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- PDB-25wf: Cryo-EM structure of the human SAM50-engaged SAM complex -

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Basic information

Entry
Database: PDB / ID: 25wf
TitleCryo-EM structure of the human SAM50-engaged SAM complex
Components
  • Metaxin-2
  • Sorting and assembly machinery component 50 homolog
KeywordsTRANSLOCASE / SAM complex / SAM50-engaged.
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsYan, L. / Guan, Z. / Wang, Q. / Yin, P.
Funding support China, 1items
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, 2026Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 30, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 30, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sorting and assembly machinery component 50 homolog
B: Metaxin-2
C: Sorting and assembly machinery component 50 homolog


Theoretical massNumber of molelcules
Total (without water)141,7963
Polymers141,7963
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Sorting and assembly machinery component 50 homolog / Transformation-related gene 3 protein / TRG-3


Mass: 54364.301 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SAMM50, SAM50, CGI-51, TRG3 / Production host: Homo sapiens (human) / References: UniProt: Q9Y512
#2: Protein Metaxin-2 / Mitochondrial outer membrane import complex protein 2


Mass: 33067.570 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MTX2 / Production host: Homo sapiens (human) / References: UniProt: O75431
Has protein modificationN

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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: SAM50-engaged SAM complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
SpecimenConc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameCategory
1Topazparticle selection
13cryoSPARC3D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 254228 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0038852
ELECTRON MICROSCOPYf_angle_d0.58611961
ELECTRON MICROSCOPYf_dihedral_angle_d5.5541197
ELECTRON MICROSCOPYf_chiral_restr0.0431277
ELECTRON MICROSCOPYf_plane_restr0.0061554

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