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- EMDB-56930: Cryo-EM structure of the human SAC3D1-PCID2-SEM1 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-56930
TitleCryo-EM structure of the human SAC3D1-PCID2-SEM1 complex
Map dataCryo-EM map of the human SAC3D1-PS complex (Map C)
Sample
  • Complex: Human SAC3D1-PCID2-SEM1 complex
    • Protein or peptide: Maltose/maltodextrin-binding periplasmic protein,SAC3 domain-containing protein 1
    • Protein or peptide: PCI domain-containing protein 2
    • Protein or peptide: 26S proteasome complex subunit SEM1
KeywordsmRNA export / GENE REGULATION
Function / homology
Function and homology information


negative regulation of lymphoid progenitor cell differentiation / transcription export complex 2 / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore nuclear basket / Impaired BRCA2 translocation to the nucleus / Impaired BRCA2 binding to SEM1 (DSS1) / integrator complex / proteasome regulatory particle, lid subcomplex / positive regulation of B cell differentiation / poly(A)+ mRNA export from nucleus ...negative regulation of lymphoid progenitor cell differentiation / transcription export complex 2 / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore nuclear basket / Impaired BRCA2 translocation to the nucleus / Impaired BRCA2 binding to SEM1 (DSS1) / integrator complex / proteasome regulatory particle, lid subcomplex / positive regulation of B cell differentiation / poly(A)+ mRNA export from nucleus / Regulation of ornithine decarboxylase (ODC) / Proteasome assembly / Cross-presentation of soluble exogenous antigens (endosomes) / Somitogenesis / Homologous DNA Pairing and Strand Exchange / Defective homologous recombination repair (HRR) due to BRCA1 loss of function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA1 binding function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA2/RAD51/RAD51C binding function / Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA) / negative regulation of gene expression, epigenetic / Resolution of D-loop Structures through Holliday Junction Intermediates / detection of maltose stimulus / maltose transport complex / Impaired BRCA2 binding to RAD51 / centrosome duplication / carbohydrate transport / Presynaptic phase of homologous DNA pairing and strand exchange / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / mRNA export from nucleus / proteasome assembly / spleen development / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / spindle assembly / ATP-binding cassette (ABC) transporter complex / proteasome complex / cell chemotaxis / Regulation of activated PAK-2p34 by proteasome mediated degradation / ubiquitin binding / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / Asymmetric localization of PCP proteins / Ubiquitin-dependent degradation of Cyclin D / transcription elongation by RNA polymerase II / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / AUF1 (hnRNP D0) binds and destabilizes mRNA / TNFR2 non-canonical NF-kB pathway / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Dectin-1 mediated noncanonical NF-kB signaling / Degradation of DVL / Degradation of AXIN / Degradation of CRY and PER proteins / Hh mutants are degraded by ERAD / Activation of NF-kappaB in B cells / G2/M Checkpoints / Degradation of GLI1 by the proteasome / Hedgehog ligand biogenesis / Regulation of RUNX3 expression and activity / Autodegradation of the E3 ubiquitin ligase COP1 / Defective CFTR causes cystic fibrosis / Negative regulation of NOTCH4 signaling / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / Hedgehog 'on' state / Vif-mediated degradation of APOBEC3G / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / MAPK6/MAPK4 signaling / double-strand break repair via homologous recombination / Degradation of CDH1 / Degradation of beta-catenin by the destruction complex / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / CDK-mediated phosphorylation and removal of Cdc6 / HDR through Homologous Recombination (HRR) / spindle / ABC-family protein mediated transport / CLEC7A (Dectin-1) signaling / SCF(Skp2)-mediated degradation of p27/p21 / FCERI mediated NF-kB activation / Regulation of expression of SLITs and ROBOs / Regulation of PTEN stability and activity / Interleukin-1 signaling / Orc1 removal from chromatin / Regulation of RUNX2 expression and activity / Regulation of RAS by GAPs / The role of GTSE1 in G2/M progression after G2 checkpoint / Separation of Sister Chromatids / UCH proteinases / KEAP1-NFE2L2 pathway / Downstream TCR signaling / protein transport / Antigen processing: Ubiquitination & Proteasome degradation / outer membrane-bounded periplasmic space
Similarity search - Function
Csn12 family / SAC3/GANP/THP3, conserved domain / SAC3/GANP/THP3 / SAC3/GANP family / DSS1/SEM1 / DSS1/SEM1 family / DSS1_SEM1 / PCI/PINT associated module / PCI domain / Proteasome component (PCI) domain ...Csn12 family / SAC3/GANP/THP3, conserved domain / SAC3/GANP/THP3 / SAC3/GANP family / DSS1/SEM1 / DSS1/SEM1 family / DSS1_SEM1 / PCI/PINT associated module / PCI domain / Proteasome component (PCI) domain / PCI domain profile. / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
SAC3 domain-containing protein 1 / Maltose/maltodextrin-binding periplasmic protein / 26S proteasome complex subunit SEM1 / PCI domain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsHohmann U / Graf M / Plaschka C
Funding supportEuropean Union, 3 items
OrganizationGrant numberCountry
European Research Council (ERC)949081European Union
H2020 Marie Curie Actions of the European Commission896416European Union
European Molecular Biology Organization (EMBO)ALTF_1175-2019European Union
CitationJournal: Nature / Year: 2026
Title: Molecular basis of polyadenylated RNA fate determination in the nucleus
Authors: Hohmann U / Graf M / Plaschka C
History
DepositionFeb 25, 2026-
Header (metadata) releaseJun 24, 2026-
Map releaseJun 24, 2026-
UpdateJun 24, 2026-
Current statusJun 24, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_56930.png

