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- EMDB-63069: Cryo-EM structure of the SPATA5-SPATA5L1-CINP-C1orf109 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-63069
TitleCryo-EM structure of the SPATA5-SPATA5L1-CINP-C1orf109 complex
Map data
Sample
  • Complex: The SPATA5 complex
    • Protein or peptide: ATPase family gene 2 protein homolog A
    • Protein or peptide: Cyclin-dependent kinase 2-interacting protein
    • Protein or peptide: cDNA FLJ55172
    • Protein or peptide: ATPase family gene 2 protein homolog B
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
Keywordsribosomal biogenesis / SPATA5 / ATPase complex / CYTOSOLIC PROTEIN
Function / homology
Function and homology information


preribosome binding / mitotic spindle disassembly / VCP-NPL4-UFD1 AAA ATPase complex / retrograde protein transport, ER to cytosol / non-chaperonin molecular chaperone ATPase / polyubiquitin modification-dependent protein binding / autophagosome maturation / ribosomal large subunit biogenesis / brain development / spindle ...preribosome binding / mitotic spindle disassembly / VCP-NPL4-UFD1 AAA ATPase complex / retrograde protein transport, ER to cytosol / non-chaperonin molecular chaperone ATPase / polyubiquitin modification-dependent protein binding / autophagosome maturation / ribosomal large subunit biogenesis / brain development / spindle / spermatogenesis / proteasome-mediated ubiquitin-dependent protein catabolic process / cell differentiation / DNA replication / cell division / DNA repair / ATP hydrolysis activity / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Ribosome biogenesis protein C1orf109-like / Ribosome biogenesis protein C1orf109-like / Cyclin-dependent kinase 2-interacting protein / : / Aspartate decarboxylase-like domain superfamily / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / ATPase family associated with various cellular activities (AAA) ...Ribosome biogenesis protein C1orf109-like / Ribosome biogenesis protein C1orf109-like / Cyclin-dependent kinase 2-interacting protein / : / Aspartate decarboxylase-like domain superfamily / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
cDNA FLJ55172 / ATPase family gene 2 protein homolog A / ATPase family gene 2 protein homolog B / Cyclin-dependent kinase 2-interacting protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.51 Å
AuthorsDai Y / Zhang Y / Gao N
Funding support China, 1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)32230051 China
CitationJournal: To Be Published
Title: cryo-EM structure of the SPATA5-SPATA5L1-CINP-C1orf109 complex
Authors: Dai Y / Zhang Y / Gao N
History
DepositionJan 10, 2025-
Header (metadata) releaseApr 23, 2025-
Map releaseApr 23, 2025-
UpdateApr 23, 2025-
Current statusApr 23, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_63069.png

Downloads & links

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Map

FileDownload / File: emd_63069.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 280 pix.
= 305.76 Å		1.09 Å/pix.
x 280 pix.
= 305.76 Å		1.09 Å/pix.
x 280 pix.
= 305.76 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.092 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.0
Minimum - Maximum-0.44249752 - 18.330857999999999
Average (Standard dev.)0.071063876 (±0.70587814)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 305.76 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : The SPATA5 complex

EntireName: The SPATA5 complex
Components
  • Complex: The SPATA5 complex
    • Protein or peptide: ATPase family gene 2 protein homolog A
    • Protein or peptide: Cyclin-dependent kinase 2-interacting protein
    • Protein or peptide: cDNA FLJ55172
    • Protein or peptide: ATPase family gene 2 protein homolog B
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: The SPATA5 complex

SupramoleculeName: The SPATA5 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: ATPase family gene 2 protein homolog A

MacromoleculeName: ATPase family gene 2 protein homolog A / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: non-chaperonin molecular chaperone ATPase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 97.276453 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSSKKNRKRL NQSAENGSSL PSAASSCAEA RAPSAGSDFA ATSGTLTVTN LLEKVDDKIP KTFQNSLIHL GLNTMKSANI CIGRPVLLT SLNGKQEVYT AWPMAGFPGG KVGLSEMAQK NVGVRPGDAI QVQPLVGAVL QAEEMDVALS DKDMEINEEE L TGCILRKL ...String:
MSSKKNRKRL NQSAENGSSL PSAASSCAEA RAPSAGSDFA ATSGTLTVTN LLEKVDDKIP KTFQNSLIHL GLNTMKSANI CIGRPVLLT SLNGKQEVYT AWPMAGFPGG KVGLSEMAQK NVGVRPGDAI QVQPLVGAVL QAEEMDVALS DKDMEINEEE L TGCILRKL DGKIVLPGNF LYCTFYGRPY KLQVLRVKGA DGMILGGPQS DSDTDAQRMA FEQSSMETSS LELSLQLSQL DL EDTQIPT SRSTPYKPID DRITNKASDV LLDVTQSPGD GSGLMLEEVT GLKCNFESAR EGNEQLTEEE RLLKFSIGAK CNT DTFYFI SSTTRVNFTE IDKNSKEQDN QFKVTYDMIG GLSSQLKAIR EIIELPLKQP ELFKSYGIPA PRGVLLYGPP GTGK TMIAR AVANEVGAYV SVINGPEIIS KFYGETEAKL RQIFAEATLR HPSIIFIDQL DALCPKREGA QNEVEKRVVA SLLTL MDGI GSEVSEGQVL VLGATNRPHA LDAALRRPGR FDKEIEIGVP NAQDRLDILQ KLLRRVPHLL TEAELLQLAN SAHGYV GAD LKVLCNEAGL CALRRILKKQ PNLPDVKVAG LVKITLKDFL QAMNDIRPSA MREIAIDVPN VSWSDIGGLE SIKLKLE QA VEWPLKHPES FIRMGIQPPK GVLLYGPPGC SKTMIAKALA NESGLNFLAI KGPELMNKYV GESERAVRET FRKARAVA P SIIFFDQLDA LAVERGSSLG AGNVADRVLA QLLTEMDGIE QLKDVTILAA TNRPDRIDKA LMRPGRIDRI IYVPLPDAA TRREIFKLQF HSMPVSNEVD LDELILQTDA YSGAEIVAVC REAALLALEE DIQANLIMKR HFTQALSTVT PRIPESLRRF YEDYQE

