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- EMDB-76659: Single particle cryo-EM structure of human MTCH2 (hyperactive mut... -

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Basic information

Entry
Database: EMDB / ID: EMD-76659
TitleSingle particle cryo-EM structure of human MTCH2 (hyperactive mutant K25E Y235A V238D)
Map data
Sample
  • Complex: MTCH2 hyperactive mutant K25E Y235A V238D complexed with UCP1 nanobody
    • Protein or peptide: UCP1 Nanobody
    • Protein or peptide: Mitochondrial carrier homolog 2,Mitochondrial brown fat uncoupling protein 1
Keywordsmitochondrial outer membrane insertase / SLC25 carrier fold / hydrophilic groove / membrane protein biogenesis / MEMBRANE PROTEIN
Function / homology
Function and homology information


regulation of mitochondrial fusion / purine ribonucleotide binding / cellular response to dehydroepiandrosterone / Mitochondrial Uncoupling / The fatty acid cycling model / cellular response to radiation / oxidative phosphorylation uncoupler activity / : / mitochondrial transmembrane transport / hematopoietic stem cell migration ...regulation of mitochondrial fusion / purine ribonucleotide binding / cellular response to dehydroepiandrosterone / Mitochondrial Uncoupling / The fatty acid cycling model / cellular response to radiation / oxidative phosphorylation uncoupler activity / : / mitochondrial transmembrane transport / hematopoietic stem cell migration / membrane insertase activity / adaptive thermogenesis / protein insertion into mitochondrial outer membrane / hematopoietic stem cell homeostasis / positive regulation of stem cell differentiation / protein localization to mitochondrion / cardiolipin binding / lactate metabolic process / cellular response to fatty acid / regulation of mitochondrial membrane permeability involved in apoptotic process / negative regulation of glycolytic process / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / regulation of reactive oxygen species biosynthetic process / long-chain fatty acid binding / response to temperature stimulus / diet induced thermogenesis / cellular response to cold / hepatocyte apoptotic process / proton transmembrane transporter activity / lipid homeostasis / negative regulation of mitochondrial membrane potential / mitochondrial ATP synthesis coupled electron transport / transmembrane transporter activity / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / cellular response to hormone stimulus / proton transmembrane transport / brown fat cell differentiation / response to cold / cellular response to reactive oxygen species / response to nutrient levels / GDP binding / positive regulation of cold-induced thermogenesis / mitochondrial outer membrane / mitochondrial inner membrane / positive regulation of apoptotic process / regulation of transcription by RNA polymerase II / GTP binding / mitochondrion / membrane / nucleus
Similarity search - Function
: / Mitochondrial carrier protein / Mitochondrial substrate/solute carrier / Mitochondrial carrier domain superfamily / Mitochondrial carrier protein / Solute carrier (Solcar) repeat profile.
Similarity search - Domain/homology
Mitochondrial brown fat uncoupling protein 1 / Mitochondrial carrier homolog 2
Similarity search - Component
Biological speciesHomo sapiens (human) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsLuo Z / Stevens TA / 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_76659.png

Downloads & links

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Map

FileDownload / File: emd_76659.map.gz / Format: CCP4 / Size: 600.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 540 pix.
= 449.28 Å		0.83 Å/pix.
x 540 pix.
= 449.28 Å		0.83 Å/pix.
x 540 pix.
= 449.28 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.832 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.056
Minimum - Maximum-0.16398886 - 0.3477841
Average (Standard dev.)-0.000011490143 (±0.0026192155)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions540540540
Spacing540540540
CellA=B=C: 449.28 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_76659_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_76659_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_76659_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 : MTCH2 hyperactive mutant K25E Y235A V238D complexed with UCP1 nanobody

EntireName: MTCH2 hyperactive mutant K25E Y235A V238D complexed with UCP1 nanobody
Components
  • Complex: MTCH2 hyperactive mutant K25E Y235A V238D complexed with UCP1 nanobody
    • Protein or peptide: UCP1 Nanobody
    • Protein or peptide: Mitochondrial carrier homolog 2,Mitochondrial brown fat uncoupling protein 1

