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- EMDB-41432: C. elegans TMC-2 complex, focused refinement of dimer interface -

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Basic information

Entry
Database: EMDB / ID: EMD-41432
TitleC. elegans TMC-2 complex, focused refinement of dimer interface
Map data
Sample
  • Complex: C. elegans TMC-2 complex
    • Protein or peptide: Transmembrane channel-like protein TMC-2
    • Protein or peptide: Calcium and integrin binding protein CALM-1
    • Protein or peptide: Transmembrane inner ear protein TMIE
KeywordsMechanosensory transduction Macromolecular complex C. elegans / MEMBRANE PROTEIN
Biological speciesCaenorhabditis elegans (invertebrata)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsClark S / Jeong H / Goehring A / Posert R / Gouaux E
Funding support United States, 1 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: To Be Published
Title: Architecture of the TMC-2 complex from C. elegans
Authors: Clark S / Jeong H / Goehring A / Posert R / Gouaux E
History
DepositionAug 2, 2023-
Header (metadata) releaseAug 28, 2024-
Map releaseAug 28, 2024-
UpdateAug 28, 2024-
Current statusAug 28, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41432.png

Downloads & links

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Map

FileDownload / File: emd_41432.map.gz / Format: CCP4 / Size: 347.6 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 450 pix.
= 373.95 Å		0.83 Å/pix.
x 450 pix.
= 373.95 Å		0.83 Å/pix.
x 450 pix.
= 373.95 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.831 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.277
Minimum - Maximum-1.1272932 - 1.7369807
Average (Standard dev.)0.0011314675 (±0.026996259)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions450450450
Spacing450450450
CellA=B=C: 373.94998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_41432_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_41432_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 : C. elegans TMC-2 complex

EntireName: C. elegans TMC-2 complex
Components
  • Complex: C. elegans TMC-2 complex
    • Protein or peptide: Transmembrane channel-like protein TMC-2
    • Protein or peptide: Calcium and integrin binding protein CALM-1
    • Protein or peptide: Transmembrane inner ear protein TMIE

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Supramolecule #1: C. elegans TMC-2 complex

SupramoleculeName: C. elegans TMC-2 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Caenorhabditis elegans (invertebrata)

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Macromolecule #1: Transmembrane channel-like protein TMC-2

