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- PDB-9xrl: Structure of mouse cytoplasmic lattice (CPL) repeating unit -

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Entry
Database: PDB / ID: 9xrl
TitleStructure of mouse cytoplasmic lattice (CPL) repeating unit
Components
  • (F-box and WD-40 domain protein ...) x 2
  • (NACHT, LRR and PYD domains-containing protein ...) x 2
  • E3 ubiquitin-protein ligase UHRF1
  • Expressed sequence C85627
  • Inactive protein-arginine deiminase type-6
  • KH domain-containing protein 3
  • NLR family, pyrin domain containing 4F
  • Oocyte-expressed protein homolog
  • S-phase kinase-associated protein 1
  • Transducin-like enhancer protein 6
  • Tubulin alpha-1A chain
  • Tubulin beta-4B chain
  • Ubiquitin-conjugating enzyme E2 D3
  • Zinc finger BED domain-containing protein 3
KeywordsCYTOSOLIC PROTEIN / cytoplasmic lattice / maternal effect protein / proteostasis / protein storage
Function / homology
Function and homology information


regulation of translation by machinery localization / Prolactin receptor signaling / Signaling by BMP / subcortical maternal complex / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Cilium Assembly / Sealing of the nuclear envelope (NE) by ESCRT-III / establishment of organelle localization / Chromatin modifying enzymes / protein storage ...regulation of translation by machinery localization / Prolactin receptor signaling / Signaling by BMP / subcortical maternal complex / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Cilium Assembly / Sealing of the nuclear envelope (NE) by ESCRT-III / establishment of organelle localization / Chromatin modifying enzymes / protein storage / structural constituent of cytoplasmic lattice / cytoplasmic lattice / SCF-beta-TrCP mediated degradation of Emi1 / cortical granule exocytosis / E3 ubiquitin ligases ubiquitinate target proteins / endoplasmic reticulum localization / Carboxyterminal post-translational modifications of tubulin / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Intraflagellar transport / establishment or maintenance of apical/basal cell polarity / ooplasm / Regulation of BACH1 activity / COPI-independent Golgi-to-ER retrograde traffic / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / PINK1-PRKN Mediated Mitophagy / Inactivation of CSF3 (G-CSF) signaling / SCF(Skp2)-mediated degradation of p27/p21 / MAP3K8 (TPL2)-dependent MAPK1/3 activation / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / Regulation of TNFR1 signaling / cytoplasm organization / histone H3 ubiquitin ligase activity / Regulation of RUNX2 expression and activity / Degradation of GLI1 by the proteasome / Cyclin D associated events in G1 / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / IKK complex recruitment mediated by RIP1 / Orc1 removal from chromatin / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Dectin-1 mediated noncanonical NF-kB signaling / NIK-->noncanonical NF-kB signaling / COPI-mediated anterograde transport / Aggrephagy / spermatogonial cell division / Kinesins / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / cortical granule / Resolution of Sister Chromatid Cohesion / PKR-mediated signaling / Degradation of beta-catenin by the destruction complex / Iron uptake and transport / Activation of NF-kappaB in B cells / The role of GTSE1 in G2/M progression after G2 checkpoint / RHO GTPases activate IQGAPs / Recycling pathway of L1 / FCERI mediated NF-kB activation / CLEC7A (Dectin-1) signaling / Interleukin-1 signaling / COPI-dependent Golgi-to-ER retrograde traffic / RHO GTPases Activate Formins / apical cortex / axonemal microtubule / positive regulation of meiotic nuclear division / Separation of Sister Chromatids / regulation of RNA stability / Downstream TCR signaling / positive regulation of embryonic development / organelle transport along microtubule / Hedgehog 'off' state / F-box domain binding / Peroxisomal protein import / Loss of Nlp from mitotic centrosomes / Recruitment of mitotic centrosome proteins and complexes / Loss of proteins required for interphase microtubule organization from the centrosome / hemi-methylated DNA-binding / Anchoring of the