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- EMDB-53362: human PAN2-PAN3 deadenylase complex in the apo state -

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Basic information

Entry
Database: EMDB / ID: EMD-53362
Titlehuman PAN2-PAN3 deadenylase complex in the apo state
Map datahuman apo PAN2-PAN3 sharpened map
Sample
  • Complex: heterotrimeric PAN2-PAN3 mRNA deadenylase complex composed of the regulatory PAN3 homodimer bound to the catalytic PAN2
    • Protein or peptide: Isoform 3 of PAN2-PAN3 deadenylation complex subunit PAN3
    • Protein or peptide: PAN2-PAN3 deadenylation complex catalytic subunit PAN2
Keywordscomplex / mammalian / deadenylase / mRNA poly(A) tail / RNA processing / mRNA / RNA BINDING PROTEIN
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.6 Å
AuthorsAlbrecht JC / Reitinger T / Basquin J / Schuessler S / Schaefer IB / Conti E
Funding supportEuropean Union, Germany, Denmark, 5 items
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, 2025-
Header (metadata) releaseDec 10, 2025-
Map releaseDec 10, 2025-
UpdateDec 10, 2025-
Current statusDec 10, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53362.png

Downloads & links

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Map

FileDownload / File: emd_53362.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationhuman apo PAN2-PAN3 sharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 440 pix.
= 374.528 Å		0.85 Å/pix.
x 440 pix.
= 374.528 Å		0.85 Å/pix.
x 440 pix.
= 374.528 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8512 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.69796604 - 1.5456771
Average (Standard dev.)-0.0005740827 (±0.027597006)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 374.52798 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_53362_msk_1.map
Projections & Slices
AxesZYX

Projections

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Histogram

Histogram (log scale)

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Mask #2

Fileemd_53362_msk_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Half map: human apo PAN2-PAN3 halfmap B

Fileemd_53362_half_map_1.map
Annotationhuman apo PAN2-PAN3 halfmap B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: human apo PAN2-PAN3 halfmap A

Fileemd_53362_half_map_2.map
Annotationhuman apo PAN2-PAN3 halfmap A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : heterotrimeric PAN2-PAN3 mRNA deadenylase complex composed of the...

EntireName: heterotrimeric PAN2-PAN3 mRNA deadenylase complex composed of the regulatory PAN3 homodimer bound to the catalytic PAN2
Components
  • Complex: heterotrimeric PAN2-PAN3 mRNA deadenylase complex composed of the regulatory PAN3 homodimer bound to the catalytic PAN2
    • Protein or peptide: Isoform 3 of PAN2-PAN3 deadenylation complex subunit PAN3
    • Protein or peptide: PAN2-PAN3 deadenylation complex catalytic subunit PAN2

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Supramolecule #1: heterotrimeric PAN2-PAN3 mRNA deadenylase complex composed of the...

SupramoleculeName: heterotrimeric PAN2-PAN3 mRNA deadenylase complex composed of the regulatory PAN3 homodimer bound to the catalytic PAN2
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Isoform 3 of PAN2-PAN3 deadenylation complex subunit PAN3

MacromoleculeName: Isoform 3 of PAN2-PAN3 deadenylation complex subunit PAN3
type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 92.526539 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MNSGGGLPPP SAAASPSSSS LAAAVAVVAP PGVGGVPGGA AVGVKLKYCR YYAKDKTCFY GEECQFLHED PAAGAAPGLG LHSNSVPLA LAGAPVAGFP PGAVAGGGAG PPPGPKKPDL GDPGTGAAAG GGGSSGGLDG PRLAIPGMDG GALTDTSLTD S YFSTSFIG ...String:
MNSGGGLPPP SAAASPSSSS LAAAVAVVAP PGVGGVPGGA AVGVKLKYCR YYAKDKTCFY GEECQFLHED PAAGAAPGLG LHSNSVPLA LAGAPVAGFP PGAVAGGGAG PPPGPKKPDL GDPGTGAAAG GGGSSGGLDG PRLAIPGMDG GALTDTSLTD S YFSTSFIG VNGFGSPVET KYPLMQRMTN SSSSPSLLND SAKPYSAHDP LTSPASSLFN DFGALNISQR RKTPNPTASE FI PKGGSTS RLSNVSQSNM SAFSQVFSHP SMGSPATAGL APGMSLSAGS SPLHSPKITP HTSPAPRRRS HTPNPASYMV PSS ASTSVN NPVSQTPSSG QVIQKETVGG TTYFYTDTTP APLTGMVFPN YHIYPPTAPH VAYMQPKANA PSFFMADELR QELI NRHLI TMAQIDQADM PAVPTEVDSY HSLFPLEPLP PPNRIQKSSN FGYITSCYKA VNSKDDLPYC LRRIHGFRLV NTKCM VLVD MWKKIQHSNI VTLREVFTTK AFAEPSLVFA YDFHAGGETM MSRHFNDPNA DAYFTKRKWG QHEGPLPRQH AGLLPE SLI WAYIVQLSSA LRTIHTAGLA CRVMDPTKIL ITGKTRLRVN CVGVFDVLTF DNSQNNNPLA LMAQYQQADL ISLGKVV LA LACNSLAGIQ RENLQKAMEL VTINYSSDLK NLILYLLTDQ NRMRSVNDIM PMIGARFYTQ LDAAQMRNDV IEEDLAKE V QNGRLFRLLA KLGTINERPE FQKDPTWSET GDRYLLKLFR DHLFHQVTEA GAPWIDLSHI ISCLNKLDAG VPEKISLIS RDEKSVLVVT YSDLKRCFEN TFQELIAAAN GQLSAWSHPQ FEKGGGSGGG SGGSAWSHPQ FEK

