific site not provided by mmCIF)	AKG 2-OXOGLUTARIC ACID × 1 NI NICKEL (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；20% PEG 3350, 0.2 M Sodium citrate, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.10 Å R-free 0.264
4QWN Histone demethylase KDM2A-H3K36ME1-alpha-KG complex structure Deposited 2014-07-16	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain F 30–44（15 aa） Fragment：UNP residues 30-44	Non-standard monomer：Yes (specific site not provided by mmCIF)	AKG 2-OXOGLUTARIC ACID × 1 NI NICKEL (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；20% PEG 3350, 0.2 M Sodium citrate, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.10 Å R-free 0.264
4QX7 Crystal structure of histone demethylase kdm2a-h3k36me2 with alpha-kg Deposited 2014-07-18	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain E 30–44（15 aa） Fragment：UNP residues 30-44	Non-standard monomer：Yes (specific site not provided by mmCIF)	AKG 2-OXOGLUTARIC ACID × 1 NI NICKEL (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；0.15 M Na citrate, 18-22% PEG 3350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.34 Å R-free 0.258
4QX7 Crystal structure of histone demethylase kdm2a-h3k36me2 with alpha-kg Deposited 2014-07-18	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain F 30–44（15 aa） Fragment：UNP residues 30-44	Non-standard monomer：Yes (specific site not provided by mmCIF)	AKG 2-OXOGLUTARIC ACID × 1 NI NICKEL (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；0.15 M Na citrate, 18-22% PEG 3350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.34 Å R-free 0.258
4QX8 Crystal structure of histone demethylase kdm2a-h3k36me3 complex with alpha-kg Deposited 2014-07-19	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain E 30–44（15 aa） Fragment：UNP residues 30-44	Non-standard monomer：Yes (specific site not provided by mmCIF)	NI NICKEL (II) ION × 1 AKG 2-OXOGLUTARIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；0.1 M Na Citrate, 18-20% PEG 3350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.65 Å R-free 0.227
4QX8 Crystal structure of histone demethylase kdm2a-h3k36me3 complex with alpha-kg Deposited 2014-07-19	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain F 30–44（15 aa） Fragment：UNP residues 30-44	Non-standard monomer：Yes (specific site not provided by mmCIF)	NI NICKEL (II) ION × 1 AKG 2-OXOGLUTARIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；0.1 M Na Citrate, 18-20% PEG 3350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.65 Å R-free 0.227
4QXB crystal structure of histone demethylase KDM2A-H3K36ME3 with NOG Deposited 2014-07-19	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain E 30–44（15 aa） Fragment：UNP residues 30-44	Non-standard monomer：Yes (specific site not provided by mmCIF)	OGA N-OXALYLGLYCINE × 1 NI NICKEL (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；0.15 M CITRATE NA 20% PEG 3350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.60 Å R-free 0.207
4QXB crystal structure of histone demethylase KDM2A-H3K36ME3 with NOG Deposited 2014-07-19	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain F 30–44（15 aa） Fragment：UNP residues 30-44	Non-standard monomer：Yes (specific site not provided by mmCIF)	OGA N-OXALYLGLYCINE × 1 NI NICKEL (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；0.15 M CITRATE NA 20% PEG 3350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.60 Å R-free 0.207
4QXC Crystal structure of histone demethylase KDM2A-H3K36ME2 with NOG Deposited 2014-07-19	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain E 30–44（15 aa） Fragment：UNP residues 30-44	Non-standard monomer：Yes (specific site not provided by mmCIF)	OGA N-OXALYLGLYCINE × 1 NI NICKEL (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；0.1 M CITRATE NA 18% PEG 3350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.75 Å R-free 0.204
4QXC Crystal structure of histone demethylase KDM2A-H3K36ME2 with NOG Deposited 2014-07-19	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain F 30–44（15 aa） Fragment：UNP residues 30-44	Non-standard monomer：Yes (specific site not provided by mmCIF)	OGA N-OXALYLGLYCINE × 1 NI NICKEL (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；0.1 M CITRATE NA 18% PEG 3350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.75 Å R-free 0.204
4QXH Crystal structure of histone demethylase KDM2A-H3K36ME1 with NOG Deposited 2014-07-20	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain E 30–44（15 aa） Fragment：UNP residues 30-44	Non-standard monomer：Yes (specific site not provided by mmCIF)	OGA N-OXALYLGLYCINE × 1 NI NICKEL (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；0.15 M CITRATE NA, 20% PEG 3350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.20 Å R-free 0.243
4QXH Crystal structure of histone demethylase KDM2A-H3K36ME1 with NOG Deposited 2014-07-20	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain F 30–44（15 aa） Fragment：UNP residues 30-44	Non-standard monomer：Yes (specific site not provided by mmCIF)	OGA N-OXALYLGLYCINE × 1 NI NICKEL (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；0.15 M CITRATE NA, 20% PEG 3350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.20 Å R-free 0.243

