9XRL | pdb_00009xrl

Structure of mouse cytoplasmic lattice (CPL) repeating unit


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.74 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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Literature

Structure of the mouse cytoplasmic lattice.

Chi, P.Wang, X.Li, J.Huang, J.Ju, S.Liu, S.Yan, L.Lu, Y.Zhang, Z.Han, Z.Li, J.Qi, Q.Liu, Q.Zeng, Y.Guo, L.Zhang, X.Gui, L.Deng, D.

(2026) Nature 

  • DOI: https://doi.org/10.1038/s41586-026-10442-6
  • Primary Citation Related Structures: 
    9XRL

  • PubMed Abstract: 

    The fertilized egg relies almost entirely on maternal stores in the oocyte to ensure the successful initiation of development 1 . The cytoplasmic lattices (CPLs) in mammalian oocytes store maternal-expressed proteins and play an essential role in embryogenesis 2,3 . Impairing multiple CPL members leads to early embryonic arrest (EEA), resulting in infertility in mammals. However, the mechanism underlying the assembly and storage of CPLs remains largely unknown. Here, we report the cryo-EM structure of a native mouse CPL repeating unit (~ 4 MDa) at 3.74 Å resolution. This repeating unit exhibits a tripartite architecture comprising a framework, extended linkers, and a CPL core. The external framework is built from PADI6 decamers and the subcortical maternal complexes (SCMC). Two linkers formed by NLRP4F polymerize the frameworks into an extended filament. In CPL core, the epigenetic regulator UHRF1 is trapped by PADI6, UBE2D, and NLRP14 in a compact, autoinhibited conformation that prevents nuclear entry and ubiquitin ligase activity. Moreover, the CPL core stores GTP-bound α/β-tubulin heterodimers and inactive SCF E3-ubiquitin ligase components (FBXW-SKP1 complex) in a poised but restrained state. These features establish CPLs as a dynamic regulatory pool that enables rapid microtubule assembly and tightly controlled ubiquitination during the oocyte-to-embryo transition. Together, this semi-in-situ structure illuminates CPL assembly and storage-module organization, and establishes CPLs as specialized proteostasis organelles for maternal regulation in oocytes and early embryonic development.


  • Organizational Affiliation
    • Department of Obstetrics and Gynecology, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University, Chengdu, China.

Macromolecule Content 

  • Total Structure Weight: 4,735.88 kDa 
  • Atom Count: 281,032 
  • Modeled Residue Count: 35,602 
  • Deposited Residue Count: 41,823 
  • Unique protein chains: 16

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Zinc finger BED domain-containing protein 3A [auth 1],
B [auth 3],
E [auth 9]
228Mus musculusMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9D0L1 (Mus musculus)
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IMPC:  MGI:1919364
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UniProt GroupQ9D0L1
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
KH domain-containing protein 3C [auth 4],
D [auth 6],
TA [auth AA]
440Mus musculusMutation(s): 0 
UniProt
Find proteins for Q9CWU5 (Mus musculus)
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
F-box and WD-40 domain protein 21F [auth A]468Mus musculusMutation(s): 0 
UniProt
Find proteins for Q8BI38 (Mus musculus)
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
S-phase kinase-associated protein 1DB [auth F],
G [auth D],
UA [auth O],
V [auth p],
VA [auth q]
163Mus musculusMutation(s): 0 
UniProt
Find proteins for Q9WTX5 (Mus musculus)
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Transducin-like enhancer protein 6581Mus musculusMutation(s): 0 
UniProt
Find proteins for Q9WVB3 (Mus musculus)
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
NLR family, pyrin domain containing 4FI [auth H],
L [auth Q],
SB [auth i],
TB [auth h]
937Mus musculusMutation(s): 0 
UniProt
Find proteins for L7N1W9 (Mus musculus)
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Inactive protein-arginine deiminase type-6682Mus musculusMutation(s): 0 
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Find proteins for Q8K3V4 (Mus musculus)
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IMPC:  MGI:2655198
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
Oocyte-expressed protein homolog164Mus musculusMutation(s): 0 
UniProt
Find proteins for Q9CWE6 (Mus musculus)
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Reference Sequence
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
Expressed sequence C85627N [auth k],
O [auth l]
469Mus musculusMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q3TSA9 (Mus musculus)
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IMPC:  MGI:3505704
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Reference Sequence
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
Tubulin beta-4B chainJB [auth AN],
LA [auth AE],
P [auth t]
445Mus musculusMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P68372 (Mus musculus)
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IMPC:  MGI:1915472
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Reference Sequence
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
NACHT, LRR and PYD domains-containing protein 51,059Mus musculusMutation(s): 0 
UniProt
Find proteins for Q9R1M5 (Mus musculus)
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Reference Sequence
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
Tubulin alpha-1A chainJA [auth u],
MA [auth AF],
PA [auth AO]
451Mus musculusMutation(s): 0 
EC: 3.6.5
UniProt & NIH Common Fund Data Resources
Find proteins for P68369 (Mus musculus)
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IMPC:  MGI:98869
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Reference Sequence
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
NACHT, LRR and PYD domains-containing protein 14KA [auth w],
QB [auth AK],
RB [auth AQ]
993Mus musculusMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q6B966 (Mus musculus)
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IMPC:  MGI:1924108
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Reference Sequence
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
Ubiquitin-conjugating enzyme E2 D3LB [auth AD],
NA [auth AM],
QA [auth AS]
147Mus musculusMutation(s): 0 
EC: 2.3.2.23 (PDB Primary Data), 2.3.2.24 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P61079 (Mus musculus)
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IMPC:  MGI:1913355
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Reference Sequence
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Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase UHRF1OA [auth AL],
PB [auth x],
RA [auth AR]
782Mus musculusMutation(s): 0 
EC: 2.3.2.27
UniProt & NIH Common Fund Data Resources
Find proteins for Q8VDF2 (Mus musculus)
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IMPC:  MGI:1338889
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Reference Sequence
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Entity ID: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
F-box and WD-40 domain protein 19BB [auth L],
CB [auth C]
466Mus musculusMutation(s): 0 
UniProt
Find proteins for Q8C2W8 (Mus musculus)
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GTP

Query on GTP



Download:Ideal Coordinates CCD File
BC [auth u],
DC [auth AF],
GC [auth AO],
MC [auth AN],
YB [auth t]
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
ADP

Query on ADP



Download:Ideal Coordinates CCD File
CC [auth w],
SC [auth AK],
TC [auth AQ]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
EC [auth AL]
FC [auth AL]
IC [auth AR]
JC [auth AR]
KC [auth AR]
EC [auth AL],
FC [auth AL],
IC [auth AR],
JC [auth AR],
KC [auth AR],
LC [auth AR],
OC [auth x],
PC [auth x],
QC [auth x],
RC [auth x],
VB [auth 1],
WB [auth 3],
XB [auth 9]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
AC [auth u],
HC [auth AO],
NC [auth AN],
ZB [auth t]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.74 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China31971132

Revision History  (Full details and data files)

  • Version 1.0: 2026-03-18
    Type: Initial release
  • Version 1.1: 2026-04-15
    Changes: Data collection, Database references