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(-) Description

Title :  CRYSTAL STRUCTURE OF A DESIGNED ZINC FINGER PROTEIN BOUND TO DNA
 
Authors :  C. A. Kim, J. M. Berg
Date :  27 Sep 96  (Deposition) - 12 Mar 97  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B,C,D,E,F,G
Biol. Unit 1:  A,B,C  (1x)
Biol. Unit 2:  D,E,F  (1x)
Biol. Unit 3:  G  (1x)
Keywords :  Zinc Finger, Protein-Dna Interaction, Protein Design, Crystal Structure, Complex (Zinc Finger/Dna), Transferase/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. A. Kim, J. M. Berg
A 2. 2 A Resolution Crystal Structure Of A Designed Zinc Finger Protein Bound To Dna
Nat. Struct. Biol. V. 3 940 1996
PubMed-ID: 8901872  |  Reference-DOI: 10.1038/NSB1196-940
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA (5'- D(*AP*TP*GP*AP*GP*GP*CP*AP*GP*AP*AP*CP*T)-3')
    Chains: A, D
    Engineered: YES
    Synthetic: YES
 
Molecule 2 - DNA (5'- D(*TP*AP*GP*TP*TP*CP*TP*GP*CP*CP*TP*(C38)P*A)-3')
    Chains: B, E
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - CONSENSUS ZINC FINGER
    Chains: C, F, G
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008

 Structural Features

(-) Chains, Units

  1234567
Asymmetric Unit : ABCDEFG
Biological Unit 1 (1x): ABC    
Biological Unit 2 (1x):    DEF 
Biological Unit 3 (1x):       G

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 11)

Asymmetric Unit (3, 11)
No.NameCountTypeFull Name
1C382Mod. Nucleotide5-IODO-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE
2CL1Ligand/IonCHLORIDE ION
3ZN8Ligand/IonZINC ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1C381Mod. Nucleotide5-IODO-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE
2CL-1Ligand/IonCHLORIDE ION
3ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1C381Mod. Nucleotide5-IODO-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE
2CL-1Ligand/IonCHLORIDE ION
3ZN-1Ligand/IonZINC ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1C38-1Mod. Nucleotide5-IODO-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE
2CL-1Ligand/IonCHLORIDE ION
3ZN-1Ligand/IonZINC ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS C:7 , CYS C:10 , HIS C:23 , HIS C:27BINDING SITE FOR RESIDUE ZN C 88
2AC2SOFTWARECYS C:35 , CYS C:38 , HIS C:51 , HIS C:55BINDING SITE FOR RESIDUE ZN C 89
3AC3SOFTWARECYS C:63 , CYS C:66 , HIS C:79 , HIS C:83BINDING SITE FOR RESIDUE ZN C 90
4AC4SOFTWARECYS F:7 , CYS F:10 , HIS F:23 , HIS F:27BINDING SITE FOR RESIDUE ZN F 88
5AC5SOFTWARECYS F:35 , CYS F:38 , HIS F:51 , HIS F:55BINDING SITE FOR RESIDUE ZN F 89
6AC6SOFTWARECYS F:63 , CYS F:66 , HIS F:79 , HIS F:83BINDING SITE FOR RESIDUE ZN F 90
7AC7SOFTWARECYS G:63 , CYS G:66 , HIS G:79 , HIS G:83BINDING SITE FOR RESIDUE ZN G 90
8AC8SOFTWAREHIS C:27 , HOH C:110 , HIS G:75 , CL G:92BINDING SITE FOR RESIDUE ZN G 91
9AC9SOFTWAREHIS C:27 , LYS G:59 , ARG G:72 , HIS G:75 , ZN G:91BINDING SITE FOR RESIDUE CL G 92

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1MEY)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1MEY)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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(-) PROSITE Motifs  (0, 0)

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(-) Exons   (0, 0)

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(-) 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:DNA  Length:13
                                            
                  1mey A  1 ATGAGGCAGAACT 13
                                    10   


Chain B from PDB  Type:DNA  Length:13
                                            
                  1mey B  1 TAGTTCTGCCTcA 13
                                    10 | 
                                      12-C38


Chain C from PDB  Type:PROTEIN  Length:83
                                                                                                                  
               SCOP domains d1meyc_ C: Designed zinc finger protein                                             SCOP domains
               CATH domains 1meyC01 C:2-29              1meyC02 C:30-55           1meyC03 C:56-84               CATH domains
               Pfam domains ----------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee......ee..hhhhhhhhhhhh....ee......ee..hhhhhhhhhhhh....ee......ee..hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------- Transcript
                  1mey C  2 EKPYKCPECGKSFSQSSNLQKHQRTHTGEKPYKCPECGKSFSQSSDLQKHQRTHTGEKPYKCPECGKSFSRSDHLSRHQRTHQ 84
                                    11        21        31        41        51        61        71        81   


Chain D from PDB  Type:DNA  Length:13
                                            
                  1mey D  1 ATGAGGCAGAACT 13
                                    10   


Chain E from PDB  Type:DNA  Length:13
                                            
                  1mey E  1 TAGTTCTGCCTcA 13
                                    10 | 
                                      12-C38


Chain F from PDB  Type:PROTEIN  Length:84
                                                                                                                   
               SCOP domains d1meyf_ F: Designed zinc finger protein                                              SCOP domains
               CATH domains -1meyF01 F:2-29              1meyF02 F:30-55           1meyF03 F:56-84               CATH domains
               Pfam domains ------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....ee......ee..hhhhhhhhhhhh....ee......ee..hhhhhhhhhhhh....ee......ee..hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------ Transcript
                  1mey F  1 MEKPYKCPECGKSFSQSSNLQKHQRTHTGEKPYKCPECGKSFSQSSDLQKHQRTHTGEKPYKCPECGKSFSRSDHLSRHQRTHQ 84
                                    10        20        30        40        50        60        70        80    


Chain G from PDB  Type:PROTEIN  Length:28
                                                           
               SCOP domains d1meyg_ G:                   SCOP domains
               CATH domains 1meyG00 G:56-83              CATH domains
               Pfam domains ---------------------------- Pfam domains
         Sec.struct. author .....ee......ee..hhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------- SAPs(SNPs)
                    PROSITE ---------------------------- PROSITE
                 Transcript ---------------------------- Transcript
                  1mey G 56 TGEKPYKCPECGKSFSRSDHLSRHQRTH 83
                                    65        75
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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  (1, 3)

Asymmetric Unit
(-)
Class: Designed proteins (167)

(-) CATH Domains  (1, 7)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1MEY)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
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