9BLY | pdb_00009bly

Composite structure of full-length human dynein-1 in phi-particle conformation

  • Classification: MOTOR PROTEIN
  • Organism(s): Homo sapiens
  • Expression System: Spodoptera frugiperda
  • Mutation(s): No 

  • Deposited: 2024-05-02 Released: 2025-04-23 
  • Deposition Author(s): Chai, P., Zhang, K.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The mechanochemical cycle of reactive full-length human dynein 1.

Chai, P.Yang, J.Geohring, I.C.Markus, S.M.Wang, Y.Zhang, K.

(2025) Nat Struct Mol Biol 32: 1383-1395

  • DOI: https://doi.org/10.1038/s41594-025-01543-3
  • Primary Citation of Related Structures:  
    9BLY, 9BLZ, 9BM0, 9BM1, 9BM2, 9BM3, 9BM4, 9BM5, 9BM6, 9BM7, 9BM8, 9BMA, 9BMB, 9BMC, 9BMD, 9BMF, 9BMG, 9BMH, 9BMJ, 9BML, 9BMM, 9BMN, 9BMO, 9BMP, 9BMR, 9BMS, 9BMT, 9BMU, 9BMV, 9BMW, 9BMY, 9BMZ, 9BN0, 9BN1, 9BN3, 9BN4, 9BN5, 9BN6, 9DH5, 9DH6, 9DH7, 9DH8, 9DH9, 9DHA

  • PubMed Abstract: 

    Dynein-driven cargo transport has a pivotal role in diverse cellular activities, central to which is dynein's mechanochemical cycle. Here, we performed a systematic cryo-electron microscopic investigation of the conformational landscape of full-length human dynein 1 in reaction, in various nucleotide conditions, on and off microtubules. Our approach reveals over 40 high-resolution structures, categorized into eight states, providing a dynamic and comprehensive view of dynein throughout its mechanochemical cycle. The described intermediate states reveal mechanistic insights into dynein function, including a 'backdoor' phosphate release model that coordinates linker straightening, how microtubule binding enhances adenosine triphosphatase activity through a two-way communication mechanism and the crosstalk mechanism between AAA1 and the regulatory AAA3 site. Our findings also lead to a revised model for the force-generating powerstroke and reveal means by which dynein exhibits unidirectional stepping. These results improve our understanding of dynein and provide a more complete model of its mechanochemical cycle.


  • Organizational Affiliation
    • Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytoplasmic dynein 1 heavy chain 1
A, B
4,646Homo sapiensMutation(s): 0 
Gene Names: DYNC1H1DHC1DNCH1DNCLDNECLDYHCKIAA0325
UniProt & NIH Common Fund Data Resources
Find proteins for Q14204 (Homo sapiens)
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Go to UniProtKB:  Q14204
PHAROS:  Q14204
GTEx:  ENSG00000197102 
Entity Groups  
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UniProt GroupQ14204
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Cytoplasmic dynein 1 intermediate chain 2
C, D
638Homo sapiensMutation(s): 0 
Gene Names: DYNC1I2DNCI2DNCIC2
UniProt & NIH Common Fund Data Resources
Find proteins for Q13409 (Homo sapiens)
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PHAROS:  Q13409
GTEx:  ENSG00000077380 
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UniProt GroupQ13409
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Cytoplasmic dynein 1 light intermediate chain 2
E, F
492Homo sapiensMutation(s): 0 
Gene Names: DYNC1LI2DNCLI2LIC2
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Find proteins for O43237 (Homo sapiens)
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PHAROS:  O43237
GTEx:  ENSG00000135720 
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UniProt GroupO43237
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Dynein light chain roadblock-type 1
G, H
96Homo sapiensMutation(s): 0 
Gene Names: DYNLRB1BITHDNCL2ADNLC2AROBLD1HSPC162
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Find proteins for Q9NP97 (Homo sapiens)
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PHAROS:  Q9NP97
GTEx:  ENSG00000125971 
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UniProt GroupQ9NP97
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Dynein light chain 1, cytoplasmic
I, J
89Homo sapiensMutation(s): 0 
Gene Names: DYNLL1DLC1DNCL1DNCLC1HDLC1
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Find proteins for P63167 (Homo sapiens)
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PHAROS:  P63167
GTEx:  ENSG00000088986 
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UniProt GroupP63167
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Dynein light chain Tctex-type 1
K, L
113Homo sapiensMutation(s): 0 
Gene Names: DYNLT1TCTEL1TCTEX-1TCTEX1
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Find proteins for P63172 (Homo sapiens)
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PHAROS:  P63172
GTEx:  ENSG00000146425 
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UniProt GroupP63172
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP (Subject of Investigation/LOI)
Query on ATP

Download Ideal Coordinates CCD File 
N [auth A],
T [auth B]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
ADP (Subject of Investigation/LOI)
Query on ADP

Download Ideal Coordinates CCD File 
M [auth A]
O [auth A]
P [auth A]
S [auth B]
U [auth B]
M [auth A],
O [auth A],
P [auth A],
S [auth B],
U [auth B],
V [auth B]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
Q [auth A],
R [auth A],
W [auth B],
X [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC4

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35GM142959
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35GM139483

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-23
    Type: Initial release
  • Version 1.1: 2025-04-30
    Changes: Data collection, Database references
  • Version 1.2: 2025-08-27
    Changes: Data collection, Database references