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- PDB-4v1w: 3D structure of horse spleen apoferritin determined by electron c... -

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Basic information

Entry
Database: PDB / ID: 4v1w
Title3D structure of horse spleen apoferritin determined by electron cryomicroscopy
ComponentsFERRITIN LIGHT CHAIN
KeywordsSTORAGE PROTEIN / IRON STORAGE / IRON TRANSPORT / FERRITINS / APOFERRITINS / HORSES / METALS / SPLEEN
Function / homology
Function and homology information


ferritin complex / autolysosome / intracellular sequestering of iron ion / autophagosome / ferric iron binding / ferrous iron binding / iron ion transport / cytoplasmic vesicle / iron ion binding / 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 light chain
Similarity search - Component
Biological speciesEQUUS CABALLUS (horse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.7 Å
AuthorsRusso, C.J. / Passmore, L.A.
CitationJournal: Science / Year: 2014
Title: Electron microscopy: Ultrastable gold substrates for electron cryomicroscopy.
Authors: Christopher J Russo / Lori A Passmore /
Abstract: Despite recent advances, the structures of many proteins cannot be determined by electron cryomicroscopy because the individual proteins move during irradiation. This blurs the images so that they ...Despite recent advances, the structures of many proteins cannot be determined by electron cryomicroscopy because the individual proteins move during irradiation. This blurs the images so that they cannot be aligned with each other to calculate a three-dimensional density. Much of this movement stems from instabilities in the carbon substrates used to support frozen samples in the microscope. Here we demonstrate a gold specimen support that nearly eliminates substrate motion during irradiation. This increases the subnanometer image contrast such that α helices of individual proteins are resolved. With this improvement, we determine the structure of apoferritin, a smooth octahedral shell of α-helical subunits that is particularly difficult to solve by electron microscopy. This advance in substrate design will enable the solution of currently intractable protein structures.
History
DepositionOct 2, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 10, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 31, 2014Group: Database references
Revision 1.2Aug 2, 2017Group: Data collection / Refinement description / Category: em_3d_fitting / em_image_scans / em_software
Item: _em_3d_fitting.target_criteria / _em_software.fitting_id ..._em_3d_fitting.target_criteria / _em_software.fitting_id / _em_software.image_processing_id / _em_software.name
Revision 1.3May 8, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

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Structure visualization

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  • Deposited structure unit
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  • EMDB-2788
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Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FERRITIN LIGHT CHAIN
B: 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
U: FERRITIN LIGHT CHAIN
V: FERRITIN LIGHT CHAIN
W: FERRITIN LIGHT CHAIN
X: FERRITIN LIGHT CHAIN


Theoretical massNumber of molelcules
Total (without water)476,93824
Polymers476,93824
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.000196, -1, -6.0E-5), (1, -0.000196, 0.000815), (-0.000815, -6.0E-5, 1)177.56935, -0.09345, 0.04647

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Components

#1: Protein ...
FERRITIN LIGHT CHAIN / FERRITIN L SUBUNIT


Mass: 19872.428 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Source: (natural) EQUUS CABALLUS (horse) / Tissue: SPLEEN / 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 / Type: COMPLEX
Buffer solutionName: PBS / pH: 7.4 / Details: PBS
SpecimenConc.: 3.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: OTHER
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Details: LIQUID ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300 / Date: Mar 8, 2013
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 59000 X / Calibrated magnification: 104012 X / Nominal defocus max: 3639 nm / Nominal defocus min: 1573 nm / Cs: 2 mm
Image recordingFilm or detector model: FEI FALCON II (4k x 4k)
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategory
1REFMACmodel fitting
2RELION3D reconstruction
CTF correctionDetails: PER PARTICLE
SymmetryPoint symmetry: O (octahedral)
3D reconstructionResolution: 4.7 Å / Num. of particles: 483 / Actual pixel size: 1.346 Å
Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2788. (DEPOSITION ID: 12832).
Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Target criteria: Maximum likelihood / Details: METHOD--FLEXIBLE REFINEMENT PROTOCOL--X-RAY
Atomic model buildingPDB-ID: 2W0O

2w0o


Accession code: 2W0O / Source name: PDB / Type: experimental model
RefinementHighest resolution: 4.7 Å
Refinement stepCycle: LAST / Highest resolution: 4.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms32736 0 0 0 32736

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