UniProtKB: PAN2-PAN3 deadenylation complex subunit PAN3

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Macromolecule #2: PAN2-PAN3 deadenylation complex catalytic subunit PAN2

MacromoleculeName: PAN2-PAN3 deadenylation complex catalytic subunit PAN2
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: poly(A)-specific ribonuclease
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 135.523094 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MNFEGLDPGL AEYAPAMHSA LDPVLDAHLN PSLLQNVELD PEGVALEALP VQESVHIMEG VYSELHSVVA EVGVPVSVSH FDLHEEMLW VGSHGGHATS FFGPALERYS SFQVNGSDDI RQIQSLENGI LFLTKNNLKY MARGGLIIFD YLLDENEDMH S LLLTDSST ...String:
MNFEGLDPGL AEYAPAMHSA LDPVLDAHLN PSLLQNVELD PEGVALEALP VQESVHIMEG VYSELHSVVA EVGVPVSVSH FDLHEEMLW VGSHGGHATS FFGPALERYS SFQVNGSDDI RQIQSLENGI LFLTKNNLKY MARGGLIIFD YLLDENEDMH S LLLTDSST LLVGGLQNHI LEIDLNTVQE TQKYAVETPG VTIMRQTNRF FFCGHTSGKV SLRDLRTFKV EHEFDAFSGS LS DFDVHGN LLAACGFSSR LTGLACDRFL KVYDLRMMRA ITPLQVHVDP AFLRFIPTYT SRLAIISQSG QCQFCEPTGL ANP ADIFHV NPVGPLLMTF DVSASKQALA FGDSEGCVHL WTDSPEPSFN PYSRETEFAL PCLVDSLPPL DWSQDLLPLS LIPV PLTTD TLLSDWPAAN SAPAPRRAPP VDAEILRTMK KVGFIGYAPN PRTRLRNQIP YRLKESDSEF DSFSQVTESP VGREE EPHL HMVSKKYRKV TIKYSKLGLE DFDFKHYNKT LFAGLEPHIP NAYCNCMIQV LYFLEPVRCL IQNHLCQKEF CLACEL GFL FHMLDLSRGD PCQGNNFLRA FRTIPEASAL GLILADSDEA SGKGNLARLI QRWNRFILTQ LHQDMQELEI PQAYRGA GG SSFCSSGDSV IGQLFSCEME NCSLCRCGSE TVRASSTLLF TLSYPDGSKS DKTGKNYDFA QVLKRSICLD QNTQAWCD T CEKYQPTIQT RNIRHLPDIL VINCEVNSSK EADFWRMQAE VAFKMAVKKH GGEISKNKEF ALADWKELGS PEGVLVCPS IEELKNVWLP FSIRMKMTKN KGLDVCNWTD GDEMQWGPAR AEEEHGVYVY DLMATVVHIL DSRTGGSLVA HIKVGETYHQ RKEGVTHQQ WYLFNDFLIE PIDKHEAVQF DMNWKVPAIL YYVKRNLNSR YNLNIKNPIE ASVLLAEASL ARKQRKTHTT F IPLMLNEM PQIGDLVGLD AEFVTLNEEE AELRSDGTKS TIKPSQMSVA RITCVRGQGP NEGIPFIDDY ISTQEQVVDY LT QYSGIKP GDLDAKISSK HLTTLKSTYL KLRFLIDIGV KFVGHGLQKD FRVINLMVPK DQVLDTVYLF HMPRKRMISL RFL AWYFLD LKIQGETHDS IEDARTALQL YRKYLELSKN GTEPESFHKV LKGLYEKGRK MDWKVPEPEG QTSPKNAAVF SSVL AL

UniProtKB: PAN2-PAN3 deadenylation complex catalytic subunit PAN2

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.12 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 40 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.022 kPa
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Average exposure time: 3.5 sec. / Average electron dose: 70.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.62 mm / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 0.5 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 4) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionNumber classes used: 1 / Resolution.type: BY AUTHOR / Resolution: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4) / Number images used: 34171
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4)
Final 3D classificationNumber classes: 3 / Software - Name: cryoSPARC (ver. 4)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementProtocol: RIGID BODY FIT
Output model

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

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