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- EMDB-50535: Cryo-EM structure of human AK2 bound to reduced human AIFM1 (resi... -

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Basic information

Entry
Database: EMDB / ID: EMD-50535
TitleCryo-EM structure of human AK2 bound to reduced human AIFM1 (residues 102-613), class 2
Map dataMain map (sharpened)
Sample
  • Complex: 2:1 complex of Apoptosis-inducing factor 1:Adenylate kinase 2
    • Protein or peptide: Apoptosis-inducing factor 1, mitochondrial
    • Protein or peptide: Adenylate kinase 2, mitochondrial
KeywordsMitochondria / Mitochondrial Intermembrane Space / IMS / Mitochondrial Inner Membrane / IM / Apoptosis-inducing Factor 1 / Adenylate Kinase / FLAVOPROTEIN
Function / homology
Function and homology information


Oxidoreductases; Acting on NADH or NADPH; With unknown physiological acceptors / AMP metabolic process / mitochondrial disulfide relay system / regulation of apoptotic DNA fragmentation / mitochondrial respiratory chain complex assembly / ADP biosynthetic process / protein import into mitochondrial intermembrane space / NAD(P)H oxidase H2O2-forming activity / poly-ADP-D-ribose binding / adenylate kinase ...Oxidoreductases; Acting on NADH or NADPH; With unknown physiological acceptors / AMP metabolic process / mitochondrial disulfide relay system / regulation of apoptotic DNA fragmentation / mitochondrial respiratory chain complex assembly / ADP biosynthetic process / protein import into mitochondrial intermembrane space / NAD(P)H oxidase H2O2-forming activity / poly-ADP-D-ribose binding / adenylate kinase / AMP kinase activity / nucleobase-containing small molecule interconversion / cellular response to aldosterone / positive regulation of necroptotic process / Interconversion of nucleotide di- and triphosphates / oxidoreductase activity, acting on NAD(P)H / sperm mitochondrial sheath / response to L-glutamate / NADH dehydrogenase activity / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / ATP metabolic process / FAD binding / cellular response to nitric oxide / response to ischemia / cellular response to estradiol stimulus / mitochondrial intermembrane space / cellular response to hydrogen peroxide / response to toxic substance / neuron differentiation / positive regulation of neuron apoptotic process / neuron apoptotic process / cellular response to hypoxia / mitochondrial inner membrane / protein dimerization activity / positive regulation of apoptotic process / apoptotic process / perinuclear region of cytoplasm / mitochondrion / DNA binding / extracellular exosome / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Adenylate kinase 2 / Mitochondrial apoptosis-inducing factor, C-terminal domain / Apoptosis-inducing factor, mitochondrion-associated, C-term / Apoptosis-inducing factor, mitochondrion-associated, C-term / : / Adenylate kinase, active site lid domain / Adenylate kinase, active site lid / Adenylate kinase subfamily / Adenylate kinase, conserved site / Adenylate kinase signature. ...Adenylate kinase 2 / Mitochondrial apoptosis-inducing factor, C-terminal domain / Apoptosis-inducing factor, mitochondrion-associated, C-term / Apoptosis-inducing factor, mitochondrion-associated, C-term / : / Adenylate kinase, active site lid domain / Adenylate kinase, active site lid / Adenylate kinase subfamily / Adenylate kinase, conserved site / Adenylate kinase signature. / Adenylate kinase/UMP-CMP kinase / Adenylate kinase / FAD/NAD-linked reductase, dimerisation domain superfamily / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / FAD/NAD(P)-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Apoptosis-inducing factor 1, mitochondrial / Adenylate kinase 2, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.2 Å
AuthorsLauer SM / Spahn CMT / Schwefel D
Funding support Germany, 1 items
OrganizationGrant numberCountry
German Research Foundation (DFG)SCHW 1851/1-1 Germany
CitationJournal: To Be Published
Title: Cryo-EM structure of human AK2 bound to reduced human AIFM1 (residues 102-613)
Authors: Lauer SM / Spahn CMT / Schwefel D
History
DepositionJun 4, 2024-
Header (metadata) releaseMay 14, 2025-
Map releaseMay 14, 2025-
UpdateMay 14, 2025-
Current statusMay 14, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50535.png

Downloads & links

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Map

FileDownload / File: emd_50535.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMain map (sharpened)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.7 Å/pix.
x 160 pix.
= 272. Å		1.7 Å/pix.
x 160 pix.
= 272. Å		1.7 Å/pix.
x 160 pix.
= 272. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.7 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.8
Minimum - Maximum-2.70214 - 5.512174
Average (Standard dev.)-0.0030247676 (±0.16051309)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 272.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_50535_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Main map (unsharpened)

