8CLA | pdb_00008cla

Z-SBTubA4 photoswitch bound to tubulin-DARPin D1 complex

• PDB DOI: https://doi.org/10.2210/pdb8CLA/pdb

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


• Deposited: 2023-02-16 Released: 2024-02-28 
• Deposition Author(s): Wranik, M., Bertrand, Q., Kepa, M.W., Weinert, T., Steinmetz, M., Standfuss, J.
• Funding Organization(s): Swiss National Science Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.206 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.155 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.156 (Depositor) 

Starting Model: experimental

Literature

A multi-reservoir extruder for time-resolved serial protein crystallography and compound screening at X-ray free electron lasers

Wranik, M., Kepa, M.W., Beale, E.V., James, D., Bertrand, Q., Weinert, T., Furrer, A., Glover, H., Gashi, D., Carrillo, M., Kondo, Y., Stipp, R.T., Khusainov, G., Nass, K., Ozerov, D., Cirelli, C., Johnson, P.J.M., Dworkowski, F., Beale, J.H., Stubbs, S., Schneider, M., Krauskopf, K., Gao, L., Thorn-Seshold, O., Bostedt, C., Bacellar, C., Steinmetz, M.O., Milne, C., 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: 114.51 kDa 
• Atom Count: 8,413 
• Modelled Residue Count: 1,020 
• Deposited Residue Count: 1,020 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin alpha-1B chain	A	435	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	430	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]	155	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GTP	D [auth A]	GUANOSINE-5'-TRIPHOSPHATE C10 H16 N5 O14 P3 XKMLYUALXHKNFT-UUOKFMHZSA-N
GDP	G [auth B]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
I8R (Subject of Investigation/LOI)	H [auth B]	2-methoxy-5-[2-(5,6,7-trimethoxy-1,3-benzothiazol-2-yl)ethyl]phenol C19 H21 N O5 S AGSIMEHHCHGERU-UHFFFAOYSA-N
CA	F [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG	E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.206 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.155 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.156 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.23	α = 90
b = 90.94	β = 96.74
c = 82.43	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: 2024-02-28 
Deposition Author(s): Wranik, M., Bertrand, Q., Kepa, M.W., Weinert, T., Steinmetz, M., Standfuss, J.

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Funding Organization	Location	Grant Number
Swiss National Science Foundation	Switzerland	31003A_179351
Swiss National Science Foundation	Switzerland	310030_207462
Swiss National Science Foundation	Switzerland	310030_192566

Revision History  

• Version 1.0: 2024-02-28
  Type: Initial release