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- PDB-9qtu: human PAN2-PAN3 deadenylase complex in the apo state -

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Basic information

Entry
Database: PDB / ID: 9qtu
Titlehuman PAN2-PAN3 deadenylase complex in the apo state
Components
  • Isoform 3 of PAN2-PAN3 deadenylation complex subunit PAN3
  • PAN2-PAN3 deadenylation complex catalytic subunit PAN2
KeywordsRNA BINDING PROTEIN / complex / mammalian / deadenylase / mRNA poly(A) tail / RNA processing / mRNA
Function / homology
Function and homology information


PAN complex / positive regulation of cytoplasmic mRNA processing body assembly / poly(A)-specific ribonuclease / poly(A)-specific ribonuclease activity / nuclear-transcribed mRNA poly(A) tail shortening / deadenylation-dependent decapping of nuclear-transcribed mRNA / Deadenylation of mRNA / poly(A) binding / protein targeting / P-body ...PAN complex / positive regulation of cytoplasmic mRNA processing body assembly / poly(A)-specific ribonuclease / poly(A)-specific ribonuclease activity / nuclear-transcribed mRNA poly(A) tail shortening / deadenylation-dependent decapping of nuclear-transcribed mRNA / Deadenylation of mRNA / poly(A) binding / protein targeting / P-body / mRNA processing / 3'-5'-RNA exonuclease activity / nucleic acid binding / protein kinase activity / zinc ion binding / ATP binding / metal ion binding / nucleus / cytosol
Similarity search - Function
PAN2-PAN3 deadenylation complex subunit PAN3 / Pan3 pseudokinase domain / Pan3 C-terminal knob domain / PAN2, UCH domain / PAN2-PAN3 deadenylation complex catalytic subunit PAN2 / : / : / Ubiquitin carboxyl-terminal hydrolase / PAN2 N-terminal / Exonuclease ...PAN2-PAN3 deadenylation complex subunit PAN3 / Pan3 pseudokinase domain / Pan3 C-terminal knob domain / PAN2, UCH domain / PAN2-PAN3 deadenylation complex catalytic subunit PAN2 / : / : / Ubiquitin carboxyl-terminal hydrolase / PAN2 N-terminal / Exonuclease / Exonuclease, RNase T/DNA polymerase III / EXOIII / Zinc finger, CCCH-type superfamily / zinc finger / Zinc finger, CCCH-type / Zinc finger C3H1-type profile. / Ubiquitin specific protease domain / Ubiquitin specific protease (USP) domain profile. / Papain-like cysteine peptidase superfamily / Ribonuclease H superfamily / Ribonuclease H-like superfamily / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
PAN2-PAN3 deadenylation complex catalytic subunit PAN2 / PAN2-PAN3 deadenylation complex subunit PAN3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.6 Å
AuthorsAlbrecht, J.C. / Reitinger, T. / Basquin, J. / Schuessler, S. / Schaefer, I.B. / Conti, E.
Funding supportEuropean Union, Germany, Denmark, 5items
OrganizationGrant numberCountry
European Research Council (ERC)740329European Union
European Research Council (ERC)101054447European Union
German Research Foundation (DFG)SFB1035 Germany
Novo Nordisk Foundation31199 Denmark
German Federal Ministry for Education and ResearchDZD Germany
CitationJournal: Cell Rep / Year: 2025
Title: Mechanisms governing poly(A)-tail-length specificity of the human PAN2-PAN3 deadenylase complex.
Authors: Jana C Albrecht / Timo Reitinger / Jérôme Basquin / Steffen Schüssler / Margot Riggi / Ingmar B Schäfer / Elena Conti /
Abstract: The lifespan of most eukaryotic mRNAs is modulated by the gradual shortening of the poly(A) tail and removal of the associated poly(A)-binding protein. The human PAN2-PAN3 complex catalyzes initial ...The lifespan of most eukaryotic mRNAs is modulated by the gradual shortening of the poly(A) tail and removal of the associated poly(A)-binding protein. The human PAN2-PAN3 complex catalyzes initial deadenylation by shortening long poly(A) tails associated with PABPC1. Both PAN2-PAN3 and PABPC1 are evolutionarily conserved from fungi to humans. How the human complex has adapted to recognize and act on longer poly(A) tails characteristic of mammalian mRNAs remains unclear. Here, we report a method to obtain homo-polymeric poly(A) RNAs up to 240 nt, mimicking the synthesis length of poly(A) tails in mammals. We recapitulate human deadenylation properties in vitro, with PAN2-PAN3 showing greater activity on long poly(A)-PABPC1 ribonucleoprotein substrates. Single-particle cryo-electron microscopy (cryo-EM) analyses of PAN2-PAN3 bound to poly(A)-PABPC1 ribonucleoproteins uncover a longer substrate-binding path in the case of the human deadenylase compared to fungi. Altogether, these data provide a rationale for the co-evolution of deadenylase properties and poly(A) tail lengths.
History
DepositionApr 9, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 10, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Isoform 3 of PAN2-PAN3 deadenylation complex subunit PAN3
B: Isoform 3 of PAN2-PAN3 deadenylation complex subunit PAN3
C: PAN2-PAN3 deadenylation complex catalytic subunit PAN2


