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(-) Description

Title :  CRYSTAL STRUCTURE OF RAG2-PHD FINGER IN COMPLEX WITH H3R2ME1K4ME3 PEPTIDE
 
Authors :  S. Ramon-Maiques, W. Yang
Date :  02 Aug 07  (Deposition) - 11 Dec 07  (Release) - 21 Dec 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B,D,E
Biol. Unit 1:  A,D  (1x)
Biol. Unit 2:  B,E  (1x)
Keywords :  V(D)J Recombination, Covalent Modifications, Rag2, Histone, Nucleus, Nuclease, Hydrolase, Phd Finger, Dna-Binding, Recombinase, Endonuclease, Trimethyl Lysine, Dna Recombination, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Ramon-Maiques, A. J. Kuo, D. Carney, A. G. W. Matthews, M. A. Oettinger, O. Gozani, W. Yang
The Plant Homeodomain Finger Of Rag2 Recognizes Histone H3 Methylated At Both Lysine-4 And Arginine-2.
Proc. Nat. Acad. Sci. Usa V. 104 18993 2007
PubMed-ID: 18025461  |  Reference-DOI: 10.1073/PNAS.0709170104
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - VDJ RECOMBINATION-ACTIVATING PROTEIN 2
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPGEX-6P-1
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    FragmentRESIDUES 414-487
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    SynonymRAG2, RAG2-PHD FINGER
 
Molecule 2 - H3R2ME1K4ME3 PEPTIDE
    ChainsD, E
    FragmentH3 (1-21), BIOTINILATED AT C-TERMINUS
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsR2 MONOMETHYLATED AND K4 TRIMETHYLATED
    SyntheticYES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABDE
Biological Unit 1 (1x)A D 
Biological Unit 2 (1x) B E

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric Unit (3, 8)
No.NameCountTypeFull Name
1M3L2Mod. Amino AcidN-TRIMETHYLLYSINE
2NMM2Mod. Amino Acid(2S)-2-AMINO-5-[(N-METHYLCARBAMIMIDOYL)AMINO]PENTANOIC ACID
3ZN4Ligand/IonZINC ION
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1M3L1Mod. Amino AcidN-TRIMETHYLLYSINE
2NMM1Mod. Amino Acid(2S)-2-AMINO-5-[(N-METHYLCARBAMIMIDOYL)AMINO]PENTANOIC ACID
3ZN-1Ligand/IonZINC ION
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1M3L1Mod. Amino AcidN-TRIMETHYLLYSINE
2NMM1Mod. Amino Acid(2S)-2-AMINO-5-[(N-METHYLCARBAMIMIDOYL)AMINO]PENTANOIC ACID
3ZN-1Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:419 , CYS A:423 , HIS A:455 , CYS A:458BINDING SITE FOR RESIDUE ZN A1488
2AC2SOFTWARECYS A:446 , HIS A:452 , CYS A:478 , HIS A:481BINDING SITE FOR RESIDUE ZN A1489
3AC3SOFTWARECYS B:419 , CYS B:423 , HIS B:455 , CYS B:458BINDING SITE FOR RESIDUE ZN B1487
4AC4SOFTWARECYS B:446 , HIS B:452 , CYS B:478 , HIS B:481BINDING SITE FOR RESIDUE ZN B1488

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2V85)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2V85)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2V85)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2V85)

(-) Exons   (1, 2)

Asymmetric Unit (1, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENSMUST000000440311aENSMUSE00000230550chr2:101464875-101465027153RAG2_MOUSE-00--
1.2ENSMUST000000440312ENSMUSE00000230542chr2:101468294-10146835663RAG2_MOUSE-00--
1.3bENSMUST000000440313bENSMUSE00000230533chr2:101469479-1014726853207RAG2_MOUSE1-5365362A:414-487
B:406-487 (gaps)
74
115

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:74
 aligned with RAG2_MOUSE | P21784 from UniProtKB/Swiss-Prot  Length:527

    Alignment length:74
                                   423       433       443       453       463       473       483    
           RAG2_MOUSE   414 GYWITCCPTCDVDINTWVPFYSTELNKPAMIYCSHGDGHWVHAQCMDLEERTLIHLSEGSNKYYCNEHVQIARA 487
               SCOP domains d2v85a_ A: automated matches                                               SCOP domains
               CATH domains -------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............................eeee.....eeee.hhhh.hhhhhhhhhh................ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.3b  PDB: A:414-487 UniProt: 1-536 [INCOMPLETE]                      Transcript 1
                 2v85 A 414 GYWITCCPTCDVDINTWVPFYSTELNKPAMIYCSHGDGHWVHAQCMDLEERTLIHLSEGSNKYYCNEHVQIARA 487
                                   423       433       443       453       463       473       483    

