5EFW | pdb_00005efw

Crystal structure of LOV2-Zdk1 - the complex of oat LOV2 and the affibody protein Zdark1

PDB DOI: https://doi.org/10.2210/pdb5EFW/pdb

Classification: SIGNALING PROTEIN
Organism(s): Avena sativa, Staphylococcus aureus
Expression System: Escherichia coli BL21(DE3), Escherichia coli
Mutation(s): Yes

Deposited: 2015-10-26 Released: 2016-07-20
Deposition Author(s): Winkler, A., Wang, H., Hartmann, E., Hahn, K., Schlichting, I.
Funding Organization(s): German Research Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.257 (Depositor), 0.260 (DCC)
R-Value Work:
0.202 (Depositor), 0.200 (DCC)
R-Value Observed:
0.204 (Depositor)

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

LOVTRAP: an optogenetic system for photoinduced protein dissociation.

Wang, H., Vilela, M., Winkler, A., Tarnawski, M., Schlichting, I., Yumerefendi, H., Kuhlman, B., Liu, R., Danuser, G., Hahn, K.M.

(2016) Nat Methods 13: 755-758

PubMed: 27427858 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/nmeth.3926
Primary Citation of Related Structures:
5DJT, 5DJU, 5EFW

PubMed Abstract:
LOVTRAP is an optogenetic approach for reversible light-induced protein dissociation using protein A fragments that bind to the LOV domain only in the dark, with tunable kinetics and a >150-fold change in the dissociation constant (Kd). By reversibly sequestering proteins at mitochondria, we precisely modulated the proteins' access to the cell edge, demonstrating a naturally occurring 3-mHz cell-edge oscillation driven by interactions of Vav2, Rac1, and PI3K proteins.

Organizational Affiliation

Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.

Macromolecule Content

Total Structure Weight: 30.8 kDa
Atom Count: 2,114
Modelled Residue Count: 245
Deposited Residue Count: 265
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NPH1-1	A	145	Avena sativa	Mutation(s): 1 Gene Names: NPH1-1 EC: 2.7.11.1
UniProt
Find proteins for O49003 (Avena sativa) Explore O49003 Go to UniProtKB: O49003
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O49003
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Z-dark, a small protein based on the Z domain affibody	B, C	60	Staphylococcus aureus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FMN Query on FMN Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	FLAVIN MONONUCLEOTIDE C₁₇ H₂₁ N₄ O₉ P FVTCRASFADXXNN-SCRDCRAPSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain J [auth B] SDF format, chain I [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B]	E [auth A] F [auth A] G [auth A] H [auth A] I [auth B] E [auth A], F [auth A], G [auth A], H [auth A], I [auth B], J [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain J [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain J [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.257 (Depositor), 0.260 (DCC)
R-Value Work: 0.202 (Depositor), 0.200 (DCC)
R-Value Observed: 0.204 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.7	α = 90
b = 54.7	β = 90
c = 188.03	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
Coot	model building
PHENIX	refinement
PDB_EXTRACT	data extraction
XSCALE	data scaling
PHASER	phasing
XSCALE	data reduction

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2016-07-20

Deposition Author(s):

Funding Organization	Location	Grant Number
German Research Foundation	Germany	FOR1279

Revision History (Full details and data files)

Version 1.0: 2016-07-20
Type: Initial release
Version 1.1: 2016-07-27
Changes: Database references
Version 1.2: 2016-09-07
Changes: Database references
Version 1.3: 2018-01-31
Changes: Author supporting evidence, Database references
Version 1.4: 2024-01-10
Changes: Data collection, Database references, Refinement description