UniProtKB: ATPase family gene 2 protein homolog A

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Macromolecule #2: Cyclin-dependent kinase 2-interacting protein

MacromoleculeName: Cyclin-dependent kinase 2-interacting protein / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 27.42109 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MWSHPQFEKG GGSGGGSGGS AWSHPQFEKG MEAKTLGTVT PRKPVLSVSA RKIKDNAADW HNLILKWETL NDAGFTTANN IANLKISLL NKDKIELDSS SPASKENEEK VCLEYNEELE KLCEELQATL DGLTKIQVKM EKLSSTTKGI CELENYHYGE E SKRPPLFH ...String:
MWSHPQFEKG GGSGGGSGGS AWSHPQFEKG MEAKTLGTVT PRKPVLSVSA RKIKDNAADW HNLILKWETL NDAGFTTANN IANLKISLL NKDKIELDSS SPASKENEEK VCLEYNEELE KLCEELQATL DGLTKIQVKM EKLSSTTKGI CELENYHYGE E SKRPPLFH TWPTTHFYEV SHKLLEMYRK ELLLKRTVAK ELAHTGDPDL TLSYLSMWLH QPYVESDSRL HLESMLLETG HR AL

UniProtKB: Cyclin-dependent kinase 2-interacting protein

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Macromolecule #3: cDNA FLJ55172

MacromoleculeName: cDNA FLJ55172 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 31.59227 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MYPYDVPDYA MSEKRRRLDA RNPLKQETAL SRLPFPRGNQ GLLQKAEAGR ARWLTPVIPA LWKTEAGGSP EKMTQDRPLL AVQEALKKC FPVVEEQQGL WQSALRDCQP LLSSLSNLAE QLQAAQNLRF EDVPALRAFP DLKERLRRKQ LVAGDIVLDK L GERLAILL ...String:
MYPYDVPDYA MSEKRRRLDA RNPLKQETAL SRLPFPRGNQ GLLQKAEAGR ARWLTPVIPA LWKTEAGGSP EKMTQDRPLL AVQEALKKC FPVVEEQQGL WQSALRDCQP LLSSLSNLAE QLQAAQNLRF EDVPALRAFP DLKERLRRKQ LVAGDIVLDK L GERLAILL KVRDMVSSHV ERVFQIYEQH ADTVGIDAVL QPSAVSPSVA DMLEWLQDIE RHYRKSYLKR KYLLSSIQWG DL ANIQALP KAWDRISKDE HQDLVQDILL NVSFFLEE

UniProtKB: cDNA FLJ55172

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Macromolecule #4: ATPase family gene 2 protein homolog B

MacromoleculeName: ATPase family gene 2 protein homolog B / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO / EC number: non-chaperonin molecular chaperone ATPase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 80.409742 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAPDSDPFPE GPLLKLLPLD ARDRGTQRCR LGPAALHALG ARLGSAVKIS LPDGGSCLCT AWPRRDGADG FVQLDPLCAS PGAAVGASR SRRSLSLNRL LLVPCPPLRR VAVWPVLRER AGAPGARNTA AVLEAAQELL RNRPISLGHV VVAPPGAPGL V AALHIVGG ...String:
MAPDSDPFPE GPLLKLLPLD ARDRGTQRCR LGPAALHALG ARLGSAVKIS LPDGGSCLCT AWPRRDGADG FVQLDPLCAS PGAAVGASR SRRSLSLNRL LLVPCPPLRR VAVWPVLRER AGAPGARNTA AVLEAAQELL RNRPISLGHV VVAPPGAPGL V AALHIVGG TPSPDPAGLV TPRTRVSLGG EPPSEAQPQP EVPLGGLSEA ADSLRELLRL PLRYPRALTA LGLAVPRGVL LA GPPGVGK TQLVRAVARE AGAELLAVSA PALQGSRPGE TEENVRRVFQ RARELASRGP SLLFLDEMDA LCPQRGSRAP ESR VVAQVL TLLDGASGDR EVVVVGATNR PDALDPALRR PGRFDREVVI GTPTLKQRKE ILQVITSKMP ISSHVDLGLL AEMT VGYVG ADLTALCREA AMHALLHSEK NQDNPVIDEI DFLEAFKNIQ PSSFRSVIGL MDIKPVDWEE IGGLEDVKLK LKQSI EWPL KFPWEFVRMG LTQPKGVLLY GPPGCAKTTL VRALATSCHC SFVSVSGADL FSPFVGDSEK VLSQIFRQAR ASTPAI LFL DEIDSILGAR SASKTGCDVQ ERVLSVLLNE LDGVGLKTIE RRGSKSSQQE FQEVFNRSVM IIAATNRPDV LDTALLR PG RLDKIIYIPP PDHKGRLSIL KVCTKTMPIG PDVSLENLAA ETCFFSGADL RNLCTEAALL ALQENGLDAT TVKQEHFL K SLKTVKPSLS CKDLALYENL FKKEGFSN

UniProtKB: ATPase family gene 2 protein homolog B

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Macromolecule #5: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 8 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

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Macromolecule #6: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 6 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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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

Concentration1.2 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.51 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 194789
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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