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- EMDB-15521: Cryo-EM structure of ASCC3 in complex with ASC1 -

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Basic information

Entry
Database: EMDB / ID: EMD-15521
TitleCryo-EM structure of ASCC3 in complex with ASC1
Map data
Sample
  • Complex: ASCC3-ASC1
    • Protein or peptide: Activating signal cointegrator 1
    • Protein or peptide: Activating signal cointegrator 1 complex subunit 3
  • Ligand: ZINC ION
Keywordshelicase / zinc finger / activator / DNA binding / DNA BINDING PROTEIN
Function / homology
Function and homology information


ALKBH3 mediated reversal of alkylation damage / RQC-trigger complex / regulation of myoblast differentiation / DNA alkylation repair / ribosome disassembly / DNA repair complex / ribosome-associated ubiquitin-dependent protein catabolic process / 3'-5' DNA helicase activity / histone acetyltransferase binding / ubiquitin-like protein ligase binding ...ALKBH3 mediated reversal of alkylation damage / RQC-trigger complex / regulation of myoblast differentiation / DNA alkylation repair / ribosome disassembly / DNA repair complex / ribosome-associated ubiquitin-dependent protein catabolic process / 3'-5' DNA helicase activity / histone acetyltransferase binding / ubiquitin-like protein ligase binding / estrogen receptor signaling pathway / cytosolic ribosome / rescue of stalled ribosome / nuclear receptor binding / nuclear estrogen receptor binding / neuromuscular junction / protease binding / DNA helicase / forked DNA-dependent helicase activity / single-stranded 3'-5' DNA helicase activity / four-way junction helicase activity / double-stranded DNA helicase activity / transcription coactivator activity / nuclear speck / nuclear body / centrosome / regulation of DNA-templated transcription / protein kinase binding / positive regulation of DNA-templated transcription / protein-containing complex / ATP hydrolysis activity / RNA binding / zinc ion binding / nucleoplasm / ATP binding / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
TRIP4, third domain / TRI4 N-terminal domain / Zinc finger, C2HC5-type / Activating signal cointegrator 1-like / Putative zinc finger motif, C2HC5-type / ASCH / ASCH domain / ASCH domain / Winged Helix-turn-helix domain / Sec63 Brl domain ...TRIP4, third domain / TRI4 N-terminal domain / Zinc finger, C2HC5-type / Activating signal cointegrator 1-like / Putative zinc finger motif, C2HC5-type / ASCH / ASCH domain / ASCH domain / Winged Helix-turn-helix domain / Sec63 Brl domain / : / Sec63 domain / Sec63 Brl domain / PUA-like superfamily / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / C2 domain superfamily / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Immunoglobulin E-set / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Activating signal cointegrator 1 / Activating signal cointegrator 1 complex subunit 3
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsJia J / Hilal T / Loll B / Wahl MC
Funding support Germany, 5 items
OrganizationGrant numberCountry
German Research Foundation (DFG)INST 130/1064-1 FUGG Germany
German Research Foundation (DFG)GRK 2473 Germany
German Research Foundation (DFG)501_BIS-CryoFac Germany
German Research Foundation (DFG)BO3442/1-2 Germany
German Research Foundation (DFG)SFB860 Germany
CitationJournal: Nat Commun / Year: 2023
Title: Cryo-EM structure of ASCC3 in complex with ASC1
Authors: Jia J / Hilal T / Loll B / Wahl MC
History
DepositionAug 1, 2022-
Header (metadata) releaseMar 8, 2023-
Map releaseMar 8, 2023-
UpdateJul 24, 2024-
Current statusJul 24, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_15521.png

Downloads & links

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Map

FileDownload / File: emd_15521.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 320 pix.
= 266.24 Å		0.83 Å/pix.
x 320 pix.
= 266.24 Å		0.83 Å/pix.
x 320 pix.
= 266.24 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.832 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.157
Minimum - Maximum0.0 - 1.6571364
Average (Standard dev.)0.0057553123 (±0.04354681)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 266.24 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_15521_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_15521_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : ASCC3-ASC1

