2V85: RAG2-PHD finger

Crystal structure of RAG2-PHD finger in complex with H3R2me1K4me3 peptide. Determined by X-ray diffraction at 2.0 Å resolution. Released 11 Dec 2007.

Method: X-ray diffraction
Resolution: 2.0 Å
Organisms: MUS MUSCULUS, HOMO SAPIENS
Chains: 4
Atoms: 1,582
Mol. weight: 21.62 kDa
Ligands: ZN
Released: 11 Dec 2007

Explore 2V85 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2V85 contains 6 α-helices and 7 β-strands across 4 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 2 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	443-446	4	1
β-strand	452-455	4	1
α-helix	456-459	4
α-helix	463-470	8
β-strand	476	1	1

Chain B: 3 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	411-414	4
β-strand	443-446	4	2
β-strand	452-455	4	2
α-helix	457-459	3
α-helix	463-471	9

Chain D: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
β-strand	3-4	2	1
α-helix	8-9	2

Chain E: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	3-4	2	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Vdj recombination-activating protein 2	A, B	protein	82	MUS MUSCULUS	P21784 (AlphaFold model)
H3R2ME1K4ME3 peptide	D, E	protein	12	HOMO SAPIENS	P68431 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>2V85_1 VDJ RECOMBINATION-ACTIVATING PROTEIN 2 (chains A, B)
GPLGSPEFGYWITCCPTCDVDINTWVPFYSTELNKPAMIYCSHGDGHWVHAQCMDLEERT
LIHLSEGSNKYYCNEHVQIARA

Sequence of entity 2 (D, E), FASTA

>2V85_2 H3R2ME1K4ME3 PEPTIDE (chains D, E)
ARTKQTARKAAG

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	4

Primary citation

The Plant Homeodomain Finger of Rag2 Recognizes Histone H3 Methylated at Both Lysine-4 and Arginine-2. Ramon-Maiques, S., Kuo, A.J., Carney, D. et al. Proc Natl Acad Sci U S A (2007) 104:18993. DOI 10.1073/PNAS.0709170104 · PubMed

Other PDB entries of the same protein (UniProt P21784 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2V89 1.1 Å, Crystal structure of RAG2-PHD finger in complex with H3K4me3 peptide at 1.1A resolution
2V87 1.8 Å, Crystal structure of RAG2-PHD finger in complex with H3R2me2sK4me3 peptide
2V88 2.0 Å, Crystal structure of RAG2-PHD finger in complex with H3R2me2sK4me2 peptide
2V86 2.05 Å, Crystal structure of RAG2-PHD finger in complex with H3R2me2aK4me3 peptide
2V83 2.4 Å, Crystal structure of RAG2-PHD finger in complex with H3K4me3 peptide
6XNX 2.7 Å, Structure of RAG1 (R848M/E649V)-RAG2-DNA Strand Transfer Complex (Dynamic-Form)
5ZE0 2.75 Å, Hairpin Forming Complex, RAG1/2-Nicked(with Dideoxy) 12RSS/23RSS complex in Mg2+
5ZDZ 2.8 Å, Hairpin Forming Complex, RAG1/2-Nicked 12RSS/23RSS complex in Ca2+
6XNY 2.9 Å, Structure of RAG1 (R848M/E649V)-RAG2-DNA Strand Transfer Complex (Paired-Form)
9JPX 2.95 Å, CryoEM structure of mouse RAG SEC-0
5ZE1 3.0 Å, Hairpin Forming Complex, RAG1/2-Nicked 12RSS/23RSS complex in 2mM Mn2+ for 10 min at 4'C
9LQO 3.0 Å, Structure of RAG transposon end complex (TEC)

Browse structure collections

About this viewer

MolViewer shows 2V85 directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.