[English] 日本語
Yorodumi
- EMDB-57249: Focused refinement of the helix-stabilized MEGF8-MOSMO complex wi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-57249
TitleFocused refinement of the helix-stabilized MEGF8-MOSMO complex with nanobody 270
Map data
Sample
  • Complex: Helix-stabilized human MEGF8-MOSMO binary complex bound to nanobody 270
    • Complex: MOSMO
      • Protein or peptide: Modulator of smoothened protein
    • Complex: Helix-stabilized MEGF8
      • Protein or peptide: Isoform 2 of Multiple epidermal growth factor-like domains protein 8
    • Complex: Nanobody 270
    • Protein or peptide: Nanobody 270
KeywordsE3 Ubiquitin Ligase / Hedgehog Signaling / Single-pass Membrane Protein / Membrane Protein Complex / Smoothened / Tetraspanin / Cell Surface Receptor / Primary Cilium / Morphogen / Signal Transduction / Human / Carpenter Syndrome / Cancer / Nanobody / Palmitoylation / GDN / MEMBRANE PROTEIN
Function / homology
Function and homology information


left/right pattern formation / embryonic skeletal system development / embryonic limb morphogenesis / regulation of neuron differentiation / ciliary membrane / smoothened signaling pathway / lung development / negative regulation of smoothened signaling pathway / regulation of protein stability / intracellular protein localization ...left/right pattern formation / embryonic skeletal system development / embryonic limb morphogenesis / regulation of neuron differentiation / ciliary membrane / smoothened signaling pathway / lung development / negative regulation of smoothened signaling pathway / regulation of protein stability / intracellular protein localization / heart development / gene expression / in utero embryonic development / cell differentiation / Golgi apparatus / plasma membrane
Similarity search - Function
Modulator of smoothened protein / Attenuator of Hedgehog
Similarity search - Domain/homology
Isoform 2 of Multiple epidermal growth factor-like domains protein 8 / Modulator of smoothened protein
Similarity search - Component
Biological speciesHomo sapiens (human) / Lama glama (llama)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.95 Å
AuthorsWilliams C / Carrique L / Pardon E / Nocka LM / Hedger G / Pusapati GV / Parashara P / Latorraca NR / Sarkar P / Lartey D ...Williams C / Carrique L / Pardon E / Nocka LM / Hedger G / Pusapati GV / Parashara P / Latorraca NR / Sarkar P / Lartey D / Gao L / Milenkovic L / Chalk R / Steyaert J / Bazan F / Rouse SL / Marqusee S / Kong JH / Rohatgi R / Siebold C
Funding support United Kingdom, 5 items
OrganizationGrant numberCountry
Cancer Research UKDRCRPG-May23/100002 United Kingdom
Cancer Research UKC20724/A26752 United Kingdom
Wellcome Trust218482/Z/19/Z United Kingdom
Wellcome Trust060208/Z/00/Z United Kingdom
Wellcome Trust093305/Z/10/Z United Kingdom
CitationJournal: Mol Cell / Year: 2026
Title: Design principles of a membrane-spanning ubiquitin ligase
Authors: Williams C / Nocka LM / Hedger G / Carrique L / Pusapati GV / Parashara P / Latorraca NR / Sarkar P / Lartey D / Gao L / Pardon E / Milenkovic L / Chalk R / Steyaert J / Bazan F / Rouse SL / ...Authors: Williams C / Nocka LM / Hedger G / Carrique L / Pusapati GV / Parashara P / Latorraca NR / Sarkar P / Lartey D / Gao L / Pardon E / Milenkovic L / Chalk R / Steyaert J / Bazan F / Rouse SL / Marqusee S / Kong JH / Siebold C / Rohatgi R
History
DepositionMar 19, 2026-
Header (metadata) releaseMay 27, 2026-
Map releaseMay 27, 2026-
UpdateMay 27, 2026-
Current statusMay 27, 2026Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_57249.png

Downloads & links

-
Map

FileDownload / File: emd_57249.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 480 pix.
= 350.544 Å		0.73 Å/pix.
x 480 pix.
= 350.544 Å		0.73 Å/pix.
x 480 pix.
= 350.544 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.7303 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.22
Minimum - Maximum-1.0473651 - 1.5849276
Average (Standard dev.)-0.0002872428 (±0.02247272)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 350.544 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_57249_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_57249_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_57249_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Helix-stabilized human MEGF8-MOSMO binary complex bound to nanobo...

EntireName: Helix-stabilized human MEGF8-MOSMO binary complex bound to nanobody 270
Components
  • Complex: Helix-stabilized human MEGF8-MOSMO binary complex bound to nanobody 270
    • Complex: MOSMO
      • Protein or peptide: Modulator of smoothened protein
    • Complex: Helix-stabilized MEGF8
      • Protein or peptide: Isoform 2 of Multiple epidermal growth factor-like domains protein 8
    • Complex: Nanobody 270
    • Protein or peptide: Nanobody 270

-
Supramolecule #1: Helix-stabilized human MEGF8-MOSMO binary complex bound to nanobo...

