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- EMDB-31584: Structure of the human Meckelin -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-31584
TitleStructure of the human Meckelin
Map data
Sample
  • Complex: homodimer of Meckelin
    • Protein or peptide: Meckelin
KeywordsCryo-EM / MEMBRANE PROTEIN
Function / homology
Function and homology information


MKS complex / negative regulation of centrosome duplication / filamin binding / ciliary transition zone / non-canonical Wnt signaling pathway / ciliary membrane / cilium assembly / ERAD pathway / Anchoring of the basal body to the plasma membrane / cytoplasmic vesicle membrane ...MKS complex / negative regulation of centrosome duplication / filamin binding / ciliary transition zone / non-canonical Wnt signaling pathway / ciliary membrane / cilium assembly / ERAD pathway / Anchoring of the basal body to the plasma membrane / cytoplasmic vesicle membrane / unfolded protein binding / centrosome / endoplasmic reticulum membrane
Similarity search - Function
Meckelin / Meckelin (Transmembrane protein 67) / Growth factor receptor cysteine-rich domain superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.34 Å
AuthorsGong DS
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Sci Adv / Year: 2021
Title: Structure of the human Meckel-Gruber protein Meckelin.
Authors: Dongliang Liu / Dandan Qian / Huaizong Shen / Deshun Gong /
Abstract: Mutations in the gene account for most cases of the Meckel-Gruber syndrome, the most severe ciliopathy with a 100% mortality rate. Here, we report a 3.3-Å cryo–electron microscopy structure of ...Mutations in the gene account for most cases of the Meckel-Gruber syndrome, the most severe ciliopathy with a 100% mortality rate. Here, we report a 3.3-Å cryo–electron microscopy structure of human Meckelin (also known as TMEM67 and MKS3). The structure reveals a unique protein fold consisting of an unusual cysteine-rich domain that folds as an arch bridge stabilized by 11 pairs of disulfide bonds, a previously uncharacterized domain named β sheet–rich domain, a previously unidentified seven-transmembrane fold wherein TM4 to TM6 are broken near the cytoplasmic surface of the membrane, and a coiled-coil domain placed below the transmembrane domain. Meckelin forms a stable homodimer with an extensive dimer interface. Our structure establishes a framework for dissecting the function and disease mechanisms of Meckelin.
History
DepositionJul 29, 2021-
Header (metadata) releaseDec 1, 2021-
Map releaseDec 1, 2021-
UpdateNov 6, 2024-
Current statusNov 6, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.022
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.022
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7fh1
  • Surface level: 0.022
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_31584.png

Downloads & links

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Map

FileDownload / File: emd_31584.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 240 pix.
= 260.88 Å		1.09 Å/pix.
x 240 pix.
= 260.88 Å		1.09 Å/pix.
x 240 pix.
= 260.88 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.087 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.022 / Movie #1: 0.022
Minimum - Maximum-0.05895717 - 0.117475115
Average (Standard dev.)0.00018673774 (±0.0037168593)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 260.88 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0871.0871.087
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z260.880260.880260.880
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ450450450
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS240240240
D min/max/mean-0.0590.1170.000

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Supplemental data

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Sample components

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Entire : homodimer of Meckelin

EntireName: homodimer of Meckelin
Components
  • Complex: homodimer of Meckelin
    • Protein or peptide: Meckelin

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Supramolecule #1: homodimer of Meckelin

SupramoleculeName: homodimer of Meckelin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Meckelin

MacromoleculeName: Meckelin / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 114.980438 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MATRGGAGVA MAVWSLLSAR AVTAFLLLFL PRFLQAQTFS FPFQQPEKCD NNQYFDISAL SCVPCGANQR QDARGTSCVC LPGFQMISN NGGPAIICKK CPENMKGVTE DGWNCISCPS DLTAEGKCHC PIGHILVERD INGTLLSQAT CELCDGNENS F MVVNALGD ...String:
MATRGGAGVA MAVWSLLSAR AVTAFLLLFL PRFLQAQTFS FPFQQPEKCD NNQYFDISAL SCVPCGANQR QDARGTSCVC LPGFQMISN NGGPAIICKK CPENMKGVTE DGWNCISCPS DLTAEGKCHC PIGHILVERD INGTLLSQAT CELCDGNENS F MVVNALGD RCVRCEPTFV NTSRSCACSE PNILTGGLCF SSTGNFPLRR ISAARYGEVG MSLTSEWFAK YLQSSAAACW VY ANLTSCQ ALGNMCVMNM NSYDFATFDA CGLFQFIFEN TAGLSTVHSI SFWRQNLPWL FYGDQLGLAP QVLSSTSLPT NFS FKGENQ NTKLKFVAAS YDIRGNFLKW QTLEGGVLQL CPDTETRLNA AYSFGTTYQQ NCEIPISKIL IDFPTPIFYD VYLE YTDEN QHQYILAVPV LNLNLQHNKI FVNQDSNSGK WLLTRRIFLV DAVSGRENDL GTQPRVIRVA TQISLSVHLV PNTIN GNIY PPLITIAYSD IDIKDANSQS VKVSFSVTYE MDHGEAHVQT DIALGVLGGL AVLASLLKTA GWKRRIGSPM IDLQTV VKF LVYYAGDLAN VFFIITVGTG LYWLIFFKAQ KSVSVLLPMP IQEERFVTYV GCAFALKALQ FLHKLISQIT IDVFFID WE RPKGKVLKAV EGEGGVRSAT VPVSIWRTYF VANEWNEIQT VRKINSLFQV LTVLFFLEVV GFKNLALMDS SSSLSRNP P SYIAPYSCIL RYAVSAALWL AIGIIQVVFF AVFYERFIED KIRQFVDLCS MSNISVFLLS HKCFGYYIHG RSVHGHADT NMEEMNMNLK REAENLCSQR GLVPNTDGQT FEIAISNQMR QHYDRIHETL IRKNGPARLL SSSASTFEQS IKAYHMMNKF LGSFIDHVH KEMDYFIKDK LLLERILGME FMEPMEKSIF YNDEGYSFSS VLYYGNEATL LIFDLLFFCV VDLACQNFIL A SFLTYLQQ EIFRYIRNTV GQKNLASKTL VDQRFLILEG SHHHHHHHHH HGSVEDYKDD DDK

UniProtKB: Meckelin

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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

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.34 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 219967
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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