8QL2

Ultrafast structural transitions in an azobenzene photoswitch at near-atomic resolution: dark structure

• PDB DOI: https://doi.org/10.2210/pdb8QL2/pdb
• Entry: 8QL2 supersedes: 7YYQ

• Classification: CELL CYCLE
• Organism(s): Bos taurus, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-09-19 Released: 2024-10-30 
• Deposition Author(s): Weinert, T., Wranik, M., Seidel, H.-P., Church, J., Steinmetz, M.O., Schapiro, I., Standfuss, J.
• Funding Organization(s): Swiss National Science Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.181 
• R-Value Work: 0.162 
• R-Value Observed: 0.162 

Starting Model: experimental

Literature

Ultrafast structural transitions in an azobenzene photoswitch at near-atomic resolution

Weinert, T., Wranik, M., Seidel, H.-P., Church, J., Steinmetz, M.O., Schapiro, I., Standfuss, J.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 119.73 kDa 
• Atom Count: 9,026 
• Modelled Residue Count: 1,017 
• Deposited Residue Count: 1,065 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin alpha-1B chain	A	451	Bos taurus	Mutation(s): 0  EC: 3.6.5
UniProt
Find proteins for P81947 (Bos taurus) Explore P81947  Go to UniProtKB:  P81947

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin beta-2B chain	B	445	Bos taurus	Mutation(s): 0
UniProt
Find proteins for Q6B856 (Bos taurus) Explore Q6B856  Go to UniProtKB:  Q6B856

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Designed Ankyrin Repeat Protein (DARPIN) D1	C [auth F]	169	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GTP	E [auth A], H [auth B]	GUANOSINE-5'-TRIPHOSPHATE C10 H16 N5 O14 P3 XKMLYUALXHKNFT-UUOKFMHZSA-N
IBL (Subject of Investigation/LOI)	G [auth B]	Azo-Combretastatin A4 (cis) C16 H18 N2 O5 AIRZFEKQGRSBNX-UHFFFAOYSA-N
CA	F [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG	D [auth A], I [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.181 
• R-Value Work: 0.162 
• R-Value Observed: 0.162 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.53	α = 90
b = 92.58	β = 96.71
c = 83.99	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
CrystFEL	data reduction
CrystFEL	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-10-30 
Deposition Author(s): Weinert, T., Wranik, M., Seidel, H.-P., Church, J., Steinmetz, M.O., Schapiro, I., Standfuss, J.
• This entry supersedes: 7YYQ

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Funding Organization	Location	Grant Number
Swiss National Science Foundation	Switzerland	310030_207462
Swiss National Science Foundation	Switzerland	310030_197674
Swiss National Science Foundation	Switzerland	310030_192566
Swiss National Science Foundation	Switzerland	CRSII5_213507

Revision History  

• Version 1.0: 2024-10-30
  Type: Initial release