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- EMDB-31910: 1.96 A structure of human apoferritin obtained from Talos Arctica... -

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Basic information

Entry
Database: EMDB / ID: EMD-31910
Title1.96 A structure of human apoferritin obtained from Talos Arctica microscope
Map data
Sample
  • Complex: Human apoferritinFerritin
    • Protein or peptide: Ferritin heavy chain
  • Ligand: ZINC ION
  • Ligand: SODIUM IONSodium
  • Ligand: water
Function / homology
Function and homology information


iron ion sequestering activity / Scavenging by Class A Receptors / intracellular ferritin complex / autolysosome / Golgi Associated Vesicle Biogenesis / ferroxidase / intracellular sequestering of iron ion / ferroxidase activity / negative regulation of fibroblast proliferation / ferric iron binding ...iron ion sequestering activity / Scavenging by Class A Receptors / intracellular ferritin complex / autolysosome / Golgi Associated Vesicle Biogenesis / ferroxidase / intracellular sequestering of iron ion / ferroxidase activity / negative regulation of fibroblast proliferation / ferric iron binding / ferrous iron binding / Iron uptake and transport / tertiary granule lumen / iron ion transport / intracellular iron ion homeostasis / ficolin-1-rich granule lumen / immune response / iron ion binding / negative regulation of cell population proliferation / Neutrophil degranulation / extracellular exosome / extracellular region / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Ferritin iron-binding regions signature 1. / Ferritin iron-binding regions signature 2. / Ferritin, conserved site / Ferritin / Ferritin-like diiron domain / Ferritin-like diiron domain profile. / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily
Similarity search - Domain/homology
Ferritin heavy chain
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 1.96 Å
AuthorsFan HC / Zhang Y / Sun F
Funding support China, 5 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2017YFA0504700 China
National Natural Science Foundation of China (NSFC)31830020 China
Chinese Academy of SciencesXDB37040102 China
National Natural Science Foundation of China (NSFC)31925026 China
Ministry of Science and Technology (MoST, China)2015DFG32140 China
CitationJournal: Nat Commun / Year: 2021
Title: A cryo-electron microscopy support film formed by 2D crystals of hydrophobin HFBI.
Authors: Hongcheng Fan / Bo Wang / Yan Zhang / Yun Zhu / Bo Song / Haijin Xu / Yujia Zhai / Mingqiang Qiao / Fei Sun /
Abstract: Cryo-electron microscopy (cryo-EM) has become a powerful tool to resolve high-resolution structures of biomacromolecules in solution. However, air-water interface induced preferred orientations, ...Cryo-electron microscopy (cryo-EM) has become a powerful tool to resolve high-resolution structures of biomacromolecules in solution. However, air-water interface induced preferred orientations, dissociation or denaturation of biomacromolecules during cryo-vitrification remains a limiting factor for many specimens. To solve this bottleneck, we developed a cryo-EM support film using 2D crystals of hydrophobin HFBI. The hydrophilic side of the HFBI film adsorbs protein particles via electrostatic interactions and sequesters them from the air-water interface, allowing the formation of sufficiently thin ice for high-quality data collection. The particle orientation distribution can be regulated by adjusting the buffer pH. Using this support, we determined the cryo-EM structures of catalase (2.29 Å) and influenza haemagglutinin trimer (2.56 Å), which exhibited strong preferred orientations using a conventional cryo-vitrification protocol. We further show that the HFBI film is suitable to obtain high-resolution structures of small proteins, including aldolase (150 kDa, 3.28 Å) and haemoglobin (64 kDa, 3.6 Å). Our work suggests that HFBI films may have broad future applications in increasing the success rate and efficiency of cryo-EM.
History
DepositionSep 6, 2021-
Header (metadata) releaseDec 29, 2021-
Map releaseDec 29, 2021-
UpdateDec 29, 2021-
Current statusDec 29, 2021Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 3
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7vd8
  • Surface level: 3
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7vd8
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_31910.png

Downloads & links

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Map

FileDownload / File: emd_31910.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.588 Å
Density
Contour LevelBy AUTHOR: 1.0 / Movie #1: 3
Minimum - Maximum-10.44443 - 23.80413
Average (Standard dev.)2.5581166e-05 (±0.6152295)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 282.24 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.5880.5880.588
M x/y/z480480480
origin x/y/z0.0000.0000.000
length x/y/z282.240282.240282.240
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ480480480
MAP C/R/S321
start NC/NR/NS000
NC/NR/NS480480480
D min/max/mean-10.44423.8040.000

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Supplemental data

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Additional map: #1

Fileemd_31910_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_31910_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_31910_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Human apoferritin

EntireName: Human apoferritinFerritin
Components
  • Complex: Human apoferritinFerritin
    • Protein or peptide: Ferritin heavy chain
  • Ligand: ZINC ION
  • Ligand: SODIUM IONSodium
  • Ligand: water

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Supramolecule #1: Human apoferritin

SupramoleculeName: Human apoferritin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Molecular weightTheoretical: 480 KDa

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Macromolecule #1: Ferritin heavy chain

MacromoleculeName: Ferritin heavy chain / type: protein_or_peptide / ID: 1 / Number of copies: 24 / Enantiomer: LEVO / EC number: ferroxidase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 20.116547 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString:
TSQVRQNYHQ DSEAAINRQI NLELYASYVY LSMSYYFDRD DVALKNFAKY FLHQSHEERE HAEKLMKLQN QRGGRIFLQD IKKPDCDDW ESGLNAMECA LHLEKNVNQS LLELHKLATD KNDPHLCDFI ETHYLNEQVK AIKELGDHVT NLRKMGAPES G LAEYLFDK HTLG

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Macromolecule #2: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 2 / Number of copies: 254 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #3: SODIUM ION

MacromoleculeName: SODIUM ION / type: ligand / ID: 3 / Number of copies: 75
Molecular weightTheoretical: 22.99 Da

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Macromolecule #4: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 2472 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER / Water

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration2 mg/mL
BufferpH: 6.5
Component:
ConcentrationFormula
20.0 mMTris-HClTris
150.0 mMNaClSodium chloride
GridMaterial: NICKEL/TITANIUM / Mesh: 300
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 165000
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: SUPER-RESOLUTION / Number real images: 2649 / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 351565
CTF correctionSoftware - Name: Gctf (ver. 1.06)
Startup modelType of model: EMDB MAP
EMDB ID:

30084

Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final 3D classificationSoftware - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final reconstructionApplied symmetry - Point group: O (octahedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 1.96 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 108183
FSC plot (resolution estimation)

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