+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-23494 | |||||||||
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Title | Cryo-EM of the SLFN12-PDE3A complex: PDE3A body refinement | |||||||||
Map data | Body output from Relion Multibody refinement | |||||||||
Sample |
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Keywords | complex / velcrin / molecular glue / DNMDP / HYDROLASE | |||||||||
Function / homology | Function and homology information 3',5'-cGMP-inhibited cyclic-nucleotide phosphodiesterase activity / estrogen binding / regulation of ribonuclease activity / positive regulation of oocyte development / regulation of meiotic nuclear division / cellular response to cGMP / rRNA catabolic process / negative regulation of cAMP-mediated signaling / negative regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / positive regulation of vascular permeability ...3',5'-cGMP-inhibited cyclic-nucleotide phosphodiesterase activity / estrogen binding / regulation of ribonuclease activity / positive regulation of oocyte development / regulation of meiotic nuclear division / cellular response to cGMP / rRNA catabolic process / negative regulation of cAMP-mediated signaling / negative regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / positive regulation of vascular permeability / negative regulation of vascular permeability / oocyte maturation / 3',5'-cyclic-nucleotide phosphodiesterase / cGMP-mediated signaling / nuclear estrogen receptor activity / 3',5'-cyclic-nucleotide phosphodiesterase activity / 3',5'-cyclic-GMP phosphodiesterase activity / 3',5'-cyclic-AMP phosphodiesterase activity / RNA nuclease activity / cellular response to transforming growth factor beta stimulus / cAMP-mediated signaling / lipid metabolic process / apoptotic signaling pathway / ribosome binding / G alpha (s) signalling events / Hydrolases; Acting on ester bonds / response to xenobiotic stimulus / G protein-coupled receptor signaling pathway / negative regulation of apoptotic process / membrane / nucleus / metal ion binding / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.97 Å | |||||||||
Authors | Fuller JR / Garvie CW / Lemke CT | |||||||||
Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_23494.map.gz | 95 MB | EMDB map data format | |
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Header (meta data) | emd-23494-v30.xml emd-23494.xml | 25.3 KB 25.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_23494_fsc.xml | 11.4 KB | Display | FSC data file |
Images | emd_23494.png | 90.2 KB | ||
Masks | emd_23494_msk_1.map | 129.7 MB | Mask map | |
Filedesc metadata | emd-23494.cif.gz | 7.7 KB | ||
Others | emd_23494_additional_1.map.gz emd_23494_half_map_1.map.gz emd_23494_half_map_2.map.gz | 75.4 MB 93.1 MB 93.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-23494 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-23494 | HTTPS FTP |
-Validation report
Summary document | emd_23494_validation.pdf.gz | 707.9 KB | Display | EMDB validaton report |
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Full document | emd_23494_full_validation.pdf.gz | 707.4 KB | Display | |
Data in XML | emd_23494_validation.xml.gz | 18.7 KB | Display | |
Data in CIF | emd_23494_validation.cif.gz | 24.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23494 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23494 | HTTPS FTP |
-Related structure data
Related structure data | 7lrcMC 7kweC 7l27C 7l28C 7l29C 7lrdC 7lreC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_23494.map.gz / Format: CCP4 / Size: 129.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Body output from Relion Multibody refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.063 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_23494_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Sharpened by an automatically-determined B-factor (-117.379) and filtered...