basal body to the plasma membrane / Recruitment of NuMA to mitotic centrosomes / regulation of establishment of protein localization / forebrain morphogenesis / AURKA Activation by TPX2 / GLI3 is processed to GLI3R by the proteasome / Regulation of PLK1 Activity at G2/M Transition / PcG protein complex / cerebellar cortex morphogenesis / Neddylation / glial cell differentiation / dentate gyrus development / neuron projection arborization / embryonic pattern specification / (E3-independent) E2 ubiquitin-conjugating enzyme / MHC class II antigen presentation / embryonic cleavage / protein K6-linked ubiquitination / mitochondrion localization / flagellated sperm motility / establishment of spindle localization / gap junction / Cul7-RING ubiquitin ligase complex
Similarity search - Function
Zinc finger BED domain-containing protein 2/3 / : / BED zinc finger / KH-like RNA-binding domain / : / KH-like RNA-binding domain / Groucho/transducin-like enhancer / : / UHRF1, tandem tudor domain / Tandem tudor domain within UHRF1 ...Zinc finger BED domain-containing protein 2/3 / : / BED zinc finger / KH-like RNA-binding domain / : / KH-like RNA-binding domain / Groucho/transducin-like enhancer / : / UHRF1, tandem tudor domain / Tandem tudor domain within UHRF1 / UHRF1/2-like / Protein-arginine deiminase / Protein-arginine deiminase, C-terminal / Protein-arginine deiminase (PAD), N-terminal / Protein-arginine deiminase (PAD), central domain / Protein-arginine deiminase, central domain superfamily / PAD, N-terminal domain superfamily / Protein-arginine deiminase (PAD) / Protein-arginine deiminase (PAD) N-terminal domain / Protein-arginine deiminase (PAD) middle domain / SRA-YDG / SRA-YDG superfamily / SAD/SRA domain / YDG domain profile. / SET and RING finger associated domain. Domain of unknown function in SET domain containing proteins and in Deinococcus radiodurans DRA1533. / : / A Receptor for Ubiquitination Targets / NACHT, LRR and PYD domains-containing protein, helical domain HD2 / NLRC4 helical domain HD2 / NOD2, winged helix domain / NOD2 winged helix domain / F-box domain profile. / NACHT nucleoside triphosphatase / NACHT domain / F-box-like / NACHT-NTPase domain profile. / F-box-like domain superfamily / DAPIN domain / PAAD/DAPIN/Pyrin domain / SKP1 component, dimerisation / S-phase kinase-associated protein 1 / SKP1-like, dimerisation domain superfamily / Skp1 family, dimerisation domain / PAAD/DAPIN/Pyrin domain / F-box domain / Leucine rich repeat, ribonuclease inhibitor type / Leucine Rich repeat / K Homology domain, type 1 superfamily / S-phase kinase-associated protein 1-like / SKP1 component, POZ domain / Skp1 family, tetramerisation domain / Found in Skp1 protein family / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / PUA-like superfamily / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme/RWD-like / PHD-finger / Alpha tubulin / Tubulin-beta mRNA autoregulation signal. / Beta tubulin, autoregulation binding site / Beta tubulin / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain / Tubulin, conserved site / Tubulin subunits alpha, beta, and gamma signature. / Death-like domain superfamily / Zinc finger C2H2 superfamily / Zinc finger PHD-type signature. / Tubulin/FtsZ family, C-terminal domain / Tubulin/FtsZ-like, C-terminal domain / Tubulin/FtsZ, C-terminal / Tubulin/FtsZ, 2-layer sandwich domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, GTPase domain superfamily / SKP1/BTB/POZ domain superfamily / Ring finger / Cupredoxin / Zinc finger PHD-type profile. / Leucine-rich repeat / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Leucine-rich repeat domain superfamily / Zinc finger RING-type profile. / Zinc finger, RING-type / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / NLR family, pyrin domain containing 4F / Ubiquitin-conjugating enzyme E2 D3 / Tubulin alpha-1A chain / Tubulin beta-4B chain / Expressed sequence C85627 / NACHT, LRR and PYD domains-containing protein 14 / F-box and WD-40 domain protein 21 / F-box and WD-40 domain protein 19 ...ADENOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / NLR family, pyrin domain containing 4F / Ubiquitin-conjugating enzyme E2 D3 / Tubulin alpha-1A chain / Tubulin beta-4B chain / Expressed sequence C85627 / NACHT, LRR and PYD domains-containing protein 14 / F-box and WD-40 domain protein 21 / F-box and WD-40 domain protein 19 / Inactive protein-arginine deiminase type-6 / E3 ubiquitin-protein ligase UHRF1 / Oocyte-expressed protein homolog / KH domain-containing protein 3 / Zinc finger BED domain-containing protein 3 / NACHT, LRR and PYD domains-containing protein 5 / S-phase kinase-associated protein 1 / Transducin-like enhancer protein 6
