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(-) Description

Title :  CRYSTAL STRUCTURE OF CARM1, SINEFUNGIN, AND METHYLATED PABP1 PEPTIDE (R460)
 
Authors :  P. A. Boriack-Sjodin
Date :  23 Sep 15  (Deposition) - 25 Nov 15  (Release) - 30 Mar 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.07
Chains :  Asym. Unit :  A,B,C,D,F,G,I
Biol. Unit 1:  A,B,F,G  (1x)
Biol. Unit 2:  C,D,I  (1x)
Keywords :  Protein-Substrate Ternary Complex, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. A. Boriack-Sjodin, L. Jin, S. L. Jacques, A. Drew, C. Sneeringer, M. P. Scott, M. P. Moyer, S. Ribich, O. Moradei, R. A. Copeland
Structural Insights Into Ternary Complex Formation Of Human Carm1 With Various Substrates.
Acs Chem. Biol. V. 11 763 2016
PubMed-ID: 26551522  |  Reference-DOI: 10.1021/ACSCHEMBIO.5B00773

(-) Compounds

Molecule 1 - HISTONE-ARGININE METHYLTRANSFERASE CARM1
    Chains: A, B, C, D
    EC Number: 2.1.1.-, 2.1.1.125
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Cell Line: SF9
    Expression System Common: FALL ARMYWORM
    Expression System Plasmid: PFASTBAC
    Expression System Taxid: 7108
    Expression System Vector Type: BACULOVIRUS
    Fragment: CATALYTIC DOMAIN (UNP RESIDUES 134-479)
    Gene: CARM1, PRMT4
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: COACTIVATOR-ASSOCIATED ARGININE METHYLTRANSFERASE 1,PROTEIN ARGININE N-METHYLTRANSFERASE 4
 
Molecule 2 - METHYLATED PABP1 PEPTIDE
    Chains: F, G, I
    Engineered: YES
    Fragment: UNP RESIDUES 449-466
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: POLY(A)-BINDING PROTEIN 1
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234567
Asymmetric Unit : ABCDFGI
Biological Unit 1 (1x): AB  FG 
Biological Unit 2 (1x):   CD  I

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 10)

Asymmetric Unit (3, 10)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
2NMM3Mod. Amino Acid(2S)-2-AMINO-5-[(N-METHYLCARBAMIMIDOYL)AMINO]PENTANOICACID
3SFG4Ligand/IonSINEFUNGIN
Biological Unit 1 (3, 6)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2NMM2Mod. Amino Acid(2S)-2-AMINO-5-[(N-METHYLCARBAMIMIDOYL)AMINO]PENTANOICACID
3SFG2Ligand/IonSINEFUNGIN
Biological Unit 2 (3, 4)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2NMM1Mod. Amino Acid(2S)-2-AMINO-5-[(N-METHYLCARBAMIMIDOYL)AMINO]PENTANOICACID
3SFG2Ligand/IonSINEFUNGIN

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:149 , PHE A:150 , TYR A:153 , GLN A:159 , MET A:162 , ARG A:168 , GLY A:192 , CYS A:193 , ILE A:197 , LEU A:198 , GLU A:214 , ALA A:215 , GLY A:240 , LYS A:241 , VAL A:242 , GLU A:243 , GLU A:257 , MET A:268 , SER A:271 , HOH A:619 , HOH A:620 , HOH A:643 , HOH A:645 , NMM F:12binding site for residue SFG A 501
2AC2SOFTWAREASP A:392 , HOH A:617 , HOH A:628binding site for residue GOL A 502
3AC3SOFTWARETYR B:149 , PHE B:150 , TYR B:153 , GLN B:159 , MET B:162 , ARG B:168 , GLY B:192 , CYS B:193 , ILE B:197 , LEU B:198 , GLU B:214 , ALA B:215 , GLY B:240 , LYS B:241 , VAL B:242 , GLU B:243 , GLU B:257 , MET B:268 , SER B:271 , HOH B:602 , HOH B:617 , HOH B:631 , HOH B:653 , NMM G:12binding site for residue SFG B 501
4AC4SOFTWAREASP B:392 , HOH B:605 , HOH B:680binding site for residue GOL B 502
5AC5SOFTWARETYR C:149 , PHE C:150 , TYR C:153 , GLN C:159 , MET C:162 , ARG C:168 , GLY C:192 , CYS C:193 , GLY C:194 , ILE C:197 , LEU C:198 , GLU C:214 , ALA C:215 , GLY C:240 , LYS C:241 , VAL C:242 , GLU C:243 , GLU C:257 , MET C:268 , SER C:271 , HOH C:623 , HOH C:632 , HOH C:637 , HOH C:666binding site for residue SFG C 501
6AC6SOFTWARETRP C:403binding site for residue GOL C 502
7AC7SOFTWARETYR D:149 , PHE D:150 , TYR D:153 , GLN D:159 , MET D:162 , ARG D:168 , GLY D:192 , CYS D:193 , GLY D:194 , ILE D:197 , LEU D:198 , GLU D:214 , ALA D:215 , GLY D:240 , LYS D:241 , VAL D:242 , GLU D:243 , GLU D:257 , MET D:268 , SER D:271 , HOH D:606 , HOH D:622 , HOH D:642 , HOH D:676 , NMM I:12binding site for residue SFG D 501

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Phe A:286 -Pro A:287
2Phe B:286 -Pro B:287
3Phe C:286 -Pro C:287
4Phe D:286 -Pro D:287

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5DXA)