File | emd_23494_additional_1.map | ||||||||||||
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Annotation | Sharpened by an automatically-determined B-factor (-117.379) and filtered to local resolution, using the Relion local resolution implementation. Model was primarily refined against this map. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Body half-map 2 from Relion Multibody refinement
File | emd_23494_half_map_1.map | ||||||||||||
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Annotation | Body half-map 2 from Relion Multibody refinement | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Body half-map 1 from Relion Multibody refinement
File | emd_23494_half_map_2.map | ||||||||||||
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Annotation | Body half-map 1 from Relion Multibody refinement | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : SLFN12-PDE3A complex, PDE3A body with interacting peptide from SLFN12
Entire | Name: SLFN12-PDE3A complex, PDE3A body with interacting peptide from SLFN12 |
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Components |
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-Supramolecule #1: SLFN12-PDE3A complex, PDE3A body with interacting peptide from SLFN12
Supramolecule | Name: SLFN12-PDE3A complex, PDE3A body with interacting peptide from SLFN12 type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: cGMP-inhibited 3',5'-cyclic phosphodiesterase A
Macromolecule | Name: cGMP-inhibited 3',5'-cyclic phosphodiesterase A / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: 3',5'-cyclic-nucleotide phosphodiesterase |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 57.352996 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: GEDETECLRE PLRKASACST YAPETMMFLD KPILAPEPLV MDNLDSIMEQ LNTWNFPIFD LVENIGRKCG RILSQVSYRL FEDMGLFEA FKIPIREFMN YFHALEIGYR DIPYHNRIHA TDVLHAVWYL TTQPIPGLST VINDHGSTSD SDSDSGFTHG H MGYVFSKT ...String: GEDETECLRE PLRKASACST YAPETMMFLD KPILAPEPLV MDNLDSIMEQ LNTWNFPIFD LVENIGRKCG RILSQVSYRL FEDMGLFEA FKIPIREFMN YFHALEIGYR DIPYHNRIHA TDVLHAVWYL TTQPIPGLST VINDHGSTSD SDSDSGFTHG H MGYVFSKT YNVTDDKYGC LSGNIPALEL MALYVAAAMH DYDHPGRTNA FLVATSAPQA VLYNDRSVLE NHHAAAAWNL FM SRPEYNF LINLDHVEFK HFRFLVIEAI LATDLKKHFD FVAKFNGKVN DDVGIDWTNE NDRLLVCQMC IKLADINGPA KCK ELHLQW TDGIVNEFYE QGDEEASLGL PISPFMDRSA PQLANLQESF ISHIVGPLCN SYDSAGLMPG KWVEDSDESG DTDD PEEEE EEAPAPNEEE TCENNESPKK KTFKRRKIYC QITQHLLQNH KMWKKVIEEE QRLAGIENQS LDQTPQSHSS EQIQA IKEE EEEKGKPRGE EIPTQKPDQ UniProtKB: cGMP-inhibited 3',5'-cyclic phosphodiesterase 3A |
-Macromolecule #2: Schlafen family member 12
Macromolecule | Name: Schlafen family member 12 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 67.383734 KDa |
Recombinant expression | Organism: unidentified baculovirus |
Sequence | String: 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 |
-Macromolecule #3: MANGANESE (II) ION
Macromolecule | Name: MANGANESE (II) ION / type: ligand / ID: 3 / Number of copies: 2 / Formula: MN |
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Molecular weight | Theoretical: 54.938 Da |
-Macromolecule #4: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 2 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Macromolecule #5: (4~{R})-3-[4-(diethylamino)-3-[oxidanyl(oxidanylidene)-$l^{4}-aza...
Macromolecule | Name: (4~{R})-3-[4-(diethylamino)-3-[oxidanyl(oxidanylidene)-$l^{4}-azanyl]phenyl]-4-methyl-4,5-dihydro-1~{H}-pyridazin-6-one type: ligand / ID: 5 / Number of copies: 2 / Formula: X5M |
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Molecular weight | Theoretical: 305.352 Da |
Chemical component information | ChemComp-X5M: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.6 mg/mL | |||||||||||||||
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Buffer | pH: 7.4 Component:
Details: 0.0038% NP-40s detergent (CAS 9016-45-9) added immediately prior to plunge freezing | |||||||||||||||
Grid | Model: C-flat / Material: GOLD / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec. | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 291 K / Instrument: FEI VITROBOT MARK IV / Details: 4.5 second blot time. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film 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 beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal magnification: 81000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Initial model | PDB ID: Chain - Source name: PDB / Chain - Initial model type: experimental model |
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Details | The atomic model (including per-residue ADP/B-factors) was refined in Phenix against the sharpened/local resolution-filtered map |
Refinement | Space: REAL |
Output model | PDB-7lrc: |