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Yorodumi- EMDB-8887: Vps4p-Vta1p complex with peptide binding to the central pore of Vps4p -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-8887 | |||||||||
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Title | Vps4p-Vta1p complex with peptide binding to the central pore of Vps4p | |||||||||
Map data | Vps4-Vta1 complex | |||||||||
Sample |
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Function / homology | Function and homology information ESCRT IV complex / Sealing of the nuclear envelope (NE) by ESCRT-III / late endosome to lysosome transport via multivesicular body sorting pathway / intralumenal vesicle formation / Macroautophagy / protein retention in Golgi apparatus / Endosomal Sorting Complex Required For Transport (ESCRT) / ESCRT III complex / endosome transport via multivesicular body sorting pathway / ATP export ...ESCRT IV complex / Sealing of the nuclear envelope (NE) by ESCRT-III / late endosome to lysosome transport via multivesicular body sorting pathway / intralumenal vesicle formation / Macroautophagy / protein retention in Golgi apparatus / Endosomal Sorting Complex Required For Transport (ESCRT) / ESCRT III complex / endosome transport via multivesicular body sorting pathway / ATP export / late endosome to vacuole transport via multivesicular body sorting pathway / sterol metabolic process / nuclear membrane reassembly / midbody abscission / multivesicular body sorting pathway / vacuole organization / plasma membrane repair / membrane fission / late endosome to vacuole transport / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / multivesicular body assembly / lipid transport / reticulophagy / endosomal transport / nucleus organization / ATPase complex / ATPase activator activity / autophagosome maturation / nuclear pore / multivesicular body / macroautophagy / autophagy / protein transport / protein-macromolecule adaptor activity / midbody / endosome / endoplasmic reticulum / protein homodimerization activity / ATP hydrolysis activity / extracellular region / ATP binding / identical protein binding / membrane / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) / Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria) / Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||
Authors | Han H / Monroe N / Shen P / Sundquist WI / Hill CP | |||||||||
Citation | Journal: Elife / Year: 2017 Title: The AAA ATPase Vps4 binds ESCRT-III substrates through a repeating array of dipeptide-binding pockets. Authors: Han Han / Nicole Monroe / Wesley I Sundquist / Peter S Shen / Christopher P Hill / Abstract: The hexameric AAA ATPase Vps4 drives membrane fission by remodeling and disassembling ESCRT-III filaments. Building upon our earlier 4.3 Å resolution cryo-EM structure (Monroe et al., 2017), we now ...The hexameric AAA ATPase Vps4 drives membrane fission by remodeling and disassembling ESCRT-III filaments. Building upon our earlier 4.3 Å resolution cryo-EM structure (Monroe et al., 2017), we now report a 3.2 Å structure of Vps4 bound to an ESCRT-III peptide substrate. The new structure reveals that the peptide approximates a β-strand conformation whose helical symmetry matches that of the five Vps4 subunits it contacts directly. Adjacent Vps4 subunits make equivalent interactions with successive substrate dipeptides through two distinct classes of side chain binding pockets formed primarily by Vps4 pore loop 1. These pockets accommodate a wide range of residues, while main chain hydrogen bonds may help dictate substrate-binding orientation. The structure supports a 'conveyor belt' model of translocation in which ATP binding allows a Vps4 subunit to join the growing end of the helix and engage the substrate, while hydrolysis and release promotes helix disassembly and substrate release at the lagging end. | |||||||||
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_8887.map.gz | 4.8 MB | EMDB map data format | |
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Header (meta data) | emd-8887-v30.xml emd-8887.xml | 15.5 KB 15.5 KB | Display Display | EMDB header |
Images | emd_8887.png | 54.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-8887 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8887 | HTTPS FTP |
-Validation report
Summary document | emd_8887_validation.pdf.gz | 327.5 KB | Display | EMDB validaton report |
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Full document | emd_8887_full_validation.pdf.gz | 327 KB | Display | |
Data in XML | emd_8887_validation.xml.gz | 6 KB | Display | |
