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- EMDB-53424: human PAN2-PAN3 bound to a 180Ai/PABPC1 RNP -

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Basic information

Entry
Database: EMDB / ID: EMD-53424
Titlehuman PAN2-PAN3 bound to a 180Ai/PABPC1 RNP
Map datahuman PAN2-PAN3 bound to the 180Ai/PABPC1 RNP 20 Angstrom low-pass filtered map
Sample
  • Complex: heteromultimeric mRNA deadenylase assembly of the human PAN2-PAN3 complex bound to a 180Ai/PABPC1 substrate RNP
    • Protein or peptide: human PAN2
    • Protein or peptide: human PAN3 short isoform
    • Protein or peptide: hPABPC1
    • RNA: 180Ai RNA
Keywordspoly(A) tail / deadenylase / PAN2-PAN3 / PABPC1 / mRNA / RNA BINDING PROTEIN
Biological speciesHomo sapiens (human) / Homo (humans)
Methodsingle particle reconstruction / cryo EM / Resolution: 14.0 Å
AuthorsAlbrecht JC / Reitinger T / Basquin J / Schuessler S / Schaefer IB / Conti E
Funding support Germany, European Union, Denmark, 6 items
OrganizationGrant numberCountry
Max Planck Society Germany
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 15, 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_53424.png

Downloads & links

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Map

FileDownload / File: emd_53424.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationhuman PAN2-PAN3 bound to the 180Ai/PABPC1 RNP 20 Angstrom low-pass filtered map
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
3.19 Å/pix.
x 128 pix.
= 408.32 Å		3.19 Å/pix.
x 128 pix.
= 408.32 Å		3.19 Å/pix.
x 128 pix.
= 408.32 Å

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Images are generated by Spider.

Voxel sizeX=Y=Z: 3.19 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.45
Minimum - Maximum-1.7861477 - 4.35824
Average (Standard dev.)0.015688846 (±0.15443483)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 408.32 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_53424_msk_1.map
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Mask #2

Fileemd_53424_msk_2.map
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Additional map: human PAN2-PAN3 bound to the 180Ai/PABPC1 RNP auto-sharpened map

Fileemd_53424_additional_1.map
Annotationhuman PAN2-PAN3 bound to the 180Ai/PABPC1 RNP auto-sharpened map
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Half map: human PAN2-PAN3 bound to the 180Ai/PABPC1 RNP half map B

Fileemd_53424_half_map_1.map
Annotationhuman PAN2-PAN3 bound to the 180Ai/PABPC1 RNP half map B
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Half map: human PAN2-PAN3 bound to the 180Ai/PABPC1 RNP half map A

Fileemd_53424_half_map_2.map
Annotationhuman PAN2-PAN3 bound to the 180Ai/PABPC1 RNP half map A
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Sample components

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Entire : heteromultimeric mRNA deadenylase assembly of the human PAN2-PAN3...

EntireName: heteromultimeric mRNA deadenylase assembly of the human PAN2-PAN3 complex bound to a 180Ai/PABPC1 substrate RNP
Components
  • Complex: heteromultimeric mRNA deadenylase assembly of the human PAN2-PAN3 complex bound to a 180Ai/PABPC1 substrate RNP
    • Protein or peptide: human PAN2
    • Protein or peptide: human PAN3 short isoform
    • Protein or peptide: hPABPC1
    • RNA: 180Ai RNA

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Supramolecule #1: heteromultimeric mRNA deadenylase assembly of the human PAN2-PAN3...

SupramoleculeName: heteromultimeric mRNA deadenylase assembly of the human PAN2-PAN3 complex bound to a 180Ai/PABPC1 substrate RNP
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: PAN2-PAN3 is a heterotrimer with one copy of the catalytic PAN2 subunit and a homodimer of the regulatory PAN3 subunit (short isoform). This deadenylase is engaging a staling poly(A) ...Details: PAN2-PAN3 is a heterotrimer with one copy of the catalytic PAN2 subunit and a homodimer of the regulatory PAN3 subunit (short isoform). This deadenylase is engaging a staling poly(A) substrate of 180A bound by theoretically at least six PABPC1 protomers