7 other PDB entries and 14 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	H32_MOUSE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain D； PDBConstruct 1–13； UniProt 2–14 Author chain E； PDBConstruct 1–13； UniProt 2–14

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	2v87
Deposition date deposition_date	2007-08-02
Structure title title	Crystal structure of RAG2-PHD finger in complex with H3R2me2sK4me3 peptide
Keywords keywords	;V(D)J RECOMBINATION, COVALENT MODIFICATIONS, RAG, HISTONE, NUCLEUS, NUCLEASE, HYDROLASE, PHD FINGER, DNA-BINDING, RECOMBINASE, ENDONUCLEASE, SYMMETRIC DIMETHYLATED ARGININE, PROTEIN BINDING, TRIMETHYL LYSINE, DNA RECOMBINATION ;; PROTEIN BINDING
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	18.45 Å
Radius of gyration Rg (electron density) rg_electron	17.53 Å
Forward intensity I(0) i0	8962770.00
Molecular weight molecular_weight	20677.0 kDa
Excluded volume excluded_volume	25223 Å³
Envelope volume envelope_volume	30944 Å³
Hydration-shell volume shell_volume	15247 Å³
Envelope diameter envelope_diameter	64.1 Å
Shell Rg shell_rg	23.01 Å
Envelope Rg envelope_rg	17.86 Å
Shape Rg shape_rg	17.55 Å
Total Rg total_rg	18.37 Å
Total atoms total_atoms	1434
Residues n_residues	176
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	62.7 Å
Rg (real space) rg_real	18.44 Å
Rg uncertainty (real space) rg_real_error	0.48 Å
I(0) (real space) i0_real	8.9630e+06
I(0) uncertainty (real space) i0_real_error	1.2770e+05
Rg (reciprocal space) rg_reciprocal	18.44 Å
I(0) (reciprocal space) i0_reciprocal	8963000.0000
Solution quality estimate total_estimate	0.8016
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	22.3 Å
Skewness Skewness skewness	0.333
Kurtosis Kurtosis kurtosis	-0.273
Angular range angular_range	— – 0.4300 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1570000.0000
Real-space data points n_real_points	74
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.814; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.976; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	VDJ RECOMBINATION-ACTIVATING PROTEIN 2
Molecular weight formula_weight	9360.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	1671

GPLGSPEFGYWITCCPTCDVDINTWVPFYSTELNKPAMIYCSHGDGHWVHAQCMDLEERTLIHLSEGSNKYYCNEHVQIARA

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 polymer

Description description	HISTONE H3.2
Molecular weight formula_weight	1434.7 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

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

ARTKQTARKSTGG

Entity 3 Entity 3 non-polymer

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

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	237

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d2v87a2
Class class	g — Small proteins
Fold Fold fold	g.50 — FYVE/PHD zinc finger
Superfamily Superfamily superfamily	g.50.1 — FYVE/PHD zinc finger
Family Family family	g.50.1.2 — PHD domain

Domain ID domain_id	d2v87a3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d2v87b2
Class class	g — Small proteins
Fold Fold fold	g.50 — FYVE/PHD zinc finger
Superfamily Superfamily superfamily	g.50.1 — FYVE/PHD zinc finger
Family Family family	g.50.1.2 — PHD domain

Domain ID domain_id	d2v87b3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (2 domains)

Domain ID domain_id	2v87A01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	160 — Double Stranded RNA Binding Domain
Homologous superfamily homologous superfamily	290 — Rag2 PHD finger

Domain ID domain_id	2v87B01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	160 — Double Stranded RNA Binding Domain
Homologous superfamily homologous superfamily	290 — Rag2 PHD finger

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8. Citations (2)

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Unit-cell length a length_a	40.407 Å
Unit-cell length b length_b	46.630 Å
Unit-cell length c length_c	57.005 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	95.13 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.1810
R_work r_work	0.1810
R_free r_free	0.2081

fit	/app/data/saxs_computation/v8/2v87/2v87.fit
pddf	/app/data/pr_computation/v8/2v87/2v87.pr.out
profile	/app/data/saxs_computation/v8/2v87/2v87.dat

Crystal structure of RAG2-PHD finger in complex with H3R2me2sK4me3 peptide

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

VDJ RECOMBINATION-ACTIVATING PROTEIN 2

State in the Current Structure

Other States of the Same Protein in the Database

HISTONE H3.2

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

CATH v4.4 (2 domains)

8. Citations (2)

9. Files and Curves (10)

Files (7)

Curves (3)