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- PDB-6bdf: 2.8 A resolution reconstruction of the Thermoplasma acidophilum 2... -

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Entry
Database: PDB / ID: 6bdf
Title2.8 A resolution reconstruction of the Thermoplasma acidophilum 20S proteasome using cryo-electron microscopy
DescriptorProteasome subunit alpha
Proteasome subunit beta
KeywordsHYDROLASE / proteasome
Specimen sourceThermoplasma acidophilum / archaea / thermophilic / acidophilic / サーモプラズマ・アシドフィラム
MethodElectron microscopy (2.8 Å resolution / Particle / Single particle)
AuthorsCampbell, M.G. / Veesler, D. / Cheng, A. / Potter, C.S. / Carragher, B.
CitationElife, 2015, 4

Elife, 2015, 4 Yorodumi Papers
2.8 Å resolution reconstruction of the Thermoplasma acidophilum 20S proteasome using cryo-electron microscopy.
Melody G Campbell / David Veesler / Anchi Cheng / Clinton S Potter / Bridget Carragher

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Oct 23, 2017 / Release: Dec 27, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Dec 27, 2017Structure modelrepositoryInitial release
1.1Jan 17, 2018Structure modelAuthor supporting evidencepdbx_audit_support_pdbx_audit_support.funding_organization

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Assembly

Deposited unit
A: Proteasome subunit alpha
B: Proteasome subunit beta
C: Proteasome subunit alpha
D: Proteasome subunit beta
E: Proteasome subunit alpha
F: Proteasome subunit beta
G: Proteasome subunit alpha
H: Proteasome subunit beta
I: Proteasome subunit alpha
J: Proteasome subunit beta
K: Proteasome subunit alpha
L: Proteasome subunit beta
M: Proteasome subunit alpha
N: Proteasome subunit beta
O: Proteasome subunit alpha
P: Proteasome subunit beta
Q: Proteasome subunit alpha
R: Proteasome subunit beta
S: Proteasome subunit alpha
T: Proteasome subunit beta
U: Proteasome subunit alpha
V: Proteasome subunit beta
W: Proteasome subunit alpha
X: Proteasome subunit beta
Y: Proteasome subunit alpha
Z: Proteasome subunit beta
0: Proteasome subunit alpha
1: Proteasome subunit beta


Theoretical massNumber of molelcules
Total (without water)685,99028
Polyers685,99028
Non-polymers00
Water13,115728
#1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)94450
ΔGint (kcal/M)-238
Surface area (Å2)215480

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Components

#1: Polypeptide(L)
Proteasome subunit alpha / 20S proteasome alpha subunit / Proteasome core protein PsmA


Mass: 25829.447 Da / Num. of mol.: 14
Source: (gene. exp.) Thermoplasma acidophilum / archaea / thermophilic / acidophilic / サーモプラズマ・アシドフィラム
References: UniProt: P25156, EC: 3.4.25.1
#2: Polypeptide(L)
Proteasome subunit beta / 20S proteasome beta subunit / Proteasome core protein PsmB


Mass: 23169.811 Da / Num. of mol.: 14
Source: (gene. exp.) Thermoplasma acidophilum / archaea / thermophilic / acidophilic / サーモプラズマ・アシドフィラム
References: UniProt: P28061, EC: 3.4.25.1
#3: WaterChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 728 / Formula: H2O

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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: Thermoplasma acidophilum 20S proteasome / Type: COMPLEX / Entity ID: 1,2 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Thermoplasma acidophilum
Source (recombinant)Organism: Escherichia coli
Buffer solutionpH: 7.8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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 recordingElectron dose: 53 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameVersionCategoryImage processing IDImaging ID
1FindEMPARTICLE SELECTION1
2LeginonIMAGE ACQUISITION1
4CTFFIND3CTF CORRECTION1
10RELIONINITIAL EULER ASSIGNMENT1
11RELIONFINAL EULER ASSIGNMENT1
13RELIONRECONSTRUCTION1
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: D7
3D reconstructionResolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 49954 / Symmetry type: POINT

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