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(-) Description

Title :  CRYSTAL STRUCTURE OF MOUSE CARM1 IN COMPLEX WITH LIGAND P2C3U
 
Authors :  N. Marechal, N. Troffer-Charlier, V. Cura, L. Bonnefond, J. Cavarelli
Date :  08 Jul 16  (Deposition) - 22 Mar 17  (Release) - 12 Apr 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F,G,H
Keywords :  Protein Arginine Methyltransferase, Catalytic Domain, Chromatin Regulator, Mrna Processing, Mrna Splicing, Nucleus, S-Adenosyl-L- Methionine, Transcription, Transcription Regulation, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. J. Van Haren, N. Marechal, N. Troffer-Charlier, A. Cianciulli, G. Sbardella, J. Cavarelli, N. I. Martin
Transition State Mimics Are Valuable Mechanistic Probes For Structural Studies With The Arginine Methyltransferase Carm1.
Proc. Natl. Acad. Sci. V. 114 3625 2017 U. S. A.
PubMed-ID: 28330993  |  Reference-DOI: 10.1073/PNAS.1618401114

(-) Compounds

Molecule 1 - HISTONE-ARGININE METHYLTRANSFERASE CARM1
    Chains: A, B, C, D
    EC Number: 2.1.1.319
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Common: FALL ARMYWORM
    Expression System Taxid: 7108
    Gene: CARM1, PRMT4
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: COACTIVATOR-ASSOCIATED ARGININE METHYLTRANSFERASE 1,PROTEIN ARGININE N-METHYLTRANSFERASE 4
 
Molecule 2 - POLYADENYLATE-BINDING PROTEIN 1
    Chains: E, F, G, H
    Engineered: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: PABP1(456-466) PAAPRPPFSTM
    Synonym: POLY(A)-BINDING PROTEIN 1
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345678
Asymmetric/Biological Unit : ABCDEFGH

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 13)

Asymmetric/Biological Unit (6, 13)
No.NameCountTypeFull Name
1DXE3Ligand/Ion1,2-DIMETHOXYETHANE
2EDO3Ligand/Ion1,2-ETHANEDIOL
3PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
4PG41Ligand/IonTETRAETHYLENE GLYCOL
5QVR4Ligand/Ion(2~{R},3~{R},4~{S},5~{R})-2-(6-AMINOPURIN-9-YL)-5-[(~{E})-PROP-1-ENYL]OXOLANE-3,4-DIOL
6SO41Ligand/IonSULFATE ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:444 , LYS A:445 , HOH A:618 , HOH A:673 , ARG B:209binding site for residue SO4 A 501
02AC2SOFTWAREGLY A:398binding site for residue DXE A 502
03AC3SOFTWAREASP B:393binding site for residue DXE B 501
04AC4SOFTWARELYS A:463 , SER B:136 , GLU B:244 , GLU B:245binding site for residue PG4 B 502
05AC5SOFTWARETRP C:404binding site for residue EDO C 501
06AC6SOFTWAREGLN C:205binding site for residue EDO C 502
07AC7SOFTWAREASP D:393binding site for residue EDO D 501
08AC8SOFTWARELEU A:178 , GLN A:205 , GLY D:461binding site for residue DXE D 502
09AC9SOFTWARETYR A:150 , PHE A:151 , TYR A:154 , MET A:163 , GLY A:193 , GLU A:215 , ALA A:216 , GLY A:241 , LYS A:242 , VAL A:243 , GLU A:244 , GLU A:258 , MET A:260 , GLU A:267 , MET A:269 , SER A:272 , HIS A:415 , HOH A:642 , ALA E:-1 , PRO E:0 , PRO E:2 , PRO E:3 , HOH E:1103 , HOH E:1104 , HOH E:1105binding site for Di-peptide QVR E 1001 and ARG E 1
10AD1SOFTWARETYR B:150 , PHE B:151 , TYR B:154 , MET B:163 , GLY B:193 , GLU B:215 , ALA B:216 , GLY B:241 , LYS B:242 , VAL B:243 , GLU B:244 , GLU B:258 , MET B:260 , GLU B:267 , MET B:269 , SER B:272 , HIS B:415 , HOH B:671 , ALA F:-1 , PRO F:0 , PRO F:2 , PRO F:3 , HOH F:1103 , HOH F:1104 , HOH F:1106binding site for Di-peptide QVR F 1001 and ARG F 1
11AD2SOFTWARETYR C:150 , PHE C:151 , TYR C:154 , MET C:163 , GLY C:193 , GLU C:215 , ALA C:216 , LYS C:242 , VAL C:243 , GLU C:244 , GLU C:258 , MET C:260 , GLU C:267 , MET C:269 , SER C:272 , HIS C:415 , HOH C:628 , ALA G:-1 , PRO G:0 , PRO G:2 , PRO G:3 , HOH G:201binding site for Di-peptide QVR G 101 and ARG G 1
12AD3SOFTWARETYR D:150 , TYR D:154 , MET D:163 , GLY D:193 , GLU D:215 , ALA D:216 , LYS D:242 , VAL D:243 , GLU D:244 , GLU D:258 , MET D:260 , GLU D:267 , MET D:269 , SER D:272 , HIS D:415 , ALA H:-1 , PRO H:0 , PRO H:2 , PRO H:3 , HOH H:202 , HOH H:203 , HOH H:204binding site for Di-peptide QVR H 101 and ARG H 1

