2V89: RAG2-PHD finger

Crystal structure of RAG2-PHD finger in complex with H3K4me3 peptide at 1.1A resolution. Determined by X-ray diffraction at 1.1 Å resolution. Released 11 Dec 2007.

Method: X-ray diffraction
Resolution: 1.1 Å
Organisms: MUS MUSCULUS, HOMO SAPIENS
Chains: 4
Atoms: 1,728
Mol. weight: 21.16 kDa
Ligands: ZN
Released: 11 Dec 2007

Explore 2V89 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2V89 contains 5 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, 2 β-strands

Element	Residues	Length	Sheet
β-strand	1443-1446	4	1
β-strand	1452-1455	4	1
α-helix	1457-1459	3
α-helix	1463-1471	9

Chain B: 2 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	443-446	4	2
β-strand	452-455	4	2
α-helix	457-459	3
α-helix	463-470	8
β-strand	476	1	2

Chain D: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
β-strand	3003-3004	2	2
α-helix	3008-3009	2

Chain E: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	2003-2004	2	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Vdj recombination-activating protein 2	A, B	protein	82	MUS MUSCULUS	P21784 (AlphaFold model)
Histone H3	D, E	protein	10	HOMO SAPIENS	P68431 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>2V89_1 VDJ RECOMBINATION-ACTIVATING PROTEIN 2 (chains A, B)
GPLGSPEFGYWITCCPTCDVDINTWVPFYSTELNKPAMIYCSHGDGHWVHAQCMDLEERT
LIHLSEGSNKYYCNEHVQIARA

Sequence of entity 2 (D, E), FASTA

>2V89_2 HISTONE H3 (chains D, E)
ARTKQTAAKA

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	4

Primary citation

Rag2 Phd Finger Couples Histone H3 Lysine 4 Trimethylation with V(D)J Recombination. Matthews, A.G.W., Kuo, A.J., Ramon-Maiques, S. et al. Nature (2007) 450:1106. DOI 10.1038/NATURE06431 · PubMed

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

2V87 1.8 Å, Crystal structure of RAG2-PHD finger in complex with H3R2me2sK4me3 peptide
2V85 2.0 Å, Crystal structure of RAG2-PHD finger in complex with H3R2me1K4me3 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)

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