6QRI

Structure of rabbit G-actin in complex with chivosazole A

PDB DOI: https://doi.org/10.2210/pdb6QRI/pdb

Classification: CYTOSOLIC PROTEIN
Organism(s): Oryctolagus cuniculus
Expression System: Oryctolagus cuniculus
Mutation(s): No

Deposited: 2019-02-19 Released: 2019-07-03
Deposition Author(s): Schneider, S., Wang, S., Zahler, S.
Funding Organization(s): German Research Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.268
R-Value Work: 0.236
R-Value Observed: 0.238

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Chivosazole A Modulates Protein-Protein Interactions of Actin.

Wang, S., Gegenfurtner, F.A., Crevenna, A.H., Ziegenhain, C., Kliesmete, Z., Enard, W., Muller, R., Vollmar, A.M., Schneider, S., Zahler, S.

(2019) J Nat Prod 82: 1961-1970

PubMed: 31260301 Search on PubMed
DOI: https://doi.org/10.1021/acs.jnatprod.9b00335
Primary Citation of Related Structures:
6QRI

PubMed Abstract:
Actin is a protein of central importance for many cellular key processes. It is regulated by local interactions with a large number of actin binding proteins (ABPs). Various compounds are known to either increase or decrease the polymerization dynamics of actin. However, no actin binding compound has been developed for clinical applications yet because of selectivity issues. We provide a crystal structure of the natural product chivosazole A (ChivoA) bound to actin and show that-in addition to inhibiting nucleation, polymerization, and severing of F-actin filaments-it selectively modulates binding of ABPs to G-actin: Although unphysiological actin dimers are induced by ChivoA, interaction with gelsolin, profilin, cofilin, and thymosin-β4 is inhibited. Moreover, ChivoA causes transcriptional effects differing from latrunculin B, an actin binder with a different binding site. Our data show that ChivoA and related compounds could serve as scaffolds for the development of actin binding molecules selectively targeting specific actin functions.

Organizational Affiliation

Department of Pharmacy , Ludwig-Maximilians-University , 81377 Munich , Germany.

Macromolecule Content

Total Structure Weight: 87.02 kDa
Atom Count: 5,861
Modelled Residue Count: 718
Deposited Residue Count: 754
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Actin, alpha skeletal muscle	A [auth B], B [auth A]	377	Oryctolagus cuniculus	Mutation(s): 0 Gene Names: ACTA1, ACTA
UniProt
Find proteins for P68135 (Oryctolagus cuniculus) Explore P68135 Go to UniProtKB: P68135
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P68135
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CV9 (Subject of Investigation/LOI) Query on CV9 Download Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain H [auth A] MOL2 format, chain E [auth B] MOL2 format, chain H [auth A]	E [auth B], H [auth A]	(2~{R},3~{R},5~{S},6~{E},8~{E},10~{Z},12~{S},13~{R},16~{Z},18~{E},20~{Z},22~{E},24~{R},25~{S},26~{E},28~{Z})-13-[(2~{S},3~{S},5~{S})-3,5-bis(oxidanyl)hexan-2-yl]-25-[(2~{R},3~{R},4~{S},5~{R},6~{R})-3,4-dimethoxy-6-methyl-5-oxidanyl-oxan-2-yl]oxy-3-methoxy-2,12,22,24-tetramethyl-5-oxidanyl-14,32-dioxa-33-azabicyclo[28.2.1]tritriaconta-1(33),6,8,10,16,18,20,22,26,28,30-undecaen-15-one C₄₉ H₇₁ N O₁₂ OVMUGRSUGHRYEC-QKLXNKFISA-N		Interactions Focus chain E [auth B] Focus chain H [auth A] Interactions & Density Focus chain E [auth B] Focus chain H [auth A]
ATP Query on ATP Download Ideal Coordinates CCD File SDF format, chain C [auth B] SDF format, chain F [auth A] MOL2 format, chain C [auth B] MOL2 format, chain F [auth A]	C [auth B], F [auth A]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain C [auth B] Focus chain F [auth A] Interactions & Density Focus chain C [auth B] Focus chain F [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain G [auth A] MOL2 format, chain D [auth B] MOL2 format, chain G [auth A]	D [auth B], G [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain D [auth B] Focus chain G [auth A] Interactions & Density Focus chain D [auth B] Focus chain G [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
HIC Query on HIC	A [auth B], B [auth A]	L-PEPTIDE LINKING	C₇ H₁₁ N₃ O₂		HIS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.268
R-Value Work: 0.236
R-Value Observed: 0.238
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.54	α = 90
b = 78.619	β = 115.11
c = 77.055	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2019-07-03

Deposition Author(s):

Schneider, S.

Wang, S.

Zahler, S.

Funding Organization	Location	Grant Number
German Research Foundation	Germany	SCHN1273/6-1
German Research Foundation	Germany	SFB1032

Revision History (Full details and data files)

Version 1.0: 2019-07-03
Type: Initial release
Version 1.1: 2019-07-10
Changes: Data collection, Database references
Version 1.2: 2019-08-07
Changes: Data collection, Database references
Version 1.3: 2024-01-24
Changes: Data collection, Database references, Derived calculations, Refinement description