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- EMDB-30083: Human apo ferritin chain A frozen on TEM grid with amorphous carb... -

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Basic information

Entry
Database: EMDB / ID: EMD-30083
TitleHuman apo ferritin chain A frozen on TEM grid with amorphous carbon supporting film
Map dataHuman apo ferritin chain A frozen on TEM grid with amorphous carbon supporting film
Sample
  • Complex: apoferritin heavy chain, 24 homologous polymer
    • Protein or peptide: Ferritin heavy chain
  • Ligand: FE (II) ION
  • Ligand: water
KeywordsApoferritin heavy chain / Homo sapiens / METAL TRANSPORT / OXIDOREDUCTASE
Function / homology
Function and homology information


iron ion sequestering activity / ferritin complex / Scavenging by Class A Receptors / negative regulation of ferroptosis / Golgi Associated Vesicle Biogenesis / ferroxidase / autolysosome / ferroxidase activity / intracellular sequestering of iron ion / negative regulation of fibroblast proliferation ...iron ion sequestering activity / ferritin complex / Scavenging by Class A Receptors / negative regulation of ferroptosis / Golgi Associated Vesicle Biogenesis / ferroxidase / autolysosome / ferroxidase activity / intracellular sequestering of iron ion / negative regulation of fibroblast proliferation / autophagosome / ferric iron binding / Iron uptake and transport / ferrous iron binding / 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 / membrane / 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: 2.6 Å
AuthorsHuang X / Zhang L
Funding support China, 4 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31830020 China
National Natural Science Foundation of China (NSFC)31925026 China
National Natural Science Foundation of China (NSFC)31500608 China
Ministry of Science and Technology (MoST, China)2017YFA0504702 China
CitationJournal: Prog Biophys Mol Biol / Year: 2020
Title: Amorphous nickel titanium alloy film: A new choice for cryo electron microscopy sample preparation.
Authors: Xiaojun Huang / Lei Zhang / Zuoling Wen / Hui Chen / Shuoguo Li / Gang Ji / Chang-Cheng Yin / Fei Sun /
Abstract: Cryo-electron microscopy (cryoEM) has become one of the most important approach for structural biology. However, barriers are still there for an increased successful rate, a better resolution and ...Cryo-electron microscopy (cryoEM) has become one of the most important approach for structural biology. However, barriers are still there for an increased successful rate, a better resolution and improved efficiency from sample preparation, data collection to image processing. CryoEM sample preparation is one of the bottlenecks with many efforts made recently, including the optimization of supporting substrate (e.g. ultra-thin carbon, graphene, pure gold, 2d crystal of streptavidin, and affinity modification), which was aimed to solve air-water interface problem, or reduce beam induced motion (BIM), or change particle distribution in the grid hole. Here, we report another effort of developing a new supporting substrate, the amorphous nickel-titanium alloy (ANTA) film, for cryoEM sample preparation as a layer of holey supporting film covering on TEM grid. Our investigations showed advantages of ANTA film in comparison with conventional carbon film, including much better electron conductivity and trace non-specific interaction with protein. These advantages yield less BIM and significantly improved particle distribution during cryoEM experiment of human apo-ferritn, thus resulting an improved reconstruction resolution from a reduced number of micrographs and particles. Unlike the pure gold film, the usage of the ANTA film is just same with the carbon film, compatible to conventional automatic cryoEM data collection procedure.
History
DepositionMar 9, 2020-
Header (metadata) releaseMay 13, 2020-
Map releaseMay 13, 2020-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0457
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0457
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6m52
  • Surface level: 0.0457
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30083.png

Downloads & links

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Map

FileDownload / File: emd_30083.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHuman apo ferritin chain A frozen on TEM grid with amorphous carbon supporting film
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.87 Å/pix.
x 288 pix.
= 250.56 Å		0.87 Å/pix.
x 288 pix.
= 250.56 Å		0.87 Å/pix.
x 288 pix.
= 250.56 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.87 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0457 / Movie #1: 0.0457
Minimum - Maximum-0.076049455 - 0.14081201
Average (Standard dev.)0.0003965073 (±0.0078109642)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 250.56 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.870.870.87
M x/y/z288288288
origin x/y/z0.0000.0000.000
length x/y/z250.560250.560250.560
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS288288288
D min/max/mean-0.0760.1410.000

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Supplemental data

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Sample components

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Entire : apoferritin heavy chain, 24 homologous polymer

EntireName: apoferritin heavy chain, 24 homologous polymer
Components
  • Complex: apoferritin heavy chain, 24 homologous polymer
    • Protein or peptide: Ferritin heavy chain
  • Ligand: FE (II) ION
  • Ligand: water

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Supramolecule #1: apoferritin heavy chain, 24 homologous polymer

SupramoleculeName: apoferritin heavy chain, 24 homologous polymer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Details: frozen on TEM grid with amorphous carbon supporting film
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 440 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: 21.255656 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MTTASTSQVR QNYHQDSEAA INRQINLELY ASYVYLSMSY YFDRDDVALK NFAKYFLHQS HEEREHAEKL MKLQNQRGGR IFLQDIKKP DCDDWESGLN AMECALHLEK NVNQSLLELH KLATDKNDPH LCDFIETHYL NEQVKAIKEL GDHVTNLRKM G APESGLAE YLFDKHTLGD SDNES

UniProtKB: Ferritin heavy chain

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Macromolecule #2: FE (II) ION

MacromoleculeName: FE (II) ION / type: ligand / ID: 2 / Number of copies: 6 / Formula: FE2
Molecular weightTheoretical: 55.845 Da

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Macromolecule #3: water

MacromoleculeName: water / type: ligand / ID: 3 / Number of copies: 8 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
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

Concentration1.3 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
50.0 mMTris-HClTRIS hydrochloride
150.0 mMNaClsodium chloride
GridModel: Homemade / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Support film - Film thickness: 25 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

2fha

Final reconstructionApplied symmetry - Point group: O (octahedral) / Resolution.type: BY AUTHOR / Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 64667
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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