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- PDB-8j5a: Single-particle cryo-EM structure of mouse apoferritin at 1.19 An... -

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Basic information

Entry
Database: PDB / ID: 8j5a
TitleSingle-particle cryo-EM structure of mouse apoferritin at 1.19 Angstrom resolution (Dataset A)
ComponentsFerritin heavy chain
KeywordsSTRUCTURAL PROTEIN / single-particle cryo-EM / Cold field emission / CFEG / Apoferritin / CRYO ARM
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 / intracellular sequestering of iron ion / negative regulation of fibroblast proliferation / endocytic vesicle lumen ...Iron uptake and transport / Golgi Associated Vesicle Biogenesis / iron ion sequestering activity / negative regulation of ferroptosis / ferroxidase / autolysosome / ferroxidase activity / intracellular sequestering of iron ion / negative regulation of fibroblast proliferation / endocytic vesicle lumen / autophagosome / Neutrophil degranulation / ferric iron binding / ferrous iron binding / iron ion transport / immune response / iron ion binding / negative regulation of cell population proliferation / mitochondrion / extracellular region / identical protein binding / membrane / 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 speciesMus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 1.19 Å
AuthorsKawakami, K. / Maki-Yonekura, S. / Hamaguchi, T. / Takaba, K. / Yonekura, K.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JPMJMI20G5 Japan
Japan Society for the Promotion of Science (JSPS)JPMJCR18J2 Japan
CitationJournal: Commun Chem / Year: 2023
Title: Measurement of charges and chemical bonding in a cryo-EM structure.
Authors: Saori Maki-Yonekura / Keisuke Kawakami / Kiyofumi Takaba / Tasuku Hamaguchi / Koji Yonekura /
Abstract: Hydrogen bonding, bond polarity, and charges in protein molecules play critical roles in the stabilization of protein structures, as well as affecting their functions such as enzymatic catalysis, ...Hydrogen bonding, bond polarity, and charges in protein molecules play critical roles in the stabilization of protein structures, as well as affecting their functions such as enzymatic catalysis, electron transfer, and ligand binding. These effects can potentially be measured in Coulomb potentials using cryogenic electron microscopy (cryo-EM). We here present charges and bond properties of hydrogen in a sub-1.2 Å resolution structure of a protein complex, apoferritin, by single-particle cryo-EM. A weighted difference map reveals positive densities for most hydrogen atoms in the core region of the complex, while negative densities around acidic amino-acid side chains are likely related to negative charges. The former positive densities identify the amino- and oxo-termini of asparagine and glutamine side chains. The latter observations were verified by spatial-resolution selection and a dose-dependent frame series. The average position of the hydrogen densities depends on the parent bonded-atom type, and this is validated by the estimated level of the standard uncertainties in the bond lengths.
History
DepositionApr 21, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 12, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond / em_admin / Item: _em_admin.last_update

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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)20,1032
Polymers20,0801
Non-polymers231
Water2,540141
1
A: Ferritin heavy chain
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)482,46248
Polymers481,91024
Non-polymers55224
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation23
2


  • Idetical with deposited unit
  • point asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit in distinct coordinate
  • point asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: O (octahedral))

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Components

#1: Protein Ferritin heavy chain


Mass: 20079.594 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 (E. coli) / References: UniProt: P09528
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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 from Mus musculus / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Mus musculus (house mouse)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: NITROGEN

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Electron microscopy imaging

MicroscopyModel: JEOL CRYO ARM 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1000 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / C2 aperture diameter: 150 µm
Image recordingElectron dose: 36.47 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: REFMAC / Version: 5.8.0267 / Classification: refinement
EM software
IDNameVersionCategory
7UCSF Chimera1.15model fitting
8Coot0.9.6model fitting
10REFMAC5.8.0267model refinement
14RELION3.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 1.19 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 2235864 / Symmetry type: POINT
RefinementResolution: 1.19→126.72 Å / Cor.coef. Fo:Fc: 0.801 / SU B: 0.528 / SU ML: 0.022 / ESU R: 0.007
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rwork0.24069 --
obs0.24069 2529386 100 %
Solvent computationSolvent model: PARAMETERS FOR MASK CACLULATION
Displacement parametersBiso mean: 15.683 Å2
Refinement stepCycle: 1 / Total: 1632
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0170.0131542
ELECTRON MICROSCOPYr_bond_other_d0.0110.0151381
ELECTRON MICROSCOPYr_angle_refined_deg1.4951.6322123
ELECTRON MICROSCOPYr_angle_other_deg1.861.5783187
ELECTRON MICROSCOPYr_dihedral_angle_1_deg4.7225214
ELECTRON MICROSCOPYr_dihedral_angle_2_deg38.11623.04982
ELECTRON MICROSCOPYr_dihedral_angle_3_deg13.28815254
ELECTRON MICROSCOPYr_dihedral_angle_4_deg19.938157
ELECTRON MICROSCOPYr_chiral_restr0.0770.2200
ELECTRON MICROSCOPYr_gen_planes_refined0.0070.021875
ELECTRON MICROSCOPYr_gen_planes_other0.0030.02379
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it0.8231.523769
ELECTRON MICROSCOPYr_mcbond_other0.8021.52767
ELECTRON MICROSCOPYr_mcangle_it1.3512.286984
ELECTRON MICROSCOPYr_mcangle_other1.3382.285984
ELECTRON MICROSCOPYr_scbond_it1.5641.757773
ELECTRON MICROSCOPYr_scbond_other1.5631.758774
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other2.5532.5591129
ELECTRON MICROSCOPYr_long_range_B_refined6.10533.8628721
ELECTRON MICROSCOPYr_long_range_B_other6.04933.2218598
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
LS refinement shellResolution: 1.19→1.221 Å / Total num. of bins used: 20
Num. reflection% reflection
Rfree0 -
Rwork187647 -
obs-100 %

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