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(-) Description

Title :  DNA BINDING PROTEIN AND DNA COMPLEX STRUCTURE
 
Authors :  G. Sheng, H. Zhao, J. Wang, Y. Rao, Y. Wang
Date :  14 May 13  (Deposition) - 29 Jan 14  (Release) - 29 Jan 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.41
Chains :  Asym. Unit :  A,B,C,D,E,F,M,N
Biol. Unit 1:  A,C,D,N  (1x)
Biol. Unit 2:  B,E,F,M  (1x)
Keywords :  Argonaute, Rna Interference, Dna Interference, Dna Binding Protein- Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Sheng, H. Zhao, J. Wang, Y. Rao, W. Tian, D. C. Swarts, J. Van Der Oost, D. J. Patel, Y. Wang
Structure-Based Cleavage Mechanism Of Thermus Thermophilus Argonaute Dna Guide Strand-Mediated Dna Target Cleavage.
Proc. Natl. Acad. Sci. Usa V. 111 652 2014
PubMed-ID: 24374628  |  Reference-DOI: 10.1073/PNAS.1321032111

(-) Compounds

Molecule 1 - UNCHARACTERIZED PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-SUMO
    Expression System Strain: ROSETTA
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: TT_P0026
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 262724
    Strain: HB27
 
Molecule 2 - DNA (5'- D(P*TP*GP*AP*GP*GP*TP*AP*GP*TP*AP*GP*GP*TP*TP*GP*TP*AP*TP*AP*GP*T)- 3')
    Chains: C, E
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - DNA (5'-D(P*TP*AP*CP*TP*AP*CP*CP*TP*CP*G)-3')
    Chains: D, F
    Engineered: YES
    Synthetic: YES
 
Molecule 4 - DNA (5'-D(*TP*AP*TP*AP*CP*AP*AP*CP*C)-3')
    Chains: M, N
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEFMN
Biological Unit 1 (1x): A CD   N
Biological Unit 2 (1x):  B  EFM 

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 8)
No.NameCountTypeFull Name
1DT2Ligand/IonTHYMIDINE-5'-MONOPHOSPHATE
2MN6Ligand/IonMANGANESE (II) ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1DT-1Ligand/IonTHYMIDINE-5'-MONOPHOSPHATE
2MN-1Ligand/IonMANGANESE (II) ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1DT-1Ligand/IonTHYMIDINE-5'-MONOPHOSPHATE
2MN-1Ligand/IonMANGANESE (II) ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:195 , TYR A:197 , ARG A:200 , TRP A:202 , LEU A:217 , PRO A:218 , TYR A:226 , HIS A:227 , ARG A:232 , ILE A:254 , PRO A:255 , HIS A:256 , HOH A:893 , PRO B:37 , GLY B:38 , ARG B:39BINDING SITE FOR RESIDUE DT A 701
2AC2SOFTWAREASP A:478 , ASP A:660 , MN A:703 , HOH A:822 , DT D:10 , HOH D:107BINDING SITE FOR RESIDUE MN A 702
3AC3SOFTWAREASP A:478 , ASP A:546 , MN A:702 , HOH A:803 , HOH A:806 , DT D:10 , DC N:9BINDING SITE FOR RESIDUE MN A 703
4AC4SOFTWAREPRO A:37 , GLY A:38 , ARG A:39 , TYR B:197 , ARG B:200 , TYR B:226 , HIS B:227 , ARG B:232 , PRO B:255 , HIS B:256BINDING SITE FOR RESIDUE DT B 701
5AC5SOFTWAREASP B:478 , ASP B:546 , MN B:703 , HOH B:801 , HOH B:936 , DT F:10 , DC M:9BINDING SITE FOR RESIDUE MN B 702
6AC6SOFTWAREASP B:478 , ASP B:660 , MN B:702 , HOH B:823 , HOH B:867 , DT F:10BINDING SITE FOR RESIDUE MN B 703
7AC7SOFTWAREVAL A:685 , HOH A:824 , DT C:1 , DA C:3 , HOH C:202BINDING SITE FOR RESIDUE MN C 101
8AC8SOFTWAREVAL B:685 , HOH B:838 , DT E:1 , DA E:3 , HOH E:203BINDING SITE FOR RESIDUE MN E 101

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Asp A:34 -Pro A:35
2Glu A:125 -Gly A:126
3Val A:437 -Pro A:438
4Asp B:34 -Pro B:35
5Glu B:125 -Gly B:126
6Val B:437 -Pro B:438

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4KPY)

