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- PDB-6wuh: Mitochondrial SAM complex in lipid nanodiscs -

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Basic information

Entry
Database: PDB / ID: 6wuh
TitleMitochondrial SAM complex in lipid nanodiscs
Components
  • Bac_surface_Ag domain-containing protein
  • Sam35
  • Tom37 domain-containing protein
KeywordsMEMBRANE PROTEIN / Mitochondrial SAM complex / Sam35 / Sam37 / Sam50.
Function / homology
Function and homology information


SAM complex / protein insertion into mitochondrial outer membrane / mitochondrion organization / protein transport / mitochondrial outer membrane
Similarity search - Function
Metaxin, glutathione S-transferase domain / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase N-terminal domain / Mitochondrial outer membrane transport complex Sam37/metaxin, N-terminal domain / : / Outer mitochondrial membrane transport complex protein / membrane protein fhac: a member of the omp85/tpsb transporter family / Thioredoxin-like fold / Surface antigen D15-like / Bacterial surface antigen (D15) ...Metaxin, glutathione S-transferase domain / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase N-terminal domain / Mitochondrial outer membrane transport complex Sam37/metaxin, N-terminal domain / : / Outer mitochondrial membrane transport complex protein / membrane protein fhac: a member of the omp85/tpsb transporter family / Thioredoxin-like fold / Surface antigen D15-like / Bacterial surface antigen (D15) / Omp85 superfamily domain / Porin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Mitochondrial outer membrane transport complex Sam37/metaxin N-terminal domain-containing protein / Thioredoxin-like fold domain-containing protein / Bacterial surface antigen (D15) domain-containing protein
Similarity search - Component
Biological speciesThermothelomyces thermophilus (fungus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsNi, X. / Botos, I. / Diederichs, K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK) United States
CitationJournal: Nat Commun / Year: 2020
Title: Structural insight into mitochondrial β-barrel outer membrane protein biogenesis.
Authors: Kathryn A Diederichs / Xiaodan Ni / Sarah E Rollauer / Istvan Botos / Xiaofeng Tan / Martin S King / Edmund R S Kunji / Jiansen Jiang / Susan K Buchanan /
Abstract: In mitochondria, β-barrel outer membrane proteins mediate protein import, metabolite transport, lipid transport, and biogenesis. The Sorting and Assembly Machinery (SAM) complex consists of three ...In mitochondria, β-barrel outer membrane proteins mediate protein import, metabolite transport, lipid transport, and biogenesis. The Sorting and Assembly Machinery (SAM) complex consists of three proteins that assemble as a 1:1:1 complex to fold β-barrel proteins and insert them into the mitochondrial outer membrane. We report cryoEM structures of the SAM complex from Myceliophthora thermophila, which show that Sam50 forms a 16-stranded transmembrane β-barrel with a single polypeptide-transport-associated (POTRA) domain extending into the intermembrane space. Sam35 and Sam37 are located on the cytosolic side of the outer membrane, with Sam35 capping Sam50, and Sam37 interacting extensively with Sam35. Sam35 and Sam37 each adopt a GST-like fold, with no functional, structural, or sequence similarity to their bacterial counterparts. Structural analysis shows how the Sam50 β-barrel opens a lateral gate to accommodate its substrates.
History
DepositionMay 4, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2020Provider: repository / Type: Initial release
Revision 1.0Aug 12, 2020Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Aug 12, 2020Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Aug 12, 2020Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Aug 12, 2020Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Aug 12, 2020Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Aug 12, 2020Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Aug 12, 2020Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Aug 19, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Jun 4, 2025Group: Data collection / Structure summary / Category: em_admin / em_software / pdbx_entry_details / Item: _em_admin.last_update / _em_software.name
Revision 1.1Jun 4, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

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Assembly

Deposited unit
A: Sam35
B: Bac_surface_Ag domain-containing protein
C: Tom37 domain-containing protein


Theoretical massNumber of molelcules
Total (without water)136,2723
Polymers136,2723
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area7160 Å2
ΔGint-30 kcal/mol
Surface area48910 Å2

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Components

#1: Protein Sam35


Mass: 36795.602 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermothelomyces thermophilus (fungus) / Gene: MYCTH_2142789 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: G2QAT9
#2: Protein Bac_surface_Ag domain-containing protein / Sam50


Mass: 53380.969 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermothelomyces thermophilus (fungus) / Gene: MYCTH_2094326 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: G2QFF9
#3: Protein Tom37 domain-containing protein / Sam37


Mass: 46095.207 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermothelomyces thermophilus (fungus) / Gene: MYCTH_2293977 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: G2Q6R7
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: Mitochondrial SAM complex in lipid nanodiscs / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Thermothelomyces thermophilus (fungus)
Source (recombinant)Organism: Saccharomyces cerevisiae (brewer's yeast)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: unspecified
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 69 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.17.1_3660: / Classification: refinement
EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 179509 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0037966
ELECTRON MICROSCOPYf_angle_d0.62510843
ELECTRON MICROSCOPYf_dihedral_angle_d18.5291130
ELECTRON MICROSCOPYf_chiral_restr0.0431224
ELECTRON MICROSCOPYf_plane_restr0.0051412

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