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- PDB-9b85: Cryo-EM structure of human dynactin complex bound to Chlamydia ef... -

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Basic information

Entry
Database: PDB / ID: 9b85
TitleCryo-EM structure of human dynactin complex bound to Chlamydia effector Dre1
Components
  • (Dynactin subunit ...) x 4
  • (F-actin-capping protein subunit ...) x 2
  • Actin, cytoplasmic 1
  • Actin-related protein 10
  • Alpha-centractin
KeywordsMOTOR PROTEIN / Human dynactin / Chlamydia effector / host-pathogen interaction
Function / homology
Function and homology information


retrograde axonal transport of mitochondrion / dynactin complex / sperm head-tail coupling apparatus / F-actin capping protein complex / WASH complex / positive regulation of norepinephrine uptake / bBAF complex / cellular response to cytochalasin B / npBAF complex / nBAF complex ...retrograde axonal transport of mitochondrion / dynactin complex / sperm head-tail coupling apparatus / F-actin capping protein complex / WASH complex / positive regulation of norepinephrine uptake / bBAF complex / cellular response to cytochalasin B / npBAF complex / nBAF complex / brahma complex / regulation of transepithelial transport / cell junction assembly / Formation of annular gap junctions / Formation of the dystrophin-glycoprotein complex (DGC) / morphogenesis of a polarized epithelium / structural constituent of postsynaptic actin cytoskeleton / Gap junction degradation / barbed-end actin filament capping / GBAF complex / Folding of actin by CCT/TriC / melanosome transport / regulation of G0 to G1 transition / protein localization to adherens junction / Cell-extracellular matrix interactions / dense body / actin polymerization or depolymerization / Tat protein binding / postsynaptic actin cytoskeleton / coronary vasculature development / Prefoldin mediated transfer of substrate to CCT/TriC / RSC-type complex / RHOD GTPase cycle / regulation of double-strand break repair / regulation of nucleotide-excision repair / regulation of cell morphogenesis / Adherens junctions interactions / RHOF GTPase cycle / dynein complex / protein localization to centrosome / COPI-independent Golgi-to-ER retrograde traffic / adherens junction assembly / apical protein localization / Sensory processing of sound by outer hair cells of the cochlea / Interaction between L1 and Ankyrins / tight junction / lamellipodium assembly / microtubule associated complex / SWI/SNF complex / regulation of mitotic metaphase/anaphase transition / Sensory processing of sound by inner hair cells of the cochlea / cytoplasmic dynein complex / aorta development / ventricular septum development / positive regulation of T cell differentiation / apical junction complex / mitotic metaphase chromosome alignment / spectrin binding / positive regulation of double-strand break repair / maintenance of blood-brain barrier / regulation of norepinephrine uptake / nitric-oxide synthase binding / transporter regulator activity / cortical cytoskeleton / establishment or maintenance of cell polarity / NuA4 histone acetyltransferase complex / positive regulation of stem cell population maintenance / Recycling pathway of L1 / Regulation of MITF-M-dependent genes involved in pigmentation / dynein complex binding / brush border / Advanced glycosylation endproduct receptor signaling / regulation of G1/S transition of mitotic cell cycle / EPH-ephrin mediated repulsion of cells / negative regulation of cell differentiation / kinesin binding / RHO GTPases Activate WASPs and WAVEs / regulation of synaptic vesicle endocytosis / positive regulation of myoblast differentiation / RHO GTPases activate IQGAPs / regulation of protein localization to plasma membrane / positive regulation of double-strand break repair via homologous recombination / COPI-mediated anterograde transport / stress fiber / vesicle-mediated transport / EPHB-mediated forward signaling / cytoskeleton organization / axon cytoplasm / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / MHC class II antigen presentation / substantia nigra development / Recruitment of NuMA to mitotic centrosomes / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / axonogenesis / Anchoring of the basal body to the plasma membrane / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / calyx of Held / hippocampal mossy fiber to CA3 synapse
Similarity search - Function
Dynactin subunit 4 / Dynactin p62 family / Dynamitin / : / Dynamitin / Dynactin subunit 6 / Dynactin subunit 5 / F-actin-capping protein subunit beta / F-actin capping protein, beta subunit, conserved site / F-actin-capping protein subunit beta, N-terminal domain ...Dynactin subunit 4 / Dynactin p62 family / Dynamitin / : / Dynamitin / Dynactin subunit 6 / Dynactin subunit 5 / F-actin-capping protein subunit beta / F-actin capping protein, beta subunit, conserved site / F-actin-capping protein subunit beta, N-terminal domain / F-actin capping protein, beta subunit / F-actin capping protein beta subunit signature. / F-actin capping protein, alpha subunit, conserved site / F-actin capping protein alpha subunit signature 1. / F-actin capping protein alpha subunit signature 2. / F-actin-capping protein subunit alpha / F-actin-capping protein subunit alpha/beta / F-actin-capping protein subunit alpha/beta, domain 2 / F-actin capping protein, alpha subunit, domain 1 / F-actin capping protein alpha subunit / Trimeric LpxA-like superfamily / 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
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Dynactin subunit 6 / F-actin-capping protein subunit beta / F-actin-capping protein subunit alpha-1 / Actin, cytoplasmic 1 / Alpha-centractin / Dynactin subunit 2 / Dynactin subunit 5 / Actin-related protein 10 / Dynactin subunit 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.47 Å
AuthorsPawar, K.I. / Verba, K.A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Cell Rep / Year: 2025
Title: The Chlamydia effector Dre1 binds dynactin to reposition host organelles during infection.
Authors: Jessica Sherry / Komal Ishwar Pawar / Lee Dolat / Erin Smith / I-Chang Chang / Khavong Pha / Robyn Kaake / Danielle L Swaney / Clara Herrera / Eleanor McMahon / Robert J Bastidas / Jeffrey R ...Authors: Jessica Sherry / Komal Ishwar Pawar / Lee Dolat / Erin Smith / I-Chang Chang / Khavong Pha / Robyn Kaake / Danielle L Swaney / Clara Herrera / Eleanor McMahon / Robert J Bastidas / Jeffrey R Johnson / Raphael H Valdivia / Nevan J Krogan / Cherilyn A Elwell / Kliment Verba / Joanne N Engel /
Abstract: The obligate intracellular pathogen Chlamydia trachomatis replicates in a specialized membrane-bound compartment where it repositions host organelles during infection to acquire nutrients and evade ...The obligate intracellular pathogen Chlamydia trachomatis replicates in a specialized membrane-bound compartment where it repositions host organelles during infection to acquire nutrients and evade host surveillance. We describe a bacterial effector, Dre1, that binds specifically to dynactin associated with host microtubule organizing centers without globally impeding dynactin function. Dre1 is required to reposition the centrosome, mitotic spindle, Golgi apparatus, and primary cilia around the inclusion and contributes to pathogen fitness in cell-based and mouse models of infection. We utilized Dre1 to affinity purify the megadalton dynactin protein complex and determined the first cryoelectron microscopy (cryo-EM) structure of human dynactin. Our results suggest that Dre1 binds to the pointed end of dynactin and uncovers the first bacterial effector that modulates dynactin function. Our work highlights how a pathogen employs a single effector to evoke targeted, large-scale changes in host cell organization that facilitate pathogen growth without inhibiting host viability.
History
DepositionMar 28, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 16, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alpha-centractin
B: Alpha-centractin
C: Alpha-centractin
D: Alpha-centractin
E: Alpha-centractin
F: Alpha-centractin
G: Alpha-centractin
H: Actin, cytoplasmic 1
I: Alpha-centractin
J: Actin-related protein 10
K: Dynactin subunit 4
L: Dynactin subunit 5
M: Dynactin subunit 6
N: F-actin-capping protein subunit alpha-1
O: F-actin-capping protein subunit beta
P: Dynactin subunit 2
Q: Dynactin subunit 2
p: Dynactin subunit 2
q: Dynactin subunit 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)767,73631
Polymers763,61619
Non-polymers4,12012
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