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5LGS)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Phe A:287 -Pro A:288
2Phe B:287 -Pro B:288
3Phe C:287 -Pro C:288
4Phe D:287 -Pro D:288

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5LGS)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5LGS)

(-) Exons   (0, 0)

(no "Exon" information available for 5LGS)

(-) Sequences/Alignments

Asymmetric/Biological 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:344
                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhh...eeeeee..hhhhhhhhhhhhh.....eeeee...........eeeeee...........hhhhhhhh...eeeeeeee..eeeeeeeee.hhhhhhhhhhhhhhhh........hhhhhhhhhhhhhh..eee..hhhhh....eeeeee....hhhhh.eeeeeeeee....eeeeeeeeeeeeeee....eeeee...........eeeeeeeeeeee....eeeeeeeeee.....eeeeeeeee.....eeeeeee....ee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5lgs A 135 RSVFSERTEESSAVQYFQFYGYLSQQQNMMQDYVRTGTYQRAILQNHTDFKDKIVLDVGCGSGILSFFAAQAGARKIYAVEASTMAQHAEVLVKSNNLTDRIVVIPGKVEEVSLPEQVDIIISEPMGYMLFNERMLESYLHAKKYLKPSGNMFPTIGDVHLAPFTDEQLYMEQFTKANFWYQPSFHGVDLSALRGAAVDEYFRQPVVDTFDIRILMAKSVKYTVNFLEAKEGDLHRIEIPFKFHMLHSGLVHGLAFWFDVAFIGSIMTVWLSTAPTEPLTHWYQVRCLFQSPLFAKAGDTLSGTCLLIANKRQSYDISIVAQVDQTGSKSSNLLDLKNPFFRYT 478
                                   144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474    


Chain B from PDB  Type:PROTEIN  Length:343
                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhh...eeeeee..hhhhhhhhhhhhh.....eeeee...........eeeeee.......hhhhhhhhhhhh...eeeeeeee..eeeeeeeee.hhhhhhhhhhhhhhhhh.hhhhh.hhhhhhhhhhhhhh..eee..hhhhh....eeeeee....hhhhh.eeeeeeeee....eeeeeeeeeeeeeee....eeeee...........eeeeeeeeeeee....eeeeeeeeeee...eeeeeeeeee.....eeeeeee....ee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5lgs B 135 RSVFSERTEESSAVQYFQFYGYLSQQQNMMQDYVRTGTYQRAILQNHTDFKDKIVLDVGCGSGILSFFAAQAGARKIYAVEASTMAQHAEVLVKSNNLTDRIVVIPGKVEEVSLPEQVDIIISEPMGYMLFNERMLESYLHAKKYLKPSGNMFPTIGDVHLAPFTDEQLYMEQFTKANFWYQPSFHGVDLSALRGAAVDEYFRQPVVDTFDIRILMAKSVKYTVNFLEAKEGDLHRIEIPFKFHMLHSGLVHGLAFWFDVAFIGSIMTVWLSTAPTEPLTHWYQVRCLFQSPLFAKAGDTLSGTCLLIANKRQSYDISIVAQVDQTGSKSSNLLDLKNPFFRY 477
                                   144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474   


