3G37

Cryo-EM structure of actin filament in the presence of phosphate

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.00 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


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


Literature

Structural basis for actin assembly, activation of ATP hydrolysis, and delayed phosphate release

Murakami, K., Yasunaga, T., Noguchi, T.Q., Gomibuchi, Y., Ngo, K.X., Uyeda, T.Q., Wakabayashi, T.

(2010) Cell 143: 275-287

  • DOI: https://doi.org/10.1016/j.cell.2010.09.034
  • Primary Citation of Related Structures:  
    3A5L, 3A5M, 3A5N, 3A5O, 3G37

  • PubMed Abstract: 

    Assembled actin filaments support cellular signaling, intracellular trafficking, and cytokinesis. ATP hydrolysis triggered by actin assembly provides the structural cues for filament turnover in vivo. Here, we present the cryo-electron microscopic (cryo-EM) structure of filamentous actin (F-actin) in the presence of phosphate, with the visualization of some α-helical backbones and large side chains. A complete atomic model based on the EM map identified intermolecular interactions mediated by bound magnesium and phosphate ions. Comparison of the F-actin model with G-actin monomer crystal structures reveals a critical role for bending of the conserved proline-rich loop in triggering phosphate release following ATP hydrolysis. Crystal structures of G-actin show that mutations in this loop trap the catalytic site in two intermediate states of the ATPase cycle. The combined structural information allows us to propose a detailed molecular mechanism for the biochemical events, including actin polymerization and ATPase activation, critical for actin filament dynamics.

    • Organizational Affiliation: 

    Department of Biosciences, School of Science and Engineering, Teikyo University, Toyosatodai 1-1, Utsunomiya 320-8551, Japan.


Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Actin, alpha skeletal muscle376Oryctolagus cuniculusMutation(s): 1 
UniProt
Find proteins for P68135 (Oryctolagus cuniculus)
Explore P68135 
Go to UniProtKB:  P68135
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP68135
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP
Download Ideal Coordinates CCD File 
AB [auth S]
AD [auth X]
FA [auth Q]
FC [auth V]
JD [auth Y]
AB [auth S],
AD [auth X],
FA [auth Q],
FC [auth V],
JD [auth Y],
M [auth O],
NB [auth T],
PC [auth W],
RA [auth R],
UD [auth Z],
VB [auth U],
X [auth P]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
PO4
Query on PO4
Download Ideal Coordinates CCD File 
BB [auth S]
BD [auth X]
CB [auth S]
CD [auth X]
EC [auth U]
BB [auth S],
BD [auth X],
CB [auth S],
CD [auth X],
EC [auth U],
GA [auth Q],
GC [auth V],
HA [auth Q],
HC [auth V],
JB [auth S],
KD [auth Y],
LB [auth T],
LD [auth Y],
MB [auth T],
N [auth O],
O,
OB [auth T],
PA [auth Q],
PB [auth T],
QA [auth R],
QC [auth W],
RC [auth W],
RD [auth Y],
SA [auth R],
TA [auth R],
TD [auth Z],
V [auth O],
VD [auth Z],
W [auth P],
WB [auth U],
WD [auth Z],
XB [auth U],
XC [auth W],
Y [auth P],
Z [auth P],
ZC [auth X]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
MG
Query on MG
Download Ideal Coordinates CCD File 
AA [auth P]
AC [auth U]
AE [auth Z]
BA [auth P]
BC [auth U]
AA [auth P],
AC [auth U],
AE [auth Z],
BA [auth P],
BC [auth U],
BE [auth Z],
CA [auth P],
CC [auth U],
DA [auth P],
DB [auth S],
DC [auth U],
DD [auth X],
EA [auth P],
EB [auth S],
ED [auth X],
FB [auth S],
FD [auth X],
GB [auth S],
GD [auth X],
HB [auth S],
HD [auth X],
IA [auth Q],
IB [auth S],
IC [auth V],
ID [auth Y],
JA [auth Q],
JC [auth V],
KA [auth Q],
KB [auth T],
KC [auth V],
LA [auth Q],
LC [auth V],
MA [auth Q],
MC [auth V],
MD [auth Y],
NA [auth Q],
NC [auth V],
ND [auth Y],
OA [auth Q],
OC [auth W],
OD [auth Y],
P [auth O],
PD [auth Y],
Q [auth O],
QB [auth T],
QD [auth Y],
R [auth O],
RB [auth T],
S [auth O],
SB [auth T],
SC [auth W],
SD [auth Z],
T [auth O],
TB [auth T],
TC [auth W],
U [auth O],
UA [auth R],
UB [auth T],
UC [auth W],
VA [auth R],
VC [auth W],
WA [auth R],
WC [auth W],
XA [auth R],
XD [auth Z],
YA [auth R],
YB [auth U],
YC [auth X],
YD [auth Z],
ZA [auth R],
ZB [auth U],
ZD [auth Z]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
HIC
Query on HIC
A [auth O]
B [auth P]
C [auth Q]
D [auth R]
E [auth S]
A [auth O],
B [auth P],
C [auth Q],
D [auth R],
E [auth S],
F [auth T],
G [auth U],
H [auth V],
I [auth W],
J [auth X],
K [auth Y],
L [auth Z]
L-PEPTIDE LINKINGC7 H11 N3 O2HIS
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.00 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONEOS

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-11-03
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2019-12-04
    Changes: Author supporting evidence, Data collection, Database references, Derived calculations
  • Version 1.3: 2019-12-18
    Changes: Data collection