PDBsum entry 1rmd

Go to PDB code: 
protein metals links
DNA-binding protein PDB id
Protein chain
116 a.a. *
_ZN ×4
Waters ×52
* Residue conservation analysis
PDB id:
Name: DNA-binding protein
Title: Rag1 dimerization domain
Structure: Rag1. Chain: a. Fragment: zinc-binding dimerization domain. Synonym: v(d)j recombination activating protein 1. Engineered: yes
Source: Mus musculus. House mouse. Organism_taxid: 10090. Cell_line: bl21. Expressed in: escherichia coli. Expression_system_taxid: 562. Expression_system_cell_line: bl21
Biol. unit: Dimer (from PQS)
2.10Å     R-factor:   0.209     R-free:   0.257
Authors: S.F.Bellon,K.K.Rodgers,D.G.Schatz,J.E.Coleman,T.A.Steitz
Key ref: S.F.Bellon et al. (1997). Crystal structure of the RAG1 dimerization domain reveals multiple zinc-binding motifs including a novel zinc binuclear cluster. Nat Struct Biol, 4, 586-591. PubMed id: 9228952
10-Jan-97     Release date:   23-Jul-97    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P15919  (RAG1_MOUSE) -  V(D)J recombination-activating protein 1
1040 a.a.
116 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     V(D)J recombination   1 term 
  Biochemical function     nucleic acid binding     6 terms  


Nat Struct Biol 4:586-591 (1997)
PubMed id: 9228952  
Crystal structure of the RAG1 dimerization domain reveals multiple zinc-binding motifs including a novel zinc binuclear cluster.
S.F.Bellon, K.K.Rodgers, D.G.Schatz, J.E.Coleman, T.A.Steitz.
The crystal structure of the dimerization domain of the V(D)J recombination-activating protein, RAG1, was solved using zinc anomalous scattering. The structure reveals an unusual combination of multi-class zinc-binding motifs, including a zinc RING finger and a C2H2 zinc finger, that together from a single structural domain. The domain also contains a unique zinc binuclear cluster in place of a normally mononuclear zinc site in the RING finger. Together, four zinc ions help organize the entire domain, including the two helices that form the dimer interface.

Literature references that cite this PDB file's key reference

  PubMed id Reference
19740377 C.Simkus, A.Bhattacharyya, M.Zhou, T.D.Veenstra, and J.M.Jones (2009).
Correlation between recombinase activating gene 1 ubiquitin ligase activity and V(D)J recombination.
  Immunology, 128, 206-217.  
19118899 C.Simkus, M.Makiya, and J.M.Jones (2009).
Karyopherin alpha 1 is a putative substrate of the RAG1 ubiquitin ligase.
  Mol Immunol, 46, 1319-1325.  
19396172 F.F.Yin, S.Bailey, C.A.Innis, M.Ciubotaru, S.Kamtekar, T.A.Steitz, and D.G.Schatz (2009).
Structure of the RAG1 nonamer binding domain with DNA reveals a dimer that mediates DNA synapsis.
  Nat Struct Mol Biol, 16, 499-508.
PDB codes: 3gna 3gnb
19333736 J.M.Jones, and C.Simkus (2009).
The roles of the RAG1 and RAG2 "non-core" regions in V(D)J recombination and lymphocyte development.
  Arch Immunol Ther Exp (Warsz), 57, 105-116.  
19500590 L.M.Gwyn, M.M.Peak, P.De, N.S.Rahman, and K.K.Rodgers (2009).
A zinc site in the C-terminal domain of RAG1 is essential for DNA cleavage activity.
  J Mol Biol, 390, 863-878.  
18253864 K.J.Brayer, and D.J.Segal (2008).
Keep your fingers off my DNA: protein-protein interactions mediated by C2H2 zinc finger domains.
  Cell Biochem Biophys, 50, 111-131.  