MacromoleculeName: Transmembrane channel-like protein TMC-2 / type: protein_or_peptide / ID: 1 / Enantiomer: DEXTRO
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
SequenceString: MPKSGAHQPL VRHDTDDGGE TGQSVKSLAD VSEEEIDSRM SRRSSVIADL LSLFRRSSSV LVRPHTRLGN PNFDDDDDEF DEEDDKEASK DRILKKIQQK KEIIQKLRGQ PWYMKRKRRT LKVAQKHLQQ QEAKVSKARL YKAEAGRRLT QASRWLDNLK IYLIPWEAKI ...String:
MPKSGAHQPL VRHDTDDGGE TGQSVKSLAD VSEEEIDSRM SRRSSVIADL LSLFRRSSSV LVRPHTRLGN PNFDDDDDEF DEEDDKEASK DRILKKIQQK KEIIQKLRGQ PWYMKRKRRT LKVAQKHLQQ QEAKVSKARL YKAEAGRRLT QASRWLDNLK IYLIPWEAKI RKIESHFGSV VSSYFTFHRW VLGVNITITF IMCMFVVIPE WLADSRTQFG DDRYNKTKAI KVMPPAVRAR ADELSTVWDF GGYFQYSLLF YGFYSKETFF GETIKYRVPV AYFFCNIFIL GFSLFIILRK MAANNRRGTL SSGKTQQYLF NWKAFTGWDY TIGNPETAGN VYMANVIKFR EAINDDKQKP SDKHPWIRFV ARVLTNLFIC AMYVFSIWAI MQCGTLKGEH FFAQNATAIT ISLITLVFPN IFDLLGKIEK LHPRNALRFQ LGRVLVLYIL NYYTLIYSLM LQLEHLQKEK NASDNPISAL GHPGDAIGRT IRETVLPRYP VDNNPHTYYS YAPVTTTPIP ATSSWTTVLP DFGPFGVYNP KASVTKDDTV FSSPVVETHM FGPNSDWNET TVNAASPTGA TTRASLRMSQ GGLCWETIIG QEITKLVTMD LYMTVASIFL IDFLRGLACR YLNLYWPWDL ERTFPEYGEF KVAENVLHLV NNQGMIWLGL FFVPLLPMLN NIKLIILMYI RGWAAMTCNV PASQIFRASR SSNFFFALLI LFLFLCTLPV GFVIASKTPS KSCGPFGNQS FFYSVITDVL HENLDKTLVN GIKYSLSPGI IIPVLVLLSL VIYFLIAMVT GLSQANQDLS FQLMVERTEE KKKIFELAGG KKKKSKDNTF GKQKPKQLLP PPTKGVSSDD DSQHNRSTAK SVSGRQFVPS LGSVSEVDHS TGEEQSSDSE STTSSLPPKL SLRQRFLVCI GWADPNKYGR HDDIEMEEGG GRLRELSTGS ETDSDDEDSE KSNRDMSYRT AIQSFDQNSQ SASASSSKST TTAPSNSEMR IEITENPLHT YITPLRIEKK SSASSSSSSH QPSSSIEKQA ARRLLQPIST THNIRYGVAT VENSSQDPTR PPSTDDSLGD PALHEPLWAN LNPHSSYTSA MMSPIMNEVM SNDETTDDEK GRLIPDRPPI PHSPRELKRL KREKDQQSES GSKPSTPRPP RFRISMSPPR KPPSEKNDSD SSNRKYEMRV EKSPKKPKKS DND

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Macromolecule #2: Calcium and integrin binding protein CALM-1

MacromoleculeName: Calcium and integrin binding protein CALM-1 / type: protein_or_peptide / ID: 2 / Enantiomer: DEXTRO
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
SequenceString: MGNNASSLSE LNLFSKGGVF TREQLDEYQD CTFFTRKDII RLYKRFYALN PHKVPTNMQG NRPAITTLTF EEVEKMPELK ENPFKRRICE VFSEDGRGNL SFDDFLDMFS VFSEMAPLQL KLKYAFRIYD YDGDELLGHD DLSKMIRSLT RDELSDVEVE FIIERIIEEA ...String:
MGNNASSLSE LNLFSKGGVF TREQLDEYQD CTFFTRKDII RLYKRFYALN PHKVPTNMQG NRPAITTLTF EEVEKMPELK ENPFKRRICE VFSEDGRGNL SFDDFLDMFS VFSEMAPLQL KLKYAFRIYD YDGDELLGHD DLSKMIRSLT RDELSDVEVE FIIERIIEEA DLDGDSSINF AEFEHVVSRS PDFIRTFHIR I

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Macromolecule #3: Transmembrane inner ear protein TMIE

MacromoleculeName: Transmembrane inner ear protein TMIE / type: protein_or_peptide / ID: 3 / Enantiomer: DEXTRO
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
SequenceString:
MPSGNEEINH LSALDQFVAP GLRLWMLIAL VGGVLLIMIV IVCCFMRIRI PRTKRQIDLI AAKRKLRKST KNSAEANAHN DERAQAIVMN SMPSGGGGGA PSTSSSRHTG SRIQSQV

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statetissue

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Sample preparation

Concentration0.003 mg/mL
BufferpH: 8 / Details: 50 mM Tris pH 8.0, 150 mM NaCl, 0.02% GDN
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV
DetailsNative TMC-2 complex, isolated from transgenic C. elegans.

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Electron microscopy

MicroscopeFEI TITAN 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 / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7usw

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 207726
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC

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