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- PDB-8pvc: Structure of mouse heavy-chain apoferritin determined by cryoEM a... -

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Basic information

Entry
Database: PDB / ID: 8pvc
TitleStructure of mouse heavy-chain apoferritin determined by cryoEM at 100 keV
ComponentsFerritin heavy chain
KeywordsMETAL BINDING PROTEIN / Iron storage
Function / homology
Function and homology information


Iron uptake and transport / Golgi Associated Vesicle Biogenesis / iron ion sequestering activity / negative regulation of ferroptosis / ferroxidase / autolysosome / ferroxidase activity / negative regulation of fibroblast proliferation / endocytic vesicle lumen / Neutrophil degranulation ...Iron uptake and transport / Golgi Associated Vesicle Biogenesis / iron ion sequestering activity / negative regulation of ferroptosis / ferroxidase / autolysosome / ferroxidase activity / negative regulation of fibroblast proliferation / endocytic vesicle lumen / Neutrophil degranulation / ferric iron binding / autophagosome / ferrous iron binding / iron ion transport / intracellular iron ion homeostasis / immune response / iron ion binding / negative regulation of cell population proliferation / mitochondrion / extracellular region / identical protein binding / membrane / cytosol
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 speciesMus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsMcMullan, G. / Naydenova, K. / Mihaylov, D. / Peet, M.J. / Wilson, H. / Yamashita, K. / Dickerson, J.L. / Chen, S. / Cannone, G. / Lee, Y. ...McMullan, G. / Naydenova, K. / Mihaylov, D. / Peet, M.J. / Wilson, H. / Yamashita, K. / Dickerson, J.L. / Chen, S. / Cannone, G. / Lee, Y. / Hutchings, K.A. / Gittins, O. / Sobhy, M. / Wells, T. / El-Gomati, M.M. / Dalby, J. / Meffert, M. / Schulze-Briese, C. / Henderson, R. / Russo, C.J.
Funding support United Kingdom, 6items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MC UP 120117 United Kingdom
Medical Research Council (MRC, United Kingdom)MC U105184322 United Kingdom
Wellcome Trust220526/B/20/Z United Kingdom
Engineering and Physical Sciences Research CouncilR122522 United Kingdom
Innovate UK103806 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/T003677/1 United Kingdom
CitationJournal: Proc Natl Acad Sci U S A / Year: 2023
Title: Structure determination by cryoEM at 100 keV.
Authors: Greg McMullan / Katerina Naydenova / Daniel Mihaylov / Keitaro Yamashita / Mathew J Peet / Hugh Wilson / Joshua L Dickerson / Shaoxia Chen / Giuseppe Cannone / Yang Lee / Katherine A ...Authors: Greg McMullan / Katerina Naydenova / Daniel Mihaylov / Keitaro Yamashita / Mathew J Peet / Hugh Wilson / Joshua L Dickerson / Shaoxia Chen / Giuseppe Cannone / Yang Lee / Katherine A Hutchings / Olivia Gittins / Mohamed A Sobhy / Torquil Wells / Mohamed M El-Gomati / Jason Dalby / Matthias Meffert / Clemens Schulze-Briese / Richard Henderson / Christopher J Russo /
Abstract: Electron cryomicroscopy can, in principle, determine the structures of most biological molecules but is currently limited by access, specimen preparation difficulties, and cost. We describe a purpose- ...Electron cryomicroscopy can, in principle, determine the structures of most biological molecules but is currently limited by access, specimen preparation difficulties, and cost. We describe a purpose-built instrument operating at 100 keV-including advances in electron optics, detection, and processing-that makes structure determination fast and simple at a fraction of current costs. The instrument attains its theoretical performance limits, allowing atomic resolution imaging of gold test specimens and biological molecular structure determination in hours. We demonstrate its capabilities by determining the structures of eleven different specimens, ranging in size from 140 kDa to 2 MDa, using a fraction of the data normally required. CryoEM with a microscope designed specifically for high-efficiency, on-the-spot imaging of biological molecules will expand structural biology to a wide range of previously intractable problems.
History
DepositionJul 17, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 29, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2023Group: Database references / Category: citation / citation_author
