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(-) Description

Title :  CRYSTAL STRUCTURE OF DNMT3A-DNMT3L IN COMPLEX WITH HISTONE H3
 
Authors :  X. Guo, L. Wang, X. Yin, J. Li, J. Xiao, S. He, J. Wang, Y. Xu
Date :  31 Jul 14  (Deposition) - 12 Nov 14  (Release) - 04 Feb 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym./Biol. Unit :  A,B,C,D,F,G
Keywords :  Dna Methyltransferase, Active Form, Transferase-Transferase Regulator Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  X. Guo, L. Wang, J. Li, Z. Ding, J. Xiao, X. Yin, S. He, P. Shi, L. Dong, G. Li, C. Tian, J. Wang, Y. Cong, Y. Xu
Structural Insight Into Autoinhibition And Histone H3-Induced Activation Of Dnmt3A
Nature V. 517 640 2015
PubMed-ID: 25383530  |  Reference-DOI: 10.1038/NATURE13899

(-) Compounds

Molecule 1 - DNA (CYTOSINE-5)-METHYLTRANSFERASE 3A
    Chains: A, C
    EC Number: 2.1.1.37
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 476-912
    Gene: DNMT3A
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: DNA METHYLTRANSFERASES DNMT3A
 
Molecule 2 - DNA (CYTOSINE-5)-METHYLTRANSFERASE 3-LIKE
    Chains: B, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 178-379
    Gene: DNMT3L
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: DNA METHYLTRANSFERASES DNMT3L
 
Molecule 3 - PEPTIDE FROM HISTONE H3.3
    Chains: F, G
    Engineered: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: HISTONE H3 PEPTIDE
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDFG

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric/Biological Unit (2, 8)
No.NameCountTypeFull Name
1SAH2Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
2ZN6Ligand/IonZINC ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:494 , CYS A:497 , CYS A:514 , CYS A:517binding site for residue ZN A 1001
2AC2SOFTWARECYS A:537 , CYS A:540 , CYS A:559 , CYS A:562binding site for residue ZN A 1002
3AC3SOFTWARECYS A:549 , CYS A:554 , CYS A:583 , CYS A:586binding site for residue ZN A 1003
4AC4SOFTWAREPHE A:640 , ASP A:641 , GLY A:642 , ILE A:643 , THR A:645 , SER A:663 , GLU A:664 , VAL A:665 , CYS A:666 , ASP A:686 , VAL A:687 , ARG A:688 , GLY A:707 , ARG A:891 , SER A:892 , TRP A:893binding site for residue SAH A 1004
5AC5SOFTWARECYS C:494 , CYS C:497 , CYS C:514 , CYS C:517binding site for residue ZN C 1001
6AC6SOFTWARECYS C:537 , CYS C:540 , CYS C:559 , CYS C:562binding site for residue ZN C 1002
7AC7SOFTWARECYS C:549 , CYS C:554 , CYS C:583 , CYS C:586binding site for residue ZN C 1003
8AC8SOFTWAREPHE C:640 , ASP C:641 , GLY C:642 , ILE C:643 , THR C:645 , SER C:663 , GLU C:664 , VAL C:665 , CYS C:666 , ASP C:686 , VAL C:687 , ARG C:688 , GLY C:707 , LEU C:730 , ARG C:891 , SER C:892 , TRP C:893binding site for residue SAH C 1004

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4U7T)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Pro B:274 -Gly B:275
2Pro D:274 -Gly D:275
3Pro D:360 -Thr D:361

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4U7T)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4U7T)

(-) Exons   (0, 0)

(no "Exon" information available for 4U7T)

(-) 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:417
                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhh...hhhhh..........ee......eehhhhhhhhhhhh...................eeee........eeehhhhhhhh..hhhhhhhhh.....................hhhhhhhhhh.......hhhhh..eeeeee....hhhhhhhhhhh..eeeeeee..hhhhhhhhhhhhh...eee.hhhhhhhhhhhhh....eeee......................hhhhhhhhhhhhhh.........eeeeeee...hhhhhhhhhhhh....eeee.hhh..ee.eeeeee.................hhhhhh...eee....ee......eee..eee..hhhhhhhhh............hhhhhhhhhhhh.hhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4u7t A 474 EFRERLVYEVRQKCRNIEDICISCGSLNVTLEHPLFVGGMCQNCKNCFLECAYQYDDDGYQSYCTICCGGREVLMCGNNNCCRCFCVECVDLLVGPGAAQAAIKEDPWNCYMCGHKGTYGLLRRREDWPSRLQMFFAKVYPPVPAEKRKPIRVLSLFDGIATGLLVLKDLGIQVDRYIASEVCEDSITVGMVRHQGKIMYVGDVRSVTQKHIQEWGPFDLVIGGSPCNDLSIVNPARKGLYEGTGRLFFEFYRLLHDARPKEGDDRPFFWLFENVVAMGVSDKRDISRFLESNPVMIDAKEVSAAHRARYFWGNLPGMNRPLASTVNDKLELQECLEHGRIAKFSKVRTIQHFPVFMNEKEDILWCTEMERVFGFPVHYTDVSNMSRLARQRLLGRSWSVPVIRHLFAPLKEYFACV 912
                                   483       493       503       513       523       533       543       553       563       573       583       593       603      |623       633       643       653       663       673       683       693       703       713       723       733       743       753       763       773       783       793       803       813       823       833|      855       865       875       885       895       905       
                                                                                                                                                                  610|                                                                                                                                                                                                                 833|                                                                  
                                                                                                                                                                   621                                                                                                                                                                                                                  846                                                                  


