9W2M | pdb_00009w2m

Cryo-EM structure of the Cytoplasmic lattice(CPL) from mouse oocyte


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.20 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 9W2M

This is version 1.2 of the entry. See complete history

Literature

Molecular basis of oocyte cytoplasmic lattice assembly.

Liu, S.Liu, Y.Xue, J.Li, Z.Zhang, Y.Li, B.Xu, L.Li, L.Yu, Z.Yu, H.Gao, H.Shen, E.Z.

(2026) Nature 

  • DOI: https://doi.org/10.1038/s41586-026-10360-7
  • Primary Citation Related Structures: 
    9W2M

  • PubMed Abstract: 

    Mammalian oocytes are filled with fibric structures called cytoplasmic lattice (CPL) that are essential for oocyte maturation and early embryonic development 1-3 . CPL comprises subcortical maternal complex (SCMC) and multiple components, including PADI6 2,4,5 . Although it was first discovered in the 1960s, the molecular architecture and assembly mechanisms of CPL remain poorly understood. Here we present the cryo-electron microscopy structure of CPL isolated from mouse oocytes. Our analysis identified 14 constitutive protein subunits and revealed that CPL is composed of repeating units comprising U-shaped basket (UB) and adapter ring (AR) features, forming a filamentous architecture. The AR adopts a two-fold symmetric conformation, containing two NLRP4F, four SCMC and two ZBED3 subunits circularized via two distinct interaction clusters. The UB is anchored by PADI6, a didecamer composed of ten homodimers assembled by two back-to-back pentamers, each forming the lateral side of the UB. The underfoot base and up and down sides of the UB are formed by multiple central-symmetric assemblies (UBE2D3-UHRF1-NLRP14) and (TUBB2B-TUBB2A-FBXW24-SKP1), respectively, associating with the PADI6 pentamers to construct the intact UB structure. Two SCMC dimers within each AR connect the up and down sides of two adjacent UBs with an extensive protein-protein interaction network, and thus maintain the repetitive connection between the neighbouring CPL units. Our work unveils the architectural principles underlying the assembly of this large, periodic CPL filament, offering a molecular basis for understanding the functions of CPL in early mammalian embryogenesis and female reproductive disorders.


  • Organizational Affiliation
    • College of Life Sciences, Zhejiang University, Hangzhou, China.

Macromolecule Content 

  • Total Structure Weight: 3,656.58 kDa 
  • Atom Count: 234,055 
  • Modeled Residue Count: 29,468 
  • Deposited Residue Count: 32,226 
  • Unique protein chains: 14

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Inactive protein-arginine deiminase type-6682Mus musculusMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q8K3V4 (Mus musculus)
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IMPC:  MGI:2655198
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UniProt GroupQ8K3V4
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Oocyte-expressed protein homologB [auth C],
E [auth H],
M [auth c],
P [auth h]
125Mus musculusMutation(s): 0 
UniProt
Find proteins for Q9CWE6 (Mus musculus)
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UniProt GroupQ9CWE6
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
KH domain-containing protein 3C [auth D],
N [auth d]
128Mus musculusMutation(s): 0 
UniProt
Find proteins for Q9CWU5 (Mus musculus)
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UniProt GroupQ9CWU5
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
NLR family, pyrin domain containing 4FD [auth E],
F [auth I],
O [auth e],
Q [auth i]
933Mus musculusMutation(s): 0 
UniProt
Find proteins for L7N1W9 (Mus musculus)
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
FBXW24G [auth J],
R [auth j]
466Mus musculusMutation(s): 0 
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
S-phase kinase-associated protein 1H [auth K],
S [auth k]
163Mus musculusMutation(s): 0 
UniProt
Find proteins for Q9WTX5 (Mus musculus)
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Ubiquitin-conjugating enzyme E2 D3I [auth O],
T [auth o]
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: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase UHRF1HA [auth P],
J [auth Q],
PA [auth p],
U [auth q]
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: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
Zinc finger BED domain-containing protein 3K [auth R],
V [auth r]
55Mus 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: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
NACHT, LRR and PYD domains-containing protein 14GA [auth N],
OA [auth n]
966Mus 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: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
Tubulin beta-2A chainIA [auth L],
QA [auth l]
445Mus musculusMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q7TMM9 (Mus musculus)
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IMPC:  MGI:107861
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Reference Sequence
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
Tubulin beta-2B chainJA [auth M],
RA [auth m]
445Mus musculusMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9CWF2 (Mus musculus)
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IMPC:  MGI:1920960
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Reference Sequence
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
Isoform 4 of NACHT, LRR and PYD domains-containing protein 5KA [auth A],
MA [auth F],
SA [auth a],
UA [auth f]
963Mus musculusMutation(s): 0 
UniProt
Find proteins for Q9R1M5 (Mus musculus)
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UniProt GroupQ9R1M5-4
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Reference Sequence
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
Transducin-like enhancer protein 6LA [auth B],
NA [auth G],
TA [auth b],
VA [auth g]
436Mus musculusMutation(s): 0 
UniProt
Find proteins for Q9WVB3 (Mus musculus)
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GDP
(Subject of Investigation/LOI)

Query on GDP



Download:Ideal Coordinates CCD File
EB [auth L],
FB [auth M],
IB [auth l],
JB [auth m]
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
ADP
(Subject of Investigation/LOI)

Query on ADP



Download:Ideal Coordinates CCD File
GB [auth A],
HB [auth F],
KB [auth a],
LB [auth f]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.20 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.2_5419:
RECONSTRUCTIONcryoSPARC

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China32070628
National Natural Science Foundation of China (NSFC)China32271258

Revision History  (Full details and data files)

  • Version 1.0: 2026-02-25
    Type: Initial release
  • Version 1.1: 2026-04-29
    Changes: Data collection, Database references
  • Version 1.2: 2026-05-06
    Changes: Data collection