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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 / dynactin complex / centriolar subdistal appendage / centriole-centriole cohesion / positive regulation of neuromuscular junction development / microtubule anchoring at centrosome / F-actin capping protein complex / WASH complex / lysosome to ER cholesterol transport ...cell cortex region / retrograde axonal transport of mitochondrion / dynactin complex / centriolar subdistal appendage / centriole-centriole cohesion / positive regulation of neuromuscular junction development / microtubule anchoring at centrosome / F-actin capping protein complex / WASH complex / lysosome to ER cholesterol transport / maintenance of synapse structure / ventral spinal cord development / positive regulation of norepinephrine uptake / bBAF complex / cytoskeleton-dependent cytokinesis / GBAF complex / dynein complex / microtubule plus-end / brahma complex / mitotic nuclear membrane disassembly / cellular response to cytochalasin B / XBP1(S) activates chaperone genes / positive regulation of microtubule nucleation / Formation of the embryonic stem cell BAF (esBAF) complex / npBAF complex / nBAF complex / Formation of the canonical BAF (cBAF) complex / regulation of transepithelial transport / morphogenesis of a polarized epithelium / cell junction assembly / structural constituent of postsynaptic actin cytoskeleton / Formation of annular gap junctions / Formation of the dystrophin-glycoprotein complex (DGC) / Formation of the polybromo-BAF (pBAF) complex / Formation of neuronal progenitor and neuronal BAF (npBAF and nBAF) / Gap junction degradation / protein localization to adherens junction / Formation of the non-canonical BAF (ncBAF) complex / regulation of G0 to G1 transition / sperm head-tail coupling apparatus / Cell-extracellular matrix interactions / regulation of cell morphogenesis / barbed-end actin filament capping / non-motile cilium assembly / actin polymerization or depolymerization / dense body / Folding of actin by CCT/TriC / Tat protein binding / RSC-type complex / postsynaptic actin cytoskeleton / RHOD GTPase cycle / protein localization to centrosome / Regulation of CDH1 Function / regulation of double-strand break repair / apical protein localization / Prefoldin mediated transfer of substrate to CCT/TriC / motor behavior / Adherens junctions interactions / retrograde transport, endosome to Golgi / adherens junction assembly / RHOF GTPase cycle / regulation of nucleotide-excision repair / COPI-independent Golgi-to-ER retrograde traffic / neuromuscular process / Sensory processing of sound by outer hair cells of the cochlea / microtubule associated complex / lamellipodium assembly / cytoplasmic dynein complex / tight junction / regulation of mitotic metaphase/anaphase transition / SWI/SNF complex / Sensory processing of sound by inner hair cells of the cochlea / nuclear migration / Interaction between L1 and Ankyrins / positive regulation of T cell differentiation / apical junction complex / spectrin binding / maintenance of blood-brain barrier / positive regulation of stem cell population maintenance / establishment of mitotic spindle orientation / intercellular bridge / regulation of norepinephrine uptake / transporter regulator activity / NuA4 histone acetyltransferase complex / positive regulation of double-strand break repair / Recycling pathway of L1 / cell leading edge / cortical cytoskeleton / Regulation of MITF-M-dependent genes involved in pigmentation / cleavage furrow / establishment or maintenance of cell polarity / neuromuscular junction development / dynein complex binding / nitric-oxide synthase binding / brush border / Advanced glycosylation endproduct receptor signaling / EPH-ephrin mediated repulsion of cells / mitotic metaphase chromosome alignment / negative regulation of cell differentiation / regulation of synaptic vesicle endocytosis
Similarity search - Function
Dynactin subunit 3 / Dynactin subunit p22 / Dynactin subunit 4 / Dynactin p62 family / Dynamitin / Dynamitin / Dynactin subunit 6 / : / : / Domain of unknown function (DUF8221) ...Dynactin subunit 3 / Dynactin subunit p22 / Dynactin subunit 4 / Dynactin p62 family / Dynamitin / Dynamitin / Dynactin subunit 6 / : / : / Domain of unknown function (DUF8221) / Dynein associated protein / Dynein associated protein / 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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