3GNB: RAG1 nonamer-binding domain with DNA

Crystal structure of the RAG1 nonamer-binding domain with DNA. Determined by X-ray diffraction at 3.0 Å resolution. Released 28 Apr 2009.

Method: X-ray diffraction
Resolution: 3.0 Å
Organism: Mus musculus
Chains: 3
Atoms: 1,112
Mol. weight: 19.36 kDa
Released: 28 Apr 2009

Explore 3GNB in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3GNB contains 5 α-helices and 0 β-strands across 1 chain. 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: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	391-395	5
α-helix	396-398	3
α-helix	401-423	23
α-helix	427-440	14
α-helix	445-455	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
V(D)J recombination-activating protein 1	A	protein	96	Mus musculus	P15919 (AlphaFold model)
5'-d(apaptptptptpcpapgpapapapcpc)-3'	D	DNA	14
5'-d(apgpgptptptpcptpgpapapapapc)-3'	E	DNA	14

Sequence of entity 1 (A), FASTA

>3GNB_1 V(D)J recombination-activating protein 1 (chains A)
MGSSHHHHHHSSGLVPGSHMGGRPRQHLLSLTRRAQKHRLRELKIQVKEFADKEEGGDVK
AVCLTLFLLALRARNEHRQADELEAIMQGRGSGLQP

Sequence of entity 2 (D), FASTA

>3GNB_2 5'-D(*AP*AP*TP*TP*TP*TP*CP*AP*GP*AP*AP*AP*CP*C)-3' (chains D)
AATTTTCAGAAACC

Sequence of entity 3 (E), FASTA

>3GNB_3 5'-D(*AP*GP*GP*TP*TP*TP*CP*TP*GP*AP*AP*AP*AP*C)-3' (chains E)
AGGTTTCTGAAAAC

Primary citation

Structure of the RAG1 nonamer binding domain with DNA reveals a dimer that mediates DNA synapsis. Yin, F.F., Bailey, S., Innis, C.A. et al. Nat Struct Mol Biol (2009) 16:499-508. DOI 10.1038/nsmb.1593 · PubMed

Other PDB entries of the same protein (UniProt P15919 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1RMD 2.1 Å, RAG1 dimerization domain
3GNA 2.4 Å, Crystal structure of the RAG1 nonamer-binding domain with DNA
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)
9JQN 3.03 Å, CryoEM structure of mouse RAG SEC-2DNA
6OES 3.06 Å, Cryo-EM structure of mouse RAG1/2 STC complex (without NBD domain)
9LQV 3.1 Å, Structure of transposase-activated RAG strand transfer complex in state 1 (STC-1)

Browse structure collections

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