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- PDB-9zzj: One Lmod2 at the pointed end of F-actin -

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Basic information

Entry
Database: PDB / ID: 9zzj
TitleOne Lmod2 at the pointed end of F-actin
Components
  • Actin, alpha skeletal muscle
  • Leiomodin-2
KeywordsSTRUCTURAL PROTEIN / actin / Lmod2 / leiomodin
Function / homology
Function and homology information


pointed-end actin filament capping / actin nucleation / myofibril assembly / M band / sarcomere organization / cytoskeletal motor activator activity / myosin heavy chain binding / tropomyosin binding / actin filament bundle / troponin I binding ...pointed-end actin filament capping / actin nucleation / myofibril assembly / M band / sarcomere organization / cytoskeletal motor activator activity / myosin heavy chain binding / tropomyosin binding / actin filament bundle / troponin I binding / filamentous actin / mesenchyme migration / positive regulation of actin filament polymerization / myofibril / skeletal muscle myofibril / actin filament bundle assembly / striated muscle thin filament / skeletal muscle thin filament assembly / actin monomer binding / skeletal muscle fiber development / stress fiber / titin binding / actin filament polymerization / muscle contraction / actin filament organization / sarcomere / filopodium / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / calcium-dependent protein binding / lamellipodium / actin binding / cell body / cytoskeleton / protein domain specific binding / hydrolase activity / calcium ion binding / positive regulation of gene expression / magnesium ion binding / ATP binding / identical protein binding / cytoplasm
Similarity search - Function
TMOD/LMOD Leucine-rich domain / Tropomodulin / Tropomodulin / WH2 domain / WH2 domain profile. / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. ...TMOD/LMOD Leucine-rich domain / Tropomodulin / Tropomodulin / WH2 domain / WH2 domain profile. / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / Leucine-rich repeat domain superfamily / ATPase, nucleotide binding domain
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Actin, alpha skeletal muscle / Leiomodin-2
Similarity search - Component
Biological speciesHomo sapiens (human)
Oryctolagus cuniculus (rabbit)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.28 Å
AuthorsBrotzman, S.B. / Palmer, N.J. / Dominguez, R.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM161161 United States
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)5T32AR053461-20 United States
CitationJournal: To Be Published
Title: Mechanism of Actin Thin Filament Pointed-End Elongation by Leiomodin
Authors: Brotzman, S.B. / Palmer, N.J. / Boczkowska, M. / Dominguez, R.
History
DepositionJan 7, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2026Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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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
L: Leiomodin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)274,50116
Polymers272,2446
Non-polymers2,25810
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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


Mass: 41875.633 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
References: UniProt: P68135, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
#2: Protein Leiomodin-2 / Cardiac leiomodin / C-LMOD / Leiomodin


Mass: 62865.445 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LMOD2
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q6P5Q4
#3: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1One Lmod2 at the pointed end of F-actinCOMPLEX#1-#20MULTIPLE SOURCES
2F-actinCOMPLEX#11NATURAL
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
11NO
211.5 kDa/nmYES
31NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-IDTissue
21Oryctolagus cuniculus (rabbit)9986Skeletal muscle
32Oryctolagus cuniculus (rabbit)9986Skeletal muscle
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMHEPESC8H18N2O4S1
250 mMPotassium acetateKAc1
31 mMEGTAC14H24N2O101
41 mMmagnesium chlorideMgCl21
50.2 mMadenosine triphosphateATP1
61 mMDTTC4H10O2S21
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 81000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm
Image recording
IDImaging-IDElectron dose (e/Å2)Film or detector model
1149GATAN K3 (6k x 4k)
2149GATAN K3 (6k x 4k)
3149GATAN K3 (6k x 4k)
4149GATAN K3 (6k x 4k)
5149GATAN K3 (6k x 4k)
6149GATAN K3 (6k x 4k)
7149GATAN K3 (6k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
2EPUimage acquisition
7Cootmodel fitting
9PHENIXmodel refinement
13PHENIX3D reconstruction
Image processing
IDImage recording-ID
11
22
CTF correction
IDEM image processing-IDType
11NONE
22NONE
3D reconstruction
IDResolution (Å)Resolution methodNum. of particlesImage processing-IDEntry-IDSymmetry type
13.28FSC 0.143 CUT-OFF5539619ZZJPOINT
23.28FSC 0.143 CUT-OFF5539619ZZJPOINT
33.28FSC 0.143 CUT-OFF5539619ZZJPOINT
43.28FSC 0.143 CUT-OFF5539619ZZJPOINT
53.28FSC 0.143 CUT-OFF5539629ZZJPOINT
63.28FSC 0.143 CUT-OFF5539629ZZJPOINT
73.28FSC 0.143 CUT-OFF5539629ZZJPOINT
83.28FSC 0.143 CUT-OFF5539629ZZJPOINT
Atomic model buildingPDB-ID: 8F8S

8f8s


Accession code: 8F8S / Source name: PDB / Type: experimental model

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