Fileemd_50535_additional_1.map
AnnotationMain map (unsharpened)
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_50535_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_50535_half_map_2.map
AnnotationHalf map B
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : 2:1 complex of Apoptosis-inducing factor 1:Adenylate kinase 2

EntireName: 2:1 complex of Apoptosis-inducing factor 1:Adenylate kinase 2
Components
  • Complex: 2:1 complex of Apoptosis-inducing factor 1:Adenylate kinase 2
    • Protein or peptide: Apoptosis-inducing factor 1, mitochondrial
    • Protein or peptide: Adenylate kinase 2, mitochondrial

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Supramolecule #1: 2:1 complex of Apoptosis-inducing factor 1:Adenylate kinase 2

SupramoleculeName: 2:1 complex of Apoptosis-inducing factor 1:Adenylate kinase 2
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 140 KDa

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Macromolecule #1: Apoptosis-inducing factor 1, mitochondrial

MacromoleculeName: Apoptosis-inducing factor 1, mitochondrial / type: protein_or_peptide / ID: 1 / Details: Residues 1-101 deleted / Enantiomer: LEVO
EC number: Oxidoreductases; Acting on NADH or NADPH; With unknown physiological acceptors
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: GIDPFT LGL TPEQKQKKAA LSASEGEEVP QDKAPSHVPF LLIGGGTAAF AAARSIRARD PGARVLIVSE DPELPYMRPP LSKELWFSDD PNVTKTLRFK QWNGKERSIY FQPPSFYVSA QDLPHIENGG VAVLTGKKVV QLDVRDNMVK LNDGSQITYE KCLIATGGTP ...String:
GIDPFT LGL TPEQKQKKAA LSASEGEEVP QDKAPSHVPF LLIGGGTAAF AAARSIRARD PGARVLIVSE DPELPYMRPP LSKELWFSDD PNVTKTLRFK QWNGKERSIY FQPPSFYVSA QDLPHIENGG VAVLTGKKVV QLDVRDNMVK LNDGSQITYE KCLIATGGTP RSLSAIDRAG AEVKSRTTLF RKIGDFRSLE KISREVKSIT IIGGGFLGSE LACALGRKAR ALGTEVIQLF PEKGNMGKIL PEYLSNWTME KVRREGVKVM PNAIVQSVGV SSGKLLIKLK DGRKVETDHI VAAVGLEPNV ELAKTGGLEI DSDFGGFRVN AELQARSNIW VAGDAACFYD IKLGRRRVEH HDHAVVSGRL AGENMTGAAK PYWHQSMFWS DLGPDVGYEA IGLVDSSLPT VGVFAKATAQ DNPKSATEQS GTGIRSESET ESEASEITIP PSTPAVPQAP VQGEDYGKGV IFYLRDKVVV GIVLWNIFNR MPIARKIIKD GEQHEDLNEV AKLFNIHED

UniProtKB: Apoptosis-inducing factor 1, mitochondrial

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Macromolecule #2: Adenylate kinase 2, mitochondrial

MacromoleculeName: Adenylate kinase 2, mitochondrial / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO / EC number: adenylate kinase
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: GIDPFT MAP SVPAAEPEYP KGIRAVLLGP PGAGKGTQAP RLAENFCVCH LATGDMLRAM VASGSEL GK KLKATMDAGK LVSDEMVVEL IEKNLETPLC KNGFLLDGFP RTVRQAEMLD DLMEKRKE K LDSVIEFSIP DSLLIRRITG RLIHPKSGRS YHEEFNPPKE ...String:
GIDPFT MAP SVPAAEPEYP KGIRAVLLGP PGAGKGTQAP RLAENFCVCH LATGDMLRAM VASGSEL GK KLKATMDAGK LVSDEMVVEL IEKNLETPLC KNGFLLDGFP RTVRQAEMLD DLMEKRKE K LDSVIEFSIP DSLLIRRITG RLIHPKSGRS YHEEFNPPKE PMKDDITGEP LIRRSDDNE KALKIRLQAY HTQTTPLIEY YRKRGIHSAI DASQTPDVVF ASILAAFSKA TCKDLVMFI

UniProtKB: Adenylate kinase 2, mitochondrial

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.1 mg/mL
BufferpH: 7.8
Component:
ConcentrationFormulaName
10.0 mMTris-HClTris-HCl
150.0 mMNaClSodium chloride
4.0 mMMgCl2Magnesium chloride
0.5 mMTCEPTris(2-carboxyethyl)phosphine
VitrificationCryogen name: ETHANE / Chamber humidity: 99 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1748043
CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: ab initio
Final reconstructionResolution.type: BY AUTHOR / Resolution: 6.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 111646
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationNumber classes: 6 / Software - Name: cryoSPARC

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL

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