PDBsum entry 3jbw

Recombination/DNA

PDB id: 3jbw

Contents

Protein chains

622 a.a.

351 a.a.

DNA/RNA

Metals

_ZN ×2

PDB id:

3jbw

Name:

Recombination/DNA

Title:

Cryo-electron microscopy structure of rag paired complex (with nbd, no symmetry)

Structure:

V(d)j recombination-activating protein 1. Chain: a, c. Synonym: rag-1, endonuclease rag1, e3 ubiquitin-protein ligase rag1. Engineered: yes. V(d)j recombination-activating protein 2. Chain: b, d. Synonym: rag-2. Engineered: yes. 12-rss signal end forward strand.

Source:

Danio rerio. Zebra fish. Organism_taxid: 7955. Strain: ab. Cell: b and t lymphocyte. Organelle: nucleus. Gene: rag1. Expressed in: spodoptera frugiperda. Expression_system_taxid: 7108.

Authors:

H.Ru,M.G.Chambers,T.-M.Fu,A.B.Tong,M.Liao,H.Wu

Key ref:

H.Ru et al. (2015). Molecular Mechanism of V(D)J Recombination from Synaptic RAG1-RAG2 Complex Structures. Cell, 163, 1138-1152. PubMed id: 26548953 DOI: 10.1016/j.cell.2015.10.055

Date:

21-Oct-15 Release date: 09-Dec-15

Protein chains

O13033  (RAG1_DANRE) -  V(D)J recombination-activating protein 1 from Danio rerio

Seq: 1057 a.a.

Struc: 622 a.a.

Protein chains

O13034  (RAG2_DANRE) -  V(D)J recombination-activating protein 2 from Danio rerio

Seq: 530 a.a.

Struc: 351 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

DNA/RNA chains

C-A-C-A-G-T-G-C-T-A-C-A-G-A-C-T-G-G-A-A-C-A-A-A-A-A-C-C-C-T-G-C-A-G 34 bases

C-T-G-C-A-G-G-G-T-T-T-T-T-G-T-T-C-C-A-G-T-C-T-G-T-A-G-C-A-C-T-G-T-G-T-A-A-G-A- 50 bases

C-T-G-C-A-G-G-G-T-T-T-T-T-G-T-A-C-A-G-C-C-A-G-A-C-A-G-T-G-G-A-G-T-A-C-T-A-C-C- 61 bases

C-A-C-A-G-T-G-G-T-A-G-T-A-C-T-C-C-A-C-T-G-T-C-T-G-G-C-T-G-T-A-C-A-A-A-A-A-C-C- 45 bases

G-A-T-C-T-G-G-C-C-T-G-T-C-T-T-A 16 bases

G-A-T-C-T-G-G-C-C-T-G-T-C-T-T-A 16 bases

Enzyme reactions

• Enzyme class 2: Chains A, C: E.C.2.3.2.27 - RING-type E3 ubiquitin transferase.
• Reaction: S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N₆- ubiquitinyl-[acceptor protein]-L-lysine
• Enzyme class 3: Chains A, C: E.C.3.1.-.-
• Enzyme class 4: Chains B, D: E.C.?

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

DOI no: 10.1016/j.cell.2015.10.055

Cell 163:1138-1152 (2015)

PubMed id: 26548953

Molecular Mechanism of V(D)J Recombination from Synaptic RAG1-RAG2 Complex Structures.

H.Ru, M.G.Chambers, T.M.Fu, A.B.Tong, M.Liao, H.Wu.

ABSTRACT

Diverse repertoires of antigen-receptor genes that result from combinatorial splicing of coding segments by V(D)J recombination are hallmarks of vertebrate immunity. The (RAG1-RAG2)2 recombinase (RAG) recognizes recombination signal sequences (RSSs) containing a heptamer, a spacer of 12 or 23 base pairs, and a nonamer (12-RSS or 23-RSS) and introduces precise breaks at RSS-coding segment junctions. RAG forms synaptic complexes only with one 12-RSS and one 23-RSS, a dogma known as the 12/23 rule that governs the recombination fidelity. We report cryo-electron microscopy structures of synaptic RAG complexes at up to 3.4 Å resolution, which reveal a closed conformation with base flipping and base-specific recognition of RSSs. Distortion at RSS-coding segment junctions and base flipping in coding segments uncover the two-metal-ion catalytic mechanism. Induced asymmetry involving tilting of the nonamer-binding domain dimer of RAG1 upon binding of HMGB1-bent 12-RSS or 23-RSS underlies the molecular mechanism for the 12/23 rule.