1RMD: RAG1 dimerization domain

RAG1 dimerization domain. Determined by X-ray diffraction at 2.1 Å resolution. Released 23 Jul 1997.

Method: X-ray diffraction
Resolution: 2.1 Å
Organism: Mus musculus
Chains: 1
Atoms: 967
Mol. weight: 13.41 kDa
Ligands: ZN
Released: 23 Jul 1997

Explore 1RMD in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1RMD contains 9 α-helices and 10 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: 9 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	2-4	3
α-helix	9-11	3
β-strand	12	1	1
α-helix	18-23	6
β-strand	25	1	2
β-strand	32	1	2
β-strand	36-38	3	3
β-strand	44-46	3	3
α-helix	47-56	10
β-strand	60	1	4
β-strand	67	1	4
α-helix	70-72	3
β-strand	74	1	3
α-helix	75-77	3
α-helix	78-86	9
β-strand	88-90	3	1
β-strand	99-101	3	1
α-helix	102-110	9
α-helix	113-114	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
RAG1	A	protein	116	Mus musculus	P15919 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>1RMD_1 RAG1 (chains A)
NCSKIHLSTKLLAVDFPAHFVKSISCQICEHILADPVETSCKHLFCRICILRCLKVMGSY
CPSCRYPCFPTDLESPVKSFLNILNSLMVKCPAQDCNEEVSLEKYNHHVSSHKESK

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	4

Primary citation

Crystal structure of the RAG1 dimerization domain reveals multiple zinc-binding motifs including a novel zinc binuclear cluster. Bellon, S.F., Rodgers, K.K., Schatz, D.G. et al. Nat Struct Biol (1997) 4:586-591. DOI 10.1038/nsb0797-586 · PubMed

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

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
3GNB 3.0 Å, Crystal structure of the RAG1 nonamer-binding domain with DNA
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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