9W2M | pdb_00009w2m

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

PDB DOI: https://doi.org/10.2210/pdb9W2M/pdb
EM Map EMD-65575: EMDB EMDataResource

Classification: STRUCTURAL PROTEIN
Organism(s): Mus musculus
Mutation(s): No

Deposited: 2025-07-28 Released: 2026-02-25
Deposition Author(s): Liu, S.X., Xue, J.C., Zhang, Y., Liu, Y.S., Gao, H.S., Shen, E.Z.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

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

Liu, S.X., Xue, J.C., Zhang, Y., Liu, Y.S., Gao, H.S., Shen, E.Z.

To be published.

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
Molecule	Chains	Sequence Length	Organism	Details	Image
Inactive protein-arginine deiminase type-6	A [auth 1] AA [auth 5] AB [auth 14] BA [auth 6] BB [auth 13] A [auth 1], AA [auth 5], AB [auth 14], BA [auth 6], BB [auth 13], CA [auth 7], CB [auth 17], DA [auth 8], DB [auth 18], EA [auth 9], FA [auth 12], L [auth Z], W [auth z], WA [auth 11], X [auth 2], XA [auth 19], Y [auth 3], YA [auth 15], Z [auth 4], ZA [auth 16]	682	Mus musculus	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q8K3V4 (Mus musculus) Explore Q8K3V4 Go to UniProtKB: Q8K3V4
IMPC: MGI:2655198
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8K3V4
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Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Oocyte-expressed protein homolog	B [auth C], E [auth H], M [auth c], P [auth h]	125	Mus musculus	Mutation(s): 0
UniProt
Find proteins for Q9CWE6 (Mus musculus) Explore Q9CWE6 Go to UniProtKB: Q9CWE6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9CWE6
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
KH domain-containing protein 3	C [auth D], N [auth d]	128	Mus musculus	Mutation(s): 0
UniProt
Find proteins for Q9CWU5 (Mus musculus) Explore Q9CWU5 Go to UniProtKB: Q9CWU5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9CWU5
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
NLR family, pyrin domain containing 4F	D [auth E], F [auth I], O [auth e], Q [auth i]	933	Mus musculus	Mutation(s): 0
UniProt
Find proteins for L7N1W9 (Mus musculus) Explore L7N1W9 Go to UniProtKB: L7N1W9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	L7N1W9
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
FBXW24	G [auth J], R [auth j]	466	Mus musculus	Mutation(s): 0
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Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
S-phase kinase-associated protein 1	H [auth K], S [auth k]	163	Mus musculus	Mutation(s): 0
UniProt
Find proteins for Q9WTX5 (Mus musculus) Explore Q9WTX5 Go to UniProtKB: Q9WTX5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9WTX5
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Reference Sequence

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin-conjugating enzyme E2 D3	I [auth O], T [auth o]	147	Mus musculus	Mutation(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) Explore P61079 Go to UniProtKB: P61079
IMPC: MGI:1913355
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P61079
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Reference Sequence

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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase UHRF1	HA [auth P], J [auth Q], PA [auth p], U [auth q]	782	Mus musculus	Mutation(s): 0 EC: 2.3.2.27
UniProt & NIH Common Fund Data Resources
Find proteins for Q8VDF2 (Mus musculus) Explore Q8VDF2 Go to UniProtKB: Q8VDF2
IMPC: MGI:1338889
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8VDF2
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Reference Sequence

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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Zinc finger BED domain-containing protein 3	K [auth R], V [auth r]	55	Mus musculus	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q9D0L1 (Mus musculus) Explore Q9D0L1 Go to UniProtKB: Q9D0L1
IMPC: MGI:1919364
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9D0L1
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Reference Sequence

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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
NACHT, LRR and PYD domains-containing protein 14	GA [auth N], OA [auth n]	966	Mus musculus	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q6B966 (Mus musculus) Explore Q6B966 Go to UniProtKB: Q6B966
IMPC: MGI:1924108
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q6B966
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Reference Sequence

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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin beta-2A chain	IA [auth L], QA [auth l]	445	Mus musculus	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q7TMM9 (Mus musculus) Explore Q7TMM9 Go to UniProtKB: Q7TMM9
IMPC: MGI:107861
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q7TMM9
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Reference Sequence

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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin beta-2B chain	JA [auth M], RA [auth m]	445	Mus musculus	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q9CWF2 (Mus musculus) Explore Q9CWF2 Go to UniProtKB: Q9CWF2
IMPC: MGI:1920960
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9CWF2
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Reference Sequence

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Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
Isoform 4 of NACHT, LRR and PYD domains-containing protein 5	KA [auth A], MA [auth F], SA [auth a], UA [auth f]	963	Mus musculus	Mutation(s): 0
UniProt
Find proteins for Q9R1M5 (Mus musculus) Go to UniProtKB: Q9R1M5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9R1M5-4
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Reference Sequence

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Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
Transducin-like enhancer protein 6	LA [auth B], NA [auth G], TA [auth b], VA [auth g]	436	Mus musculus	Mutation(s): 0
UniProt
Find proteins for Q9WVB3 (Mus musculus) Explore Q9WVB3 Go to UniProtKB: Q9WVB3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9WVB3
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Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GDP (Subject of Investigation/LOI) Query on GDP Download Ideal Coordinates CCD File SDF format, chain EB [auth L] SDF format, chain FB [auth M] SDF format, chain IB [auth l] SDF format, chain JB [auth m] MOL2 format, chain EB [auth L] MOL2 format, chain FB [auth M] MOL2 format, chain IB [auth l] MOL2 format, chain JB [auth m] mmCIF format, chain EB [auth L] mmCIF format, chain FB [auth M] mmCIF format, chain IB [auth l] mmCIF format, chain JB [auth m]	EB [auth L], FB [auth M], IB [auth l], JB [auth m]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain EB [auth L] Focus chain FB [auth M] Focus chain IB [auth l] Focus chain JB [auth m] Interactions & Density Focus chain EB [auth L] Focus chain FB [auth M] Focus chain IB [auth l] Focus chain JB [auth m]
ADP (Subject of Investigation/LOI) Query on ADP Download Ideal Coordinates CCD File SDF format, chain GB [auth A] SDF format, chain HB [auth F] SDF format, chain KB [auth a] SDF format, chain LB [auth f] MOL2 format, chain GB [auth A] MOL2 format, chain HB [auth F] MOL2 format, chain KB [auth a] MOL2 format, chain LB [auth f] mmCIF format, chain GB [auth A] mmCIF format, chain HB [auth F] mmCIF format, chain KB [auth a] mmCIF format, chain LB [auth f]	GB [auth A], HB [auth F], KB [auth a], LB [auth f]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain GB [auth A] Focus chain HB [auth F] Focus chain KB [auth a] Focus chain LB [auth f] Interactions & Density Focus chain GB [auth A] Focus chain HB [auth F] Focus chain KB [auth a] Focus chain LB [auth f]