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- EMDB-53392: human PAN2-PAN3 bound to a 90Ai/PABPC1 RNP -

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Basic information

Entry
Database: EMDB / ID: EMD-53392
Titlehuman PAN2-PAN3 bound to a 90Ai/PABPC1 RNP
Map datahuman PAN2-PAN3 bound to the 90Ai/PABPC1 RNP, sharpened map
Sample
  • Complex: heterotrimeric PAN2-PAN3 mRNA deadenylase complex composed of the regulatory PAN3 homodimer bound to the catalytic PAN2 in complex with an inhibitory 90Ai/PABPC1 RNP
    • Protein or peptide: human PAN2
  • Protein or peptide: human PAN3 short isoform
  • Protein or peptide: human PABPC1
  • RNA: 90Ai RNA
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: 7.0 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 11, 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_53392.png

Downloads & links

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Map

FileDownload / File: emd_53392.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationhuman PAN2-PAN3 bound to the 90Ai/PABPC1 RNP, sharpened map
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.7 Å/pix.
x 220 pix.
= 374. Å		1.7 Å/pix.
x 220 pix.
= 374. Å		1.7 Å/pix.
x 220 pix.
= 374. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.7 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.28
Minimum - Maximum-0.9091213 - 2.3995857
Average (Standard dev.)0.00079705333 (±0.073507115)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions220220220
Spacing220220220
CellA=B=C: 374.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_53392_msk_1.map
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Mask #2

Fileemd_53392_msk_2.map
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Half map: human PAN2-PAN3 bound to the 90Ai/PABPC1 RNP, half map B

Fileemd_53392_half_map_1.map
Annotationhuman PAN2-PAN3 bound to the 90Ai/PABPC1 RNP, half map B
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: human PAN2-PAN3 bound to the 90Ai/PABPC1 RNP, half map A

Fileemd_53392_half_map_2.map
Annotationhuman PAN2-PAN3 bound to the 90Ai/PABPC1 RNP, half map A
Projections & Slices
AxesZYX

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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 in complex with an inhibitory 90Ai/PABPC1 RNP
Components
  • Complex: heterotrimeric PAN2-PAN3 mRNA deadenylase complex composed of the regulatory PAN3 homodimer bound to the catalytic PAN2 in complex with an inhibitory 90Ai/PABPC1 RNP
    • Protein or peptide: human PAN2
  • Protein or peptide: human PAN3 short isoform
  • Protein or peptide: human PABPC1
  • RNA: 90Ai RNA

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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 in complex with an inhibitory 90Ai/PABPC1 RNP
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: human PAN2

MacromoleculeName: human PAN2 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MHSALDPVLD AHLNPSLLQN VELDPEGVA LEALPVQESV H IMEGVYSE LHSVVAEVGV PV SVSHFDL HEEMLWVGSH GGH ATSFFG PALERYSSFQ VNGS DDIRQ IQSLENGILF LTKNN LKYM ARGGLIIFDY LLDENE DMH SLLLTDSSTL LVGGLQN HI ...String:
MHSALDPVLD AHLNPSLLQN VELDPEGVA LEALPVQESV H IMEGVYSE LHSVVAEVGV PV SVSHFDL HEEMLWVGSH GGH ATSFFG PALERYSSFQ VNGS DDIRQ IQSLENGILF LTKNN LKYM ARGGLIIFDY LLDENE DMH SLLLTDSSTL LVGGLQN HI LEIDLNTVQE TQKYAVET P GVTIMRQTNR FFFCGHTSG KVSLRDLRTF KVEHEFDAFS GSLSDFDVH GNLLAACGFS S RLTGLACD RFLKVYDLRM MR AITPLQV HVDPAFLRFI PTY TSRLAI ISQSGQCQFC EPTG LANPA DIFHVNPVGP LLMTF DVSA SKQALAFGDS EGCVHL WTD SPEPSFNPYS RETEFAL PC LVDSLPPLDW SQDLLPLS L IPVPLTTDTL LSDWPAANS APAPRRAPPV DAEILRTMKK VGFIGYAPN PRTRLRNQIP Y RLKESDSE FDSFSQVTES PV GREEEPH LHMVSKKYRK VTI KYSKLG LEDFDFKHYN KTLF AGLEP HIPNAYCNCM IQVLY FLEP VRCLIQNHLC QKEFCL ACE LGFLFHMLDL SRGDPCQ GN NFLRAFRTIP EASALGLI L ADSDEASGKG NLARLIQRW NRFILTQLHQ DMQELEIPQA YRGAGGSSF CSSGDSVIGQ L FSCEMENC SLCRCGSETV RA SSTLLFT LSYPDGSKSD KTG KNYDFA QVLKRSICLD QNTQ AWCDT CEKYQPTIQT RNIRH LPDI LVINCEVNSS KEADFW RMQ AEVAFKMAVK KHGGEIS KN KEFALADWKE LGSPEGVL V CPSIEELKNV WLPFSIRMK MTKNKGLDVC NWTDGDEMQW GPARAEEEH GVYVYDLMAT V VHILDSRT GGSLVAHIKV GE TYHQRKE GVTHQQWYLF NDF LIEPID KHEAVQFDMN WKVP AILYY VKRNLNSRYN LNIKN PIEA SVLLAEASLA RKQRKT HTT FIPLMLNEMP QIGDLVG LD AEFVTLNEEE AELRSDGT K STIKPSQMSV ARITCVRGQ GPNEGIPFID DYISTQEQVV DYLTQYSGI KPGDLDAKIS S KHLTTLKS TYLKLRFLID IG VKFVGHG LQKDFRVINL MVP KDQVLD TVYLFHMPRK RMIS LRFLA WYFLDLKIQG ETHDS IEDA RTALQLYRKY LELSKN GTE PESFHKVLKG LYEKGRK MD WKVPEPEGQT SPKNAAVF S SVLAL

