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- PDB-6eny: Structure of the human PLC editing module -

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Basic information

Entry
Database: PDB / ID: 6eny
TitleStructure of the human PLC editing module
DescriptorBeta-2-microglobulin
Tapasin
Protein disulfide-isomerase A3
HLA class I histocompatibility antigen
A-3 alpha chain
Calreticulin
KeywordsIMMUNE SYSTEM / adaptive immunity / antigen processing / chaperone / MHC class I
Specimen sourceHomo sapiens / human
MethodElectron microscopy (5.8 Å resolution / Particle / Single particle)
AuthorsTrowitzsch, S. / Januliene, D. / Blees, A. / Moeller, A. / Tampe, R.
CitationNature, 2017, 551, 525-528

Nature, 2017, 551, 525-528 Yorodumi Papers
Structure of the human MHC-I peptide-loading complex.
Andreas Blees / Dovile Januliene / Tommy Hofmann / Nicole Koller / Carla Schmidt / Simon Trowitzsch / Arne Moeller / Robert Tampé

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Oct 7, 2017 / Release: Nov 29, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Nov 29, 2017Structure modelrepositoryInitial release
1.1Dec 6, 2017Structure modelDatabase referencescitation_citation.journal_volume / _citation.page_first / _citation.page_last

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Assembly

Deposited unit
B: Beta-2-microglobulin
C: Tapasin
D: Protein disulfide-isomerase A3
F: HLA class I histocompatibility antigen, A-3 alpha chain
G: Calreticulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)197,88411
Polyers196,7215
Non-polymers1,1636
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Polypeptide(L) , 5 types, 5 molecules BCDFG

#1: Polypeptide(L)Beta-2-microglobulin


Mass: 11748.160 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens / References: UniProt: P61769
#2: Polypeptide(L)Tapasin / TPSN / NGS-17 / TAP-associated protein / TAP-binding protein


Mass: 45761.184 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens / References: UniProt: O15533
#3: Polypeptide(L)Protein disulfide-isomerase A3 / 58 kDa glucose-regulated protein / 58 kDa microsomal protein / p58 / Disulfide isomerase ER-60 / Endoplasmic reticulum resident protein 57 / ERp57 / Endoplasmic reticulum resident protein 60 / ERp60


Mass: 54341.102 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens / References: UniProt: P30101, EC: 5.3.4.1
#4: Polypeptide(L)HLA class I histocompatibility antigen, A-3 alpha chain / MHC class I antigen A*3


Mass: 38363.535 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens / References: UniProt: P04439
#5: Polypeptide(L)Calreticulin / CRP55 / Calregulin / Endoplasmic reticulum resident protein 60 / ERp60 / HACBP / grp60


Mass: 46507.145 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens / References: UniProt: P27797

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Non-polymers , 3 types, 6 molecules

#6: ChemicalChemComp-NAG / N-ACETYL-D-GLUCOSAMINE


Mass: 221.208 Da / Num. of mol.: 2 / Formula: C8H15NO6
#7: ChemicalChemComp-MAN / ALPHA-D-MANNOSE


Mass: 180.156 Da / Num. of mol.: 3 / Formula: C6H12O6
#8: ChemicalChemComp-BGC / BETA-D-GLUCOSE


Mass: 180.156 Da / Num. of mol.: 1 / Formula: C6H12O6

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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: Protein Complex / Type: COMPLEX / Entity ID: 1, 2, 3, 4, 5 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens
Buffer solutionpH: 7.5
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: C-flat-2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / 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 recordingElectron dose: 55 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

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Processing

EM software
IDNameVersionCategoryImage processing IDImaging IDFitting ID
2GautomatchPARTICLE SELECTION1
3EPUIMAGE ACQUISITION1
5GctfCTF CORRECTION1
8CootMODEL FITTING1
9Flex-EMMODEL FITTING1
11RELION2.1INITIAL EULER ASSIGNMENT1
14FREALIGNXRECONSTRUCTION1
15PHENIXMODEL REFINEMENT1
CTF correctionDetails: CTF correction was performed internally in Relion and Frealign
Type: NONE
SymmetryPoint symmetry: C1
3D reconstructionResolution: 5.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 141078 / Symmetry type: POINT
Least-squares processHighest resolution: 5.8 Å

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