Chain B from PDB  Type:PROTEIN  Length:187
                                                                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhh....eee....hhhhhh.............eee..hhhhhhhhhhhhh....eeeee..........hhhhhhhhhhhhhhhhh.........eeeeee....hhhhhhhhhhhh....ee........eeee..........hhhhhhhhhhhh.....hhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4u7t B 177 FMFETVPVWRRQPVRVLSLFEDIKKELTSLGFLESGSDPGQLKHVVDVTDTVRKDVEEWGPFDLVYGATPPLGHTCDRPPSWYLFQFHRLLQYARPKPGSPRPFFWMFVDNLVLNKEDLDVASRFLEMEPVTIPDVHGGVRVWSNIPAIRSALVSEEELSLLAQNKSSTKLVKNCFLPLREYFKYFS 379
                                   186       196       206       216       226       236       246       256       266       276       286       296       306       321       331||     344     ||362       372       
                                                                                                                                                                    315|        332|           350|||                  
                                                                                                                                                                     321         336            352||                  
                                                                                                                                                                                                 353|                  
                                                                                                                                                                                                  361                  


Chain C from PDB  Type:PROTEIN  Length:418
                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhh...hhhhh..........ee......eehhhhhhhhhhhh...................eeee........eeehhhhhhhh..hhhhhhhhh.....................hhhhhhhhhh...............eeeeee....hhhhhhhhhh...eeeeeee..hhhhhhhhhhhhh...eee.hhhhhhhhhhhhh....eeee......................hhhhhhhhhhhhhh.........eeeeeee...hhhhhhhhhhhh....eeee.hhh..ee.eeeeee.................hhhhhh...eee....ee......eee..eee..hhhhhhhhh............hhhhhhhhhhhh.hhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4u7t C 474 EFRERLVYEVRQKCRNIEDICISCGSLNVTLEHPLFVGGMCQNCKNCFLECAYQYDDDGYQSYCTICCGGREVLMCGNNNCCRCFCVECVDLLVGPGAAQAAIKEDPWNCYMCGHKGTYGLLRRREDWPSRLQMFFAPKVYPPVPAEKRKPIRVLSLFDGIATGLLVLKDLGIQVDRYIASEVCEDSITVGMVRHQGKIMYVGDVRSVTQKHIQEWGPFDLVIGGSPCNDLSIVNPARKGLYEGTGRLFFEFYRLLHDARPKEGDDRPFFWLFENVVAMGVSDKRDISRFLESNPVMIDAKEVSAAHRARYFWGNLPGMNRPLASTVNDKLELQECLEHGRIAKFSKVRTIQHFPVFMNEKEDILWCTEMERVFGFPVHYTDVSNMSRLARQRLLGRSWSVPVIRHLFAPLKEYFACV 912
                                   483       493       503       513       523       533       543       553       563       573       583       593       603      |622       632       642       652       662       672       682       692       702       712       722       732       742       752       762       772       782       792       802       812       822       832||     854       864       874       884       894       904        
                                                                                                                                                                  610|                                                                                                                                                                                                                  833|                                                                  
                                                                                                                                                                   620                                                                                                                                                                                                                   846                                                                  


Chain D from PDB  Type:PROTEIN  Length:191
                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhh....eee....hhhhhhhh...........eee..hhhhhhhhhhhhh....eeeee..........hhhhhhhhhhhhhhhhh.........eeeeee....hhhhhhhhhhhh....eee.....eeeee...hhhhh.....hhhhhhhhhhhh.......hhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4u7t D 177 FMFETVPVWRRQPVRVLSLFEDIKKELTSLGFLESGSDPGQLKHVVDVTDTVRKDVEEWGPFDLVYGATPPLGHTCDRPPSWYLFQFHRLLQYARPKPGSPRPFFWMFVDNLVLNKEDLDVASRFLEMEPVTIPDVHAVRVWSNIPAIRSRHWALVSEEELSLLAQNKQSSPTKLVKNCFLPLREYFKYFS 379
                                   186       196       206       216       226       236       246       256       266       276       286       296       306      |322       332       342       352||     368       378 
                                                                                                                                                                  313|                              353|                   
                                                                                                                                                                   320                               360                   


Chain F from PDB  Type:PROTEIN  Length:10
                                          
               SCOP domains ---------- SCOP domains
               CATH domains ---------- CATH domains
               Pfam domains ---------- Pfam domains
         Sec.struct. author ..eee..... Sec.struct. author
                 SAPs(SNPs) ---------- SAPs(SNPs)
                    PROSITE ---------- PROSITE
                 Transcript ---------- Transcript
                 4u7t F   1 ARTKQTARKS  10
                                    10


Chain G from PDB  Type:PROTEIN  Length:10
                                          
               SCOP domains ---------- SCOP domains
               CATH domains ---------- CATH domains
               Pfam domains ---------- Pfam domains
         Sec.struct. author ..eee..... Sec.struct. author
                 SAPs(SNPs) ---------- SAPs(SNPs)
                    PROSITE ---------- PROSITE
                 Transcript ---------- Transcript
                 4u7t G   1 ARTKQTARKS  10
                                    10
   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 4U7T)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4U7T)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4U7T)

(-) Gene Ontology  (85, 96)

Asymmetric/Biological Unit(hide GO term definitions)

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  4u7t
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  DNM3A_HUMAN | Q9Y6K1
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  2.1.1.37
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 Related Entries

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

UniProtKB/Swiss-Prot
        DNM3A_HUMAN | Q9Y6K1: 2qrv 3a1a 3a1b 3llr 3svm 4qbq 4qbr 4qbs 4u7p
        DNM3L_HUMAN | Q9UJW3: 2pv0 2pvc 2qrv 4u7p
        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 4w5a 5ay8 5b32 5b33 5bnv 5bnx 5dwq 5dx0 5ja4 5jjy 5jlb 5kdm 5x7x

(-) Related Entries Specified in the PDB File

4u7p