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Protein , 3 types, 10 molecules ABCDEFGIHJ

#1: Protein
Alpha-centractin / Centractin / ARP1 / Actin-RPV / Centrosome-associated actin homolog


Mass: 42670.688 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61163
#2: Protein Actin, cytoplasmic 1 / Beta-actin


Mass: 41782.660 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P60709
#3: Protein Actin-related protein 10 / Actin-related protein 11 / hARP11


Mass: 46360.863 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9NZ32

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Dynactin subunit ... , 4 types, 7 molecules KLMPQpq

#4: Protein Dynactin subunit 4 / Dyn4 / Dynactin subunit p62


Mass: 52409.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9UJW0
#5: Protein Dynactin subunit 5 / Dynactin subunit p25


Mass: 20150.533 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BTE1
#6: Protein Dynactin subunit 6 / Dynactin subunit p27 / Protein WS-3


Mass: 20769.002 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O00399
#9: Protein
Dynactin subunit 2 / 50 kDa dynein-associated polypeptide / Dynactin complex 50 kDa subunit / DCTN-50 / p50 dynamitin


Mass: 44285.891 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q13561

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F-actin-capping protein subunit ... , 2 types, 2 molecules NO

#7: Protein F-actin-capping protein subunit alpha-1 / CapZ alpha-1


Mass: 32964.727 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P52907
#8: Protein F-actin-capping protein subunit beta / CapZ beta


Mass: 30669.768 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P47756

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Non-polymers , 3 types, 12 molecules

#10: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#11: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#12: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn

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Details

Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Human dynactin complex bound to Chlamydia effector Dre1
Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightValue: 1.1 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 57.7 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.47 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 50376 / Symmetry type: POINT

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