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- PDB-6ap1: Vps4p-Vta1p complex with peptide binding to the central pore of Vps4p -

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Basic information

Entry
Database: PDB / ID: 6ap1
TitleVps4p-Vta1p complex with peptide binding to the central pore of Vps4p
DescriptorVacuolar protein sorting-associated protein 4
DOA4-independent degradation protein 4
Vacuolar protein sorting-associated protein VTA1
KeywordsTRANSPORT PROTEIN / Vps4 / ESCRT / Vta1 / AAA ATPase
Specimen sourceSaccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast / Baker's yeast /
Pseudomonas aeruginosa (strain atcc 15692 / dsm 22644 / cip 104116 / jcm 14847 / lmg 12228 / 1c / prs 101 / pao1) / bacteria
Saccharomyces cerevisiae / yeast / サッカロミセス・セレビシエ /
MethodElectron microscopy (3.2 Å resolution / Particle / Single particle)
AuthorsHan, H. / Monroe, N. / Shen, P. / Sundquist, W.I. / Hill, C.P.
CitationElife, 2017, 6

Elife, 2017, 6 Yorodumi Papers
The AAA ATPase Vps4 binds ESCRT-III substrates through a repeating array of dipeptide-binding pockets.
Han Han / Nicole Monroe / Wesley I Sundquist / Peter S Shen / Christopher P Hill

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Aug 16, 2017 / Release: Dec 6, 2017

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Assembly

Deposited unit
A: Vacuolar protein sorting-associated protein 4,Protein hcp1
B: Vacuolar protein sorting-associated protein 4,Protein hcp1
C: Vacuolar protein sorting-associated protein 4,Protein hcp1
D: Vacuolar protein sorting-associated protein 4,Protein hcp1
E: Vacuolar protein sorting-associated protein 4,Protein hcp1
G: ACE-ASP-GLU-ILE-VAL-ASN-LYS-VAL-LEU-NH2
F: Vacuolar protein sorting-associated protein 4,Protein hcp1
H: Vacuolar protein sorting-associated protein VTA1
I: Vacuolar protein sorting-associated protein VTA1
J: Vacuolar protein sorting-associated protein VTA1
K: Vacuolar protein sorting-associated protein VTA1
L: Vacuolar protein sorting-associated protein VTA1
M: Vacuolar protein sorting-associated protein VTA1
N: Vacuolar protein sorting-associated protein VTA1
O: Vacuolar protein sorting-associated protein VTA1
P: Vacuolar protein sorting-associated protein VTA1
Q: Vacuolar protein sorting-associated protein VTA1
R: Vacuolar protein sorting-associated protein VTA1
S: Vacuolar protein sorting-associated protein VTA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)786,31231
Polyers783,88019
Non-polymers2,43112
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)44080
ΔGint (kcal/M)-230
Surface area (Å2)107790

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Components

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Vacuolar protein sorting-associated protein ... , 2 types, 18 molecules ABCDEFHIJK...

#1: Polypeptide(L)
Vacuolar protein sorting-associated protein 4,Protein hcp1 / DOA4-independent degradation protein 6 / Protein END13 / Vacuolar protein-targeting protein 10


Mass: 55768.402 Da / Num. of mol.: 6
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c), (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)
References: UniProt: P52917, UniProt: Q9I747
#3: Polypeptide(L)
Vacuolar protein sorting-associated protein VTA1 / VPS20-associated protein 1


Mass: 37359.660 Da / Num. of mol.: 12
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: Q06263

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Polypeptide(L) , 1 types, 1 molecules G

#2: Polypeptide(L)ACE-ASP-GLU-ILE-VAL-ASN-LYS-VAL-LEU-NH2


Mass: 954.122 Da / Num. of mol.: 1 / Source: (synth.) Saccharomyces cerevisiae

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Non-polymers , 3 types, 12 molecules

#4: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / ADP *YM


Mass: 427.201 Da / Num. of mol.: 5 / Formula: C10H15N5O10P2
#5: ChemicalChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 3 / Formula: BeF3
#6: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Formula: Mg

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

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Sample preparation

ComponentName: Vps4-Vta1 complex / Type: COMPLEX / Entity ID: 1, 2, 3 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Saccharomyces cerevisiae
Source (recombinant)Organism: Escherichia coli BL21(DE3)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 / Grid type: Quantifoil R1.2/1.3 holey carbon
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 80 % / Chamber temperature: 277 kelvins

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingAverage exposure time: 0.25 sec. / Electron dose: 1.55 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.11.1_2575: / Classification: refinement
EM software
IDNameVersionCategoryImaging IDImage processing ID
2SerialEMIMAGE ACQUISITION1
13RELION1.4RECONSTRUCTION1
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 82225 / Symmetry type: POINT
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01812700
ELECTRON MICROSCOPYf_angle_d1.53317171
ELECTRON MICROSCOPYf_dihedral_angle_d5.9427740
ELECTRON MICROSCOPYf_chiral_restr0.0781949
ELECTRON MICROSCOPYf_plane_restr0.0102197

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