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- PDB-7a6a: 1.15 A structure of human apoferritin obtained from Titan Mono- B... -

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Basic information

Entry
Database: PDB / ID: 7a6a
Title1.15 A structure of human apoferritin obtained from Titan Mono- BCOR microscope
ComponentsFerritin heavy chain
KeywordsMETAL BINDING PROTEIN / Apoferritin
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 1.15 Å
AuthorsYip, K.M. / Fischer, N. / Chari, A. / Stark, H.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG)SFB860 Germany
Max Planck Society Germany
CitationJournal: Nature / Year: 2020
Title: Atomic-resolution protein structure determination by cryo-EM.
Authors: Ka Man Yip / Niels Fischer / Elham Paknia / Ashwin Chari / Holger Stark /
Abstract: Single-particle electron cryo-microscopy (cryo-EM) is a powerful method for solving the three-dimensional structures of biological macromolecules. The technological development of transmission ...Single-particle electron cryo-microscopy (cryo-EM) is a powerful method for solving the three-dimensional structures of biological macromolecules. The technological development of transmission electron microscopes, detectors and automated procedures in combination with user-friendly image processing software and ever-increasing computational power have made cryo-EM a successful and expanding technology over the past decade. At resolutions better than 4 Å, atomic model building starts to become possible, but the direct visualization of true atomic positions in protein structure determination requires much higher (better than 1.5 Å) resolution, which so far has not been attained by cryo-EM. The direct visualization of atom positions is essential for understanding the mechanisms of protein-catalysed chemical reactions, and for studying how drugs bind to and interfere with the function of proteins. Here we report a 1.25 Å-resolution structure of apoferritin obtained by cryo-EM with a newly developed electron microscope that provides, to our knowledge, unprecedented structural detail. Our apoferritin structure has almost twice the 3D information content of the current world record reconstruction (at 1.54 Å resolution). We can visualize individual atoms in a protein, see density for hydrogen atoms and image single-atom chemical modifications. Beyond the nominal improvement in resolution, we also achieve a substantial improvement in the quality of the cryo-EM density map, which is highly relevant for using cryo-EM in structure-based drug design.
History
DepositionAug 25, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 2, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 10, 2021Group: Data collection / Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / em_software / pdbx_struct_assembly / pdbx_struct_assembly_prop
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_software.category / _em_software.fitting_id / _em_software.imaging_id / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details

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Structure visualization

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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
  • EMDB-11668
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  • Superimposition on EM map
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Structure viewerMolecule:
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Assembly

Deposited unit
A: Ferritin heavy chain
1: Ferritin heavy chain
K: Ferritin heavy chain
a: Ferritin heavy chain
B: Ferritin heavy chain
E: Ferritin heavy chain
e: Ferritin heavy chain
r: Ferritin heavy chain
G: Ferritin heavy chain
I: Ferritin heavy chain
M: Ferritin heavy chain
O: Ferritin heavy chain
Q: Ferritin heavy chain
S: Ferritin heavy chain
U: Ferritin heavy chain
W: Ferritin heavy chain
Y: Ferritin heavy chain
2: Ferritin heavy chain
4: Ferritin heavy chain
F: Ferritin heavy chain
H: Ferritin heavy chain
P: Ferritin heavy chain
X: Ferritin heavy chain
6: Ferritin heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)511,23056
Polymers510,49524
Non-polymers73632
Water83,2474621
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area95720 Å2
ΔGint-708 kcal/mol
Surface area142700 Å2
MethodPISA

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Components

#1: Protein ...
Ferritin heavy chain / Ferritin H subunit / Cell proliferation-inducing gene 15 protein


Mass: 21270.605 Da / Num. of mol.: 24
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FTH1, FTH, FTHL6, OK/SW-cl.84, PIG15 / Production host: Escherichia coli (E. coli) / References: UniProt: P02794, ferroxidase
#2: Chemical...
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 32 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4621 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Apoferritin / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.6
SpecimenConc.: 3.5 mg/ml / Embedding 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
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 50 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k)
EM imaging opticsChromatic aberration corrector: TFS Monochromator / Spherical aberration corrector: CEOS B-COR

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Processing

EM software
IDNameCategory
2EPUimage acquisition
13RELION3D reconstruction
CTF correctionType: PHASE FLIPPING ONLY
SymmetryPoint symmetry: O (octahedral)
3D reconstructionResolution: 1.15 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 797000 / Algorithm: FOURIER SPACE / Symmetry type: POINT

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