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- EMDB-75003: One Lmod2 at the pointed end of F-actin -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-75003
TitleOne Lmod2 at the pointed end of F-actin
Map data
Sample
  • Complex: One Lmod2 at the pointed end of F-actin
    • Complex: F-actin
      • Protein or peptide: Actin, alpha skeletal muscle
    • Protein or peptide: Leiomodin-2
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
Keywordsactin / Lmod2 / leiomodin / STRUCTURAL PROTEIN
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
Actin, alpha skeletal muscle / Leiomodin-2
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.28 Å
AuthorsBrotzman SB / Palmer NJ / Dominguez R
Funding support United States, 2 items
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 SB / Palmer NJ / Boczkowska M / Dominguez R
History
DepositionJan 7, 2026-
Header (metadata) releaseJun 24, 2026-
Map releaseJun 24, 2026-
UpdateJun 24, 2026-
Current statusJun 24, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_75003.png

Downloads & links

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Map

FileDownload / File: emd_75003.map.gz / Format: CCP4 / Size: 274.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 416 pix.
= 439.712 Å		1.06 Å/pix.
x 416 pix.
= 439.712 Å		1.06 Å/pix.
x 416 pix.
= 439.712 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.057 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.122
Minimum - Maximum0.0 - 0.79525644
Average (Standard dev.)0.0011192291 (±0.016307715)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions416416416
Spacing416416416
CellA=B=C: 439.712 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : One Lmod2 at the pointed end of F-actin

EntireName: One Lmod2 at the pointed end of F-actin
Components
  • Complex: One Lmod2 at the pointed end of F-actin
    • Complex: F-actin
      • Protein or peptide: Actin, alpha skeletal muscle
    • Protein or peptide: Leiomodin-2
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: One Lmod2 at the pointed end of F-actin

SupramoleculeName: One Lmod2 at the pointed end of F-actin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Oryctolagus cuniculus (rabbit) / Tissue: Skeletal muscle

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Supramolecule #2: F-actin

SupramoleculeName: F-actin / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Oryctolagus cuniculus (rabbit) / Tissue: Skeletal muscle

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Macromolecule #1: Actin, alpha skeletal muscle

MacromoleculeName: Actin, alpha skeletal muscle / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
EC number: Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Molecular weightTheoretical: 41.875633 KDa
SequenceString: DEDETTALVC DNGSGLVKAG FAGDDAPRAV FPSIVGRPRH QGVMVGMGQK DSYVGDEAQS KRGILTLKYP IE(HIC)GII TNW DDMEKIWHHT FYNELRVAPE EHPTLLTEAP LNPKANREKM TQIMFETFNV PAMYVAIQAV LSLYASGRTT GIVLDSG DG VTHNVPIYEG ...String:
DEDETTALVC DNGSGLVKAG FAGDDAPRAV FPSIVGRPRH QGVMVGMGQK DSYVGDEAQS KRGILTLKYP IE(HIC)GII TNW DDMEKIWHHT FYNELRVAPE EHPTLLTEAP LNPKANREKM TQIMFETFNV PAMYVAIQAV LSLYASGRTT GIVLDSG DG VTHNVPIYEG YALPHAIMRL DLAGRDLTDY LMKILTERGY SFVTTAEREI VRDIKEKLCY VALDFENEMA TAASSSSL E KSYELPDGQV ITIGNERFRC PETLFQPSFI GMESAGIHET TYNSIMKCDI DIRKDLYANN VMSGGTTMYP GIADRMQKE ITALAPSTMK IKIIAPPERK YSVWIGGSIL ASLSTFQQMW ITKQEYDEAG PSIVHRKCF

UniProtKB: Actin, alpha skeletal muscle

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Macromolecule #2: Leiomodin-2

MacromoleculeName: Leiomodin-2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 62.865445 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: MHHHHHHSGM STFGYRRGLS KYESIDEDEL LASLSAEELK ELERELEDIE PDRNLPVGLR QKSLTEKTPT GTFSREALMA YWEKESQKL LEKERLGECG KVAEDKEESE EELIFTESNS EVSEEVYTEE EEEESQEEEE EEDSDEEERT IETAKGINGT V NYDSVNSD ...String:
MHHHHHHSGM STFGYRRGLS KYESIDEDEL LASLSAEELK ELERELEDIE PDRNLPVGLR QKSLTEKTPT GTFSREALMA YWEKESQKL LEKERLGECG KVAEDKEESE EELIFTESNS EVSEEVYTEE EEEESQEEEE EEDSDEEERT IETAKGINGT V NYDSVNSD NSKPKIFKSQ IENINLTNGS NGRNTESPAA IHPCGNPTVI EDALDKIKSN DPDTTEVNLN NIENITTQTL TR FAEALKD NTVVKTFSLA NTHADDSAAM AIAEMLKVNE HITNVNVESN FITGKGILAI MRALQHNTVL TELRFHNQRH IMG SQVEME IVKLLKENTT LLRLGYHFEL PGPRMSMTSI LTRNMDKQRQ KRLQEQKQQE GYDGGPNLRT KVWQRGTPSS SPYV SPRHS PWSSPKLPKK VQTVRSRPLS PVATPPPPPP PPPPPPPSSQ RLPPPPPPPP PPLPEKKLIT RNIAEVIKQQ ESAQR ALQN GQKKKKGKKV KKQPNSILKE IKNSLRSVQE KKMEDSSRPS TPQRSAHENL MEAIRGSSIK QLKRVEVPEA LR

UniProtKB: Leiomodin-2

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Macromolecule #3: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 5 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 5 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7.5
Component:
ConcentrationFormulaName
20.0 mMC8H18N2O4SHEPES
50.0 mMKAcPotassium acetate
1.0 mMC14H24N2O10EGTA
1.0 mMMgCl2magnesium chloride
0.2 mMATPadenosine triphosphate
1.0 mMC4H10O2S2DTT
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recording#0 - Image recording ID: 1 / #0 - Film or detector model: GATAN K3 (6k x 4k) / #0 - Average electron dose: 49.0 e/Å2 / #1 - Image recording ID: 2 / #1 - Film or detector model: GATAN K3 (6k x 4k) / #1 - Average electron dose: 49.0 e/Å2 / #2 - Image recording ID: 3 / #2 - Film or detector model: GATAN K3 (6k x 4k) / #2 - Average electron dose: 49.0 e/Å2 / #3 - Image recording ID: 4 / #3 - Film or detector model: GATAN K3 (6k x 4k) / #3 - Average electron dose: 49.0 e/Å2 / #4 - Image recording ID: 5 / #4 - Film or detector model: GATAN K3 (6k x 4k) / #4 - Average electron dose: 49.0 e/Å2 / #5 - Image recording ID: 6 / #5 - Film or detector model: GATAN K3 (6k x 4k) / #5 - Average electron dose: 49.0 e/Å2 / #6 - Image recording ID: 7 / #6 - Film or detector model: GATAN K3 (6k x 4k) / #6 - Average electron dose: 49.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 81000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing #1

Image processing ID1
Image recording ID1
CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.28 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: PHENIX / Number images used: 55396
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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Image processing #2

Image processing ID2
Image recording ID2
CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.28 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 55396

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Atomic model buiding 1

Initial modelPDB ID:

8f8s


Chain - Source name: PDB / Chain - Initial model type: experimental model
Output model

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

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