6IUG | pdb_00006iug

Cryo-EM structure of the plant actin filaments from Zea mays pollen


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history

Literature

Cryo-EM Structure of Actin Filaments fromZea maysPollen.

Ren, Z.Zhang, Y.Zhang, Y.He, Y.Du, P.Wang, Z.Sun, F.Ren, H.

(2019) Plant Cell 31: 2855-2867

  • DOI: https://doi.org/10.1105/tpc.18.00973
  • Primary Citation Related Structures: 
    6IUG

  • PubMed Abstract: 

    Actins are among the most abundant and conserved proteins in eukaryotic cells, where they form filamentous structures that perform vital roles in key cellular processes. Although large amounts of data on the biochemical activities, dynamic behaviors, and important cellular functions of plant actin filaments have accumulated, their structural basis remains elusive. Here, we report a 3.9 Å structure of the plant actin filament from Zea mays pollen (ZMPA) using cryo-electron microscopy. The structure shows a right-handed, double-stranded (two parallel strands) and staggered architecture that is stabilized by intra- and interstrand interactions. While the overall structure resembles that of other actin filaments, its DNase I binding loop bends farther outward, adopting an open conformation similar to that of the jasplakinolide- or beryllium fluoride (BeF x )-stabilized rabbit skeletal muscle actin (RSMA) filament. Single-molecule magnetic tweezers analysis revealed that the ZMPA filament can resist a greater stretching force than the RSMA filament. Overall, these data provide evidence that plant actin filaments have greater stability than animal actin filaments, which might be important to their role as tracks for long-distance vesicle and organelle transportation.plantcell;31/12/2855/FX1F1fx1.


  • Organizational Affiliation
    • Key Laboratory of Cell Proliferation and Regulation Biology of Ministry of Education, Center for Biological Science and Technology, College of Life Sciences, Beijing Normal University, Zhuhai 519087, China feisun@ibp.ac.cn hren@bnu.edu.cn.

Macromolecule Content 

  • Total Structure Weight: 208.31 kDa 
  • Atom Count: 14,585 
  • Modeled Residue Count: 1,855 
  • Deposited Residue Count: 1,855 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
pollen F-actin
A, B, C, D, E
371Zea maysMutation(s): 0 
UniProt
Find proteins for B6TQ08 (Zea mays)
Explore B6TQ08 
Go to UniProtKB:  B6TQ08
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB6TQ08
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP
(Subject of Investigation/LOI)

Query on ADP



Download:Ideal Coordinates CCD File
F [auth A],
H [auth B],
J [auth C],
L [auth D],
N [auth E]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
G [auth A],
I [auth B],
K [auth C],
M [auth D],
O [auth E]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.11.1
RECONSTRUCTIONSPIDER24.08

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina91854206
National Natural Science Foundation of ChinaChina31770206
National Natural Science Foundation of ChinaChina31770794
Ministry of Science and Technology (China)China2013CB126902
Ministry of Science and Technology (China)China2017YFA0504700

Revision History  (Full details and data files)

  • Version 1.0: 2019-11-06
    Type: Initial release
  • Version 1.1: 2019-12-25
    Changes: Database references
  • Version 1.2: 2024-03-27
    Changes: Data collection, Database references, Derived calculations, Refinement description