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.74 Å
AuthorsChi, P.L. / Wang, X. / Li, J.L. / Deng, D.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31971132 China
CitationJournal: To Be Published
Title: Structure of mouse cytoplasmic lattice (CPL) repeating unit
Authors: Chi, P.L. / Wang, X. / Li, J.L. / Deng, D.
History
DepositionNov 19, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 18, 2026Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
1: Zinc finger BED domain-containing protein 3
3: Zinc finger BED domain-containing protein 3
4: KH domain-containing protein 3
6: KH domain-containing protein 3
9: Zinc finger BED domain-containing protein 3
A: F-box and WD-40 domain protein 21
D: S-phase kinase-associated protein 1
E: Transducin-like enhancer protein 6
H: NLR family, pyrin domain containing 4F
I: Transducin-like enhancer protein 6
S: Inactive protein-arginine deiminase type-6
Q: NLR family, pyrin domain containing 4F
e: Oocyte-expressed protein homolog
k: Expressed sequence C85627
l: Expressed sequence C85627
t: Tubulin beta-4B chain
g: Oocyte-expressed protein homolog
T: Inactive protein-arginine deiminase type-6
z: Transducin-like enhancer protein 6
y: NACHT, LRR and PYD domains-containing protein 5
AH: Oocyte-expressed protein homolog
p: S-phase kinase-associated protein 1
Y: Inactive protein-arginine deiminase type-6
b: Inactive protein-arginine deiminase type-6
X: Inactive protein-arginine deiminase type-6
Z: Inactive protein-arginine deiminase type-6
V: Inactive protein-arginine deiminase type-6
W: Inactive protein-arginine deiminase type-6
n: Inactive protein-arginine deiminase type-6
f: Inactive protein-arginine deiminase type-6
s: Inactive protein-arginine deiminase type-6
m: Inactive protein-arginine deiminase type-6
o: Inactive protein-arginine deiminase type-6
d: Inactive protein-arginine deiminase type-6
j: Inactive protein-arginine deiminase type-6
u: Tubulin alpha-1A chain
w: NACHT, LRR and PYD domains-containing protein 14
AE: Tubulin beta-4B chain
AF: Tubulin alpha-1A chain
AM: Ubiquitin-conjugating enzyme E2 D3
AL: E3 ubiquitin-protein ligase UHRF1
AO: Tubulin alpha-1A chain
AS: Ubiquitin-conjugating enzyme E2 D3
AR: E3 ubiquitin-protein ligase UHRF1
P: Transducin-like enhancer protein 6
AA: KH domain-containing protein 3
O: S-phase kinase-associated protein 1
q: S-phase kinase-associated protein 1
AC: Transducin-like enhancer protein 6
AB: NACHT, LRR and PYD domains-containing protein 5
AJ: Oocyte-expressed protein homolog
0: NACHT, LRR and PYD domains-containing protein 5
r: Inactive protein-arginine deiminase type-6
L: F-box and WD-40 domain protein 19
C: F-box and WD-40 domain protein 19
F: S-phase kinase-associated protein 1
8: Transducin-like enhancer protein 6
7: NACHT, LRR and PYD domains-containing protein 5
5: NACHT, LRR and PYD domains-containing protein 5
B: Inactive protein-arginine deiminase type-6
K: Inactive protein-arginine deiminase type-6
AN: Tubulin beta-4B chain
AI: Oocyte-expressed protein homolog
AD: Ubiquitin-conjugating enzyme E2 D3
2: NACHT, LRR and PYD domains-containing protein 5
U: Inactive protein-arginine deiminase type-6
c: Inactive protein-arginine deiminase type-6
x: E3 ubiquitin-protein ligase UHRF1
AK: NACHT, LRR and PYD domains-containing protein 14
AQ: NACHT, LRR and PYD domains-containing protein 14
i: NLR family, pyrin domain containing 4F
h: NLR family, pyrin domain containing 4F
AT: Oocyte-expressed protein homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,735,88298
Polymers4,731,03773
Non-polymers4,84525
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 12 types, 61 molecules 13946AADpOqFEIzPAC8HQihSTYbXZVWn...

