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- EMDB-16468: Cryo-EM structure of the yeast SPT-Orm1-Sac1 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-16468
TitleCryo-EM structure of the yeast SPT-Orm1-Sac1 complex
Map dataSPOTS-Orm1-Sac1-Map
Sample
  • Complex: Heteropentameric complex of Orm1 with Lcb1, Lcb2, Tsc3 and Sac1
    • Protein or peptide: Protein ORM1
    • Protein or peptide: Serine palmitoyltransferase 1
    • Protein or peptide: Serine palmitoyltransferase 2
    • Protein or peptide: Serine palmitoyltransferase-regulating protein TSC3
    • Protein or peptide: Phosphatidylinositol-3-phosphatase SAC1
  • Ligand: ERGOSTEROL
  • Ligand: N-[(2S,3S,4R)-1,3,4-trihydroxyoctadecan-2-yl]hexacosanamide
  • Ligand: 2-{[(4-O-alpha-D-glucopyranosyl-alpha-D-glucopyranosyl)oxy]methyl}-4-{[(3beta,9beta,14beta,17beta,25R)-spirost-5-en-3-yl]oxy}butyl 4-O-alpha-D-glucopyranosyl-alpha-D-glucopyranoside
  • Ligand: PYRIDOXAL-5'-PHOSPHATE
KeywordsSerine-Palmitoyl-Transferase / SPT / Orm-Protein / TRANSFERASE
Function / homology
Function and homology information


phosphatidylinositol-3-phosphatase / Synthesis of PIPs at the ER membrane / phosphatidylinositol-4-phosphate phosphatase activity / negative regulation of sphingolipid biosynthetic process / positive regulation of sphingolipid biosynthetic process / 3-keto-sphinganine metabolic process / phosphatidylinositol-3,5-bisphosphate 3-phosphatase activity / host cell viral assembly compartment / phosphatidylinositol-3-phosphate phosphatase activity / Synthesis of PIPs at the Golgi membrane ...phosphatidylinositol-3-phosphatase / Synthesis of PIPs at the ER membrane / phosphatidylinositol-4-phosphate phosphatase activity / negative regulation of sphingolipid biosynthetic process / positive regulation of sphingolipid biosynthetic process / 3-keto-sphinganine metabolic process / phosphatidylinositol-3,5-bisphosphate 3-phosphatase activity / host cell viral assembly compartment / phosphatidylinositol-3-phosphate phosphatase activity / Synthesis of PIPs at the Golgi membrane / serine palmitoyltransferase complex / intracellular sphingolipid homeostasis / serine C-palmitoyltransferase activity / serine C-palmitoyltransferase / cortical endoplasmic reticulum / ceramide metabolic process / autophagosome-lysosome fusion / sphingosine biosynthetic process / sphingolipid biosynthetic process / phosphatidylinositol dephosphorylation / ceramide biosynthetic process / Golgi medial cisterna / response to unfolded protein / enzyme activator activity / Neutrophil degranulation / pyridoxal phosphate binding / mitochondrial outer membrane / Golgi membrane / endoplasmic reticulum membrane / endoplasmic reticulum / mitochondrion / membrane
Similarity search - Function
SAC domain / SacI homology domain / Sac phosphatase domain profile. / ORMDL family / ORMDL family / : / Aminotransferase, class-II, pyridoxal-phosphate binding site / Aminotransferases class-II pyridoxal-phosphate attachment site. / Aminotransferase, class I/classII / Aminotransferase class I and II ...SAC domain / SacI homology domain / Sac phosphatase domain profile. / ORMDL family / ORMDL family / : / Aminotransferase, class-II, pyridoxal-phosphate binding site / Aminotransferases class-II pyridoxal-phosphate attachment site. / Aminotransferase, class I/classII / Aminotransferase class I and II / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
Serine palmitoyltransferase 1 / Phosphatidylinositol-3-phosphatase SAC1 / Serine palmitoyltransferase 2 / Protein ORM1 / Serine palmitoyltransferase-regulating protein TSC3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsSchaefer J / Koerner C / Parey K / Januliene D / Moeller A / Froehlich F
Funding support Germany, 2 items
OrganizationGrant numberCountry
German Research Foundation (DFG)SFB944 Germany
German Research Foundation (DFG)SFB15 Germany
CitationJournal: Nat Commun / Year: 2023
Title: Structure of the ceramide-bound SPOTS complex.
Authors: Jan-Hannes Schäfer / Carolin Körner / Bianca M Esch / Sergej Limar / Kristian Parey / Stefan Walter / Dovile Januliene / Arne Moeller / Florian Fröhlich /
Abstract: Sphingolipids are structural membrane components that also function in cellular stress responses. The serine palmitoyltransferase (SPT) catalyzes the rate-limiting step in sphingolipid biogenesis. ...Sphingolipids are structural membrane components that also function in cellular stress responses. The serine palmitoyltransferase (SPT) catalyzes the rate-limiting step in sphingolipid biogenesis. Its activity is tightly regulated through multiple binding partners, including Tsc3, Orm proteins, ceramides, and the phosphatidylinositol-4-phosphate (PI4P) phosphatase Sac1. The structural organization and regulatory mechanisms of this complex are not yet understood. Here, we report the high-resolution cryo-EM structures of the yeast SPT in complex with Tsc3 and Orm1 (SPOT) as dimers and monomers and a monomeric complex further carrying Sac1 (SPOTS). In all complexes, the tight interaction of the downstream metabolite ceramide and Orm1 reveals the ceramide-dependent inhibition. Additionally, observation of ceramide and ergosterol binding suggests a co-regulation of sphingolipid biogenesis and sterol metabolism within the SPOTS complex.
History
DepositionJan 18, 2023-
Header (metadata) releaseOct 11, 2023-
Map releaseOct 11, 2023-
UpdateOct 11, 2023-
Current statusOct 11, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16468.png

