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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN NEIL1(242K) BOUND TO DUPLEX DNA CONTAINING THF
 
Authors :  C. Zhu, L. Lu, J. Zhang, Z. Yue, J. Song, S. Zong, M. Liu, O. Stovicek, Y. Ga
Date :  17 Mar 16  (Deposition) - 06 Jul 16  (Release) - 03 Aug 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.41
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H,I
Biol. Unit 1:  A,D,E  (1x)
Biol. Unit 2:  B,F,G  (1x)
Biol. Unit 3:  C,H,I  (1x)
Keywords :  Dna Glycosylase Neil1 Fpg Nei Base Excision Repair, Dna Binding Protein-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Zhu, L. Lu, J. Zhang, Z. Yue, J. Song, S. Zong, M. Liu, O. Stovicek, Y. Q. Gao, C. Yi
Tautomerization-Dependent Recognition And Excision Of Oxidation Damage In Base-Excision Dna Repair
Proc. Natl. Acad. Sci. Usa V. 113 7792 2016
PubMed-ID: 27354518  |  Reference-DOI: 10.1073/PNAS.1604591113

(-) Compounds

Molecule 1 - ENDONUCLEASE 8-LIKE 1
    Chains: A, B, C
    EC Number: 3.2.2.-, 4.2.99.18
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: NEIL1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: DNA GLYCOSYLASE/AP LYASE NEIL1,DNA-(APURINIC OR APYRIMIDINIC SITE) LYASE NEIL1,ENDONUCLEASE VIII-LIKE 1,FPG1,NEI HOMOLOG 1,NEH1, NEI-LIKE PROTEIN 1
 
Molecule 2 - DNA (5'-D(*CP*GP*TP*CP*CP*AP*CP*GP*TP*CP*TP*AP*C)-3')
    Chains: D, F, H
    Engineered: YES
    Organism Scientific: UNIDENTIFIED
    Organism Taxid: 32644
    Synthetic: YES
 
Molecule 3 - DNA (5'-D(*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*GP*G)-3')
    Chains: E, G, I
    Engineered: YES
    Organism Scientific: UNIDENTIFIED
    Organism Taxid: 32644
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456789
Asymmetric Unit : ABCDEFGHI
Biological Unit 1 (1x): A  DE    
Biological Unit 2 (1x):  B   FG  
Biological Unit 3 (1x):   C    HI

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 5ITU)

(-) Sites  (0, 0)

(no "Site" information available for 5ITU)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Gln B:67 -Pro B:68

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5ITU)

(-) 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:268
                                                                                                                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh....eeeeeee...........eeeeeeeeeeee..eeeeeeee..........eeeeee.....eeeeee.......eeeeeee......eeeeee......eeee..............hhhhhhhhhhh...hhhhhhhhhhhh.........hhhhhhhhhhhhh.....hhhhhhh....hhhhhhhhhhhhhhhhh.hhhhh...hhhhhhhhhh........eeee.....eeee......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5itu A   2 PEGPELHLASQFVNEACRALVFGGCVEKSSVSRNPEVPFESSAYRISASARGKELRLILSPLPGAQPQQEPLALVFRFGMSGSFQLVPREELPRHAHLRFYTAPPGPRLALCFVDIRRFGRWDLGGKWQPGRGPCVLQEYQQFRENVLRNLADKAFDRPICEALLDQRFFNGIGNYLRAEILYRLKIPPFEKARSVLEALNPDLLELCHSVPKEVVQLGGKGYGSSGEEDFAAFRAWLRCYGMPGMSSLQDRHGRTIWFQGDPGPLAP 290
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201|      231       241    || 252       262       272       282        
                                                                                                                                                                                                                                 201|                     246|                                          
                                                                                                                                                                                                                                  222                      248                                          


Chain B from PDB  Type:PROTEIN  Length:255
                                                                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh...eeeeeee...........eeeeeeeeeeee..eeeeeeee..........eeeeee....eeeeeee.......eeeeeee......eeeeeee.....eeee..............hhhhhhhhhhh...hhhhhhhhhhhh.........hhhhhhhhhhhh......hhhhhhhh...hhhhhhhhhhhhhhhh.hhhhhh........eeee.....eeee......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5itu B   2 PEGPELHLASQFVNEACRALVFGGCVEKSSVSRNPEVPFESSAYRISASARGKELRLILSPLPGAQPQQEPLALVFRFGMSGSFQLVPREELPRHAHLRFYTAPPGPRLALCFVDIRRFGRWDLGGKWQPGRGPCVLQEYQQFRENVLRNLADKAFDRPICEALLDQRFFNGIGNYLRAEILYRLKIPPFEKARSVLEALQPDLLELCHSVPKEVVQLAAFRAWLRCYGMPGMSSLQDRHGRTIWFQGDPGPLAP 290
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201||     231       255       265       275       285     
                                                                                                                                                                                                                                  202|             239|                                    
                                                                                                                                                                                                                                   223              254                                    


Chain C from PDB  Type:PROTEIN  Length:271
                                                                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh..........................eeee....eeee.............eeee.......eeee........eeeeee........eeeee.......ee..............hhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhh.......hhhhhhh...............hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh........eeee...eeee......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5itu C   2 PEGPELHLASQFVNEACRALVFGCEKSSVSRNPEVPFESSAYRISASARGKELRLILSPLPGAPQQEPLALVFRFGMSGSFQLVPREELPRHAHLRFYTAPPGPRLALCFVDIRRFGRWDLGKWQPGRGPCVLQEYQQFRENVLRNLDKAFDRPICEALLDQRFFNGIGNYLRAEILYRLKIPPFEKARSVLEALQTLSQKITKLQNPDLLELCHSVPKEVVQLGGKYGESGEEDFAAFRAWLRCYGMPGMSSLQDGRTIWFQGDPGPLAP 290
                                    11        21 ||||   33        43        53        63  ||    74        84        94       104       114       124 ||    135       145      |156       166       176       186       196     ||214 ||    225       235      |247       257       267     ||279       289 
                                                23|||                                    66|                                                       126|                     152|                                             202|  216|                     242|||                       273|              
                                                 25||                                     68                                                        128                      154                                              211   218                      244||                        276              
                                                  26|                                                                                                                                                                                                         245|                                         
                                                   28                                                                                                                                                                                                          247                                         


Chain D from PDB  Type:DNA  Length:13
                                             
                 5itu D   1 CGTCCACGTCTAC  13
                                    10   


Chain E from PDB  Type:DNA  Length:13
                                             
                 5itu E   1 TAGACCTGGACGG  13
                                    10   


Chain F from PDB  Type:DNA  Length:13
                                             
                 5itu F   1 CGTCCACGTCTAC  13
                                    10   


Chain G from PDB  Type:DNA  Length:13
                                             
                 5itu G   1 TAGACCTGGACGG  13
                                    10   


Chain H from PDB  Type:DNA  Length:13
                                             
                 5itu H   1 CGTCCACGTCTAC  13
                                    10   


Chain I from PDB  Type:DNA  Length:13
                                             
                 5itu I   1 TAGACCTGGACGG  13
                                    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 5ITU)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (26, 26)

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    Gln B:67 - Pro B:68   [ RasMol ]  
 
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 Related Entries

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

UniProtKB/Swiss-Prot
        NEIL1_HUMAN | Q96FI4: 1tdh 4nrv 5itq 5itr 5itt 5itx 5ity

(-) Related Entries Specified in the PDB File

5itq 5itr 5itt 5itx 5ity