(-) 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:344
                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhh...eeeeee..hhhhhhhhhhhhh.....eeeee...........eeeeee..........hhhhhhhhh...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
                 5dxa A 134 RSVFSERTEESSAVQYFQFYGYLSQQQNMMQDYVRTGTYQRAILQNHTDFKDKIVLDVGCGSGILSFFAAQAGARKIYAVEASTMAQHAEVLVKSNNLTDRIVVIPGKVEEVSLPEQVDIIISEPMGYMLFNERMLESYLHAKKYLKPSGNMFPTIGDVHLAPFTDEQLYMEQFTKANFWYQPSFHGVDLSALRGAAVDEYFRQPVVDTFDIRILMAKSVKYTVNFLEAKEGDLHRIEIPFKFHMLHSGLVHGLAFWFDVAFIGSIMTVWLSTAPTEPLTHWYQVRCLFQSPLFAKAGDTLSGTCLLIANKRQSYDISIVAQVDQTGSKSSNLLDLKNPFFRYT 477
                                   143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473    


Chain B from PDB  Type:PROTEIN  Length:343
                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhh...eeeeee..hhhhhhhhhhhhh.....eeeee...........eeeeee..........hhhhhhhhh...eeeeeeee..eeeeeeeee.hhhhhhhhhhhhhhhhh.hhhhh.hhhhhhhhhhhhhh..eee..hhhhh....eeeeee....hhhhh.eeeeeeeee....eeeeeeeeeeeeeee....eeeee...........eeeeeeeeeeee....eeeeeeeeee.....eeeeeeeee.....eeeeeee....ee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dxa B 135 SVFSERTEESSAVQYFQFYGYLSQQQNMMQDYVRTGTYQRAILQNHTDFKDKIVLDVGCGSGILSFFAAQAGARKIYAVEASTMAQHAEVLVKSNNLTDRIVVIPGKVEEVSLPEQVDIIISEPMGYMLFNERMLESYLHAKKYLKPSGNMFPTIGDVHLAPFTDEQLYMEQFTKANFWYQPSFHGVDLSALRGAAVDEYFRQPVVDTFDIRILMAKSVKYTVNFLEAKEGDLHRIEIPFKFHMLHSGLVHGLAFWFDVAFIGSIMTVWLSTAPTEPLTHWYQVRCLFQSPLFAKAGDTLSGTCLLIANKRQSYDISIVAQVDQTGSKSSNLLDLKNPFFRYT 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 .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhh...eeeeee..hhhhhhhhhhhhh.....eeeee...........eeeeee..........hhhhhhhhh...eeeeeeee..eeeeeeeee.hhhhhhhhhhhhhhhhh.hhhhh.hhhhhhhhhhhhhh..eee..hhhhh....eeeeee....hhhhh.eeeeeeeee....eeeeeeeeeeeeeee....eeeee...........eeeeeeeeeeee....eeeeeeeeee.....eeeeeeeee.....eeeeeee....ee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dxa C 134 RSVFSERTEESSAVQYFQFYGYLSQQQNMMQDYVRTGTYQRAILQNHTDFKDKIVLDVGCGSGILSFFAAQAGARKIYAVEASTMAQHAEVLVKSNNLTDRIVVIPGKVEEVSLPEQVDIIISEPMGYMLFNERMLESYLHAKKYLKPSGNMFPTIGDVHLAPFTDEQLYMEQFTKANFWYQPSFHGVDLSALRGAAVDEYFRQPVVDTFDIRILMAKSVKYTVNFLEAKEGDLHRIEIPFKFHMLHSGLVHGLAFWFDVAFIGSIMTVWLSTAPTEPLTHWYQVRCLFQSPLFAKAGDTLSGTCLLIANKRQSYDISIVAQVDQTGSKSSNLLDLKNPFFRY 476
                                   143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473   


Chain D from PDB  Type:PROTEIN  Length:343
                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhh...eeeeee..hhhhhhhhhhhhh.....eeeee...........eeeeee..........hhhhhhhhh...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
                 5dxa D 135 SVFSERTEESSAVQYFQFYGYLSQQQNMMQDYVRTGTYQRAILQNHTDFKDKIVLDVGCGSGILSFFAAQAGARKIYAVEASTMAQHAEVLVKSNNLTDRIVVIPGKVEEVSLPEQVDIIISEPMGYMLFNERMLESYLHAKKYLKPSGNMFPTIGDVHLAPFTDEQLYMEQFTKANFWYQPSFHGVDLSALRGAAVDEYFRQPVVDTFDIRILMAKSVKYTVNFLEAKEGDLHRIEIPFKFHMLHSGLVHGLAFWFDVAFIGSIMTVWLSTAPTEPLTHWYQVRCLFQSPLFAKAGDTLSGTCLLIANKRQSYDISIVAQVDQTGSKSSNLLDLKNPFFRYT 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 F from PDB  Type:PROTEIN  Length:7
                                       
               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
                 5dxa F  10 APrPPFS  16
                              |    
                             12-NMM


Chain G from PDB  Type:PROTEIN  Length:6
                                      
               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
                 5dxa G  10 APrPPF  15
                              |   
                             12-NMM


Chain I from PDB  Type:PROTEIN  Length:7
                                       
               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
                 5dxa I  10 APrPPFS  16
                              |    
                              |    
                             12-NMM
   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 5DXA)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (75, 79)

Asymmetric Unit(hide GO term definitions)

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  PABP1_HUMAN | P11940
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 Related Entries

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

UniProtKB/Swiss-Prot
        CARM1_HUMAN | Q86X55: 2y1w 2y1x 4ikp 5dwq 5dx0 5dx1 5dx8 5dxj 5u4x
        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 5lgp 5lgq 5lgr 5lgs

(-) Related Entries Specified in the PDB File

5dwq 5dx0 5dx1 5dx8 5dxj