(-) 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:676
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeeeeeeee........eeeeeeee......hhhhhhhhhhhhhh..eeee..eeee..hhhhh..eeee......eeeeeeeeee......hhhhhhhhhhhhhhhhhhhhhh....eee..eeeeeeeeee..eeeeeeeeeeeee....eeeeeeeeeeeeee..hhhhhhh.......eeee.....eeeeeeee.............hhhhhhhhh..........eeeee...eeeee...eee..hhhhh......hhhhhhhhhhhhhhhhhhhh.....eeeeeeeee.....ee...ee.hhhhhhhhh......eeeeeee.......hhhhhhhhhhhhhhhh..eeeee...hhhhhhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhhhhhh...eeeee......hhhhhhhhhhhhhhhh.....ee.......eeeeeeee.....eeeeeeeee.....eeee...eee.....hhhhhhhhhhhhhhhhhhhhh....eeeeeee.......hhhhhhhhhhhh.eeeeeeee......eee........eeeeee..eeeee...hhhhh....eeeeeee...hhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kpy A   1 MNHLGKTEVFLNRFALRPLNPEELRPWRLEVVLDPPPGREEVYPLLAQVARRAGGVTVRMGDGLASWSPPEVLVLEGTLARMGQTYAYRLYPKGRRPLDPKDPGERSVLSALARRLLQERLRRLEGVWVEGLAVYRREHARGPGWRVLGGAVLDLWVSDSGAFLLEVDPAYRILCEMSLEAWLAQGHPLPKRVRNAYDRRTWELLRLGEEDPKELPLPGGLSLLDYHASKGRLQGREGGRVAWVADPKPIPHLTGLLVPVLTLEDLSLALSLPWEERRRRTREIASWIGRRLGLGTPEAVRAQAYRLSIPKLMGRRAVSKPADALRVGFYRAQETALALLRLDGAQGWPEFLRRALLRAFGASGASLRLHTLHAHPSQGLAFREALRKAKEEGVQAVLVLTPPMAWEDRNRLKALLLREGLPSQILNVPLREEERHRWENALLGLLAKAGLQVVALSGAYPAELAVGFDAGGRESFRFGGAACAVGGDGGHLLWTLPEAQAGERIPQEVVWDLLEETLWAFRRKAGRLPSRVLLLRDGRVPQDEFALALEALAREGIAYDLVSVRKSGGGRVYPVQGRLADGLYVPLEDKTFLLLTVHRDFRGTPRPLKLVHEAGDTPLEALAHQIFHLTRLYPASGFAFPRLPAPLHLADRLVKEVGRLGIRHLKEVDREKLFFV 685
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240      |254       264     ||279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609       619       629       639       649       659       669       679      
                                                                                                                                                                                                                                                                                247|               270|                                                                                                                                                                                                                                                                                                                                                                                                                         
                                                                                                                                                                                                                                                                                 252                276                                                                                                                                                                                                                                                                                                                                                                                                                         


Chain B from PDB  Type:PROTEIN  Length:675
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeeeeee........eeeeeeee......hhhhhhhhhhhhh...eeee..eeee..hhhhh..eeeeee..eeeeeeeeeeee......hhhhhhhhhhhhhhhhhhhhhh....eee..eeeeeeee....eeeeeeeeeeeee....eeeeeeeeeeeeee..hhhhhhh.......eeee.....eeeeeeee...........hhhhhhhh...........eeeee...eeeee...eee..hhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh.....eeeeeeeee....eee......hhhhhhhhh......eeeeeee.......hhhhhhhhhhhhhhhh..eeeee...hhhhhhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhhhhhh...eeeee......hhhhhhhhhhhhhhhhh....eee......eeeeeeee.....eeeeeeeee.....eeee...eee.....hhhhhhhhhhhhhhhhhhhhh....eeeeeee.......hhhhhhhhhhhh.eeeeeeee......eee........eeeeee..eeeee............eeeeeee...hhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kpy B   3 HLGKTEVFLNRFALRPLNPEELRPWRLEVVLDPPPGREEVYPLLAQVARRAGGVTVRMGDGLASWSPPEVLVLEGTLARMGQTYAYRLYPKGRRPLDPKDPGERSVLSALARRLLQERLRRLEGVWVEGLAVYRREHARGPGWRVLGGAVLDLWVSDSGAFLLEVDPAYRILCEMSLEAWLAQGHPLPKRVRNAYDRRTWELLRLGEEDPKELPGGLSLLDYHASKGRLQGREGGRVAWVADPKPIPHLTGLLVPVLTLEDLHEEELALSLPWEERRRRTREIASWIGRRLGLGTPEAVRAQAYRLSIPKLMGRRAVSKPADALRVGFYRAQETALALLRLDGAQGWPEFLRRALLRAFGASGASLRLHTLHAHPSQGLAFREALRKAKEEGVQAVLVLTPPMAWEDRNRLKALLLREGLPSQILNVPLREEERHRWENALLGLLAKAGLQVVALSGAYPAELAVGFDAGGRESFRFGGAACAVGGDGGHLLWTLPEAQAGERIPQEVVWDLLEETLWAFRRKAGRLPSRVLLLRDGRVPQDEFALALEALAREGIAYDLVSVRKSGGGRVYPVQGRLADGLYVPLEDKTFLLLTVHRDFRGTPRPLKLVHEAGDTPLEALAHQIFHLTRLYPASGFAFPRLPAPLHLADRLVKEVGRLGIRHLKEVDREKLFFV 685
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212   ||  224       234       244  ||   258       268     ||280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680     
                                                                                                                                                                                                                                               216|                         247|                   274|                                                                                                                                                                                                                                                                                                                                                                                                                        
                                                                                                                                                                                                                                                219                          252                    277                                                                                                                                                                                                                                                                                                                                                                                                                        


Chain C from PDB  Type:DNA  Length:16
                                                
                 4kpy C   1 TGAGGTAGTAGGTTGT  16
                                    10      


Chain D from PDB  Type:DNA  Length:10
                                          
                 4kpy D  10 TACTACCTCG  19
                                    19


Chain E from PDB  Type:DNA  Length:16
                                                
                 4kpy E   1 TGAGGTAGTAGGTTGT  16
                                    10      


Chain F from PDB  Type:DNA  Length:10
                                          
                 4kpy F  10 TACTACCTCG  19
                                    19


Chain M from PDB  Type:DNA  Length:6
                                      
                 4kpy M   4 ACAACC   9


Chain N from PDB  Type:DNA  Length:6
                                      
                 4kpy N   4 ACAACC   9
   Legend:   → Mismatch (orange background)
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  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 4KPY)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)

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  Q746M7_THET2 | Q746M7
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 Related Entries

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

UniProtKB/TrEMBL
        Q746M7_THET2 | Q746M7: 3dlb 3dlh 3f73 3hjf 3hk2 3hm9 3ho1 3hvr 3hxm 4n41 4n47 4n76 4nca 4ncb

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4KPY)