6CRO

CRYSTAL STRUCTURE OF LAMBDA-CRO BOUND TO A CONSENSUS OPERATOR AT 3.0 ANGSTROM RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Work: 0.194 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Crystal structure of lambda-Cro bound to a consensus operator at 3.0 A resolution.

Albright, R.A.Matthews, B.W.

(1998) J Mol Biol 280: 137-151

  • DOI: 10.1006/jmbi.1998.1848
  • Primary Citation of Related Structures:  
    6CRO

  • PubMed Abstract: 
  • The structure of the Cro protein from bacteriophage lambda in complex with a 19 base-pair DNA duplex that includes the 17 base-pair consensus operator has been determined at 3.0 A resolution. The structure confirms the large changes in the protein and DNA seen previously in a crystallographically distinct low-resolution structure of the complex and, for the first time, reveals the detailed interactions between the side-chains of the protein and the base-pairs of the operator ...

    The structure of the Cro protein from bacteriophage lambda in complex with a 19 base-pair DNA duplex that includes the 17 base-pair consensus operator has been determined at 3.0 A resolution. The structure confirms the large changes in the protein and DNA seen previously in a crystallographically distinct low-resolution structure of the complex and, for the first time, reveals the detailed interactions between the side-chains of the protein and the base-pairs of the operator. Relative to the crystal structure of the free protein, the subunits of Cro rotate 53 degrees with respect to each other on binding DNA. At the same time the DNA is bent by 40 degrees through the 19 base-pairs. The intersubunit connection includes a region within the protein core that is structurally reminiscent of the "ball and socket" motif seen in the immunoglobulins and T-cell receptors. The crystal structure of the Cro complex is consistent with virtually all available biochemical and related data. Some of the interactions between Cro and DNA proposed on the basis of model-building are now seen to be correct, but many are different. Tests of the original model by mutagenesis and biochemical analysis corrected some but not all of the errors. Within the limitations of the crystallographic resolution it appears that operator recognition is achieved almost entirely by direct hydrogen-bonding and van der Waals contacts between the protein and the exposed bases within the major groove of the DNA. The discrimination of Cro between the operators OR3 and OR1, which differ in sequence at just three positions, is inferred to result from a combination of small differences, both favorable and unfavorable. A van der Waals contact at one of the positions is of primary importance, while the other two provide smaller, indirect effects. Direct hydrogen bonding is not utilized in this distinction.


    Related Citations: 
    • Crystal Structure of an Engineered Cro Monomer Bound Nonspecifically to DNA: Possible Implications for Nonspecific Binding by the Wild-Type Protein
      Albright, R.A., Mossing, M.C., Matthews, B.W.
      (1998) Protein Sci 7: 1485
    • Refined Structure of Cro Repressor Protein from Bacteriophage Lambda Suggests Both Flexibility and Plasticity
      Ohlendorf, D.H., Tronrud, D.E., Matthews, B.W.
      (1998) J Mol Biol 280: 129
    • How Cro and Lambda-Repressor Distinguish between Operators: The Structural Basis Underlying a Genetic Switch
      Albright, R.A., Matthews, B.W.
      (1998) Proc Natl Acad Sci U S A 95: 3431
    • Protein-DNA Conformational Changes in the Crystal Structure of a Lambda Cro- Operator Complex
      Brennan, R.G., Roderick, S.L., Takeda, Y., Matthews, B.W.
      (1990) Proc Natl Acad Sci U S A 87: 8165

    Organizational Affiliation

    Institute of Molecular Biology Howard Hughes Medical Institute and Department of Physics, University of Oregon, Eugene, OR, 97403-1229, USA.



Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
LAMBDA CRO REPRESSORC [auth A]60Escherichia virus LambdaMutation(s): 0 
Gene Names: crolambdap57
UniProt
Find proteins for P03040 (Escherichia phage lambda)
Explore P03040 
Go to UniProtKB:  P03040
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03040
Protein Feature View
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  • Reference Sequence

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Entity ID: 1
MoleculeChainsLengthOrganismImage
DNA (5'-D(*AP*CP*TP*AP*TP*CP*AP*CP*CP*GP*CP*GP*GP*GP*TP*GP*AP*TP*AP*C)-3')A [auth R]20N/A
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
DNA (5'-D(*TP*GP*TP*AP*TP*CP*AP*CP*CP*CP*GP*CP*GP*GP*TP*GP*AP*TP*AP*G)-3')B [auth U]20N/A
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
D [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Work: 0.194 
  • Space Group: I 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.97α = 90
b = 102.97β = 90
c = 102.97γ = 90
Software Package:
Software NamePurpose
VERIFYmodel building
EDPDBmodel building
TNTrefinement
SDMSdata reduction
SDMSdata scaling
VERIFYphasing
EDPDBphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1998-09-18
    Type: Initial release
  • Version 1.1: 2008-05-22
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-11-29
    Changes: Derived calculations