Data in CIF | emd_8887_validation.cif.gz | 6.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8887 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8887 | HTTPS FTP |
-Related structure data
Related structure data | 6ap1MC 6bmfMC 8888C 8889C 8890C 8891C 8892C 8893C 8894C 8895C 8896C C: citing same article (ref.) M: atomic model generated by this map |
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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_8887.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Vps4-Vta1 complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.0961 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Vps4-Vta1 complex
Entire | Name: Vps4-Vta1 complex |
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Components |
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-Supramolecule #1: Vps4-Vta1 complex
Supramolecule | Name: Vps4-Vta1 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
-Macromolecule #1: Vacuolar protein sorting-associated protein 4,Protein hcp1
Macromolecule | Name: Vacuolar protein sorting-associated protein 4,Protein hcp1 type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria) Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1 |
Molecular weight | Theoretical: 55.768402 KDa |
Recombinant expression | Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) |
Sequence | String: GQEEGEDNGG EDNKKLRGAL SSAILSEKPN VKWEDVAGLE GAKEALKEAV ILPVKFPHLF KGNRKPTSGI LLYGPPGTGK SYLAKAVAT EANSTFFSVS SSDLVSKWMG ESEKLVKQLF AMARENKPSI IFIDEVDALT GTRGEGESEA SRRIKTELLV Q MNGVGNDS ...String: GQEEGEDNGG EDNKKLRGAL SSAILSEKPN VKWEDVAGLE GAKEALKEAV ILPVKFPHLF KGNRKPTSGI LLYGPPGTGK SYLAKAVAT EANSTFFSVS SSDLVSKWMG ESEKLVKQLF AMARENKPSI IFIDEVDALT GTRGEGESEA SRRIKTELLV Q MNGVGNDS QGVLVLGATN IPWQLDSAIR RRFERRIYIP LPDLAARTTM FEINVGDTPC VLTKEDYRTL GAMTEGYSGS DI AVVVKDA LMQPIRKIQS ATHFKDVSTE DDETRKLTPC SPGDDGAIEM SWTDIEADEL KEPDLTIKDF LKAIKSTRPT VNE DDLLKQ EQFTRDFGQE GNGGGGSGGG GSGGGGSGGG MAVDMFIKIG DVKGESKDKT HAEEIDVLAW SWGMSQSGSM HMGG GGGAG KVNVQDLSFT KYIDKSTPNL MMACSSGKHY PQAKLTIRKA GGENQVEYLI ITLKEVLVSS VSTGGSGGED RLTEN VTLN FAQVQVDYQP QKADGAKDGG PVKYGWNIRQ NVQAG |
-Macromolecule #2: ACE-ASP-GLU-ILE-VAL-ASN-LYS-VAL-LEU-NH2
Macromolecule | Name: ACE-ASP-GLU-ILE-VAL-ASN-LYS-VAL-LEU-NH2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Molecular weight | Theoretical: 954.122 Da |
Sequence | String: (ACE)DEIVNKVL(NH2) |
-Macromolecule #3: Vacuolar protein sorting-associated protein VTA1
Macromolecule | Name: Vacuolar protein sorting-associated protein VTA1 / type: protein_or_peptide / ID: 3 / Number of copies: 12 / Enantiomer: LEVO |
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Source (natural) | Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c |
Molecular weight | Theoretical: 37.35966 KDa |
Recombinant expression | Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) |
Sequence | String: MASNAARVVA TAKDFDKVGL GIIGYYLQLY AVELILSEED RSQEMTALAT ELLDTIEAFK KEIGGESEAE DSDKSLHVMN TLIHDQEKA KIYMLNFTMS LYNEKLKQLK DGPWDVMLKR SLWCCIDLFS CILHLWKENI SETSTNSLQK RIKYCKIYLS K LAKGEIGS ...String: MASNAARVVA TAKDFDKVGL GIIGYYLQLY AVELILSEED RSQEMTALAT ELLDTIEAFK KEIGGESEAE DSDKSLHVMN TLIHDQEKA KIYMLNFTMS LYNEKLKQLK DGPWDVMLKR SLWCCIDLFS CILHLWKENI SETSTNSLQK RIKYCKIYLS K LAKGEIGS SDEKTLDYAD FADDSEEIKD EDVDHQTSDL ENNNNDKVEG LAPKDQTTSY EPVDEVPEFI DDADSVNEEE QT VDKNEDA ITKDEQQVVK KEVDLTRPSA PSEPAAAEHK SYTKDELTKI MDRASKIEQI QKLAKYAISA LNYEDLPTAK DEL TKALDL LNSI |
-Macromolecule #4: ADENOSINE-5'-DIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 5 / Formula: ADP |
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Molecular weight | Theoretical: 427.201 Da |
Chemical component information | ChemComp-ADP: |
-Macromolecule #5: BERYLLIUM TRIFLUORIDE ION
Macromolecule | Name: BERYLLIUM TRIFLUORIDE ION / type: ligand / ID: 5 / Number of copies: 3 / Formula: BEF |
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Molecular weight | Theoretical: 66.007 Da |
Chemical component information | ChemComp-BEF: |
-Macromolecule #6: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 6 / Number of copies: 4 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 80 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK III |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average exposure time: 0.25 sec. / Average electron dose: 1.55 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: INSILICO MODEL / Details: e2initialmodel.py |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.4) / Number images used: 82225 |
Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: ANGULAR RECONSTITUTION |