Downloads & links

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Map

FileDownload / File: emd_56930.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM map of the human SAC3D1-PS complex (Map C)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.9 Å/pix.
x 256 pix.
= 229.888 Å		0.9 Å/pix.
x 256 pix.
= 229.888 Å		0.9 Å/pix.
x 256 pix.
= 229.888 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.898 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.091
Minimum - Maximum-0.31030434 - 0.4782606
Average (Standard dev.)-0.00023518602 (±0.0121305315)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 229.888 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Cryo-EM map of the human SAC3D1-PS complex (Map C), half map A

Fileemd_56930_half_map_1.map
AnnotationCryo-EM map of the human SAC3D1-PS complex (Map C), half map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Cryo-EM map of the human SAC3D1-PS complex (Map C), half map B

Fileemd_56930_half_map_2.map
AnnotationCryo-EM map of the human SAC3D1-PS complex (Map C), half map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Human SAC3D1-PCID2-SEM1 complex

EntireName: Human SAC3D1-PCID2-SEM1 complex
Components
  • Complex: Human SAC3D1-PCID2-SEM1 complex
    • Protein or peptide: Maltose/maltodextrin-binding periplasmic protein,SAC3 domain-containing protein 1
    • Protein or peptide: PCI domain-containing protein 2
    • Protein or peptide: 26S proteasome complex subunit SEM1

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Supramolecule #1: Human SAC3D1-PCID2-SEM1 complex

SupramoleculeName: Human SAC3D1-PCID2-SEM1 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 125 kDa/nm

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Macromolecule #1: Maltose/maltodextrin-binding periplasmic protein,SAC3 domain-cont...

