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- EMDB-76658: Single particle cryo-EM structure of human MTCH2-BRIL fusion -

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Basic information

Entry
Database: EMDB / ID: EMD-76658
TitleSingle particle cryo-EM structure of human MTCH2-BRIL fusion
Map data
Sample
  • Complex: MTCH2-BRIL fusion complexed with FAB and anti-Fab nanobody
    • Protein or peptide: MTCH2
Keywordsmitochondrial outer membrane insertase / SLC25 carrier fold / hydrophilic groove / membrane protein biogenesis / MEMBRANE PROTEIN
Function / homology
Function and homology information


regulation of mitochondrial fusion / cellular response to radiation / : / hematopoietic stem cell migration / membrane insertase activity / protein insertion into mitochondrial outer membrane / hematopoietic stem cell homeostasis / positive regulation of stem cell differentiation / protein localization to mitochondrion / lactate metabolic process ...regulation of mitochondrial fusion / cellular response to radiation / : / hematopoietic stem cell migration / membrane insertase activity / protein insertion into mitochondrial outer membrane / hematopoietic stem cell homeostasis / positive regulation of stem cell differentiation / protein localization to mitochondrion / lactate metabolic process / regulation of mitochondrial membrane permeability involved in apoptotic process / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / negative regulation of glycolytic process / hepatocyte apoptotic process / lipid homeostasis / negative regulation of mitochondrial membrane potential / mitochondrial ATP synthesis coupled electron transport / mitochondrial outer membrane / positive regulation of apoptotic process / mitochondrion / membrane / nucleus
Similarity search - Function
Mitochondrial substrate/solute carrier / Mitochondrial carrier domain superfamily / Mitochondrial carrier protein / Solute carrier (Solcar) repeat profile.
Similarity search - Domain/homology
Mitochondrial carrier homolog 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.55 Å
AuthorsLuo Z / Stevens AS / Voorhees RM
Funding support United States, 8 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1K99GM151478 United States
Nagendranath Reddy Graduate Fellowship United States
Hevolution/AFAR new investigator award United States
Caltech Center for Evolutionary Science Grant United States
Caltech OTCCP Rothenberg Innovation Initiative Grant United States
Merkin Institute Translational Research Grant United States
Sontag Foundation United States
Howard Hughes Medical Institute (HHMI)Freeman Hrabowski Scholar United States
CitationJournal: To Be Published
Title: Structural evolution of the MTCH family of mitochondrial insertases
Authors: Luo Z / Stevens TA / Lee CA / Hazu M / Galatis EG / Inglis AJ / Guna A / Voorhees RM
History
DepositionApr 14, 2026-
Header (metadata) releaseMay 13, 2026-
Map releaseMay 13, 2026-
UpdateMay 13, 2026-
Current statusMay 13, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_76658.png

Downloads & links

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Map

FileDownload / File: emd_76658.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1 Å/pix.
x 400 pix.
= 399.36 Å		1 Å/pix.
x 400 pix.
= 399.36 Å		1 Å/pix.
x 400 pix.
= 399.36 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.9984 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.08
Minimum - Maximum-0.29357493 - 0.6956783
Average (Standard dev.)-0.000039345814 (±0.008960897)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 399.36002 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_76658_msk_1.map
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Additional map: #1

Fileemd_76658_additional_1.map
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Half map: #1

Fileemd_76658_half_map_1.map
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Half map: #2

Fileemd_76658_half_map_2.map
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Sample components

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Entire : MTCH2-BRIL fusion complexed with FAB and anti-Fab nanobody

EntireName: MTCH2-BRIL fusion complexed with FAB and anti-Fab nanobody
Components
  • Complex: MTCH2-BRIL fusion complexed with FAB and anti-Fab nanobody
    • Protein or peptide: MTCH2

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Supramolecule #1: MTCH2-BRIL fusion complexed with FAB and anti-Fab nanobody

SupramoleculeName: MTCH2-BRIL fusion complexed with FAB and anti-Fab nanobody
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Human MTCH2-BRIL fusion residues 207-214 were replaced with an engineered variant of apocytochrome b562 (BRIL) flanked by two alpha-helical linkers and complexed with Fab and anti-Fab nanobody.
Source (natural)Organism: Homo sapiens (human) / Organelle: Mitochondrion / Location in cell: Mitochondrial outer membrane

