2VTB

Structure of cryptochrome 3 - DNA complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.184 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Recognition and Repair of Uv Lesions in Loop Structures of Duplex DNA by Dash-Type Cryptochrome.

Pokorny, R.Klar, T.Hennecke, U.Carell, T.Batschauer, A.Essen, L.-O.

(2008) Proc.Natl.Acad.Sci.USA 105: 21023

  • DOI: 10.1073/pnas.0805830106

  • PubMed Abstract: 
  • DNA photolyases and cryptochromes (cry) form a family of flavoproteins that use light energy in the blue/UV-A region for the repair of UV-induced DNA lesions or for signaling, respectively. Very recently, it was shown that members of the DASH cryptoc ...

    DNA photolyases and cryptochromes (cry) form a family of flavoproteins that use light energy in the blue/UV-A region for the repair of UV-induced DNA lesions or for signaling, respectively. Very recently, it was shown that members of the DASH cryptochrome subclade repair specifically cyclobutane pyrimidine dimers (CPDs) in UV-damaged single-stranded DNA. Here, we report the crystal structure of Arabidopsis cryptochrome 3 with an in-situ-repaired CPD substrate in single-stranded DNA. The structure shows a binding mode similar to that of conventional DNA photolyases. Furthermore, CPD lesions in double-stranded DNA are bound and repaired with similar efficiency as in single-stranded DNA if the CPD lesion is present in a loop structure. Together, these data reveal that DASH cryptochromes catalyze light-driven DNA repair like conventional photolyases but lack an efficient flipping mechanism for interaction with CPD lesions within duplex DNA.


    Related Citations: 
    • Cryptochrome 3 from Arabidopsis Thaliana: Structural and Functional Analysis of its Complex with a Folate Light Antenna.
      Klar, T.,Pokorny, R.,Moldt, J.,Batschauer, A.,Essen, L.
      (2007) J.Mol.Biol. 366: 954


    Organizational Affiliation

    Department of Biology, Philipps University, Karl-von-Frisch-Strasse 8, D-35032 Marburg, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CRYPTOCHROME DASH
A, C, D, E, F
526Arabidopsis thalianaMutation(s): 0 
Gene Names: CRYD (CRY3)
Find proteins for Q84KJ5 (Arabidopsis thaliana)
Go to UniProtKB:  Q84KJ5
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
CRYPTOCHROME DASH
B
525Arabidopsis thalianaMutation(s): 0 
Gene Names: CRYD (CRY3)
Find proteins for Q84KJ5 (Arabidopsis thaliana)
Go to UniProtKB:  Q84KJ5
Entity ID: 3
MoleculeChainsLengthOrganism
5'-D(*DT*DT*DT*DT*DTP)-3'G,H,I,J,K,L5Homo sapiens
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MHF
Query on MHF

Download SDF File 
Download CCD File 
A, B, C, D, E, F
5,10-METHENYL-6,7,8-TRIHYDROFOLIC ACID
C20 H23 N7 O6
QYNUQALWYRSVHF-OLZOCXBDSA-N
 Ligand Interaction
ACT
Query on ACT

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Download CCD File 
B
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A, B, C, D, E, F
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
FAD
Query on FAD

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Download CCD File 
A, B, C, D, E, F
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TCP
Query on TCP
G, H, I, J, K, L
DNA LINKINGC11 H16 N2 O5DT
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.184 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 120.734α = 90.00
b = 136.082β = 90.00
c = 211.484γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
REFMACrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-06-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance