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- PDB-7u8k: Magic Angle Spinning NMR Structure of Human Cofilin-2 Assembled o... -

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Basic information

Entry
Database: PDB / ID: 7u8k
TitleMagic Angle Spinning NMR Structure of Human Cofilin-2 Assembled on Actin Filaments
Components
  • Actin, alpha skeletal muscle
  • Cofilin-2
KeywordsCONTRACTILE PROTEIN / CELL CYCLE / actin filament binding / actin filament severing / cytoskeletal assembly
Function / homology
Function and homology information


actin filament fragmentation / positive regulation of actin filament depolymerization / actin filament severing / actin filament depolymerization / I band / cytoskeletal motor activator activity / muscle cell cellular homeostasis / sarcomere organization / tropomyosin binding / myosin heavy chain binding ...actin filament fragmentation / positive regulation of actin filament depolymerization / actin filament severing / actin filament depolymerization / I band / cytoskeletal motor activator activity / muscle cell cellular homeostasis / sarcomere organization / tropomyosin binding / myosin heavy chain binding / troponin I binding / mesenchyme migration / filamentous actin / actin filament bundle / striated muscle thin filament / actin filament bundle assembly / skeletal muscle thin filament assembly / skeletal muscle myofibril / actin monomer binding / skeletal muscle tissue development / stress fiber / skeletal muscle fiber development / titin binding / actin filament polymerization / filopodium / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / Z disc / nuclear matrix / calcium-dependent protein binding / actin filament binding / actin cytoskeleton / lamellipodium / cell body / hydrolase activity / protein domain specific binding / calcium ion binding / positive regulation of gene expression / magnesium ion binding / extracellular space / extracellular exosome / ATP binding / identical protein binding / cytoplasm
Similarity search - Function
ADF/Cofilin / Actin-depolymerising factor homology domain / Cofilin/tropomyosin-type actin-binding protein / ADF-H domain profile. / Actin depolymerisation factor/cofilin -like domains / ADF-H/Gelsolin-like domain superfamily / ATPase, substrate binding domain, subdomain 4 / Actin; Chain A, domain 4 / Actins signature 1. / Actin, conserved site ...ADF/Cofilin / Actin-depolymerising factor homology domain / Cofilin/tropomyosin-type actin-binding protein / ADF-H domain profile. / Actin depolymerisation factor/cofilin -like domains / ADF-H/Gelsolin-like domain superfamily / ATPase, substrate binding domain, subdomain 4 / Actin; Chain A, domain 4 / 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 / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Actin, alpha skeletal muscle / Cofilin-2
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
Homo sapiens (human)
MethodSOLID-STATE NMR / molecular dynamics
AuthorsKraus, J. / Russell, R. / Kudryashova, E. / Xu, C. / Katyal, N. / Kudryashov, D. / Perilla, J.R. / Polenova, T.
Funding support United States, 3items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1247394 United States
National Science Foundation (NSF, United States)CHE0959496 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30GM110758 United States
CitationJournal: Nat Commun / Year: 2022
Title: Magic angle spinning NMR structure of human cofilin-2 assembled on actin filaments reveals isoform-specific conformation and binding mode.
Authors: Kraus, J. / Russell, R.W. / Kudryashova, E. / Xu, C. / Katyal, N. / Perilla, J.R. / Kudryashov, D.S. / Polenova, T.
History
DepositionMar 8, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 16, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 23, 2024Group: Database references / Structure summary
Category: database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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: Cofilin-2
L: Cofilin-2
M: Cofilin-2
N: Cofilin-2
O: Cofilin-2
P: Cofilin-2
Q: Cofilin-2
R: Cofilin-2


Theoretical massNumber of molelcules
Total (without water)569,18418
Polymers569,18418
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area47640 Å2
ΔGint-131 kcal/mol
Surface area210210 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)4 / 4all calculated structures submitted
RepresentativeModel #1lowest energy

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Components

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


Mass: 41886.660 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: ACTA1, ACTA / Production host: Oryctolagus cuniculus (rabbit)
References: UniProt: P68135, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
#2: Protein
Cofilin-2 / Cofilin / muscle isoform


Mass: 18789.672 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CFL2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y281
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLID-STATE NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic1Exp1 CORD50ms
121isotropic1Exp2 CORD200ms
132isotropic1Exp3 CORD50ms
142isotropic1Exp4 CORD200ms
152isotropic1Exp5 CORD500ms
163isotropic1Exp6 CORD50ms
173isotropic1Exp7 CORD200ms
183isotropic1Exp8 CORD500ms
193isotropic1Exp9 PAINCP
1101isotropic1Exp10 NCACX2d
1111isotropic1Exp11 NCACX3d
1121isotropic1Exp12 NCOCX2d
1131isotropic1Exp13 NCOCX3d

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solid120.8 % w/w [U-13C; U-15N] human cofilin-2, 79.2 % w/w F-actin, SolidUniformly labeled human cofilin-2 in complex with natural abundance actin filaments obtained using rabbit skeletal muscle actin[U-13C; U-15N]-cofilin2Solid
solid220.8 % w/w [1,6-13C]-glucose, U-15N human cofilin-2, 79.2 % w/w F-actin, SolidSelectively labeled human cofilin-2 in complex with natural abundance actin filaments obtained using rabbit skeletal muscle actin[1,6-13C]-glucose, U-15N-cofilin2Solid
solid320.8 % w/w [2-13C]-glucose, U-15N human cofilin-2, 79.2 % w/w F-actin, SolidSelectively labeled human cofilin-2 in complex with natural abundance actin filaments obtained using rabbit skeletal muscle actin[2-13C]-glucose, U-15N-cofilin2Solid
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
20.8 % w/whuman cofilin-2[U-13C; U-15N]1
79.2 % w/wF-actinnatural abundance1
20.8 % w/whuman cofilin-2[1,6-13C]-glucose, U-15N2
79.2 % w/wF-actinnatural abundance2
20.8 % w/whuman cofilin-2[2-13C]-glucose, U-15N3
79.2 % w/wF-actinnatural abundance3
Sample conditionsIonic strength: 50 mM / Label: cofilin condition / pH: 6.6 / Pressure: 1 atm / Temperature: 273 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 850 MHz

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CcpNmr AnalysisCCPNchemical shift assignment
CcpNmr AnalysisCCPNpeak picking
Rowland NMR Toolkit (RNMRTK)Hoch and Sternprocessing
TALOS-NCornilescu, Delaglio and Baxstructure calculation
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
NAMDJames C. Phillipsrefinement
RefinementMethod: molecular dynamics / Software ordinal: 9
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 4 / Conformers submitted total number: 4

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