Downloads & links

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Map

FileDownload / File: emd_16468.map.gz / Format: CCP4 / Size: 307.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSPOTS-Orm1-Sac1-Map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.92 Å/pix.
x 432 pix.
= 399.168 Å		0.92 Å/pix.
x 432 pix.
= 399.168 Å		0.92 Å/pix.
x 432 pix.
= 399.168 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.924 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.14
Minimum - Maximum-0.63460416 - 1.0689365
Average (Standard dev.)-0.000072497685 (±0.026991246)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions432432432
Spacing432432432
CellA=B=C: 399.168 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: SPOTS-Orm1-Sac1-Half-Map-A

Fileemd_16468_half_map_1.map
AnnotationSPOTS-Orm1-Sac1-Half-Map-A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: SPOTS-Orm1-Sac1-Half-Map-B

Fileemd_16468_half_map_2.map
AnnotationSPOTS-Orm1-Sac1-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 : Heteropentameric complex of Orm1 with Lcb1, Lcb2, Tsc3 and Sac1

EntireName: Heteropentameric complex of Orm1 with Lcb1, Lcb2, Tsc3 and Sac1
Components
  • Complex: Heteropentameric complex of Orm1 with Lcb1, Lcb2, Tsc3 and Sac1
    • Protein or peptide: Protein ORM1
    • Protein or peptide: Serine palmitoyltransferase 1
    • Protein or peptide: Serine palmitoyltransferase 2
    • Protein or peptide: Serine palmitoyltransferase-regulating protein TSC3
    • Protein or peptide: Phosphatidylinositol-3-phosphatase SAC1
  • Ligand: ERGOSTEROL
  • Ligand: N-[(2S,3S,4R)-1,3,4-trihydroxyoctadecan-2-yl]hexacosanamide
  • Ligand: 2-{[(4-O-alpha-D-glucopyranosyl-alpha-D-glucopyranosyl)oxy]methyl}-4-{[(3beta,9beta,14beta,17beta,25R)-spirost-5-en-3-yl]oxy}butyl 4-O-alpha-D-glucopyranosyl-alpha-D-glucopyranoside
  • Ligand: PYRIDOXAL-5'-PHOSPHATE

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Supramolecule #1: Heteropentameric complex of Orm1 with Lcb1, Lcb2, Tsc3 and Sac1

SupramoleculeName: Heteropentameric complex of Orm1 with Lcb1, Lcb2, Tsc3 and Sac1
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 230 KDa

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Macromolecule #1: Protein ORM1

MacromoleculeName: Protein ORM1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 25.221674 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MTELDYQGTA EAASTSYSRN QTDLKPFPSA GSASSSIKTT EPVKDHRRRR AAAIISHVEP ETFEDENDQQ LLPNMNATWV DQRGAWIIH VVIIILLKLF YNLFPGVTTE WSWTLTNMTY VIGSYVMFHL IKGTPFDFNG GAYDNLTMWE QIDDETLYTP S RKFLISVP ...String:
MTELDYQGTA EAASTSYSRN QTDLKPFPSA GSASSSIKTT EPVKDHRRRR AAAIISHVEP ETFEDENDQQ LLPNMNATWV DQRGAWIIH VVIIILLKLF YNLFPGVTTE WSWTLTNMTY VIGSYVMFHL IKGTPFDFNG GAYDNLTMWE QIDDETLYTP S RKFLISVP IALFLVSTHY AHYDLKLFSW NCFLTTFGAV VPKLPVTHRL RISIPGITGR AQIS

