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(-) Description

Title :  CRYSTAL STRUCTURE OF CARM1, SINEFUNGIN, AND H3 PEPTIDE (R17)
 
Authors :  P. A. Boriack-Sjodin
Date :  23 Sep 15  (Deposition) - 25 Nov 15  (Release) - 30 Mar 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.05
Chains :  Asym. Unit :  A,B,C,D,F,G,H,I
Biol. Unit 1:  A,B,F,G  (1x)
Biol. Unit 2:  C,D,H,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 - H3 PEPTIDE
    Chains: F, G, H, I
    Engineered: YES
    Fragment: UNP RESIDUES 14-31
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDFGHI
Biological Unit 1 (1x): AB  FG  
Biological Unit 2 (1x):   CD  HI

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 14)

Asymmetric Unit (4, 14)
No.NameCountTypeFull Name
1ACE4Mod. Amino AcidACETYL GROUP
2GOL2Ligand/IonGLYCEROL
3SFG4Ligand/IonSINEFUNGIN
4SO44Ligand/IonSULFATE ION
Biological Unit 1 (4, 7)
No.NameCountTypeFull Name
1ACE2Mod. Amino AcidACETYL GROUP
2GOL1Ligand/IonGLYCEROL
3SFG2Ligand/IonSINEFUNGIN
4SO42Ligand/IonSULFATE ION
Biological Unit 2 (4, 7)
No.NameCountTypeFull Name
1ACE2Mod. Amino AcidACETYL GROUP
2GOL1Ligand/IonGLYCEROL
3SFG2Ligand/IonSINEFUNGIN
4SO42Ligand/IonSULFATE ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETYR A:149 , PHE A:150 , TYR A:153 , GLN A:159 , MET A:162 , ARG A:168 , CYS A:193 , ILE A:197 , LEU A:198 , GLU A:214 , ALA A:215 , LYS A:241 , VAL A:242 , GLU A:243 , GLU A:257 , MET A:268 , SER A:271 , HOH A:606 , HOH A:608 , HOH A:610 , HOH A:625 , ARG F:5binding site for residue SFG A 501
02AC2SOFTWAREASP A:392 , SER A:405binding site for residue GOL A 502
03AC3SOFTWAREGLN A:148 , LYS A:470 , HOH A:672 , GLN B:151binding site for residue SO4 A 503
04AC4SOFTWARETYR B:149 , PHE B:150 , TYR B:153 , GLN B:159 , MET B:162 , ARG B:168 , CYS B:193 , ILE B:197 , LEU B:198 , GLU B:214 , ALA B:215 , LYS B:241 , VAL B:242 , GLU B:243 , GLU B:257 , MET B:268 , SER B:271 , HOH B:617 , HOH B:618 , HOH B:643 , HOH B:647 , ARG G:5binding site for residue SFG B 501
05AC5SOFTWAREGLN A:151 , GLN B:148 , ARG B:445 , LYS B:470 , HOH G:103binding site for residue SO4 B 502
06AC6SOFTWARETYR C:149 , PHE C:150 , TYR C:153 , GLN C:159 , MET C:162 , ARG C:168 , CYS C:193 , ILE C:197 , LEU C:198 , GLU C:214 , ALA C:215 , LYS C:241 , VAL C:242 , GLU C:243 , GLU C:257 , MET C:268 , SER C:271 , HOH C:602 , HOH C:618 , HOH C:623 , HOH C:664 , ARG H:5binding site for residue SFG C 501
07AC7SOFTWAREASP C:392 , TRP C:403binding site for residue GOL C 502
08AC8SOFTWAREGLN C:148 , ARG C:445 , LYS C:470 , GLN D:151 , LYS H:2binding site for residue SO4 C 503
09AC9SOFTWARETYR D:149 , PHE D:150 , TYR D:153 , GLN D:159 , MET D:162 , ARG D:168 , CYS D:193 , ILE D:197 , LEU D:198 , GLU D:214 , ALA D:215 , LYS D:241 , VAL D:242 , GLU D:243 , GLU D:257 , MET D:268 , SER D:271 , HOH D:612 , HOH D:613 , HOH D:640 , HOH D:655 , ARG I:5binding site for residue SFG D 501
10AD1SOFTWAREGLN C:151 , GLN D:148 , ARG D:445 , LYS D:470 , HOH D:628 , LYS I:2binding site for residue SO4 D 502

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5DX0)

(-) 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 5DX0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5DX0)

(-) Exons   (0, 0)

(no "Exon" information available for 5DX0)

(-) 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: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.hhhhhhhhhhhhhhh.eee..hhhhh....eeeeee....hhhhh.eeeeeeeee....eeeeeeeeeeeeeee....eeeee...........eeeeeeeeeeee....eeeeeeeeee.....eeeeeeeee.....eeeeeee....ee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dx0 A 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 B 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...........hhhhhhhh...eeeeeeee..eeeeeeeee.hhhhhhhhhhhhhhhh........hhhhhhhhhhhhhh..eee..hhhhh....eeeeee....hhhhh.eeeeeeeee....eeeeeeeeeeeeeee....eeeee...........eeeeeeeeeeee....eeeeeeeeeee...eeeeeeeeee....eeeeeeee....ee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dx0 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 .hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...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
                 5dx0 C 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 D from PDB  Type:PROTEIN  Length:343
                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhh..eeeeee..hhhhhhhhhhhhh.....eeeee...........eeeeee..........hhhhhhhhh...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
                 5dx0 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: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
                 5dx0 F   0 xGKAPRKQL   8
                            |        
                            0-ACE    


Chain G from PDB  Type:PROTEIN  Length:10
                                          
               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
                 5dx0 G   0 xGKAPRKQLA   9
                            |        9
                            0-ACE     


Chain H 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
                 5dx0 H   0 xGKAPRKQL   8
                            |        
                            0-ACE    


Chain I from PDB  Type:PROTEIN  Length:10
                                          
               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
                 5dx0 I   0 xGKAPRKQLA   9
                            |        9
                            0-ACE
   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 5DX0)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5DX0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5DX0)

(-) Gene Ontology  (71, 74)

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  H33_HUMAN | P84243
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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 5dx1 5dx8 5dxa 5dxj 5u4x
        H33_HUMAN | P84243: 1pdq 2l43 3ask 3asl 3av2 3jvk 3muk 3mul 3ql9 3qla 3qlc 3wtp 4gne 4gnf 4gng 4gu0 4gur 4gus 4gy5 4h9n 4h9o 4h9p 4h9q 4h9r 4h9s 4hga 4l58 4n4i 4o62 4qq4 4tmp 4u7t 4w5a 5ay8 5b32 5b33 5bnv 5bnx 5dwq 5ja4 5jjy 5jlb 5kdm 5x7x

(-) Related Entries Specified in the PDB File

5dwq 5DWQ CONTAINS THE SAME PROTEIN WITH A METHYLATED H3 PEPTIDE
5dx1
5dx8
5dxa
5dxj