#1: Protein Zinc finger BED domain-containing protein 3 / Axin-interacting protein


Mass: 25643.373 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9D0L1
#2: Protein KH domain-containing protein 3 / Protein Filia


Mass: 48055.301 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CWU5
#4: Protein
S-phase kinase-associated protein 1 / Cyclin-A/CDK2-associated protein p19 / S-phase kinase-associated protein 1A / p19A / p19skp1


Mass: 18693.992 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9WTX5
#5: Protein
Transducin-like enhancer protein 6 / Groucho-related protein 6


Mass: 65187.332 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9WVB3
#6: Protein
NLR family, pyrin domain containing 4F


Mass: 108001.281 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: L7N1W9
#7: Protein
Inactive protein-arginine deiminase type-6 / Arginine deiminase-like protein / Egg and embryo abundant PAD / ePAD / P75 / Peptidylarginine ...Arginine deiminase-like protein / Egg and embryo abundant PAD / ePAD / P75 / Peptidylarginine deiminase VI / Protein-arginine deiminase type VI / Protein-arginine deiminase type-6


Mass: 76854.109 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q8K3V4
#8: Protein
Oocyte-expressed protein homolog / Factor located in oocytes permitting embryonic development / Floped / Oocyte- and embryo-specific ...Factor located in oocytes permitting embryonic development / Floped / Oocyte- and embryo-specific protein 19 / mOEP19 / STAT3 downstream gene and differentiation regulator


Mass: 18481.295 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CWE6
#9: Protein Expressed sequence C85627 / F-box and WD-40 domain protein 18


Mass: 54205.703 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q3TSA9
#10: Protein Tubulin beta-4B chain / Tubulin beta-2C chain


Mass: 49877.824 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P68372
#12: Protein Tubulin alpha-1A chain / Alpha-tubulin 1 / Alpha-tubulin isotype M-alpha-1 / Tubulin alpha-1 chain


Mass: 50188.441 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
References: UniProt: P68369, Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement
#14: Protein Ubiquitin-conjugating enzyme E2 D3 / (E3-independent) E2 ubiquitin-conjugating enzyme D3 / E2 ubiquitin-conjugating enzyme D3 / ...(E3-independent) E2 ubiquitin-conjugating enzyme D3 / E2 ubiquitin-conjugating enzyme D3 / Ubiquitin carrier protein D3 / Ubiquitin-conjugating enzyme E2(17)KB 3 / Ubiquitin-conjugating enzyme E2-17 kDa 3 / Ubiquitin-protein ligase D3


Mass: 16706.133 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
References: UniProt: P61079, E2 ubiquitin-conjugating enzyme, (E3-independent) E2 ubiquitin-conjugating enzyme
#15: Protein E3 ubiquitin-protein ligase UHRF1


Mass: 88436.805 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q8VDF2

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F-box and WD-40 domain protein ... , 2 types, 3 molecules ALC

#3: Protein F-box and WD-40 domain protein 21


Mass: 54517.043 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q8BI38
#16: Protein F-box and WD-40 domain protein 19


Mass: 53657.457 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q8C2W8

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NACHT, LRR and PYD domains-containing protein ... , 2 types, 9 molecules yAB0752wAKAQ

#11: Protein
NACHT, LRR and PYD domains-containing protein 5 / Maternal antigen that embryos require / Mater protein / Ooplasm-specific protein 1 / OP1


Mass: 119819.859 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9R1M5
#13: Protein NACHT, LRR and PYD domains-containing protein 14 / NALP-iota / Germ cell specific leucine-rich repeat NTPase


Mass: 113527.188 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q6B966

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Non-polymers , 4 types, 25 molecules

#17: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Zn
#18: Chemical
ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#19: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#20: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM

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Details

Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: mouse cytoplasmic lattice / Type: COMPLEX / Entity ID: #1-#7, #9-#10, #8, #11-#16 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Mus musculus (house mouse)
Buffer solutionpH: 6.7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
13cryoSPARC3D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 3.74 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 349408 / Symmetry type: POINT
RefinementCross valid method: NONE

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