Theoretical massNumber of molelcules
Total (without water)320,5763
Polymers320,5763
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Isoform 3 of PAN2-PAN3 deadenylation complex subunit PAN3 / PAB1P-dependent poly(A)-specific ribonuclease / Poly(A)-nuclease deadenylation complex subunit 3 / ...PAB1P-dependent poly(A)-specific ribonuclease / Poly(A)-nuclease deadenylation complex subunit 3 / PAN deadenylation complex subunit 3


Mass: 92526.539 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PAN3 / Plasmid: PB-T / Cell line (production host): HEK293-T / Production host: Homo sapiens (human) / References: UniProt: Q58A45
#2: Protein PAN2-PAN3 deadenylation complex catalytic subunit PAN2 / Inactive ubiquitin carboxyl-terminal hydrolase 52 / PAB1P-dependent poly(A)-specific ribonuclease / ...Inactive ubiquitin carboxyl-terminal hydrolase 52 / PAB1P-dependent poly(A)-specific ribonuclease / Poly(A)-nuclease deadenylation complex subunit 2 / PAN deadenylation complex subunit 2


Mass: 135523.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PAN2, KIAA0710, USP52 / Plasmid: PB-T / Cell line (production host): HEK293-T / Production host: Homo sapiens (human) / References: UniProt: Q504Q3, poly(A)-specific ribonuclease
Has protein modificationN

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: heterotrimeric PAN2-PAN3 mRNA deadenylase complex composed of the regulatory PAN3 homodimer bound to the catalytic PAN2
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human) / Strain: HEK293-T
Buffer solutionpH: 7.5
SpecimenConc.: 0.12 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 95 % / Chamber temperature: 277 K

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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: 2800 nm / Nominal defocus min: 500 nm / Cs: 2.62 mm / C2 aperture diameter: 100 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN
Image recordingAverage exposure time: 3.5 sec. / Electron dose: 70 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1

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Processing

EM software
IDNameVersionCategory
1Topazparticle selection
2SerialEMimage acquisition
4cryoSPARC4CTF correction
7Coot1.1.14model fitting
9PHENIX1.21.2_5419model refinement
10cryoSPARC4initial Euler assignment
11cryoSPARC4final Euler assignment
12cryoSPARC4classification
13cryoSPARC43D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 34171 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT
Atomic model buildingSource name: AlphaFold / Type: in silico model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00410026
ELECTRON MICROSCOPYf_angle_d0.71813616
ELECTRON MICROSCOPYf_dihedral_angle_d4.8181342
ELECTRON MICROSCOPYf_chiral_restr0.0451539
ELECTRON MICROSCOPYf_plane_restr0.0051764

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