EntireName: ASCC3-ASC1
Components
  • Complex: ASCC3-ASC1
    • Protein or peptide: Activating signal cointegrator 1
    • Protein or peptide: Activating signal cointegrator 1 complex subunit 3
  • Ligand: ZINC ION

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Supramolecule #1: ASCC3-ASC1

SupramoleculeName: ASCC3-ASC1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Details: Protein complex was produced in baculovirus-insect system.
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 270 KDa

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Macromolecule #1: Activating signal cointegrator 1

MacromoleculeName: Activating signal cointegrator 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 66.650656 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: GAEFMAVAGA VSGEPLVHWC TQQLRKTFGL DVSEEIIQYV LSIESAEEIR EYVTDLLQGN EGKKGQFIEE LITKWQKNDQ ELISDPLQQ CFKKDEILDG QKSGDHLKRG RKKGRNRQEV PAFTEPDTTA EVKTPFDLAK AQENSNSVKK KTKFVNLYTR E GQDRLAVL ...String:
GAEFMAVAGA VSGEPLVHWC TQQLRKTFGL DVSEEIIQYV LSIESAEEIR EYVTDLLQGN EGKKGQFIEE LITKWQKNDQ ELISDPLQQ CFKKDEILDG QKSGDHLKRG RKKGRNRQEV PAFTEPDTTA EVKTPFDLAK AQENSNSVKK KTKFVNLYTR E GQDRLAVL LPGRHPCDCL GQKHKLINNC LICGRIVCEQ EGSGPCLFCG TLVCTHEEQD ILQRDSNKSQ KLLKKLMSGV EN SGKVDIS TKDLLPHQEL RIKSGLEKAI KHKDKLLEFD RTSIRRTQVI DDESDYFASD SNQWLSKLER ETLQKREEEL REL RHASRL SKKVTIDFAG RKILEEENSL AEYHSRLDET IQAIANGTLN QPLTKLDRSS EEPLGVLVNP NMYQSPPQWV DHTG AASQK KAFRSSGFGL EFNSFQHQLR IQDQEFQEGF DGGWCLSVHQ PWASLLVRGI KRVEGRSWYT PHRGRLWIAA TAKKP SPQE VSELQATYRL LRGKDVEFPN DYPSGCLLGC VDLIDCLSQK QFKEQFPDIS QESDSPFVFI CKNPQEMVVK FPIKGN PKI WKLDSKIHQG AKKGLMKQNK AV

UniProtKB: Activating signal cointegrator 1

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Macromolecule #2: Activating signal cointegrator 1 complex subunit 3