MacromoleculeName: Maltose/maltodextrin-binding periplasmic protein,SAC3 domain-containing protein 1
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 80.112484 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKIEEGKLVI WINGDKGYNG LAEVGKKFEK DTGIKVTVEH PDKLEEKFPQ VAATGDGPDI IFWAHDRFGG YAQSGLLAEI TPDKAFQDK LYPFTWDAVR YNGKLIAYPI AVEALSLIYN KDLLPNPPKT WEEIPALDKE LKAKGKSALM FNLQEPYFTW P LIAADGGY ...String:
MKIEEGKLVI WINGDKGYNG LAEVGKKFEK DTGIKVTVEH PDKLEEKFPQ VAATGDGPDI IFWAHDRFGG YAQSGLLAEI TPDKAFQDK LYPFTWDAVR YNGKLIAYPI AVEALSLIYN KDLLPNPPKT WEEIPALDKE LKAKGKSALM FNLQEPYFTW P LIAADGGY AFKYENGKYD IKDVGVDNAG AKAGLTFLVD LIKNKHMNAD TDYSIAEAAF NKGETAMTIN GPWAWSNIDT SK VNYGVTV LPTFKGQPSK PFVGVLSAGI NAASPNKELA KEFLENYLLT DEGLEAVNKD KPLGAVALKS YEEELAKDPR IAA TMENAQ KGEIMPNIPQ MSAFWYAVRT AVINAASGRQ TVDEALKDAQ TSSGLEVLFQ GPMPGCELPV GTCPDMCPAA ERAQ REREH RLHRLEVVPG CRQDPPRADP QRAVKEYSRP AAGKPRPPPS QLRPPSVLLA TVRYLAGEVA ESADIARAEV ASFVA DRLR AVLLDLALQG AGDAEAAVVL EAALATLLTV VARLGPDAAR GPADPVLLQA QVQEGFGSLR RCYARGAGPH PRQPAF QGL FLLYNLGSVE ALHEVLQLPA ALRACPPLRK ALAVDAAFRE GNAARLFRLL QTLPYLPSCA VQCHVGHARR EALARFA RA FSTPKGQTLP LGFMVNLLAL DGLREARDLC QAHGLPLDGE ERVVFLRGRY VEEGLPPAST CKVLVESKLR GRTLEEVV M AEEEDEGTDR PGSPA

UniProtKB: Maltose/maltodextrin-binding periplasmic protein, SAC3 domain-containing protein 1

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Macromolecule #2: PCI domain-containing protein 2

MacromoleculeName: PCI domain-containing protein 2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 51.844449 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGKPIPNPLL GLDSTGSGKP IPNPLLGLDS TGSGKPIPNP LLGLDSTSSG LEVLFQGPMA HITINQYLQQ VYEAIDSRDG ASCAELVSF KHPHVANPRL QMASPEEKCQ QVLEPPYDEM FAAHLRCTYA VGNHDFIEAY KCQTVIVQSF LRAFQAHKEE N WALPVMYA ...String:
MGKPIPNPLL GLDSTGSGKP IPNPLLGLDS TGSGKPIPNP LLGLDSTSSG LEVLFQGPMA HITINQYLQQ VYEAIDSRDG ASCAELVSF KHPHVANPRL QMASPEEKCQ QVLEPPYDEM FAAHLRCTYA VGNHDFIEAY KCQTVIVQSF LRAFQAHKEE N WALPVMYA VALDLRVFAN NADQQLVKKG KSKVGDMLEK AAELLMSCFR VCASDTRAGI EDSKKWGMLF LVNQLFKIYF KI NKLHLCK PLIRAIDSSN LKDDYSTAQR VTYKYYVGRK AMFDSDFKQA EEYLSFAFEH CHRSSQKNKR MILIYLLPVK MLL GHMPTV ELLKKYHLMQ FAEVTRAVSE GNLLLLHEAL AKHEAFFIRC GIFLILEKLK IITYRNLFKK VYLLLKTHQL SLDA FLVAL KFMQVEDVDI DEVQCILANL IYMGHVKGYI SHQHQKLVVS KQNPFPPLST VC

UniProtKB: PCI domain-containing protein 2

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Macromolecule #3: 26S proteasome complex subunit SEM1

MacromoleculeName: 26S proteasome complex subunit SEM1 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 8.284611 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSEKKQPVDL GLLEEDDEFE EFPAEDWAGL DEDEDAHVWE DNWDDDNVED DFSNQLRAEL EKHGYKMETS

UniProtKB: 26S proteasome complex subunit SEM1

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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

Concentration0.5 mg/mL
BufferpH: 7.9
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 281 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 17936
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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