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 / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ferritin heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2193
Polymers21,0981
Non-polymers1212
Water00
1
A: Ferritin heavy chain
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)509,25372
Polymers506,34324
Non-polymers2,91048
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation23
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(6.123234E-17, -1), (1, 6.123234E-17), (1)276.54
3generate(-1, -1.2246468E-16), (1.2246468E-16, -1), (1)276.54, 276.54
4generate(-1.8369702E-16, 1), (-1, -1.8369702E-16), (1)2.84217094E-14, 276.54
5generate(6.123234E-17, 1), (1), (-1, 6.123234E-17)276.54
6generate(-1, 1.2246468E-16), (1), (-1.2246468E-16, -1)276.54, 276.54
7generate(-1.8369702E-16, -1), (1), (1, -1.8369702E-16)276.54, 2.84217094E-14
8generate(1.11022302E-16, -1, 1.11022302E-16), (1.11022302E-16, 1.11022302E-16, 1), (-1, -1.11022302E-16, 1.11022302E-16)276.54, 276.54
9generate(-3.33066907E-16, -2.77555756E-16, -1), (-1, -3.33066907E-16, 2.77555756E-16), (-2.77555756E-16, 1, -3.33066907E-16)276.54, 276.54, 8.52651283E-14
10generate(1.11022302E-16, -1.11022302E-16, 1), (1, 1.11022302E-16, -1.11022302E-16), (-1.11022302E-16, 1, 1.11022302E-16)2.84217094E-14, 2.84217094E-14, 2.84217094E-14
11generate(-3.33066907E-16, 1, 2.77555756E-16), (2.77555756E-16, -3.33066907E-16, 1), (1, 2.77555756E-16, -3.33066907E-16)2.84217094E-14, 2.84217094E-14
12generate(2.22044605E-16, -1), (-1, 2.22044605E-16), (-1)276.54, 276.54, 276.54
13generate(2.22044605E-16, 1), (1, 2.22044605E-16), (-1)-5.68434189E-14, -5.68434189E-14, 276.54
14generate(1.11022302E-16, -1, -1.11022302E-16), (1.11022302E-16, 1.11022302E-16, -1), (1, 1.11022302E-16, 1.11022302E-16)276.54, 276.54, -2.84217094E-14
15generate(-3.33066907E-16, -2.77555756E-16, 1), (-1, -3.33066907E-16, -2.77555756E-16), (2.77555756E-16, -1, -3.33066907E-16)8.52651283E-14, 276.54, 276.54
16generate(1.11022302E-16, -1.11022302E-16, -1), (1, 1.11022302E-16, 1.11022302E-16), (1.11022302E-16, -1, 1.11022302E-16)276.54, -2.84217094E-14, 276.54
17generate(-3.33066907E-16, 1, -2.77555756E-16), (2.77555756E-16, -3.33066907E-16, -1), (-1, -2.77555756E-16, -3.33066907E-16)8.52651283E-14, 276.54, 276.54
18generate(2.22044605E-16, -1), (-1), (-1, 2.22044605E-16)276.54, 276.54, 276.54
19generate(2.22044605E-16, 1), (-1), (1, 2.22044605E-16)-5.68434189E-14, 276.54, -5.68434189E-14
20generate(1), (-1, -1.2246468E-16), (1.2246468E-16, -1)276.54, 276.54
21generate(-1), (2.22044605E-16, 1), (1, 2.22044605E-16)276.54, -8.52651283E-14, -5.68434189E-14
22generate(1), (6.123234E-17, -1), (1, 6.123234E-17)276.54
23generate(1), (-1.8369702E-16, 1), (-1, -1.8369702E-16)2.84217094E-14, 276.54
24generate(-1), (2.22044605E-16, -1), (-1, 2.22044605E-16)276.54, 276.54, 276.54

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Components

#1: Protein Ferritin heavy chain / Ferritin H subunit


Mass: 21097.631 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Fth1, Fth / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P09528, ferroxidase
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
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: Mouse heavy-chain apoferritin / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Mus musculus (house mouse)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R1.2/1.3
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: JEOL 1400/HR + YPS FEG
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 100 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm
Specimen holderCryogen: NITROGEN
Specimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
Image recordingElectron dose: 80 e/Å2 / Film or detector model: DECTRIS SINGLA (1k x 1k)
Image scansSampling size: 75 µm / Width: 1030 / Height: 1066

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Processing

EM softwareName: Servalcat / Version: 0.4.27 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: O (octahedral)
3D reconstructionResolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 26745 / Symmetry type: POINT
Atomic model buildingSpace: RECIPROCAL
Atomic model buildingPDB-ID: 7a4m

7a4m


Accession code: 7a4m / Source name: PDB / Type: experimental model

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