9E23 | pdb_00009e23

Cryo-EM structure of Pre-Chi dynein tail

• PDB DOI: https://doi.org/10.2210/pdb9E23/pdb
• EM Map EMD-47430: EMDB EMDataResource

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


• Deposited: 2024-10-21 Released: 2025-07-09 
• Deposition Author(s): Nguyen, K.H.V., Kendrick, A.A., Leschziner, A.E.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

---

Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 6.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Cryo-EM structure of Pre-Chi dynein bound to Lis1

Nguyen, K.H.V., Kendrick, A.A., Leschziner, A.E.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 16-mer - A2B2C2D2E2F2G2H2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 16-mer - A2B2C2D2E2F2G1H1I1J1 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - C2 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - D2 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - E2 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - H2 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 2,666.18 kDa 
• Atom Count: 21,249 
• Modeled Residue Count: 4,734 
• Deposited Residue Count: 23,400 
• Unique protein chains: 6

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dynein light chain roadblock-type 1	A [auth E], B [auth F]	96	Homo sapiens	Mutation(s): 0  Gene Names: DYNLRB1, BITH, DNCL2A, DNLC2A, ROBLD1, HSPC162
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NP97 (Homo sapiens) Explore Q9NP97  Go to UniProtKB:  Q9NP97
PHAROS:  Q9NP97 GTEx:  ENSG00000125971

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Isoform 2C of Cytoplasmic dynein 1 intermediate chain 2	C [auth H], E [auth g], F [auth h], P [auth D]	612	Homo sapiens	Mutation(s): 0  Gene Names: DYNC1I2, DNCI2, DNCIC2
UniProt & NIH Common Fund Data Resources
Find proteins for Q13409 (Homo sapiens) Explore Q13409  Go to UniProtKB:  Q13409
PHAROS:  Q13409 GTEx:  ENSG00000077380

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Dynein light chain 1, cytoplasmic	D [auth d], G [auth i]	89	Homo sapiens	Mutation(s): 0  Gene Names: DYNLL1, DLC1, DNCL1, DNCLC1, HDLC1
UniProt & NIH Common Fund Data Resources
Find proteins for P63167 (Homo sapiens) Explore P63167  Go to UniProtKB:  P63167
PHAROS:  P63167 GTEx:  ENSG00000088986

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Dynein light chain Tctex-type 1	H [auth k], I [auth v]	113	Homo sapiens	Mutation(s): 0  Gene Names: DYNLT1, TCTEL1, TCTEX-1, TCTEX1
UniProt & NIH Common Fund Data Resources
Find proteins for P63172 (Homo sapiens) Explore P63172  Go to UniProtKB:  P63172
PHAROS:  P63172 GTEx:  ENSG00000146425

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytoplasmic dynein 1 light intermediate chain 2	J [auth B], K [auth C]	492	Homo sapiens	Mutation(s): 0  Gene Names: DYNC1LI2, DNCLI2, LIC2
UniProt & NIH Common Fund Data Resources
Find proteins for O43237 (Homo sapiens) Explore O43237  Go to UniProtKB:  O43237
PHAROS:  O43237 GTEx:  ENSG00000135720

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytoplasmic dynein 1 heavy chain 1	L [auth e], M [auth f], N [auth A], O [auth G]	4,843	Homo sapiens	Mutation(s): 0  Gene Names: DYNC1H1, DHC1, DNCH1, DNCL, DNECL, DYHC, KIAA0325
UniProt & NIH Common Fund Data Resources
Find proteins for Q14204 (Homo sapiens) Explore Q14204  Go to UniProtKB:  Q14204
PHAROS:  Q14204 GTEx:  ENSG00000197102

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 6.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-07-09 
Deposition Author(s): Nguyen, K.H.V., Kendrick, A.A., Leschziner, A.E.

---

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	T32 GM139795
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35 GM145296

Revision History  

• Version 1.0: 2025-07-09
  Type: Initial release