UniProtKB: Protein ORM1

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Macromolecule #2: Serine palmitoyltransferase 1

MacromoleculeName: Serine palmitoyltransferase 1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: serine C-palmitoyltransferase
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 64.98552 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MAHIPEVLPD YKDHDGDYKD HDIDYKDDDD KKSIPIPAFI VTTSSYLWYY FNLVLTQIPG GQFIVSYIKK SHHDDPYRTT VEIGLILYG IIYYLSKPQQ KKSLQAQKPN LSPQEIDALI EDWEPEPLVD PSATDEQSWR VAKTPVTMEM PIQNHITITR N NLQEKYTN ...String:
MAHIPEVLPD YKDHDGDYKD HDIDYKDDDD KKSIPIPAFI VTTSSYLWYY FNLVLTQIPG GQFIVSYIKK SHHDDPYRTT VEIGLILYG IIYYLSKPQQ KKSLQAQKPN LSPQEIDALI EDWEPEPLVD PSATDEQSWR VAKTPVTMEM PIQNHITITR N NLQEKYTN VFNLASNNFL QLSATEPVKE VVKTTIKNYG VGACGPAGFY GNQDVHYTLE YDLAQFFGTQ GSVLYGQDFC AA PSVLPAF TKRGDVIVAD DQVSLPVQNA LQLSRSTVYY FNHNDMNSLE CLLNELTEQE KLEKLPAIPR KFIVTEGIFH NSG DLAPLP ELTKLKNKYK FRLFVDETFS IGVLGATGRG LSEHFNMDRA TAIDITVGSM ATALGSTGGF VLGDSVMCLH QRIG SNAYC FSACLPAYTV TSVSKVLKLM DSNNDAVQTL QKLSKSLHDS FASDDSLRSY VIVTSSPVSA VLHLQLTPAY RSRKF GYTC EQLFETMSAL QKKSQTNKFI EPYEEEEKFL QSIVDHALIN YNVLITRNTI VLKQETLPIV PSLKICCNAA MSPEEL KNA CESVKQSILA CCQESNK

UniProtKB: Serine palmitoyltransferase 1

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Macromolecule #3: Serine palmitoyltransferase 2

MacromoleculeName: Serine palmitoyltransferase 2 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: serine C-palmitoyltransferase
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 63.189707 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MSTPANYTRV PLCEPEELPD DIQKENEYGT LDSPGHLYQV KSRHGKPLPE PVVDTPPYYI SLLTYLNYLI LIILGHVHDF LGMTFQKNK HLDLLEHDGL APWFSNFESF YVRRIKMRID DCFSRPTTGV PGRFIRCIDR ISHNINEYFT YSGAVYPCMN L SSYNYLGF ...String:
MSTPANYTRV PLCEPEELPD DIQKENEYGT LDSPGHLYQV KSRHGKPLPE PVVDTPPYYI SLLTYLNYLI LIILGHVHDF LGMTFQKNK HLDLLEHDGL APWFSNFESF YVRRIKMRID DCFSRPTTGV PGRFIRCIDR ISHNINEYFT YSGAVYPCMN L SSYNYLGF AQSKGQCTDA ALESVDKYSI QSGGPRAQIG TTDLHIKAEK LVARFIGKED ALVFSMGYGT NANLFNAFLD KK CLVISDE LNHTSIRTGV RLSGAAVRTF KHGDMVGLEK LIREQIVLGQ PKTNRPWKKI LICAEGLFSM EGTLCNLPKL VEL KKKYKC YLFIDEAHSI GAMGPTGRGV CEIFGVDPKD VDILMGTFTK SFGAAGGYIA ADQWIIDRLR LDLTTVSYSE SMPA PVLAQ TISSLQTISG EICPGQGTER LQRIAFNSRY LRLALQRLGF IVYGVADSPV IPLLLYCPSK MPAFSRMMLQ RRIAV VVVA YPATPLIESR VRFCMSASLT KEDIDYLLRH VSEVGDKLNL KSNSGKSSYD GKRQRWDIEE VIRRTPEDCK DDKYFV N

UniProtKB: Serine palmitoyltransferase 2

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Macromolecule #4: Serine palmitoyltransferase-regulating protein TSC3

MacromoleculeName: Serine palmitoyltransferase-regulating protein TSC3 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 9.590233 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString:
MTQHKSSMVY IPTTKEAKRR NGKSEGILNT IEEVVEKLYW TYYIHLPFYL MASFDSFFLH VFFLTIFSLS FFGILKYCFL

UniProtKB: Serine palmitoyltransferase-regulating protein TSC3

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Macromolecule #5: Phosphatidylinositol-3-phosphatase SAC1

