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- PDB-6pxm: Horse spleen apoferritin light chain -

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Basic information

Entry
Database: PDB / ID: 6pxm
TitleHorse spleen apoferritin light chain
ComponentsFerritin light chain
KeywordsMETAL BINDING PROTEIN / Ferritin / apoferritin / octahedral
Function / homology
Function and homology information


intracellular ferritin complex / intracellular sequestering of iron ion / ferric iron binding / ferrous iron binding / iron ion transport / iron ion binding / cytoplasm
Similarity search - Function
Ferritin iron-binding regions signature 1. / Ferritin iron-binding regions signature 2. / Ferritin, conserved site / Ferritin, core subunit, four-helix bundle / Ferritin / Ferritin / Ferritin-like diiron domain / Ferritin-like diiron domain profile. / Ferritin/DPS protein domain / Ferritin-like domain ...Ferritin iron-binding regions signature 1. / Ferritin iron-binding regions signature 2. / Ferritin, conserved site / Ferritin, core subunit, four-helix bundle / Ferritin / Ferritin / Ferritin-like diiron domain / Ferritin-like diiron domain profile. / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Ferritin light chain
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.1 Å
AuthorsKopylov, M. / Kelley, K. / Yen, L.Y. / Rice, W.J. / Eng, E.T. / Carragher, B. / Potter, C.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)GM103310 United States
CitationJournal: To Be Published
Title: Horse spleen apoferritin light chain structure at 2.1 Angstrom resolution
Authors: Kopylov, M. / Kelley, K. / Yen, L.Y. / Rice, W.J. / Eng, E.T. / Carragher, B. / Potter, C.S.
History
DepositionJul 26, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Structure viewerMolecule:
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Assembly

Deposited unit
B: Ferritin light chain
A: Ferritin light chain
C: Ferritin light chain
D: Ferritin light chain
E: Ferritin light chain
F: Ferritin light chain
G: Ferritin light chain
H: Ferritin light chain
I: Ferritin light chain
J: Ferritin light chain
K: Ferritin light chain
L: Ferritin light chain
M: Ferritin light chain
N: Ferritin light chain
O: Ferritin light chain
P: Ferritin light chain
Q: Ferritin light chain
R: Ferritin light chain
S: Ferritin light chain
T: Ferritin light chain
V: Ferritin light chain
W: Ferritin light chain
X: Ferritin light chain
Y: Ferritin light chain


Theoretical massNumber of molelcules
Total (without water)480,08724
Polymers480,08724
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area92840 Å2
ΔGint-322 kcal/mol
Surface area133340 Å2

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Components

#1: Protein ...
Ferritin light chain / / apoferritin light chain / Ferritin L subunit


Mass: 20003.623 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Source: (natural) Equus caballus (horse) / Organ: Spleen / Plasmid details: Sigma catalog: A3641 / References: UniProt: P02791

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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: Horse spleen apoferritin light chain / Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightValue: 0.48 MDa
Source (natural)Organism: Equus caballus (horse) / Organ: Spleen
Buffer solutionpH: 7.4
SpecimenConc.: 7 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: In-house-made nanowire grids / Grid material: COPPER
VitrificationInstrument: SPOTITON / Cryogen name: ETHANE / Humidity: 80 % / Chamber temperature: 298 K / Details: Chameleon EP2 based on Spotiton

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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 FIELDBright-field microscopy / Nominal magnification: 29000 X / Nominal defocus max: -2000 nm / Nominal defocus min: -1000 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 70 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 3885

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Processing

EM software
IDNameVersionCategory
4CTFFIND4CTF correction
7Coot0.9-premodel fitting
10cryoSPARC0.6.5final Euler assignment
11cryoSPARC0.6.5classification
12cryoSPARC0.6.53D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 911171
SymmetryPoint symmetry: O (octahedral)
3D reconstructionResolution: 2.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 145495 / Symmetry type: POINT

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