18281312 P.Raval, A.N.Kriatchko, S.Kumar, and P.C.Swanson (2008).
Evidence for Ku70/Ku80 association with full-length RAG1.
  Nucleic Acids Res, 36, 2060-2072.  
17135271 B.Lamothe, A.Besse, A.D.Campos, W.K.Webster, H.Wu, and B.G.Darnay (2007).
Site-specific Lys-63-linked tumor necrosis factor receptor-associated factor 6 auto-ubiquitination is a critical determinant of I kappa B kinase activation.
  J Biol Chem, 282, 4102-4112.  
17610897 B.M.Lee, B.A.Buck-Koehntop, M.A.Martinez-Yamout, H.J.Dyson, and P.E.Wright (2007).
Embryonic neural inducing factor churchill is not a DNA-binding zinc finger protein: solution structure reveals a solvent-exposed beta-sheet and zinc binuclear cluster.
  J Mol Biol, 371, 1274-1289.
PDB code: 2jox
17933515 P.Knipscheer, and T.K.Sixma (2007).
Protein-protein interactions regulate Ubl conjugation.
  Curr Opin Struct Biol, 17, 665-673.  
16388587 C.W.Vander Kooi, M.D.Ohi, J.A.Rosenberg, M.L.Oldham, M.E.Newcomer, K.L.Gould, and W.J.Chazin (2006).
The Prp19 U-box crystal structure suggests a common dimeric architecture for a class of oligomeric E3 ubiquitin ligases.
  Biochemistry, 45, 121-130.
PDB code: 2bay
16710298 G.Buchwald, P.van der Stoop, O.Weichenrieder, A.Perrakis, M.van Lohuizen, and T.K.Sixma (2006).
Structure and E3-ligase activity of the Ring-Ring complex of polycomb proteins Bmi1 and Ring1b.
  EMBO J, 25, 2465-2474.
PDB code: 2ckl
16987000 W.Maret (2006).
Zinc coordination environments in proteins as redox sensors and signal transducers.
  Antioxid Redox Signal, 8, 1419-1441.  
15964842 J.Hennig, L.Ottosson, C.Andrésen, L.Horvath, V.K.Kuchroo, K.Broo, M.Wahren-Herlenius, and M.Sunnerhagen (2005).
Structural organization and Zn2+-dependent subdomain interactions involving autoantigenic epitopes in the Ring-B-box-coiled-coil (RBCC) region of Ro52.
  J Biol Chem, 280, 33250-33261.  
15934064 N.Gresh, J.P.Piquemal, and M.Krauss (2005).
Representation of Zn(II) complexes in polarizable molecular mechanics. Further refinements of the electrostatic and short-range contributions. Comparisons with parallel ab initio computations.
  J Comput Chem, 26, 1113-1130.  
16210246 S.Gazdoiu, K.Yamoah, K.Wu, C.R.Escalante, I.Tappin, V.Bermudez, A.K.Aggarwal, J.Hurwitz, and Z.Q.Pan (2005).
Proximity-induced activation of human Cdc34 through heterologous dimerization.
  Proc Natl Acad Sci U S A, 102, 15053-15058.  
16186120 S.Katoh, Y.Tsunoda, K.Murata, E.Minami, and E.Katoh (2005).
Active site residues and amino acid specificity of the ubiquitin carrier protein-binding RING-H2 finger domain.
  J Biol Chem, 280, 41015-41024.  
15898832 V.V.Kapitonov, and J.Jurka (2005).
RAG1 core and V(D)J recombination signal sequences were derived from Transib transposons.
  PLoS Biol, 3, e181.  
15242391 D.G.Schatz (2004).
V(D)J recombination.
  Immunol Rev, 200, 5.  
15522623 D.G.Schatz (2004).
Antigen receptor genes and the evolution of a recombinase.
  Semin Immunol, 16, 245-256.  
15231834 P.Andersen, B.B.Kragelund, A.N.Olsen, F.H.Larsen, N.H.Chua, F.M.Poulsen, and K.Skriver (2004).
Structure and biochemical function of a prototypical Arabidopsis U-box domain.
