9B85 | pdb_00009b85

Cryo-EM structure of human dynactin complex bound to Chlamydia effector Dre1


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.47 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


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Literature

The Chlamydia effector Dre1 binds dynactin to reposition host organelles during infection.

Sherry, J.Pawar, K.I.Dolat, L.Smith, E.Chang, I.C.Pha, K.Kaake, R.Swaney, D.L.Herrera, C.McMahon, E.Bastidas, R.J.Johnson, J.R.Valdivia, R.H.Krogan, N.J.Elwell, C.A.Verba, K.Engel, J.N.

(2025) Cell Rep 44: 115509-115509

  • DOI: https://doi.org/10.1016/j.celrep.2025.115509
  • Primary Citation of Related Structures:  
    9B7J, 9B85

  • PubMed 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 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.


  • Organizational Affiliation

    Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Alpha-centractin
A, B, C, D, E
A, B, C, D, E, F, G, I
376Homo sapiensMutation(s): 0 
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Find proteins for P61163 (Homo sapiens)
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PHAROS:  P61163
GTEx:  ENSG00000138107 
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UniProt GroupP61163
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Actin, cytoplasmic 1375Homo sapiensMutation(s): 0 
EC: 3.6.4
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Find proteins for P60709 (Homo sapiens)
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PHAROS:  P60709
GTEx:  ENSG00000075624 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Actin-related protein 10417Homo sapiensMutation(s): 0 
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PHAROS:  Q9NZ32
GTEx:  ENSG00000131966 
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UniProt GroupQ9NZ32
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Dynactin subunit 4460Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000132912 
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UniProt GroupQ9UJW0
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Dynactin subunit 5182Homo sapiensMutation(s): 0 
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Find proteins for Q9BTE1 (Homo sapiens)
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PHAROS:  Q9BTE1
GTEx:  ENSG00000166847 
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UniProt GroupQ9BTE1
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Dynactin subunit 6190Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000104671 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
F-actin-capping protein subunit alpha-1286Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000116489 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
F-actin-capping protein subunit beta272Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000077549 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Dynactin subunit 2P,
Q,
R [auth p],
S [auth q]
401Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000175203 
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Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ANP
Query on ANP

Download Ideal Coordinates CCD File 
AA [auth H]PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
ADP
Query on ADP

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BA [auth I]
T [auth A]
U [auth B]
V [auth C]
W [auth D]
BA [auth I],
T [auth A],
U [auth B],
V [auth C],
W [auth D],
X [auth E],
Y [auth F],
Z [auth G]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
CA [auth K],
DA [auth K],
EA [auth K]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.47 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-16
    Type: Initial release