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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: MNFEGLDPGL AEYAPAMHSA LDPVLDAHL NPSLLQNVEL D PEGVALEA LPVQESVHIM EG VYSELHS VVAEVGVPVS VSH FDLHEE MLWVGSHGGH ATSF FGPAL ERYSSFQVNG SDDIR QIQS LENGILFLTK NNLKYM ARG GLIIFDYLLD ENEDMHS LL ...String:
MNFEGLDPGL AEYAPAMHSA LDPVLDAHL NPSLLQNVEL D PEGVALEA LPVQESVHIM EG VYSELHS VVAEVGVPVS VSH FDLHEE MLWVGSHGGH ATSF FGPAL ERYSSFQVNG SDDIR QIQS LENGILFLTK NNLKYM ARG GLIIFDYLLD ENEDMHS LL LTDSSTLLVG GLQNHILE I DLNTVQETQK YAVETPGVT IMRQTNRFFF CGHTSGKVSL RDLRTFKVE HEFDAFSGSL S DFDVHGNL LAACGFSSRL TG LACDRFL KVYDLRMMRA ITP LQVHVD PAFLRFIPTY TSRL AIISQ SGQCQFCEPT GLANP ADIF HVNPVGPLLM TFDVSA SKQ ALAFGDSEGC VHLWTDS PE PSFNPYSRET EFALPCLV D SLPPLDWSQD LLPLSLIPV PLTTDTLLSD WPAANSAPAP RRAPPVDAE ILRTMKKVGF I GYAPNPRT RLRNQIPYRL KE SDSEFDS FSQVTESPVG REE EPHLHM VSKKYRKVTI KYSK LGLED FDFKHYNKTL FAGLE PHIP NAYCNCMIQV LYFLEP VRC LIQNHLCQKE FCLACEL GF LFHMLDLSRG DPCQGNNF L RAFRTIPEAS ALGLILADS DEASGKGNLA RLIQRWNRFI LTQLHQDMQ ELEIPQAYRG A GGSSFCSS GDSVIGQLFS CE MENCSLC RCGSETVRAS STL LFTLSY PDGSKSDKTG KNYD FAQVL KRSICLDQNT QAWCD TCEK YQPTIQTRNI RHLPDI LVI NCEVNSSKEA DFWRMQA EV AFKMAVKKHG GEISKNKE F ALADWKELGS PEGVLVCPS IEELKNVWLP FSIRMKMTKN KGLDVCNWT DGDEMQWGPA R AEEEHGVY VYDLMATVVH IL DSRTGGS LVAHIKVGET YHQ RKEGVT HQQWYLFNDF LIEP IDKHE AVQFDMNWKV PAILY YVKR NLNSRYNLNI KNPIEA SVL LAEASLARKQ RKTHTTF IP LMLNEMPQIG DLVGLDAE F VTLNEEEAEL RSDGTKSTI KPSQMSVARI TCVRGQGPNE GIPFIDDYI STQEQVVDYL T QYSGIKPG DLDAKISSKH LT TLKSTYL KLRFLIDIGV KFV GHGLQK DFRVINLMVP KDQV LDTVY LFHMPRKRMI SLRFL AWYF LDLKIQGETH DSIEDA RTA LQLYRKYLEL SKNGTEP ES FHKVLKGLYE KGRKMDWK V PEPEGQTSPK NAAVFSSVL AL

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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 (humans)
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

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Macromolecule #3: hPABPC1

MacromoleculeName: hPABPC1 / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
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: 180Ai RNA

MacromoleculeName: 180Ai RNA / type: rna / ID: 4 / Details: 35 nt long model RNA with a 175A-GGG-AA tail
Source (natural)Organism: Homo sapiens (human)
SequenceString: GAGACCCAAG CTGGCTAGCG TTTAAACTTa agcttAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA ...String:
GAGACCCAAG CTGGCTAGCG TTTAAACTTa agcttAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA GGGAA

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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
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) / Average exposure time: 3.0 sec. / Average electron dose: 69.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 150.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.62 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.8 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 14.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 5048
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationSoftware - Name: cryoSPARC
FSC plot (resolution estimation)

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