Chain C from PDB  Type:PROTEIN  Length:343
                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhh...eeeeee..hhhhhhhhhhhhh.....eeeee...........eeeeee.......hhhhhhhhhhhh...eeeeeeee..eeeeeeeee.hhhhhhhhhhhhhhhh........hhhhhhhhhhhhhh..eee..hhhhh....eeeeee....hhhhh.eeeeeeeee....eeeeeeeeeeeeeee....eeeee...........eeeeeeeeeeee....eeeeeeeeeee...eeeeeeeeee.....eeeeeee....ee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5lgs C 136 SVFSERTEESSAVQYFQFYGYLSQQQNMMQDYVRTGTYQRAILQNHTDFKDKIVLDVGCGSGILSFFAAQAGARKIYAVEASTMAQHAEVLVKSNNLTDRIVVIPGKVEEVSLPEQVDIIISEPMGYMLFNERMLESYLHAKKYLKPSGNMFPTIGDVHLAPFTDEQLYMEQFTKANFWYQPSFHGVDLSALRGAAVDEYFRQPVVDTFDIRILMAKSVKYTVNFLEAKEGDLHRIEIPFKFHMLHSGLVHGLAFWFDVAFIGSIMTVWLSTAPTEPLTHWYQVRCLFQSPLFAKAGDTLSGTCLLIANKRQSYDISIVAQVDQTGSKSSNLLDLKNPFFRYT 478
                                   145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475   


Chain D from PDB  Type:PROTEIN  Length:343
                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh.hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhh...eeeeee..hhhhhhhhhhhhh.....eeeee...........eeeeee.......hhhhhhhhhhhh...eeeeeeee..eeeeeeeee.hhhhhhhhhhhhhhhhh.hhhhh.hhhhhhhhhhhhhh..eee..hhhhh....eeeeee....hhhhh.eeeeeeeee....eeeeeeeeeeeeeee....eeeee...........eeeeeeeeeeee....eeeeeeeeee.....eeeeeeeee....eeeeeeee....ee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5lgs D 135 RSVFSERTEESSAVQYFQFYGYLSQQQNMMQDYVRTGTYQRAILQNHTDFKDKIVLDVGCGSGILSFFAAQAGARKIYAVEASTMAQHAEVLVKSNNLTDRIVVIPGKVEEVSLPEQVDIIISEPMGYMLFNERMLESYLHAKKYLKPSGNMFPTIGDVHLAPFTDEQLYMEQFTKANFWYQPSFHGVDLSALRGAAVDEYFRQPVVDTFDIRILMAKSVKYTVNFLEAKEGDLHRIEIPFKFHMLHSGLVHGLAFWFDVAFIGSIMTVWLSTAPTEPLTHWYQVRCLFQSPLFAKAGDTLSGTCLLIANKRQSYDISIVAQVDQTGSKSSNLLDLKNPFFRY 477
                                   144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474   


Chain E from PDB  Type:PROTEIN  Length:8
                                        
               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
                 5lgs E  -2 AAPRPPFS   5


Chain F from PDB  Type:PROTEIN  Length:9
                                         
               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
                 5lgs F  -3 PAAPRPPFS   5


Chain G from PDB  Type:PROTEIN  Length:8
                                        
               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
                 5lgs G  -2 AAPRPPFS   5


Chain H from PDB  Type:PROTEIN  Length:8
                                        
               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
                 5lgs H  -2 AAPRPPFS   5
   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  (0, 0)

(no "SCOP Domain" information available for 5LGS)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5LGS)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5LGS)

(-) Gene Ontology  (71, 75)

Asymmetric/Biological Unit(hide GO term definitions)

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  5lgs
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  PABP1_HUMAN | P11940
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  2.1.1.319
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 Related Entries

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

UniProtKB/Swiss-Prot
        CARM1_MOUSE | Q9WVG6: 2v74 2v7e 5ih3 5is6 5is7 5is8 5is9 5isa 5isb 5isc 5isd 5ise 5isf 5isg 5ish 5isi 5k8v 5k8w 5k8x 5lgp 5lgq 5lgr
        PABP1_HUMAN | P11940: 1cvj 1g9l 1jgn 1jh4 2k8g 2rqg 2rqh 2x04 3ktp 3ktr 3kui 3kuj 3kur 3kus 3kut 3pkn 3pth 4f02 4f25 4f26 5dx1 5dx8 5dxa 5lgp 5lgq 5lgr

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5LGS)