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- PDB-9b7j: Cryo-EM structure of human dynactin complex bound to Chlamydia ef... -

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Basic information

Entry
Database: PDB / ID: 9b7j
TitleCryo-EM structure of human dynactin complex bound to Chlamydia effector Dre1
Components
  • (Dynactin subunit ...) x 9
  • (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


cell cortex region / retrograde axonal transport of mitochondrion / centriolar subdistal appendage / dynactin complex / positive regulation of neuromuscular junction development / centriole-centriole cohesion / sperm head-tail coupling apparatus / F-actin capping protein complex / WASH complex / microtubule anchoring at centrosome ...cell cortex region / retrograde axonal transport of mitochondrion / centriolar subdistal appendage / dynactin complex / positive regulation of neuromuscular junction development / centriole-centriole cohesion / sperm head-tail coupling apparatus / F-actin capping protein complex / WASH complex / microtubule anchoring at centrosome / maintenance of synapse structure / ventral spinal cord development / positive regulation of norepinephrine uptake / cytoskeleton-dependent cytokinesis / microtubule plus-end / nuclear membrane disassembly / cellular response to cytochalasin B / bBAF complex / npBAF complex / nBAF complex / brahma complex / positive regulation of microtubule nucleation / XBP1(S) activates chaperone genes / regulation of transepithelial transport / Formation of annular gap junctions / morphogenesis of a polarized epithelium / Formation of the dystrophin-glycoprotein complex (DGC) / structural constituent of postsynaptic actin cytoskeleton / cell junction assembly / 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 / postsynaptic actin cytoskeleton / Tat protein binding / coronary vasculature development / non-motile cilium assembly / 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 / retrograde transport, endosome to Golgi / protein localization to centrosome / adherens junction assembly / COPI-independent Golgi-to-ER retrograde traffic / 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 / cytoplasmic dynein complex / Sensory processing of sound by inner hair cells of the cochlea / aorta development / ventricular septum development / positive regulation of T cell differentiation / neuromuscular process / nuclear migration / mitotic metaphase chromosome alignment / apical junction complex / spectrin binding / positive regulation of double-strand break repair / regulation of norepinephrine uptake / neuromuscular junction development / transporter regulator activity / maintenance of blood-brain barrier / nitric-oxide synthase binding / cortical cytoskeleton / NuA4 histone acetyltransferase complex / establishment or maintenance of cell polarity / positive regulation of stem cell population maintenance / cell leading edge / motor behavior / dynein complex binding / Regulation of MITF-M-dependent genes involved in pigmentation / Recycling pathway of L1 / cleavage furrow / brush border / establishment of mitotic spindle orientation / Advanced glycosylation endproduct receptor signaling / regulation of G1/S transition of mitotic cell cycle / EPH-ephrin mediated repulsion of cells / kinesin binding / negative regulation of cell differentiation / RHO GTPases Activate WASPs and WAVEs / regulation of synaptic vesicle endocytosis / positive regulation of myoblast differentiation
Similarity search - Function
Dynactin subunit 3 / Dynactin subunit p22 / Dynactin subunit 4 / Dynactin p62 family / Dynein associated protein / Dynein associated protein / Dynamitin / : / Dynamitin / Dynactin subunit 6 ...Dynactin subunit 3 / Dynactin subunit p22 / Dynactin subunit 4 / Dynactin p62 family / Dynein associated protein / Dynein associated protein / 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 / CAP-Gly domain signature. / CAP Gly-rich domain / CAP Gly-rich domain superfamily / CAP-Gly domain / CAP-Gly domain profile. / CAP_GLY / 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 / Dynactin subunit 3 / F-actin-capping protein subunit beta / F-actin-capping protein subunit alpha-1 / Actin, cytoplasmic 1 / Alpha-centractin / Dynactin subunit 2 / Dynactin subunit 1 ...ADENOSINE-5'-DIPHOSPHATE / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Dynactin subunit 6 / Dynactin subunit 3 / F-actin-capping protein subunit beta / F-actin-capping protein subunit alpha-1 / Actin, cytoplasmic 1 / Alpha-centractin / Dynactin subunit 2 / Dynactin subunit 1 / 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: 3.49 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 27, 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
R: Dynactin subunit 3
S: Dynactin subunit 1
T: Dynactin subunit 1, p150-glued
U: Dynactin subunit 2, p50 dynamitin
p: Dynactin subunit 2
q: Dynactin subunit 2
r: Dynactin subunit 3
s: Dynactin subunit 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,108,34337
Polymers1,104,22325
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 ... , 9 types, 13 molecules KLMPQpqRrSTUs

#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
#10: Protein Dynactin subunit 3 / Dynactin complex subunit 22 kDa subunit / p22


Mass: 21145.379 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O75935
#11: Protein Dynactin subunit 1 / 150 kDa dynein-associated polypeptide / DAP-150 / DP-150 / p135 / p150-glued


Mass: 141920.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q14203
#12: Protein Dynactin subunit 1, p150-glued


Mass: 7081.720 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#13: Protein Dynactin subunit 2, p50 dynamitin


Mass: 7422.140 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#14: Protein Dynactin subunit 1 / 150 kDa dynein-associated polypeptide / DAP-150 / DP-150 / p135 / p150-glued


Mass: 141892.547 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q14203

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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

#15: 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
#16: 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
#17: 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 modificationY

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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: #1-#14 / 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: 3.49 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 45091 / Symmetry type: POINT

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