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- EMDB-0552: human m-AAA protease AFG3L2, substrate-bound -

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Basic information

Entry
Database: EMDB / ID: EMD-0552
Titlehuman m-AAA protease AFG3L2, substrate-bound
Map data
SampleAFG3L2:
AFG3-like protein 2 / Substrate / (ligand) x 4
Function / homology
Function and homology information


Processing of SMDT1 / mitochondrial protein processing / m-AAA complex / cristae formation / calcium import into the mitochondrion / mitochondrial calcium ion transmembrane transport / mitochondrial calcium ion homeostasis / righting reflex / muscle fiber development / mitochondrial fusion ...Processing of SMDT1 / mitochondrial protein processing / m-AAA complex / cristae formation / calcium import into the mitochondrion / mitochondrial calcium ion transmembrane transport / mitochondrial calcium ion homeostasis / righting reflex / muscle fiber development / mitochondrial fusion / nerve development / myelination / ec:3.4.24.-: / neuromuscular junction development / protein autoprocessing / protein processing / axonogenesis / regulation of multicellular organism growth / metallopeptidase activity / metalloendopeptidase activity / mitochondrial inner membrane / unfolded protein binding / proteolysis / mitochondrion / zinc ion binding / ATP binding
Peptidase M41 / AAA ATPase, AAA+ lid domain / ATPase, AAA-type, core / ATPase, AAA-type, conserved site / Peptidase, FtsH / Peptidase M41, FtsH extracellular / AAA+ ATPase domain / Peptidase M41-like / P-loop containing nucleoside triphosphate hydrolase / ATPase family associated with various cellular activities (AAA) ...Peptidase M41 / AAA ATPase, AAA+ lid domain / ATPase, AAA-type, core / ATPase, AAA-type, conserved site / Peptidase, FtsH / Peptidase M41, FtsH extracellular / AAA+ ATPase domain / Peptidase M41-like / P-loop containing nucleoside triphosphate hydrolase / ATPase family associated with various cellular activities (AAA) / AAA+ lid domain / Peptidase family M41 / FtsH Extracellular / AAA-protein family signature.
AFG3-like protein 2
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsLander GC / Puchades C
CitationJournal: To Be Published
Title: Unique structural features of the mitochondrial AAA+ protease AFG3L2 reveal the molecular basis for activity in health and disease
Authors: Lander GC / Puchades C
Validation ReportPDB-ID: 6nyy

SummaryFull reportAbout validation report
DateDeposition: Feb 12, 2019 / Header (metadata) release: May 22, 2019 / Map release: May 22, 2019 / Update: May 22, 2019

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.07
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.07
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6nyy
  • Surface level: 0.07
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_0552.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.15 Å/pix.
x 128 pix.
= 147.2 Å
1.15 Å/pix.
x 128 pix.
= 147.2 Å
1.15 Å/pix.
x 128 pix.
= 147.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.15 Å
Density
Contour LevelBy AUTHOR: 0.07 / Movie #1: 0.07
Minimum - Maximum-0.03232731 - 0.078550875
Average (Standard dev.)0.0003941555 (±0.0061497614)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 147.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.151.151.15
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z147.200147.200147.200
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS128128128
D min/max/mean-0.0290.4640.010

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Supplemental data

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Sample components

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Entire AFG3L2

EntireName: AFG3L2
Details: Soluble domains of the AFG3L2, comprising the AAA+ ATPase and protease domains.
Number of components: 7

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Component #1: cellular-component, AFG3L2

Cellular-componentName: AFG3L2
Details: Soluble domains of the AFG3L2, comprising the AAA+ ATPase and protease domains.
Recombinant expression: No
MassTheoretical: 360 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #2: protein, AFG3-like protein 2

ProteinName: AFG3-like protein 2 / Number of Copies: 6 / Recombinant expression: No
MassTheoretical: 58.331629 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #3: protein, Substrate

ProteinName: Substrate / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 0.799871 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #4: ligand, ZINC ION

LigandName: ZINC ION / Number of Copies: 6 / Recombinant expression: No
MassTheoretical: 6.540905 MDa

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Component #5: ligand, PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

LigandName: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 0.506196 kDa

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Component #6: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

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Component #7: ligand, ADENOSINE-5'-DIPHOSPHATE

LigandName: ADENOSINE-5'-DIPHOSPHATE / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.427201 kDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 2 mg/mL
Buffer solution: DTT and ATP were added fresh before sample preparation
pH: 8
Support filmGrids were plasma cleaned using a Solarus plasma cleaner (Gatan, Inc.).
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Temperature: 278 K / Humidity: 100 %
Details: Sample was blotted for 3 seconds using Whatman No. 1 filter paper immediately prio to plunge-freezing..

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 40 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 36000.0 X (nominal), 43478.0 X (calibrated) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 8000.0 - 18000.0 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature: (100.0 - 100.0 K)
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 5707 / Sampling size: 5 µm / Details: Data collected with Leginon

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 1129437
3D reconstructionAlgorithm: BACK PROJECTION / Software: RELION
CTF correction: CTF estimated with CTFFIND 4, local CTF estimated with
Resolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF
Details: Multi-body refinement was used to generate 3 different reconstructions that were stitched together
Euler angles: Multi-body reconstruction
FSC plot (resolution estimation)

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Atomic model buiding

Modeling #1Refinement protocol: rigid body / Refinement space: REAL
Details: The sequence was threaded onto the PDB ID 6AZ0 and built into the EM density with Coot.
Input PDB model: 6AZ0
Overall bvalue: 85
Output model

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