  J Biol Chem, 279, 40053-40061.
PDB code: 1t1h
15242397 P.De, and K.K.Rodgers (2004).
Putting the pieces together: identification and characterization of structural domains in the V(D)J recombination protein RAG1.
  Immunol Rev, 200, 70-82.  
12620233 A.S.McCarty, G.Kleiger, D.Eisenberg, and S.T.Smale (2003).
Selective dimerization of a C2H2 zinc finger subfamily.
  Mol Cell, 11, 459-470.  
14671314 J.M.Jones, and M.Gellert (2003).
Autoubiquitylation of the V(D)J recombinase protein RAG1.
  Proc Natl Acad Sci U S A, 100, 15446-15451.  
12655019 L.J.Godderz, N.S.Rahman, G.M.Risinger, J.L.Arbuckle, and K.K.Rodgers (2003).
Self-association and conformational properties of RAG1: implications for formation of the V(D)J recombinase.
  Nucleic Acids Res, 31, 2014-2023.  
12488446 M.Ciubotaru, L.M.Ptaszek, G.A.Baker, S.N.Baker, F.V.Bright, and D.G.Schatz (2003).
RAG1-DNA binding in V(D)J recombination. Specificity and DNA-induced conformational changes revealed by fluorescence and CD spectroscopy.
  J Biol Chem, 278, 5584-5596.  
12627222 M.D.Ohi, C.W.Vander Kooi, J.A.Rosenberg, W.J.Chazin, and K.L.Gould (2003).
Structural insights into the U-box, a domain associated with multi-ubiquitination.
  Nat Struct Biol, 10, 250-255.
PDB code: 1n87
12502808 N.Imai, N.Matsuda, K.Tanaka, A.Nakano, S.Matsumoto, and W.Kang (2003).
Ubiquitin ligase activities of Bombyx mori nucleopolyhedrovirus RING finger proteins.
  J Virol, 77, 923-930.  
12588869 S.Katoh, C.Hong, Y.Tsunoda, K.Murata, R.Takai, E.Minami, T.Yamazaki, and E.Katoh (2003).
High precision NMR structure and function of the RING-H2 finger domain of EL5, a rice protein whose expression is increased upon exposure to pathogen-derived oligosaccharides.
  J Biol Chem, 278, 15341-15348.
PDB code: 1iym
12466024 C.Yi, H.Wang, N.Wei, and X.W.Deng (2002).
An initial biochemical and cell biological characterization of the mammalian homologue of a central plant developmental switch, COP1.
  BMC Cell Biol, 3, 30.  
  11983057 P.Kosarev, K.F.Mayer, and C.S.Hardtke (2002).
Evaluation and classification of RING-finger domains encoded by the Arabidopsis genome.
  Genome Biol, 3, RESEARCH0016.  
11823428 T.K.Albert, H.Hanzawa, Y.I.Legtenberg, Ruwe, F.A.van den Heuvel, M.A.Collart, R.Boelens, and H.T.Timmers (2002).
Identification of a ubiquitin-protein ligase subunit within the CCR4-NOT transcription repressor complex.
  EMBO J, 21, 355-364.  
11226167 A.D.Capili, D.C.Schultz, F.J.RauscherIII, and K.L.Borden (2001).
Solution structure of the PHD domain from the KAP-1 corepressor: structural determinants for PHD, RING and LIM zinc-binding domains.
  EMBO J, 20, 165-177.
PDB code: 1fp0
11138625 L.D.Notarangelo, S.Santagata, and A.Villa (2001).
Recombinase activating gene enzymes of lymphocytes.
  Curr Opin Hematol, 8, 41-46.  
11266539 M.J.Sadofsky (2001).
The RAG proteins in V(D)J recombination: more than just a nuclease.
  Nucleic Acids Res, 29, 1399-1409.  