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Macromolecule #1: MTCH2

MacromoleculeName: MTCH2 / type: protein_or_peptide / ID: 1
Details: Human MTCH2-BRIL fusion residues 207-214 were replaced with an engineered variant of apocytochrome b562 (BRIL) flanked by two alpha-helical linkers, in order to enable complexing with ...Details: Human MTCH2-BRIL fusion residues 207-214 were replaced with an engineered variant of apocytochrome b562 (BRIL) flanked by two alpha-helical linkers, in order to enable complexing with synthetic antibodies. No coordinate was provided due to the lac of cryo-EM density.
Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MADAASQVLL GSGLTILSQP LMYVKVLIQV GYEPLPPTIG RNIFGRQVCQ LPGLFSYAQH IASIDGRRGL FTGLTPRLCS GVLGTVVHGK VLQHYQESDK GEELGPGNVQ KEVSSSFDHV IKETTREMIA RSAATLITHP FHVITLRSMV QFIGRESKYC GLCDSIITIY ...String:
MADAASQVLL GSGLTILSQP LMYVKVLIQV GYEPLPPTIG RNIFGRQVCQ LPGLFSYAQH IASIDGRRGL FTGLTPRLCS GVLGTVVHGK VLQHYQESDK GEELGPGNVQ KEVSSSFDHV IKETTREMIA RSAATLITHP FHVITLRSMV QFIGRESKYC GLCDSIITIY REEGILGFFA GLVPRLLGDI LSLWLCNSLA YLVNTYTEQA VTHVQQGQQA DLEDNWETLN DNLKVIEKAD NAAQVKDALT KMRAAALDAQ KATPPKLEDK SPDSPEMKDF RHGFDILVGQ IDDALKLANE GKVKEAQAAA EQLKTTRNAY IQVVQNQQQA EMNEMKSYSQ AVTGFFASML TYPFVLVSNL MAVNNCGLAG GCPPYSPIYT SWIDCWCMLQ KEGNMSRGNS LFFRKVPFGK TYCCDLKMLI

UniProtKB: Mitochondrial carrier homolog 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

Concentration3.5 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
50.0 mMHEPES/KOH4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid/potassium hydroxide
2.0 mMMgOAcmagnesium acetate
0.07 %UDMn-Undecyl-beta-D-Maltopyranoside
200.0 mMNaClsodium chloride

Details: 50 mM HEPES/KOH pH 7.5, 200 mM NaCl, 2 mM Mg Acetate, and 0.07% UDM
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 12 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.03 kPa
Details: The grid was glow-discharged with a PELCO easiGlowTM (Ted Pella, Inc.) at 20 mA for 60 s.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 279.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
SoftwareName: SerialEM
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 11520 pixel / Digitization - Dimensions - Height: 8184 pixel / Number grids imaged: 3 / Number real images: 26889 / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.6 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 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: 7786491
Details: 23,738 out of 26,889 micrographs were selected for downstream processing. A total of 7,786,491 particles from blob picker and template picker were obtained. After running 11 rounds of ...Details: 23,738 out of 26,889 micrographs were selected for downstream processing. A total of 7,786,491 particles from blob picker and template picker were obtained. After running 11 rounds of heterogenous refinement, 199,397 particles were selected for further processing.
CTF correctionSoftware - Name: cryoSPARC (ver. 4.7.0)
Details: CTF parameters estimated using Patch CTF estimation in cryoSPARC. Global CTF correction for beam tilt was additionally performed.
Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionNumber classes used: 5 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.55 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7.0)
Details: Non-uniform refinement in cryoSPARC with per-particle CTF refinement
Number images used: 50000
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.7.0) / Details: Ab initio reconstruction in cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.7.0)
Details: Local refinement in cryoSPARC with a soft mask around MTCH2 only
Final 3D classificationNumber classes: 5 / Software - Name: cryoSPARC (ver. 4.7.0) / Details: Heterogeneous refinement in cryoSPARC

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Atomic model buiding 1

DetailsNo coordinate was used or fitted due to the lack of cryo-EM density.

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