+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-18517 | |||||||||
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Title | p97 (VCP) mutant - F539A with its adaptor | |||||||||
Map data | Post-processed map | |||||||||
Sample |
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Keywords | Hexameric complex / ATPase / Unfoldase / Protein Quality Control / Segregase / CHAPERONE | |||||||||
Biological species | Homo sapiens (human) / Rattus (rat) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.0 Å | |||||||||
Authors | Arie M / Matzov D / Karmona R / Szenkier N / Stanhill A / Navon A | |||||||||
Funding support | Israel, 1 items
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Citation | Journal: To Be Published Title: p97 (VCP) mutant - F539A with its adaptor Authors: Arie M / Matzov D / Karmona R / Szenkier N / Stanhill A / Navon A | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_18517.map.gz | 23.7 MB | EMDB map data format | |
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Header (meta data) | emd-18517-v30.xml emd-18517.xml | 20.3 KB 20.3 KB | Display Display | EMDB header |
Images | emd_18517.png | 166.7 KB | ||
Filedesc metadata | emd-18517.cif.gz | 6.2 KB | ||
Others | emd_18517_additional_1.map.gz emd_18517_half_map_1.map.gz emd_18517_half_map_2.map.gz | 139.9 MB 140.7 MB 140.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-18517 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-18517 | HTTPS FTP |
-Validation report
Summary document | emd_18517_validation.pdf.gz | 841.2 KB | Display | EMDB validaton report |
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Full document | emd_18517_full_validation.pdf.gz | 840.8 KB | Display | |
Data in XML | emd_18517_validation.xml.gz | 14.9 KB | Display | |
Data in CIF | emd_18517_validation.cif.gz | 17.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-18517 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-18517 | HTTPS FTP |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_18517.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Post-processed map | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.793 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: Unsharpened map
File | emd_18517_additional_1.map | ||||||||||||
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Annotation | Unsharpened map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half-map B
File | emd_18517_half_map_1.map | ||||||||||||
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Annotation | Half-map B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half-map A
File | emd_18517_half_map_2.map | ||||||||||||
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Annotation | Half-map A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Tertiary complex of the hexameric p97 F539A mutant with its adaptor
Entire | Name: Tertiary complex of the hexameric p97 F539A mutant with its adaptor |
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Components |
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-Supramolecule #1: Tertiary complex of the hexameric p97 F539A mutant with its adaptor
Supramolecule | Name: Tertiary complex of the hexameric p97 F539A mutant with its adaptor type: complex / ID: 1 / Parent: 0 / Macromolecule list: all Details: The mutant generated by the replacement of phenylalanine to alanine at position 539 |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Transitional endoplasmic reticulum ATPase
Macromolecule | Name: Transitional endoplasmic reticulum ATPase / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MASGADSKGD DLSTAILKQK NRPNRLIVDE AINEDNSVVS LSQPKMDELQ LFRGDTVLLK GKKRREAVCI VLSDDTCSDE KIRMNRVVR NNLRVRLGDV ISIQPCPDVK YGKRIHVLPI DDTVEGITGN LFEVYLKPYF LEAYRPIRKG DIFLVRGGMR A VEFKVVET ...String: MASGADSKGD DLSTAILKQK NRPNRLIVDE AINEDNSVVS LSQPKMDELQ LFRGDTVLLK GKKRREAVCI VLSDDTCSDE KIRMNRVVR NNLRVRLGDV ISIQPCPDVK YGKRIHVLPI DDTVEGITGN LFEVYLKPYF LEAYRPIRKG DIFLVRGGMR A VEFKVVET DPSPYCIVAP DTVIHCEGEP IKREDEEESL NEVGYDDIGG CRKQLAQIKE MVELPLRHPA LFKAIGVKPP RG ILLYGPP GTGKTLIARA VANETGAFFF LINGPEIMSK LAGESESNLR KAFEEAEKNA PAIIFIDELD AIAPKREKTH GEV ERRIVS QLLTLMDGLK QRAHVIVMAA TNRPNSIDPA LRRFGRFDRE VDIGIPDATG RLEILQIHTK NMKLADDVDL EQVA NETHG HVGADLAALC SEAALQAIRK KMDLIDLEDE TIDAEVMNSL AVTMDDFRWA LSQSNPSALR ETVVEVPQVT WEDIG GLED VKRELQELVQ YPVEHPDKFL KFGMTPSKGV LFYGPPGCGK TLLAKAIANE CQANAISIKG PELLTMWFGE SEANVR EIF DKARQAAPCV LFFDELDSIA KARGGNIGDG GGAADRVINQ ILTEMDGMST KKNVFIIGAT NRPDIIDPAI LRPGRLD QL IYIPLPDEKS RVAILKANLR KSPVAKDVDL EFLAKMTNGF SGADLTEICQ RACKLAIRES IESEIRRERE RQTNPSAM E VEEDDPVPEI RRDHFEEAMR FARRSVSDND IRKYEMFAQT LQQSRGFGSF RFPSGNQGGA GPSQGSGGGT GGSVYTEDN DDDLYG |
-Macromolecule #2: Nuclear protein localization protein 4 homolog
Macromolecule | Name: Nuclear protein localization protein 4 homolog / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Rattus (rat) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MAEGTIIRVQ SPDGVKRITA TKRETAATFL KKVAKEFGFQ NNGFSVYINR NKTGEITASS SKSLHLLKI KHGDLLFLFP SSLAGPSSEM ETSTSVGLKA FGAPHVVEDE IDQYLSKQDG K IYRSRDPQ LCRHGPLGKC VHCVPLEPFD EDYLNHLEPP VKHMSFHAYI ...String: MAEGTIIRVQ SPDGVKRITA TKRETAATFL KKVAKEFGFQ NNGFSVYINR NKTGEITASS SKSLHLLKI KHGDLLFLFP SSLAGPSSEM ETSTSVGLKA FGAPHVVEDE IDQYLSKQDG K IYRSRDPQ LCRHGPLGKC VHCVPLEPFD EDYLNHLEPP VKHMSFHAYI RKLTGGADKG KF VALENIS CKIKSGCEGH LPWPNGICTK CQPSAITLNR QKYRHVDNIM FENHTVADRF LDF WRKTGN QHFGYLYGRY TEHKDIPLGI RAEVAAIYEP PQIGTQNSLE LLEDPKAEVV DEIA SKLGL RKVGWIFTDL VSEDTRKGTV RYSRNKDTYF LSSEECITAG DFQNKHPNIC RLSPD GHFG SKFVTAVATG GPDNQVHFEG YQVSNQCMAL VRDECLLPCK DAPELGYAKE SSSEQY VPD VFYKDIDKFG NEITQLARPL PVEYLIIDIT TTFPKDPVYT FSISQNPFPI ENRDVLG ET QDFHSLATYL SQNTSSVFLD TISDFHLLLF LVTNEVMPLQ DSISLLLEAV RTRNEELA Q TWKKSEQWAT IEQLCSTVGV QLPGLHEFGA VGGSARAATS AMWACQHCTF MNQPGTGHC EMCSLPRT |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 3.5 mg/mL | ||||||||||||
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Buffer | pH: 7.5 Component:
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Grid | Model: Quantifoil R2/2 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV Details: pre-blotting incubation time of 20 seconds and blot for 3.5 seconds with -1 blot force. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number real images: 11807 / Average electron dose: 43.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm |
Sample stage | 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: Other / Chain - Initial model type: experimental model / Details: FROM EMDB |
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Refinement | Overall B value: 104 |