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Supramolecule #1: MTCH2 hyperactive mutant K25E Y235A V238D complexed with UCP1 nanobody

SupramoleculeName: MTCH2 hyperactive mutant K25E Y235A V238D complexed with UCP1 nanobody
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Human MTCH2 hyperactive mutant K25E V238D Y235A with the cytosolic loop between TM4 and TM5 replaced by the anti-UCP1 nanobody recognition epitope from UCP1 in complex with the anti-UCP1 ...Details: Human MTCH2 hyperactive mutant K25E V238D Y235A with the cytosolic loop between TM4 and TM5 replaced by the anti-UCP1 nanobody recognition epitope from UCP1 in complex with the anti-UCP1 nanobody pMb65 (modified to permit NabFab binding).
Source (natural)Organism: Homo sapiens (human) / Organelle: Mitochondrion / Location in cell: Mitochondrial outer membrane

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Macromolecule #1: UCP1 Nanobody

MacromoleculeName: UCP1 Nanobody / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 13.913538 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
GQRQLVESGG GLVQPGGSLR LSCAASGRTS STYTMGWFRQ APGKEREFVA AISWTGTPYY ADSVKGRFTI SRDNAKNTVY LQMNSLEPE DTAVYYCAAA RPGLFIFVSD YARTAKYDYW GKGTPVTV

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Macromolecule #2: Mitochondrial carrier homolog 2,Mitochondrial brown fat uncouplin...

MacromoleculeName: Mitochondrial carrier homolog 2,Mitochondrial brown fat uncoupling protein 1
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 33.480988 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MADAASQVLL GSGLTILSQP LMYVEVLIQV GYEPLPPTIG RNIFGRQVCQ LPGLFSYAQH IASIDGRRGL FTGLTPRLCS GVLGTVVHG KVLQHYQESD KGEELGPGNV QKEVSSSFDH VIKETTREMI ARSAATLITH PFHVITLRSM VQFIGRESKY C GLCDSIIT ...String:
MADAASQVLL GSGLTILSQP LMYVEVLIQV GYEPLPPTIG RNIFGRQVCQ LPGLFSYAQH IASIDGRRGL FTGLTPRLCS GVLGTVVHG KVLQHYQESD KGEELGPGNV QKEVSSSFDH VIKETTREMI ARSAATLITH PFHVITLRSM VQFIGRESKY C GLCDSIIT IYREEGILGF FAGLVPRLLG DILSLWLCNS VYYLMKEAFV KNNILADDVP CHLVSQAVAG FFASMLTAPF DL VSNLMAV NNCGLAGGCP PYSPIYTSWI DCWCMLQKEG NMSRGNSLFF RKVPFGKTYC CDLKMLI

UniProtKB: Mitochondrial carrier homolog 2, Mitochondrial brown fat uncoupling protein 1, 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

Concentration4.9 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: 1 / Number real images: 10816 / 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: 3547162
Details: 9,633 out of 10,816 micrographs were selected for downstream processing. A total of 3,547,162 particles from blob picker and template picker were obtained. After running 7 rounds of ...Details: 9,633 out of 10,816 micrographs were selected for downstream processing. A total of 3,547,162 particles from blob picker and template picker were obtained. After running 7 rounds of heterogenous refinement, 612,877 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: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7.0)
Details: Final map generated by local refinement in cryoSPARC using a soft mask encompassing MTCH2 only.
Number images used: 612877
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
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
ChainPDB ID
chain_id: A, source_name: AlphaFold, initial_model_type: in silico model
chain_id: B, source_name: PDB, initial_model_type: experimental model

8hbv

SoftwareName: Coot (ver. 0.9.8.95)
DetailsInitial fitting was done using Coot and refined by Phenix cryo-EM real space refinement.
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 194 / Target criteria: Real-space correlation coefficient
Output model

PDB-12pb:
Single particle cryo-EM structure of human MTCH2 (hyperactive mutant K25E Y235A V238D)

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