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- EMDB-80423: Cryo-EM structure of the human SAM50-engaged SAM complex -

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Basic information

Entry
Database: EMDB / ID: EMD-80423
TitleCryo-EM structure of the human SAM50-engaged SAM complex
Map data
Sample
  • Complex: SAM50-engaged SAM complex
    • Protein or peptide: Sorting and assembly machinery component 50 homolog
    • Protein or peptide: Metaxin-2
KeywordsSAM complex / SAM50-engaged. / TRANSLOCASE
Function / homology
Function and homology information


MIB complex / mitochondrial outer membrane translocase complex assembly / SAM complex / Cristae formation / inner mitochondrial membrane organization / cristae formation / protein insertion into mitochondrial outer membrane / Mitochondrial protein import / mitochondrial transport / protein import into mitochondrial matrix ...MIB complex / mitochondrial outer membrane translocase complex assembly / SAM complex / Cristae formation / inner mitochondrial membrane organization / cristae formation / protein insertion into mitochondrial outer membrane / Mitochondrial protein import / mitochondrial transport / protein import into mitochondrial matrix / RAC2 GTPase cycle / mitochondrial outer membrane / mitochondrion / extracellular exosome / membrane
Similarity search - Function
Metaxin, glutathione S-transferase domain / Glutathione S-transferase, C-terminal domain / Mitochondrial outer membrane transport complex Sam37/metaxin, N-terminal domain / : / Outer mitochondrial membrane transport complex protein / Surface antigen D15-like / POTRA domain / POTRA domain profile. / Bacterial surface antigen (D15) / Omp85 superfamily domain ...Metaxin, glutathione S-transferase domain / Glutathione S-transferase, C-terminal domain / Mitochondrial outer membrane transport complex Sam37/metaxin, N-terminal domain / : / Outer mitochondrial membrane transport complex protein / Surface antigen D15-like / POTRA domain / POTRA domain profile. / Bacterial surface antigen (D15) / Omp85 superfamily domain / Glutathione transferase family / Glutathione S-transferase, C-terminal domain superfamily
Similarity search - Domain/homology
Metaxin-2 / Sorting and assembly machinery component 50 homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsYan L / Guan Z / Wang Q / Yin P
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Mechanical Insights into the SAM-mediated Mitochondrial beta-barrel outer membrane protein folding in Mammalian Cells
Authors: Guan Z / Yan L / Yin P
History
DepositionApr 20, 2026-
Header (metadata) releaseSep 30, 2026-
Map releaseSep 30, 2026-
UpdateSep 30, 2026-
Current statusSep 30, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_80423.png

Downloads & links

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Map

FileDownload / File: emd_80423.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 280 pix.
= 299.6 Å		1.07 Å/pix.
x 280 pix.
= 299.6 Å		1.07 Å/pix.
x 280 pix.
= 299.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-0.0008887941 - 2.1823437
Average (Standard dev.)0.0017927097 (±0.032101218)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 299.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_80423_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_80423_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : SAM50-engaged SAM complex

EntireName: SAM50-engaged SAM complex
Components
  • Complex: SAM50-engaged SAM complex
    • Protein or peptide: Sorting and assembly machinery component 50 homolog
    • Protein or peptide: Metaxin-2

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Supramolecule #1: SAM50-engaged SAM complex

SupramoleculeName: SAM50-engaged SAM complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Sorting and assembly machinery component 50 homolog

MacromoleculeName: Sorting and assembly machinery component 50 homolog / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 54.364301 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDYKDDDDKG DYKDDDDKGS MGTVHARSLE PLPSSGPDFG GLGEEAEFVE VEPEAKQEIL ENKDVVVQHV HFDGLGRTKD DIIICEIGD VFKAKNLIEV MRKSHEAREK LLRLGIFRQV DVLIDTCQGD DALPNGLDVT FEVTELRRLT GSYNTMVGNN E GSMVLGLK ...String:
MDYKDDDDKG DYKDDDDKGS MGTVHARSLE PLPSSGPDFG GLGEEAEFVE VEPEAKQEIL ENKDVVVQHV HFDGLGRTKD DIIICEIGD VFKAKNLIEV MRKSHEAREK LLRLGIFRQV DVLIDTCQGD DALPNGLDVT FEVTELRRLT GSYNTMVGNN E GSMVLGLK LPNLLGRAEK VTFQFSYGTK ETSYGLSFFK PRPGNFERNF SVNLYKVTGQ FPWSSLRETD RGMSAEYSFP IW KTSHTVK WEGVWRELGC LSRTASFAVR KESGHSLKSS LSHAMVIDSR NSSILPRRGA LLKVNQELAG YTGGDVSFIK EDF ELQLNK QLIFDSVFSA SFWGGMLVPI GDKPSSIADR FYLGGPTSIR GFSMHSIGPQ SEGDYLGGEA YWAGGLHLYT PLPF RPGQG GFGELFRTHF FLNAGNLCNL NYGEGPKAHI RKLAECIRWS YGAGIVLRLG NIARLELNYC VPMGVQTGDR ICDGV QFGA GIRFL

UniProtKB: Sorting and assembly machinery component 50 homolog

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Macromolecule #2: Metaxin-2

MacromoleculeName: Metaxin-2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 33.06757 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSLVAEAFVS QIAAAEPWPE NATLYQQLKG EQILLSDNAA SLAVQAFLQM CNLPIKVVCR ANAEYMSPSG KVPFIHVGNQ VVSELGPIV QFVKAKGHSL SDGLEEVQKA EMKAYMELVN NMLLTAELYL QWCDEATVGE ITHARYGSPY PWPLNHILAY Q KQWEVKRK ...String:
MSLVAEAFVS QIAAAEPWPE NATLYQQLKG EQILLSDNAA SLAVQAFLQM CNLPIKVVCR ANAEYMSPSG KVPFIHVGNQ VVSELGPIV QFVKAKGHSL SDGLEEVQKA EMKAYMELVN NMLLTAELYL QWCDEATVGE ITHARYGSPY PWPLNHILAY Q KQWEVKRK MKAIGWGKKT LDQVLEDVDQ CCQALSQRLG TQPYFFNKQP TELDALVFGH LYTILTTQLT NDELSEKVKN YS NLLAFCR RIEQHYFEDR GKGRLSLESA WSHPQFEKGG GSGGGSGGSA WSHPQFEK

UniProtKB: Metaxin-2

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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

Concentration5 mg/mL
BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 254228
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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