MacromoleculeName: Activating signal cointegrator 1 complex subunit 3 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 206.276094 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: GAEFHYPHVY DSQAEAMKTS AFIAGAKMIL PEGIQRENNK LYEEVRIPYS EPMPLSFEEK PVYIQDLDEI GQLAFKGMKR LNRIQSIVF ETAYNTNENM LICAPTGAGK TNIAMLTVLH EIRQHFQQGV IKKNEFKIVY VAPMKALAAE MTDYFSRRLE P LGIIVKEL ...String:
GAEFHYPHVY DSQAEAMKTS AFIAGAKMIL PEGIQRENNK LYEEVRIPYS EPMPLSFEEK PVYIQDLDEI GQLAFKGMKR LNRIQSIVF ETAYNTNENM LICAPTGAGK TNIAMLTVLH EIRQHFQQGV IKKNEFKIVY VAPMKALAAE MTDYFSRRLE P LGIIVKEL TGDMQLSKSE ILRTQMLVTT PEKWDVVTRK SVGDVALSQI VRLLILDEVH LLHEDRGPVL ESIVARTLRQ VE STQSMIR ILGLSATLPN YLDVATFLHV NPYIGLFFFD GRFRPVPLGQ TFLGIKCANK MQQLNNMDEV CYENVLKQVK AGH QVMVFV HARNATVRTA MSLIERAKNC GHIPFFFPTQ GHDYVLAEKQ VQRSRNKQVR ELFPDGFSIH HAGMLRQDRN LVEN LFSNG HIKVLVCTAT LAWGVNLPAH AVIIKGTQIY AAKRGSFVDL GILDVMQIFG RAGRPQFDKF GEGIIITTHD KLSHY LTLL TQRNPIESQF LESLADNLNA EIALGTVTNV EEAVKWISYT YLYVRMRANP LAYGISHKAY QIDPTLRKHR EQLVIE VGR KLDKAQMIRF EERTGYFSST DLGRTASHYY IKYNTIETFN ELFDAHKTEG DIFAIVSKAE EFDQIKVREE EIEELDT LL SNFCELSTPG GVENSYGKIN ILLQTYISRG EMDSFSLISD SAYVAQNAAR IVRALFEIAL RKRWPTMTYR LLNLSKVI D KRLWGWASPL RQFSILPPHI LTRLEEKKLT VDKLKDMRKD EIGHILHHVN IGLKVKQCVH QIPSVMMEAS IQPITRTVL RVTLSIYADF TWNDQVHGTV GEPWWIWVED PTNDHIYHSE YFLALKKQVI SKEAQLLVFT IPIFEPLPSQ YYIRAVSDRW LGAEAVCII NFQHLILPER HPPHTELLDL QPLPITALGC KAYEALYNFS HFNPVQTQIF HTLYHTDCNV LLGAPTGSGK T VAAELAIF RVFNKYPTSK AVYIAPLKAL VRERMDDWKV RIEEKLGKKV IELTGDVTPD MKSIAKADLI VTTPEKWDGV SR SWQNRNY VQQVTILIID EIHLLGEERG PVLEVIVSRT NFISSHTEKP VRIVGLSTAL ANARDLADWL NIKQMGLFNF RPS VRPVPL EVHIQGFPGQ HYCPRMASMN KPAFQAIRSH SPAKPVLIFV SSRRQTRLTA LELIAFLATE EDPKQWLNMD EREM ENIIA TVRDSNLKLT LAFGIGMHHA GLHERDRKTV EELFVNCKVQ VLIATSTLAW GVNFPAHLVI IKGTEYYDGK TRRYV DFPI TDVLQMMGRA GRPQFDDQGK AVILVHDIKK DFYKKFLYEP FPVESSLLGV LSDHLNAEIA GGTITSKQDA LDYITW TYF FRRLIMNPSY YNLGDVSHDS VNKFLSHLIE KSLIELELSY CIEIGEDNRS IEPLTYGRIA SYYYLKHQTV KMFKDRL KP ECSTEELLSI LSDAEEYTDL PVRHNEDHMN SELAKCLPIE SNPHSFDSPH TKAHLLLQAH LSRAMLPCPD YDTDTKTV L DQALRVCQAM LDVAANQGWL VTVLNITNLI QMVIQGRWLK DSSLLTLPNI ENHHLHLFKK WKPIMKGPHA RGRTSIESL PELIHACGGK DHVFSSMVES ELHAAKTKQA WNFLSHLPVI NVGISVKGSW DDLVEGHNEL SVSTLTADKR DDNKWIKLHA DQEYVLQVS LQRVHFGFHK GKPESCAVTP RFPKSKDEGW FLILGEVDKR ELIALKRVGY IRNHHVASLS FYTPEIPGRY I YTLYFMSD CYLGLDQQYD IYLNVTQASL SAQVNTKVSD SLTDLALK

UniProtKB: Activating signal cointegrator 1 complex subunit 3

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Macromolecule #3: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 3 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 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

Concentration4.15 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
300.0 mMNaClsodium chloride
20.0 mMHEPES-NaOH4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid
1.0 mMDTTDithiothreitol
0.1 mg/mlDDMn-dodecyl-B-maltoside

Details: Solutions were made fresh from concentrated to avoid microbial contamination.
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283.15 K / Instrument: FEI VITROBOT MARK IV
DetailsThis sample was monodisperse.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 2 / Number real images: 6267 / Average exposure time: 40.57 sec. / Average electron dose: 42.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 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

Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.2) / Number images used: 244064
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.1)
FSC plot (resolution estimation)

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