9ZZM | pdb_00009zzm

Two Lmod2s and incoming actin at the pointed end of F-actin

PDB DOI: https://doi.org/10.2210/pdb9ZZM/pdb
EM Map EMD-75010: EMDB EMDataResource

Classification: STRUCTURAL PROTEIN
Organism(s): Oryctolagus cuniculus, Homo sapiens
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2026-01-07 Released: 2026-06-24
Deposition Author(s): Brotzman, S.B., Palmer, N.J., Dominguez, R.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.56 Å
Resolution: 3.56 Å
Resolution: 3.56 Å
Resolution: 3.56 Å
Aggregation State: FILAMENT
Reconstruction Method: SINGLE PARTICLE

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Mechanism of Actin Thin Filament Pointed-End Elongation by Leiomodin

Brotzman, S.B., Palmer, N.J., Boczkowska, M., Dominguez, R.

To be published.

Macromolecule Content

Total Structure Weight: 379.77 kDa
Atom Count: 20,218
Modeled Residue Count: 2,560
Deposited Residue Count: 3,362
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Actin, alpha skeletal muscle	A B C D E A, B, C, D, E, H [auth O]	375	Oryctolagus cuniculus	Mutation(s): 0 EC: 3.6.4
UniProt
Find proteins for P68135 (Oryctolagus cuniculus) Explore P68135 Go to UniProtKB: P68135
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P68135
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Leiomodin-2	F [auth L], G [auth M]	556	Homo sapiens	Mutation(s): 0 Gene Names: LMOD2
UniProt & NIH Common Fund Data Resources
Find proteins for Q6P5Q4 (Homo sapiens) Explore Q6P5Q4 Go to UniProtKB: Q6P5Q4
PHAROS: Q6P5Q4 GTEx: ENSG00000170807
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6P5Q4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP Query on ATP Download:Ideal Coordinates CCD File SDF format, chain S [auth O] MOL2 format, chain S [auth O] mmCIF format, chain S [auth O]	S [auth O]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain S [auth O] Interactions & Density Focus chain S [auth O]
ADP Query on ADP Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain K [auth B] SDF format, chain M [auth C] SDF format, chain O [auth D] SDF format, chain Q [auth E] MOL2 format, chain I [auth A] MOL2 format, chain K [auth B] MOL2 format, chain M [auth C] MOL2 format, chain O [auth D] MOL2 format, chain Q [auth E] mmCIF format, chain I [auth A] mmCIF format, chain K [auth B] mmCIF format, chain M [auth C] mmCIF format, chain O [auth D] mmCIF format, chain Q [auth E]	I [auth A], K [auth B], M [auth C], O [auth D], Q [auth E]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain I [auth A] Focus chain K [auth B] Focus chain M [auth C] Focus chain O [auth D] Focus chain Q [auth E] Interactions & Density Focus chain I [auth A] Focus chain K [auth B] Focus chain M [auth C] Focus chain O [auth D] Focus chain Q [auth E]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain L [auth B] SDF format, chain N [auth C] SDF format, chain R [auth E] SDF format, chain T [auth O] SDF format, chain P [auth D] MOL2 format, chain J [auth A] MOL2 format, chain L [auth B] MOL2 format, chain N [auth C] MOL2 format, chain R [auth E] MOL2 format, chain T [auth O] MOL2 format, chain P [auth D] mmCIF format, chain J [auth A] mmCIF format, chain L [auth B] mmCIF format, chain N [auth C] mmCIF format, chain R [auth E] mmCIF format, chain T [auth O] mmCIF format, chain P [auth D]	J [auth A] L [auth B] N [auth C] P [auth D] R [auth E] J [auth A], L [auth B], N [auth C], P [auth D], R [auth E], T [auth O]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain L [auth B] Focus chain N [auth C] Focus chain P [auth D] Focus chain R [auth E] Focus chain T [auth O] Interactions & Density Focus chain J [auth A] Focus chain L [auth B] Focus chain N [auth C] Focus chain P [auth D] Focus chain R [auth E] Focus chain T [auth O]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
HIC Query on HIC	A B C D E A, B, C, D, E, H [auth O]	L-PEPTIDE LINKING	C₇ H₁₁ N₃ O₂		HIS

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.56 Å
Resolution: 3.56 Å
Resolution: 3.56 Å
Resolution: 3.56 Å
Aggregation State: FILAMENT
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	PHENIX
RECONSTRUCTION	PHENIX
MODEL REFINEMENT	PHENIX

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-06-24

Deposition Author(s):

Brotzman, S.B.

Palmer, N.J.

Dominguez, R.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35 GM161161
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)	United States	5T32AR053461-20

Revision History (Full details and data files)

Version 1.0: 2026-06-24
Type: Initial release

9ZZM | pdb_00009zzm

Two Lmod2s and incoming actin at the pointed end of F-actin

Literature

Mechanism of Actin Thin Filament Pointed-End Elongation by Leiomodin

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Entity ID: 2

UniProt & NIH Common Fund Data Resources