Chain B from PDB  Type:PROTEIN  Length:82
 aligned with RAG2_MOUSE | P21784 from UniProtKB/Swiss-Prot  Length:527

    Alignment length:115
                                   382       392       402       412       422       432       442       452       462       472       482     
           RAG2_MOUSE   373 GDSTPFEDSEEFCFSAEATSFDGDDEFDTYNEDDEDDESVTGYWITCCPTCDVDINTWVPFYSTELNKPAMIYCSHGDGHWVHAQCMDLEERTLIHLSEGSNKYYCNEHVQIARA 487
               SCOP domains d   2v                85b_               B: automated matches                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----------------------------------------RAG2_PHD-2v85B01 B:414-487                                                 Pfam domains (1)
           Pfam domains (2) -----------------------------------------RAG2_PHD-2v85B02 B:414-487                                                 Pfam domains (2)
         Sec.struct. author .---..----------------.hhhh--------------hh...........................eeee.....eeee.hhhh.hhhhhhhhhhh............... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.3b  PDB: B:406-487 (gaps) UniProt: 1-536 [INCOMPLETE]                                                        Transcript 1
                 2v85 B 406 G---PL----------------GSPEF--------------GYWITCCPTCDVDINTWVPFYSTELNKPAMIYCSHGDGHWVHAQCMDLEERTLIHLSEGSNKYYCNEHVQIARA 487
                            |   ||   -         -  |   |  -         - |     422       432       442       452       462       472       482     
                          406 407|              409 413            414                                                                         
                               408                                                                                                             

Chain D from PDB  Type:PROTEIN  Length:12
 aligned with Q5TEC6_HUMAN | Q5TEC6 from UniProtKB/TrEMBL  Length:136

    Alignment length:12
                                    11  
         Q5TEC6_HUMAN     2 ARTKQTARKSTG  13
               SCOP domains ------------ SCOP domains
               CATH domains ------------ CATH domains
               Pfam domains ------------ Pfam domains
         Sec.struct. author ............ Sec.struct. author
                 SAPs(SNPs) ------------ SAPs(SNPs)
                    PROSITE ------------ PROSITE
                 Transcript ------------ Transcript
                 2v85 D   1 ArTkQTARKAAG  12
                             | |    10  
                             | |        
                             2-NMM      
                               4-M3L    

Chain E from PDB  Type:PROTEIN  Length:10
 aligned with Q5TEC6_HUMAN | Q5TEC6 from UniProtKB/TrEMBL  Length:136

    Alignment length:10
                                    11
         Q5TEC6_HUMAN     2 ARTKQTARKS  11
               SCOP domains ---------- SCOP domains
               CATH domains ---------- CATH domains
               Pfam domains ---------- Pfam domains
         Sec.struct. author .......... Sec.struct. author
                 SAPs(SNPs) ---------- SAPs(SNPs)
                    PROSITE ---------- PROSITE
                 Transcript ---------- Transcript
                 2v85 E   1 ArTkQTARKA  10
                             | |    10
                             2-NMM    
                               4-M3L  

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2V85)

(-) Pfam Domains  (1, 2)

