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- EMDB-23496: Cryo-EM of the SLFN12-PDE3A complex: SLFN12 body refinement -

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Basic information

Entry
Database: EMDB / ID: EMD-23496
TitleCryo-EM of the SLFN12-PDE3A complex: SLFN12 body refinement
Map dataBody output from Relion Multibody refinement
Sample
  • Complex: SLFN12-PDE3A complex, SLFN12 body
    • Protein or peptide: Schlafen family member 12
  • Ligand: ZINC ION
Keywordscomplex / velcrin / molecular glue / DNMDP / RNA BINDING PROTEIN
Function / homology
Function and homology information


rRNA catabolic process / RNA nuclease activity / apoptotic signaling pathway / ribosome binding / Hydrolases; Acting on ester bonds / nucleus / cytosol
Similarity search - Function
: / Schlafen, GTPase-like domain / Schlafen family / Orthopoxvirus B3 protein / Poxviridae B3 protein / Schlafen, AlbA_2 domain / Schlafen, AlbA_2 domain superfamily / Schlafen, AlbA_2
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.76 Å
AuthorsFuller JR / Garvie CW / Lemke CT
CitationJournal: Nat Commun / Year: 2021
Title: Structure of PDE3A-SLFN12 complex reveals requirements for activation of SLFN12 RNase.
Authors: Colin W Garvie / Xiaoyun Wu / Malvina Papanastasiou / Sooncheol Lee / James Fuller / Gavin R Schnitzler / Steven W Horner / Andrew Baker / Terry Zhang / James P Mullahoo / Lindsay Westlake / ...Authors: Colin W Garvie / Xiaoyun Wu / Malvina Papanastasiou / Sooncheol Lee / James Fuller / Gavin R Schnitzler / Steven W Horner / Andrew Baker / Terry Zhang / James P Mullahoo / Lindsay Westlake / Stephanie H Hoyt / Marcus Toetzl / Matthew J Ranaghan / Luc de Waal / Joseph McGaunn / Bethany Kaplan / Federica Piccioni / Xiaoping Yang / Martin Lange / Adrian Tersteegen / Donald Raymond / Timothy A Lewis / Steven A Carr / Andrew D Cherniack / Christopher T Lemke / Matthew Meyerson / Heidi Greulich /
Abstract: DNMDP and related compounds, or velcrins, induce complex formation between the phosphodiesterase PDE3A and the SLFN12 protein, leading to a cytotoxic response in cancer cells that express elevated ...DNMDP and related compounds, or velcrins, induce complex formation between the phosphodiesterase PDE3A and the SLFN12 protein, leading to a cytotoxic response in cancer cells that express elevated levels of both proteins. The mechanisms by which velcrins induce complex formation, and how the PDE3A-SLFN12 complex causes cancer cell death, are not fully understood. Here, we show that PDE3A and SLFN12 form a heterotetramer stabilized by binding of DNMDP. Interactions between the C-terminal alpha helix of SLFN12 and residues near the active site of PDE3A are required for complex formation, and are further stabilized by interactions between SLFN12 and DNMDP. Moreover, we demonstrate that SLFN12 is an RNase, that PDE3A binding increases SLFN12 RNase activity, and that SLFN12 RNase activity is required for DNMDP response. This new mechanistic understanding will facilitate development of velcrin compounds into new cancer therapies.
History
DepositionFeb 16, 2021-
Header (metadata) releaseJun 9, 2021-
Map releaseJun 9, 2021-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0175
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.0175
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7lre
  • Surface level: 0.0175
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7lre
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23496.png

Downloads & links

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Map

FileDownload / File: emd_23496.map.gz / Format: CCP4 / Size: 129.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationBody output from Relion Multibody refinement
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 324 pix.
= 344.412 Å		1.06 Å/pix.
x 324 pix.
= 344.412 Å		1.06 Å/pix.
x 324 pix.
= 344.412 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.063 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0175 / Movie #1: 0.0175
Minimum - Maximum-0.02046164 - 0.0635099
Average (Standard dev.)0.000011518381 (±0.0015845727)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions324324324
Spacing324324324
CellA=B=C: 344.412 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0631.0631.063
M x/y/z324324324
origin x/y/z0.0000.0000.000
length x/y/z344.412344.412344.412
α/β/γ90.00090.00090.000
start NX/NY/NZ727265
NX/NY/NZ157157169
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS324324324
D min/max/mean-0.0200.0640.000

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Supplemental data

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Mask #1

Fileemd_23496_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Sharpened by an automatically-determined B-factor (-100.32) and filtered...

