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- PDB-6gk3: Two protofilament beta-2-microglobulin amyloid fibril -

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Basic information

Entry
Database: PDB / ID: 6gk3
TitleTwo protofilament beta-2-microglobulin amyloid fibril
ComponentsBeta-2-microglobulinBeta-2 microglobulin
KeywordsPROTEIN FIBRIL / amyloid / b2m
Function / homologyImmunoglobulin-like fold / DAP12 signaling / Immunoglobulin C1-set domain / Immunoglobulins and major histocompatibility complex proteins signature. / Ig-like domain profile. / ER-Phagosome pathway / Beta-2-Microglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Endosomal/Vacuolar pathway / Immunoglobulin-like domain ...Immunoglobulin-like fold / DAP12 signaling / Immunoglobulin C1-set domain / Immunoglobulins and major histocompatibility complex proteins signature. / Ig-like domain profile. / ER-Phagosome pathway / Beta-2-Microglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Endosomal/Vacuolar pathway / Immunoglobulin-like domain / Nef mediated downregulation of MHC class I complex cell surface expression / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / DAP12 interactions / Immunoglobulin C1-set / Neutrophil degranulation / Interferon gamma signaling / Immunoglobulin-like domain superfamily / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / Amyloid fiber formation / antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent / early endosome lumen / regulation of membrane depolarization / antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent / antigen processing and presentation of peptide antigen via MHC class I / ER to Golgi transport vesicle membrane / recycling endosome membrane / regulation of defense response to virus by virus / go:0033216: / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / negative regulation of receptor binding / antigen processing and presentation of endogenous peptide antigen via MHC class I / regulation of erythrocyte differentiation / go:1900390: / MHC class I protein complex / HFE-transferrin receptor complex / positive regulation of T cell mediated cytotoxicity / positive regulation of T cell cytokine production / response to molecule of bacterial origin / cellular response to iron ion / positive regulation of receptor binding / positive regulation of receptor-mediated endocytosis / phagocytic vesicle membrane / interferon-gamma-mediated signaling pathway / T cell differentiation in thymus / specific granule lumen / retina homeostasis / early endosome membrane / iron ion homeostasis / negative regulation of neuron projection development / response to cadmium ion / regulation of immune response / antibacterial humoral response / tertiary granule lumen / protein refolding / positive regulation of protein binding / antimicrobial humoral immune response mediated by antimicrobial peptide / cellular response to lipopolysaccharide / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / response to drug / Golgi membrane / external side of plasma membrane / endoplasmic reticulum lumen / focal adhesion / innate immune response / cellular protein metabolic process / neutrophil degranulation / Golgi apparatus / extracellular space / extracellular exosome / membrane / extracellular region / identical protein binding / plasma membrane / cytosol / Beta-2-microglobulin
Function and homology information
Specimen sourceHomo sapiens (human)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / 3.975 Å resolution
AuthorsIadanza, M.G. / Ranson, N.A.
CitationJournal: Nat Commun / Year: 2018
Title: The structure of a β-microglobulin fibril suggests a molecular basis for its amyloid polymorphism.
Authors: Matthew G Iadanza / Robert Silvers / Joshua Boardman / Hugh I Smith / Theodoros K Karamanos / Galia T Debelouchina / Yongchao Su / Robert G Griffin / Neil A Ranson / Sheena E Radford
Validation Report
SummaryFull reportAbout validation report
DateDeposition: May 18, 2018 / Release: Nov 14, 2018

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Structure visualization

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Structure viewerMolecule:
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Assembly

Deposited unit
A: Beta-2-microglobulin
B: Beta-2-microglobulin
C: Beta-2-microglobulin
D: Beta-2-microglobulin
E: Beta-2-microglobulin
F: Beta-2-microglobulin
G: Beta-2-microglobulin
H: Beta-2-microglobulin


Theoretical massNumber of molelcules
Total (without water)61,0848
Polyers61,0848
Non-polymers00
Water0
1


  • idetical with deposited unit
  • defined by author&software
  • Evidence: microscopy, Negative stain EM SEM
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TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)35320
ΔGint (kcal/M)-152
Surface area (Å2)25000
MethodPISA

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Components

#1: Protein/peptide
Beta-2-microglobulin / Beta-2 microglobulin


Mass: 7635.446 Da / Num. of mol.: 8 / Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: Escherichia coli (E. coli) / References: UniProt: P61769

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / Reconstruction method: helical reconstruction

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Sample preparation

ComponentName: two protofilament beta-2-microglobulin amyloid fibril / Type: COMPLEX / Entity ID: 1 / Source: RECOMBINANT
Molecular weightValue: 53.3 kDa/nm / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 2.5
Buffer component
IDConc.NameFormulaBuffer ID
120 mMSodium AcetateCH3COONa1
220 mMSodium phosphateNa3PO41
30.01 %Sodium AzideNaN31
SpecimenConc.: 0.025 mg/ml
Details: Quiescent growth at 0.25 mg/ml for 5 weeks, diluted 10x with buffer
Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 / Grid type: Quantifoil R3.5/1
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Humidity: 80 % / Chamber temperature: 281.15 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 FIELDBright-field microscopy / Nominal magnification: 130000 / Nominal defocus max: 3.25 nm / Nominal defocus min: 1.75 nm / Cs: 2.7 mm / C2 aperture diameter: 100 microns / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 10 sec. / Electron dose: 38.5 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number of grids imaged: 1 / Number of real images: 5549
Image scansMovie frames/image: 40 / Used frames/image: 3-40

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Processing

EM software
IDNameVersionCategory
1RELION2.1particle selection
2EPUimage acquisition
4RELION2.1CTF correction
5GctfCTF correction
8UCSF Chimeramodel fitting
10PHENIX1.11.1model refinement
11RELION2.1initial Euler assignment
12RELION2.1final Euler assignment
13RELIONclassification
14RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -0.608 deg. / Axial rise/subunit: 4.83 Å / Axial symmetry: C2
Particle selectionDetails: 300 x 300 pixel Overlapping segments 90% overlap / Number of particles selected: 99000
3D reconstructionResolution: 3.975 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 11035 / Algorithm: FOURIER SPACE / Number of class averages: 1 / Symmetry type: HELICAL
Atomic model buildingRef protocol: OTHER / Ref space: REAL
Least-squares processHighest resolution: 3.9 Å

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