UniProtKB: PAN2-PAN3 deadenylation complex catalytic subunit PAN2

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Macromolecule #2: human PAN3 short isoform

MacromoleculeName: human PAN3 short isoform / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MNSGGGLPPP SAAASPSSSS LAAAVAVVA PPGVGGVPGG A AVGVKLKY CRYYAKDKTC FY GEECQFL HEDPAAGAAP GLG LHSNSV PLALAGAPVA GFPP GAVAG GGAGPPPGPK KPDLG DPGT GAAAGGGGSS GGLDGP RLA IPGMDGGALT DTSLTDS YF ...String:
MNSGGGLPPP SAAASPSSSS LAAAVAVVA PPGVGGVPGG A AVGVKLKY CRYYAKDKTC FY GEECQFL HEDPAAGAAP GLG LHSNSV PLALAGAPVA GFPP GAVAG GGAGPPPGPK KPDLG DPGT GAAAGGGGSS GGLDGP RLA IPGMDGGALT DTSLTDS YF STSFIGVNGF GSPVETKY P LMQRMTNSSS SPSLLNDSA KPYSAHDPLT SPASSLFNDF GALNISQRR KTPNPTASEF I PKGGSTSR LSNVSQSNMS AF SQVFSHP SMGSPATAGL APG MSLSAG SSPLHSPKIT PHTS PAPRR RSHTPNPASY MVPSS ASTS VNNPVSQTPS SGQVIQ KET VGGTTYFYTD TTPAPLT GM VFPNYHIYPP TAPHVAYM Q PKANAPSFFM ADELRQELI NRHLITMAQI DQADMPAVPT EVDSYHSLF PLEPLPPPNR I QKSSNFGY ITSCYKAVNS KD DLPYCLR RIHGFRLVNT KCM VLVDMW KKIQHSNIVT LREV FTTKA FAEPSLVFAY DFHAG GETM MSRHFNDPNA DAYFTK RKW GQHEGPLPRQ HAGLLPE SL IWAYIVQLSS ALRTIHTA G LACRVMDPTK ILITGKTRL RVNCVGVFDV LTFDNSQNNN PLALMAQYQ QADLISLGKV V LALACNSL AGIQRENLQK AM ELVTINY SSDLKNLILY LLT DQNRMR SVNDIMPMIG ARFY TQLDA AQMRNDVIEE DLAKE VQNG RLFRLLAKLG TINERP EFQ KDPTWSETGD RYLLKLF RD HLFHQVTEAG APWIDLSH I ISCLNKLDAG VPEKISLIS RDEKSVLVVT YSDLKRCFEN TFQELIAAA NGQLSAWSHP Q FEKGGGSG GGSGGSAWSH PQ FEK

UniProtKB: PAN2-PAN3 deadenylation complex subunit PAN3

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Macromolecule #3: human PABPC1

MacromoleculeName: human PABPC1 / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MNPSAPSYPM ASLYVGDLHP DVTEAMLYE KFSPAGPILS I RVCRDMIT RRSLGYAYVN FQ QPADAER ALDTMNFDVI KGK PVRIMW SQRDPSLRKS GVGN IFIKN LDKSIDNKAL YDTFS AFGN ILSCKVVCDE NGSKGY GFV HFETQEAAER AIEKMNG ML ...String:
MNPSAPSYPM ASLYVGDLHP DVTEAMLYE KFSPAGPILS I RVCRDMIT RRSLGYAYVN FQ QPADAER ALDTMNFDVI KGK PVRIMW SQRDPSLRKS GVGN IFIKN LDKSIDNKAL YDTFS AFGN ILSCKVVCDE NGSKGY GFV HFETQEAAER AIEKMNG ML LNDRKVFVGR FKSRKERE A ELGARAKEFT NVYIKNFGE DMDDERLKDL FGKFGPALSV KVMTDESGK SKGFGFVSFE R HEDAQKAV DEMNGKELNG KQ IYVGRAQ KKVERQTELK RKF EQMKQD RITRYQGVNL YVKN LDDGI DDERLRKEFS PFGTI TSAK VMMEGGRSKG FGFVCF SSP EEATKAVTEM NGRIVAT KP LYVALAQRKE ERQAHLTN Q YMQRMASVRA VPNPVINPY QPAPPSGYFM AAIPQTQNRA AYYPPSQIA QLRPSPRWTA Q GARPHPFQ NMPGAIRPAA PR PPFSTMR PASSQVPRVM STQ RVANTS TQTMGPRPAA AAAA ATPAV RTVPQYKYAA GVRNP QQHL NAQPQVTMQQ PAVHVQ GQE PLTASMLASA PPQEQKQ ML GERLFPLIQA MHPTLAGK I TGMLLEIDNS ELLHMLESP ESLRSKVDEA VAVLQAHQAK EAAQKAVNS ATGVPTVSAW SHPQFE K

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Macromolecule #4: 90Ai RNA

MacromoleculeName: 90Ai RNA / type: rna / ID: 4 / Details: 85A-GGG-AA RNA oligo
Source (natural)Organism: Homo sapiens (human)
SequenceString:
AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAGGGAA

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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
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 reconstructionResolution.type: BY AUTHOR / Resolution: 7.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4) / Number images used: 16132
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

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