Asymmetric Unit

(-) Gene Ontology  (27, 29)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (RAG2_MOUSE | P21784)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003682    chromatin binding    Interacting selectively and non-covalently with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0035064    methylated histone binding    Interacting selectively and non-covalently with a histone in which a residue has been modified by methylation. Histones are any of a group of water-soluble proteins found in association with the DNA of eukaroytic chromosomes.
    GO:0035091    phosphatidylinositol binding    Interacting selectively and non-covalently with any inositol-containing glycerophospholipid, i.e. phosphatidylinositol (PtdIns) and its phosphorylated derivatives.
    GO:0005547    phosphatidylinositol-3,4,5-trisphosphate binding    Interacting selectively and non-covalently with phosphatidylinositol-3,4,5-trisphosphate, a derivative of phosphatidylinositol in which the inositol ring is phosphorylated at the 3', 4' and 5' positions.
    GO:0043325    phosphatidylinositol-3,4-bisphosphate binding    Interacting selectively and non-covalently with phosphatidylinositol-3,4-bisphosphate, a derivative of phosphatidylinositol in which the inositol ring is phosphorylated at the 3' and 4' positions.
    GO:0080025    phosphatidylinositol-3,5-bisphosphate binding    Interacting selectively and non-covalently with phosphatidylinositol-3,5-bisphosphate, a derivative of phosphatidylinositol in which the inositol ring is phosphorylated at the 3' and 5' positions.
    GO:0005546    phosphatidylinositol-4,5-bisphosphate binding    Interacting selectively and non-covalently with phosphatidylinositol-4,5-bisphosphate, a derivative of phosphatidylinositol in which the inositol ring is phosphorylated at the 4' and 5' positions.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0061630    ubiquitin protein ligase activity    Catalysis of the transfer of ubiquitin to a substrate protein via the reaction X-ubiquitin + S -> X + S-ubiquitin, where X is either an E2 or E3 enzyme, the X-ubiquitin linkage is a thioester bond, and the S-ubiquitin linkage is an amide bond: an isopeptide bond between the C-terminal glycine of ubiquitin and the epsilon-amino group of lysine residues in the substrate or, in the linear extension of ubiquitin chains, a peptide bond the between the C-terminal glycine and N-terminal methionine of ubiquitin residues.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0030183    B cell differentiation    The process in which a precursor cell type acquires the specialized features of a B cell. A B cell is a lymphocyte of B lineage with the phenotype CD19-positive and capable of B cell mediated immunity.
    GO:0002358    B cell homeostatic proliferation    The non-specific expansion of B cell populations within a whole or part of an organism to reach to a total number of B cells which will then remain stable over time in the absence of an external stimulus.
    GO:0002326    B cell lineage commitment    The process in which a lymphoid progenitor cell becomes committed to become any type of B cell.
    GO:0006310    DNA recombination    Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction.
    GO:0030217    T cell differentiation    The process in which a precursor cell type acquires characteristics of a more mature T-cell. A T cell is a type of lymphocyte whose definin characteristic is the expression of a T cell receptor complex.
    GO:0033077    T cell differentiation in thymus    The process in which a precursor cell type acquires the specialized features of a T cell via a differentiation pathway dependent upon transit through the thymus.
    GO:0002360    T cell lineage commitment    The process in which a lymphoid progenitor cell becomes committed to becoming any type of T cell.
    GO:0033151    V(D)J recombination    The process in which immune receptor V, D, and J, or V and J gene segments, depending on the specific receptor, are recombined within a single locus utilizing the conserved heptamer and nonomer recombination signal sequences (RSS).
    GO:0046622    positive regulation of organ growth    Any process that activates or increases the frequency, rate or extent of growth of an organ of an organism.
    GO:0002331    pre-B cell allelic exclusion    Expression of a single heavy chain allele during pre-B cell differentiation.
    GO:0016567    protein ubiquitination    The process in which one or more ubiquitin groups are added to a protein.
cellular component
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

Chain D,E   (Q5TEC6_HUMAN | Q5TEC6)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0046982    protein heterodimerization activity    Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
cellular component
    GO:0005694    chromosome    A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
    GO:0000786    nucleosome    A complex comprised of DNA wound around a multisubunit core and associated proteins, which forms the primary packing unit of DNA into higher order structures.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        Q5TEC6_HUMAN | Q5TEC62cnx 2co0 2v83 2v88 2v89 2vnf 2x0l
        RAG2_MOUSE | P217842jwo 2v83 2v86 2v87 2v88 2v89 4wwx
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        Q5TEC6_HUMAN | Q5TEC64h75

(-) Related Entries Specified in the PDB File

2a23 A PHD FINGER MOTIF IN THE C-TERMINUS OF RAG2 MODULATESRECOMBINATION ACTIVITY
2v83 CRYSTAL STRUCTURE OF RAG2-PHD FINGER IN COMPLEX WITH H3K4ME3 PEPTIDE
2v86 CRYSTAL STRUCTURE OF RAG2-PHD FINGER IN COMPLEX WITH H3R2ME2AK4ME3 PEPTIDE
2v87 CRYSTAL STRUCTURE OF RAG2-PHD FINGER IN COMPLEX WITH H3R2ME2SK4ME3 PEPTIDE
2v88 CRYSTAL STRUCTURE OF RAG2-PHD FINGER IN COMPLEX WITH H3R2ME2SK4ME2 PEPTIDE
2v89 CRYSTAL STRUCTURE OF RAG2-PHD FINGER IN COMPLEX WITH H3K4ME3 PEPTIDE AT 1.1A RESOLUTION