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: 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 ...

    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
MoleculeChainsSequence LengthOrganismDetailsImage
Actin, alpha skeletal muscle376Oryctolagus cuniculusMutation(s): 1 
Gene Names: ACTA1ACTA
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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / 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
 Ligand Interaction
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
 Ligand Interaction
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
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D 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 

Structure Validation

View Full Validation Report




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