11292843 N.V.Grishin (2001).
Treble clef finger--a functionally diverse zinc-binding structural motif.
  Nucleic Acids Res, 29, 1703-1714.  
11573085 P.S.Brzovic, P.Rajagopal, D.W.Hoyt, M.C.King, and R.E.Klevit (2001).
Structure of a BRCA1-BARD1 heterodimeric RING-RING complex.
  Nat Struct Biol, 8, 833-837.
PDB code: 1jm7
11573079 R.Baer (2001).
With the ends in sight: images from the BRCA1 tumor suppressor.
  Nat Struct Biol, 8, 822-824.  
10704423 L.Aravind, and E.V.Koonin (2000).
The U box is a modified RING finger - a common domain in ubiquitination.
  Curr Biol, 10, R132-R134.  
10799597 L.C.van Dinten, H.van Tol, A.E.Gorbalenya, and E.J.Snijder (2000).
The predicted metal-binding region of the arterivirus helicase protein is involved in subgenomic mRNA synthesis, genome replication, and virion biogenesis.
  J Virol, 74, 5213-5223.  
10966114 N.Zheng, P.Wang, P.D.Jeffrey, and N.P.Pavletich (2000).
Structure of a c-Cbl-UbcH7 complex: RING domain function in ubiquitin-protein ligases.
  Cell, 102, 533-539.
PDB code: 1fbv
10652143 C.Stoop-Myer, K.U.Torii, T.W.McNellis, J.E.Coleman, and X.W.Deng (1999).
Short communication: the N-terminal fragment of Arabidopsis photomorphogenic repressor COP1 maintains partial function and acts in a concentration-dependent manner.
  Plant J, 20, 713-717.  
10026184 J.E.Meza, P.S.Brzovic, M.C.King, and R.E.Klevit (1999).
Mapping the functional domains of BRCA1. Interaction of the ring finger domains of BRCA1 and BARD1.
  J Biol Chem, 274, 5659-5665.  
10488108 K.U.Torii, C.D.Stoop-Myer, H.Okamoto, J.E.Coleman, M.Matsui, and X.W.Deng (1999).
The RING finger motif of photomorphogenic repressor COP1 specifically interacts with the RING-H2 motif of a novel Arabidopsis protein.
  J Biol Chem, 274, 27674-27681.  
10448134 L.D.Notarangelo, A.Villa, and K.Schwarz (1999).
RAG and RAG defects.
  Curr Opin Immunol, 11, 435-442.  
10394369 T.G.Kutateladze, K.D.Ogburn, W.T.Watson, Beer, S.D.Emr, C.G.Burd, and M.Overduin (1999).
Phosphatidylinositol 3-phosphate recognition by the FYVE domain.
  Mol Cell, 3, 805-811.  
  10490593 V.Aidinis, T.Bonaldi, M.Beltrame, S.Santagata, M.E.Bianchi, and E.Spanopoulou (1999).
The RAG1 homeodomain recruits HMG1 and HMG2 to facilitate recombination signal sequence binding and to enhance the intrinsic DNA-bending activity of RAG1-RAG2.
  Mol Cell Biol, 19, 6532-6542.  
9667939 J.E.Coleman (1998).
Zinc enzymes.
  Curr Opin Chem Biol, 2, 222-234.  
9755158 K.U.Torii, T.W.McNellis, and X.W.Deng (1998).
Functional dissection of Arabidopsis COP1 reveals specific roles of its three structural modules in light control of seedling development.
  EMBO J, 17, 5577-5587.  
9525870 P.S.Brzovic, J.Meza, M.C.King, and R.E.Klevit (1998).
The cancer-predisposing mutation C61G disrupts homodimer formation in the NH2-terminal BRCA1 RING finger domain.
  J Biol Chem, 273, 7795-7799.  
9345628 K.Moffat, and Z.Ren (1997).
Synchrotron radiation applications to macromolecular crystallography.
  Curr Opin Struct Biol, 7, 689-696.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.