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- PDB-3b63: Actin filament model in the extended form of acromsomal bundle in... -

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Basic information

Entry
Database: PDB / ID: 3b63
TitleActin filament model in the extended form of acromsomal bundle in the Limulus sperm
Components(Actin) x 7
KeywordsCONTRACTILE PROTEIN/STRUCTURAL PROTEIN / ACTIN FILAMENT / ACTIN / ACROMSOMAL BUNDLE / CRYOEM / STRUCTURAL PROTEIN / CONTRACTILE PROTEIN-STRUCTURAL PROTEIN COMPLEX
Function / homology
Function and homology information


Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / cytoskeleton / hydrolase activity / ATP 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
Biological speciesLimulus polyphemus (Atlantic horseshoe crab)
MethodELECTRON MICROSCOPY / 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 1.0Nov 18, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 30, 2012Group: Refinement description
Revision 1.3Jul 18, 2018Group: Author supporting evidence / Data collection
Category: em_image_scans / em_single_particle_entity / em_software
Item: _em_software.image_processing_id
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)566,21714
Polymers566,21714
Non-polymers00
Water00
1


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

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Components

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Protein , 7 types, 14 molecules AGBCIDEHJKNFLM

#1: Protein Actin


Mass: 40533.129 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Limulus polyphemus (Atlantic horseshoe crab)
References: UniProt: P41340*PLUS
#2: Protein Actin


Mass: 40460.129 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Limulus polyphemus (Atlantic horseshoe crab)
References: UniProt: P41340*PLUS
#3: Protein Actin


Mass: 40518.160 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Limulus polyphemus (Atlantic horseshoe crab)
References: UniProt: P41340*PLUS
#4: Protein Actin


Mass: 39834.418 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Limulus polyphemus (Atlantic horseshoe crab)
References: UniProt: P41340*PLUS
#5: Protein
Actin


Mass: 40598.273 Da / Num. of mol.: 5 / Source method: isolated from a natural source
Source: (natural) Limulus polyphemus (Atlantic horseshoe crab)
References: UniProt: P41340*PLUS
#6: Protein Actin


Mass: 39792.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Limulus polyphemus (Atlantic horseshoe crab)
References: UniProt: P41340*PLUS
#7: Protein Actin


Mass: 40518.211 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Limulus polyphemus (Atlantic horseshoe crab)
References: UniProt: P41340*PLUS

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Details

Sequence detailsAUTHORS STATE THAT THE EM DENSITY MAP OBTAINED CONSISTS OF 14 INDEPENDENT ACTIN MOLECULES FROM THE ...AUTHORS STATE THAT THE EM DENSITY MAP OBTAINED CONSISTS OF 14 INDEPENDENT ACTIN MOLECULES FROM THE SOURCE ORGANISM LIMULUS POLYPHEMUS. 9 DIFFERENT ACTIN PDB MODELS FROM DIFFERENT SOURCES WERE USED TO FIT INTO THESE 14 POSITIONS. THE DIFFERENT PDB ENTRIES THAT WERE USED FOR FITTING ARE 1T44,1HLU,1ATN,1YAG,1YVN,1MDU, 1HIV,1NWK, AND 1ESV.

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: electron crystallography

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Sample preparation

Component
IDNameTypeParent-IDDetails
1Acrosomal bundle from Limulus spermCOMPLEX0
2An actin filament model in the acrosomal bundle refined from multiple actin crystal structures1All the actin crystal structures as the starting coordinates before refinement in this model were listed under the Molecule Names entry
Buffer solutionpH: 7.4
SpecimenConc.: 10 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE

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Electron microscopy imaging

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 FIELD / 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
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 building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
11T44

1t44

11T441PDBexperimental model
21HLU

1hlu

11HLU2PDBexperimental model
31ATN

1atn

11ATN3PDBexperimental model
41YAG

1yag

11YAG4PDBexperimental model
51YVN

1yvn

11YVN5PDBexperimental model
61MDU

1mdu

11MDU6PDBexperimental model
71HIV

1hiv

11HIV7PDBexperimental model
81NWK

1nwk

11NWK8PDBexperimental model
91ESV

1esv

11ESV9PDBexperimental model
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms39685 0 0 0 39685

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