2VTB | pdb_00002vtb

Structure of cryptochrome 3 - DNA complex

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 
    0.222 (Depositor), 0.231 (DCC) 
  • R-Value Work: 
    0.184 (Depositor), 0.195 (DCC) 
  • R-Value Observed: 
    0.185 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 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 U S A 105: 21023

  • DOI: https://doi.org/10.1073/pnas.0805830106
  • Primary Citation Related Structures: 
    2VTB

  • 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 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.

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

Macromolecule Content 

  • Total Structure Weight: 378.97 kDa 
  • Atom Count: 26,329 
  • Modeled Residue Count: 2,974 
  • Deposited Residue Count: 3,185 
  • Unique protein chains: 2
  • Unique nucleic acid chains: 1

Macromolecules


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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
CRYPTOCHROME DASH
A, C, D, E, F
526Arabidopsis thalianaMutation(s): 0 
EC: 4.1.99.3
UniProt
Find proteins for Q84KJ5 (Arabidopsis thaliana)
Explore Q84KJ5 
Go to UniProtKB:  Q84KJ5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ84KJ5
Sequence Annotations
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Reference Sequence
Find similar proteins by:
|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
CRYPTOCHROME DASH525Arabidopsis thalianaMutation(s): 0 
EC: 4.1.99.3
UniProt
Find proteins for Q84KJ5 (Arabidopsis thaliana)
Explore Q84KJ5 
Go to UniProtKB:  Q84KJ5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ84KJ5
Sequence Annotations
Expand
Reference Sequence
Find similar nucleic acids by:  Sequence
Entity ID: 3
MoleculeChains LengthOrganismImage
5'-D(*DT*DT*DT*DT*DTP)-3'
G, H, I, J, K
G, H, I, J, K, L
5Homo sapiens
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD

Query on FAD


Download:Ideal Coordinates CCD File
BA [auth E]
EA [auth F]
M [auth A]
P [auth B]
U [auth C]
BA [auth E],
EA [auth F],
M [auth A],
P [auth B],
U [auth C],
Y [auth D]
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
MHF

Query on MHF


Download:Ideal Coordinates CCD File
CA [auth E]
FA [auth F]
N [auth A]
Q [auth B]
V [auth C]
CA [auth E],
FA [auth F],
N [auth A],
Q [auth B],
V [auth C],
Z [auth D]
5,10-METHENYL-6,7,8-TRIHYDROFOLIC ACID
C20 H23 N7 O6
QYNUQALWYRSVHF-OLZOCXBDSA-N
ACT

Query on ACT


Download:Ideal Coordinates CCD File
T [auth B]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
CL

Query on CL


Download:Ideal Coordinates CCD File
AA [auth D]
DA [auth E]
GA [auth F]
O [auth A]
R [auth B]
AA [auth D],
DA [auth E],
GA [auth F],
O [auth A],
R [auth B],
S [auth B],
W [auth C],
X [auth C]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free:  0.222 (Depositor), 0.231 (DCC) 
  • R-Value Work:  0.184 (Depositor), 0.195 (DCC) 
  • R-Value Observed: 0.185 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 120.734α = 90
b = 136.082β = 90
c = 211.484γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-06-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2019-07-24
    Changes: Advisory, Data collection, Derived calculations
  • Version 1.3: 2023-12-13
    Changes: Advisory, Data collection, Database references, Derived calculations, Other, Refinement description