8VAA | pdb_00008vaa

Actin-binding domain of Legionella pneumophila effector LFAT1 (lpg1387) bound to F-actin

PDB DOI: https://doi.org/10.2210/pdb8VAA/pdb
EM Map EMD-43087: EMDB EMDataResource

Classification: TOXIN
Organism(s): Bos taurus, Legionella pneumophila
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-12-11 Released: 2024-12-18
Deposition Author(s): Zeng, W., Mao, Y.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.58 Å
Aggregation State: FILAMENT
Reconstruction Method: HELICAL

Starting Models: in silico
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wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Cryo-EM structure revealed a novel F-actin binding motif in a Legionella pneumophila lysine fatty-acyltransferase

Zeng, W.W., Komaniecki, G., Liu, J., Lin, H., Mao, Y.

(2025) Elife

DOI: https://doi.org/10.7554/elife.106975.1

Macromolecule Content

Total Structure Weight: 496.5 kDa
Atom Count: 34,740
Modeled Residue Count: 4,390
Deposited Residue Count: 4,390
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, F, G, H, I, J	370	Bos taurus	Mutation(s): 0 EC: 3.6.4
UniProt
Find proteins for P68138 (Bos taurus) Explore P68138 Go to UniProtKB: P68138
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P68138
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
F-actin-binding Coiled-Coil domain of LFAT1	K, L, M, N, O K, L, M, N, O, P, Q, R, S, T	69	Legionella pneumophila	Mutation(s): 0 Gene Names: lpg1387
UniProt
Find proteins for Q5ZVQ3 (Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513)) Explore Q5ZVQ3 Go to UniProtKB: Q5ZVQ3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5ZVQ3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP (Subject of Investigation/LOI) Query on ADP Download:Ideal Coordinates CCD File SDF format, chain Y [auth C] SDF format, chain W [auth B] SDF format, chain U [auth A] SDF format, chain MA [auth J] SDF format, chain KA [auth I] SDF format, chain IA [auth H] SDF format, chain GA [auth G] SDF format, chain EA [auth F] SDF format, chain CA [auth E] SDF format, chain AA [auth D] MOL2 format, chain Y [auth C] MOL2 format, chain W [auth B] MOL2 format, chain U [auth A] MOL2 format, chain MA [auth J] MOL2 format, chain KA [auth I] MOL2 format, chain IA [auth H] MOL2 format, chain GA [auth G] MOL2 format, chain EA [auth F] MOL2 format, chain CA [auth E] MOL2 format, chain AA [auth D] mmCIF format, chain Y [auth C] mmCIF format, chain W [auth B] mmCIF format, chain U [auth A] mmCIF format, chain MA [auth J] mmCIF format, chain KA [auth I] mmCIF format, chain IA [auth H] mmCIF format, chain GA [auth G] mmCIF format, chain EA [auth F] mmCIF format, chain CA [auth E] mmCIF format, chain AA [auth D]	AA [auth D] CA [auth E] EA [auth F] GA [auth G] IA [auth H] AA [auth D], CA [auth E], EA [auth F], GA [auth G], IA [auth H], KA [auth I], MA [auth J], U [auth A], W [auth B], Y [auth C]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain AA [auth D] Focus chain CA [auth E] Focus chain EA [auth F] Focus chain GA [auth G] Focus chain IA [auth H] Focus chain KA [auth I] Focus chain MA [auth J] Focus chain U [auth A] Focus chain W [auth B] Focus chain Y [auth C] Interactions & Density Focus chain AA [auth D] Focus chain CA [auth E] Focus chain EA [auth F] Focus chain GA [auth G] Focus chain IA [auth H] Focus chain KA [auth I] Focus chain MA [auth J] Focus chain U [auth A] Focus chain W [auth B] Focus chain Y [auth C]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain Z [auth C] SDF format, chain X [auth B] SDF format, chain V [auth A] SDF format, chain NA [auth J] SDF format, chain LA [auth I] SDF format, chain JA [auth H] SDF format, chain HA [auth G] SDF format, chain FA [auth F] SDF format, chain DA [auth E] SDF format, chain BA [auth D] MOL2 format, chain Z [auth C] MOL2 format, chain X [auth B] MOL2 format, chain V [auth A] MOL2 format, chain NA [auth J] MOL2 format, chain LA [auth I] MOL2 format, chain JA [auth H] MOL2 format, chain HA [auth G] MOL2 format, chain FA [auth F] MOL2 format, chain DA [auth E] MOL2 format, chain BA [auth D] mmCIF format, chain Z [auth C] mmCIF format, chain X [auth B] mmCIF format, chain V [auth A] mmCIF format, chain NA [auth J] mmCIF format, chain LA [auth I] mmCIF format, chain JA [auth H] mmCIF format, chain HA [auth G] mmCIF format, chain FA [auth F] mmCIF format, chain DA [auth E] mmCIF format, chain BA [auth D]	BA [auth D] DA [auth E] FA [auth F] HA [auth G] JA [auth H] BA [auth D], DA [auth E], FA [auth F], HA [auth G], JA [auth H], LA [auth I], NA [auth J], V [auth A], X [auth B], Z [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain BA [auth D] Focus chain DA [auth E] Focus chain FA [auth F] Focus chain HA [auth G] Focus chain JA [auth H] Focus chain LA [auth I] Focus chain NA [auth J] Focus chain V [auth A] Focus chain X [auth B] Focus chain Z [auth C] Interactions & Density Focus chain BA [auth D] Focus chain DA [auth E] Focus chain FA [auth F] Focus chain HA [auth G] Focus chain JA [auth H] Focus chain LA [auth I] Focus chain NA [auth J] Focus chain V [auth A] Focus chain X [auth B] Focus chain Z [auth C]