MacromoleculeName: Phosphatidylinositol-3-phosphatase SAC1 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO / EC number: phosphatidylinositol-3-phosphatase
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 71.214352 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MTGPIVYVQN ADGIFFKLAE GKGTNDAVIH LANQDQGVRV LGAEEFPVQG EVVKIASLMG FIKLKLNRYA IIANTVEETG RFNGHVFYR VLQHSIVSTK FNSRIDSEEA EYIKLLELHL KNSTFYFSYT YDLTNSLQRN EKVGPAASWK TADERFFWNH Y LTEDLRNF ...String:
MTGPIVYVQN ADGIFFKLAE GKGTNDAVIH LANQDQGVRV LGAEEFPVQG EVVKIASLMG FIKLKLNRYA IIANTVEETG RFNGHVFYR VLQHSIVSTK FNSRIDSEEA EYIKLLELHL KNSTFYFSYT YDLTNSLQRN EKVGPAASWK TADERFFWNH Y LTEDLRNF AHQDPRIDSF IQPVIYGYAK TVDAVLNATP IVLGLITRRS IFRAGTRYFR RGVDKDGNVG NFNETEQILL AE NPESEKI HVFSFLQTRG SVPIYWAEIN NLKYKPNLVL GENSLDATKK HFDQQKELYG DNYLVNLVNQ KGHELPVKEG YES VVHALN DPKIHYVYFD FHHECRKMQW HRVKLLIDHL EKLGLSNEDF FHKVIDSNGN TVEIVNEQHS VVRTNCMDCL DRTN VVQSV LAQWVLQKEF ESADVVATGS TWEDNAPLLT SYQNLWADNA DAVSVAYSGT GALKTDFTRT GKRTRLGAFN DFLNS ASRY YQNNWTDGPR QDSYDLFLGG FRPHTASIKS PFPDRRPVYI QLIPMIICAA LTVLGATIFF PKDRFTSSKN LLYFAG ASI VLALSTKFMF KNGIQFVNWP KLVDVGFLVV HQTHDKEQQF KGLKYAQSPK FSKPDPLKRD

UniProtKB: Phosphatidylinositol-3-phosphatase SAC1

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Macromolecule #6: ERGOSTEROL

MacromoleculeName: ERGOSTEROL / type: ligand / ID: 6 / Number of copies: 3 / Formula: ERG
Molecular weightTheoretical: 396.648 Da
Chemical component information

ChemComp-ERG:
ERGOSTEROL

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Macromolecule #7: N-[(2S,3S,4R)-1,3,4-trihydroxyoctadecan-2-yl]hexacosanamide

MacromoleculeName: N-[(2S,3S,4R)-1,3,4-trihydroxyoctadecan-2-yl]hexacosanamide
type: ligand / ID: 7 / Number of copies: 1 / Formula: Z8A
Molecular weightTheoretical: 696.182 Da
Chemical component information

ChemComp-Z8A:
N-[(2S,3S,4R)-1,3,4-trihydroxyoctadecan-2-yl]hexacosanamide

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Macromolecule #8: 2-{[(4-O-alpha-D-glucopyranosyl-alpha-D-glucopyranosyl)oxy]methyl...

MacromoleculeName: 2-{[(4-O-alpha-D-glucopyranosyl-alpha-D-glucopyranosyl)oxy]methyl}-4-{[(3beta,9beta,14beta,17beta,25R)-spirost-5-en-3-yl]oxy}butyl 4-O-alpha-D-glucopyranosyl-alpha-D-glucopyranoside
type: ligand / ID: 8 / Number of copies: 1 / Formula: Q7G
Molecular weightTheoretical: 1.165315 KDa
Chemical component information

ChemComp-Q7G:
2-{[(4-O-alpha-D-glucopyranosyl-alpha-D-glucopyranosyl)oxy]methyl}-4-{[(3beta,9beta,14beta,17beta,25R)-spirost-5-en-3-yl]oxy}butyl 4-O-alpha-D-glucopyranosyl-alpha-D-glucopyranoside

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Macromolecule #9: PYRIDOXAL-5'-PHOSPHATE

MacromoleculeName: PYRIDOXAL-5'-PHOSPHATE / type: ligand / ID: 9 / Number of copies: 1 / Formula: PLP
Molecular weightTheoretical: 247.142 Da
Chemical component information

ChemComp-PLP:
PYRIDOXAL-5'-PHOSPHATE

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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

Concentration10.0 mg/mL
BufferpH: 6.8
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS GLACIOS
Specialist opticsEnergy filter - Name: TFS Selectris / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number real images: 13604 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 130000

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 53236
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL / Overall B value: 63
Output model

PDB-8c81:
Cryo-EM structure of the yeast SPT-Orm1-Sac1 complex

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