Fileemd_23496_additional_1.map
AnnotationSharpened by an automatically-determined B-factor (-100.32) and filtered to local resolution, using the Relion local resolution implementation. Model was primarily refined against this map.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Body half-map 1 from Relion Multibody refinement

Fileemd_23496_half_map_1.map
AnnotationBody half-map 1 from Relion Multibody refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Body half-map 2 from Relion Multibody refinement

Fileemd_23496_half_map_2.map
AnnotationBody half-map 2 from Relion Multibody refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : SLFN12-PDE3A complex, SLFN12 body

EntireName: SLFN12-PDE3A complex, SLFN12 body
Components
  • Complex: SLFN12-PDE3A complex, SLFN12 body
    • Protein or peptide: Schlafen family member 12
  • Ligand: ZINC ION

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Supramolecule #1: SLFN12-PDE3A complex, SLFN12 body

SupramoleculeName: SLFN12-PDE3A complex, SLFN12 body / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Schlafen family member 12

MacromoleculeName: Schlafen family member 12 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 67.383734 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: GGGGSMNISV DLETNYAELV LDVGRVTLGE NSRKKMKDCK LRKKQNESVS RAMCALLNSG GGVIKAEIEN EDYSYTKDGI GLDLENSFS NILLFVPEYL DFMQNGNYFL IFVKSWSLNT SGLRITTLSS NLYKRDITSA KVMNATAALE FLKDMKKTRG R LYLRPELL ...String:
GGGGSMNISV DLETNYAELV LDVGRVTLGE NSRKKMKDCK LRKKQNESVS RAMCALLNSG GGVIKAEIEN EDYSYTKDGI GLDLENSFS NILLFVPEYL DFMQNGNYFL IFVKSWSLNT SGLRITTLSS NLYKRDITSA KVMNATAALE FLKDMKKTRG R LYLRPELL AKRPCVDIQE ENNMKALAGV FFDRTELDRK EKLTFTESTH VEIKNFSTEK LLQRIKEILP QYVSAFANTD GG YLFIGLN EDKEIIGFKA EMSDLDDLER EIEKSIRKMP VHHFCMEKKK INYSCKFLGV YDKGSLCGYV CALRVERFCC AVF AKEPDS WHVKDNRVMQ LTRKEWIQFM VEAEPKFSSS YEEVISQINT SLPAPHSWPL LEWQRQRHHC PGLSGRITYT PENL CRKLF LQHEGLKQLI CEEMDSVRKG SLIFSRSWSV DLGLQENHKV LCDALLISQD SPPVLYTFHM VQDEEFKGYS TQTAL TLKQ KLAKIGGYTK KVCVMTKIFY LSPEGMTSCQ YDLRSQVIYP ESYYFTRRKY LLKALFKALK RLKSLRDQFS FAENLY QII GIDCFQKNDK KMFKSCRRLT

UniProtKB: Ribonuclease SLFN12

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Macromolecule #2: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 2 / 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

Concentration0.6 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
150.0 mMNaClsodium chloride
1.0 mMMgCl2magnesium chloride
20.0 mMC8H18N2O4SHEPES
0.5 mMC9H15O6PTCEP

Details: 0.0038% NP-40s detergent (CAS 9016-45-9) added immediately prior to plunge freezing
GridModel: C-flat / Material: GOLD / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 291 K / Instrument: FEI VITROBOT MARK IV / Details: 4.5 second blot time.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 3163 / Average electron dose: 50.0 e/Å2
Details: Exposures were collected in super-resolution mode, as movies fractionated over 40 frames
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal magnification: 81000
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

Particle selectionNumber selected: 2160426
Startup modelType of model: OTHER
Details: The initial startup model was calculated de novo from the data using the method implemented in cisTEM v1.0.0-beta
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.76 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Details: Multi-body refinement in Relion / Number images used: 247402
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cisTEM (ver. 1.0.0-beta)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final 3D classificationNumber classes: 9 / Software - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

5yd0


Chain - Source name: PDB / Chain - Initial model type: experimental model
DetailsThe atomic model (including per-residue ADP/B-factors) was refined in Phenix against the sharpened/local resolution-filtered map
RefinementSpace: REAL
Output model

PDB-7lre:
Cryo-EM of the SLFN12-PDE3A complex: SLFN12 body refinement

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