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- PDB-3b5u: Actin filament model from extended form of acromsomal bundle in t... -

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Basic information

Entry
Database: PDB / ID: 3b5u
TitleActin filament model from extended form of acromsomal bundle in the Limulus sperm
ComponentsActin, alpha skeletal muscle
KeywordsMOTOR PROTEIN / ACTIN FILAMENT / ACTIN / ACROMSOMAL BUNDLE / CRYOEM
Function / homology
Function and homology information


cytoskeletal motor activator activity / tropomyosin binding / myosin heavy chain binding / mesenchyme migration / troponin I binding / actin filament bundle / filamentous actin / actin filament bundle assembly / skeletal muscle thin filament assembly / striated muscle thin filament ...cytoskeletal motor activator activity / tropomyosin binding / myosin heavy chain binding / mesenchyme migration / troponin I binding / actin filament bundle / filamentous actin / actin filament bundle assembly / skeletal muscle thin filament assembly / striated muscle thin filament / skeletal muscle myofibril / actin monomer binding / skeletal muscle fiber development / stress fiber / titin binding / actin filament polymerization / filopodium / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / calcium-dependent protein binding / lamellipodium / cell body / hydrolase activity / protein domain specific binding / calcium ion binding / positive regulation of gene expression / magnesium ion binding / ATP binding / identical protein binding / cytoplasm
Similarity search - Function
Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / ATPase, nucleotide binding domain
Similarity search - Domain/homology
Actin, alpha skeletal muscle
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodELECTRON CRYSTALLOGRAPHY / electron crystallography / cryo EM / Resolution: 9.5 Å
AuthorsCong, Y. / Topf, M. / Sali, A. / Matsudaira, P. / Dougherty, M. / Chiu, W. / Schmid, M.F.
CitationJournal: J Mol Biol / Year: 2008
Title: Crystallographic conformers of actin in a biologically active bundle of filaments.
Authors: Yao Cong / Maya Topf / Andrej Sali / Paul Matsudaira / Matthew Dougherty / Wah Chiu / Michael F Schmid /
Abstract: Actin carries out many of its cellular functions through its filamentous form; thus, understanding the detailed structure of actin filaments is an essential step in achieving a mechanistic ...Actin carries out many of its cellular functions through its filamentous form; thus, understanding the detailed structure of actin filaments is an essential step in achieving a mechanistic understanding of actin function. The acrosomal bundle in the Limulus sperm has been shown to be a quasi-crystalline array with an asymmetric unit composed of a filament with 14 actin-scruin pairs. The bundle in its true discharge state penetrates the jelly coat of the egg. Our previous electron crystallographic reconstruction demonstrated that the actin filament cross-linked by scruin in this acrosomal bundle state deviates significantly from a perfect F-actin helix. In that study, the tertiary structure of each of the 14 actin protomers in the asymmetric unit of the bundle filament was assumed to be constant. In the current study, an actin filament atomic model in the acrosomal bundle has been refined by combining rigid-body docking with multiple actin crystal structures from the Protein Data Bank and constrained energy minimization. Our observation demonstrates that actin protomers adopt different tertiary conformations when they form an actin filament in the bundle. The scruin and bundle packing forces appear to influence the tertiary and quaternary conformations of actin in the filament of this biologically active bundle.
History
DepositionOct 26, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 18, 2018Group: Author supporting evidence / Data collection
Category: em_image_scans / em_single_particle_entity / em_software
Item: _em_software.image_processing_id
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
  • EMDB-1088
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  • EMDB-1088
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Structure viewerMolecule:
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Assembly

Deposited unit
A: Actin, alpha skeletal muscle
B: Actin, alpha skeletal muscle
C: Actin, alpha skeletal muscle
D: Actin, alpha skeletal muscle
E: Actin, alpha skeletal muscle
F: Actin, alpha skeletal muscle
G: Actin, alpha skeletal muscle
H: Actin, alpha skeletal muscle
I: Actin, alpha skeletal muscle
J: Actin, alpha skeletal muscle
K: Actin, alpha skeletal muscle
L: Actin, alpha skeletal muscle
M: Actin, alpha skeletal muscle
N: Actin, alpha skeletal muscle


Theoretical massNumber of molelcules
Total (without water)589,35714
Polymers589,35714
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Actin, alpha skeletal muscle / / Alpha-actin-1


Mass: 42096.953 Da / Num. of mol.: 14 / Source method: isolated from a natural source
Details: Holmes Actin model from Fiber Diffraction experiment
Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P68135

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Experimental details

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Experiment

ExperimentMethod: ELECTRON CRYSTALLOGRAPHY
EM experimentAggregation state: 3D ARRAY / 3D reconstruction method: electron crystallography

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Sample preparation

Component
IDNameTypeDetailsParent-ID
1acrosomal bundle in the Limulus spermCOMPLEXPlease refer to EMDB entry EMD-1088 http://www.ebi.ac.uk/msd-srv/emsearch/atlas/1088_summary.html0
2Refined (by energy minimization) Actin filament model in the extended form of acromsomal bundle. The starting coordinates of the protomers are the Holmes Actin model from Fiber Diffraction experiment.For more information, please refer to EMDB entry EMD-10881
Buffer solutionpH: 7.4 / Details: see J Mol Biol, 221, 711-725 (1991)
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE

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Data collection

MicroscopyModel: JEOL 4000EX
Details: For more information, please refer to EMDB entry EMD-1088 http://www.ebi.ac.uk/msd-srv/emsearch/atlas/1088_summary.html
Electron gunElectron source: LAB6 / Accelerating voltage: 400 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 40000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 800 nm
Specimen holderTemperature: 106 K
Image recordingElectron dose: 15 e/Å2 / Film or detector model: KODAK SO-163 FILM

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Processing

EM software
IDNameCategory
1Foldhuntermodel fitting
2MRC3D reconstruction
3D reconstructionMethod: Cross-correlation and merging of crystallographic reflections derived from cryoelectron micrographs of 3D crystals. For more information, please refer to EMDB entry EMD-1088 http://www.ebi.ac. ...Method: Cross-correlation and merging of crystallographic reflections derived from cryoelectron micrographs of 3D crystals. For more information, please refer to EMDB entry EMD-1088 http://www.ebi.ac.uk/msd-srv/emsearch/atlas/1088_summary.html
Resolution: 9.5 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES
Details: Cross-correlation and merging of crystallographic reflections derived from cryoelectron micrographs of 3D crystalss: application to the Limulus acrosomal bundle, Michael F. Schmid, J. Struc. ...Details: Cross-correlation and merging of crystallographic reflections derived from cryoelectron micrographs of 3D crystalss: application to the Limulus acrosomal bundle, Michael F. Schmid, J. Struc. Biol., 144 (2003) 195-208
Symmetry type: 3D CRYSTAL
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
Target criteria: Best cross-correlation score between model and cryoEM map
Details: REFINEMENT PROTOCOL--Foldhunter program from EMAN single particle analysis package
Atomic model buildingDetails: Holmes' Actin model from Fiber Diffraction experiment
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms41062 0 0 0 41062

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