SupramoleculeName: Helix-stabilized human MEGF8-MOSMO binary complex bound to nanobody 270
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: MMM complex was obtained by co-expression of MEGF8, MOSMO and MGRN1 components in HEK293S GnTI- TetR cells. The MMM complex was purified by tandem affinity purification. Purified nanobody ...Details: MMM complex was obtained by co-expression of MEGF8, MOSMO and MGRN1 components in HEK293S GnTI- TetR cells. The MMM complex was purified by tandem affinity purification. Purified nanobody 270, from E. coli WK6 cells, was added to MMM complex and the MMM-nanobody 270 complex formed on size-exclusion chromatography. A focused refinement of extracellular and transmembrane regions of the MMM complex was performed to obtain this MEGF8-MOSMO map.
Source (natural)Organism: Homo sapiens (human)

-
Supramolecule #2: MOSMO

SupramoleculeName: MOSMO / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #2
Details: Ternary complex with MEGF8 and MGRN1 was obtained by co-expressing helix-stabilized MEGF8, MOSMO and MGRN1 to form the MMM complex.
Source (natural)Organism: Homo sapiens (human)

-
Supramolecule #3: Helix-stabilized MEGF8

SupramoleculeName: Helix-stabilized MEGF8 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #4
Details: Cytoplasmic helix of MEGF8 (residues 2605-2624) were replaced with E/RK repeats (EEEEKKKREEEERRRREEEK). MEGF8 was co-expressed with MOSMO and MGRN1, then the complex was purified on size- ...Details: Cytoplasmic helix of MEGF8 (residues 2605-2624) were replaced with E/RK repeats (EEEEKKKREEEERRRREEEK). MEGF8 was co-expressed with MOSMO and MGRN1, then the complex was purified on size-exclusion chromatography with nanobody 270.
Source (natural)Organism: Homo sapiens (human)

-
Supramolecule #4: Nanobody 270

SupramoleculeName: Nanobody 270 / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Lama glama (llama)

-
Macromolecule #2: Modulator of smoothened protein

MacromoleculeName: Modulator of smoothened protein / type: protein_or_peptide / ID: 2
Details: Human MOSMO with C-terminal 3C protease site-TwinStrep tags.
Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDKLTIISGC LFLAADIFAI ASIANPDWIN TGESAGALTV GLVRQCQTIH GRDRTCIPPR LPPEWVTTLF FIIMGIISLT VTCGLLVAS HWRREATKYA RWIAFTGMIL FCMAALIFPI GFYINEVGGQ PYKLPNNTVV GSSYVLFVLS IFFTIVGLLF A GKVCLPGG ...String:
MDKLTIISGC LFLAADIFAI ASIANPDWIN TGESAGALTV GLVRQCQTIH GRDRTCIPPR LPPEWVTTLF FIIMGIISLT VTCGLLVAS HWRREATKYA RWIAFTGMIL FCMAALIFPI GFYINEVGGQ PYKLPNNTVV GSSYVLFVLS IFFTIVGLLF A GKVCLPGG TLEVLFQGPG GSGSAWSHPQ FEKGGGSGGG SGGSAWSHPQ FEK

UniProtKB: Modulator of smoothened protein

-
Macromolecule #3: Nanobody 270

MacromoleculeName: Nanobody 270 / type: protein_or_peptide / ID: 3 / Details: Nanobody 270 with C-terminal His6-EPEA tags. / Enantiomer: LEVO
Source (natural)Organism: Lama glama (llama)
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)
SequenceString:
QVQLVESGGG LVQAGGSLRL SCAASGSIFS YDDMGWYRQA PGKQRELVAT FTNVGSTNYV DSVKGRFTIS RDNAKNTVYL QMNSLKPED TAVYYCHAYT VRRFQGMEYW GKGTQVTVSS HHHHHHEPEA

-
Macromolecule #4: Isoform 2 of Multiple epidermal growth factor-like domains protein 8

MacromoleculeName: Isoform 2 of Multiple epidermal growth factor-like domains protein 8
type: protein_or_peptide / ID: 4
Details: Cytoplasmic helix of human MEGF8 (residues 2605-2624) were replaced with E/RK repeats (EEEEKKKREEEERRRREEEK). Human MEGF8 has a C-terminal 1D4 tag.
Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: KCQCNGHADT CNEQDGTGCP CQNNTETGTC QGSSPSDRRD CYKYQCAKCR ESFHGSPLGG QQCYRLISVE QECCLDPTSQ TNCFHEPKR RALGPGRTVL FGVQPKFTNV DIRLTLDVTF GAVDLYVSTS YDTFVVRVAP DTGVHTVHIQ PPPAPPPPPP P ADGGPRGA ...String:
KCQCNGHADT CNEQDGTGCP CQNNTETGTC QGSSPSDRRD CYKYQCAKCR ESFHGSPLGG QQCYRLISVE QECCLDPTSQ TNCFHEPKR RALGPGRTVL FGVQPKFTNV DIRLTLDVTF GAVDLYVSTS YDTFVVRVAP DTGVHTVHIQ PPPAPPPPPP P ADGGPRGA GDPGGAGASS GPGAPAEPRV REVWPRGLIT YVTVTEPSAV LVVRGVRDRL VITYPHEHHA LKSSRFYLLL LG VGDPSGP GANGSADSQG LLFFRQDQAH IDLFVFFSVF FSCFFLFLSL CVLLWKEEEE KKKREEEERR RREEEKMASR PFA KVTVCF PPDPTAPASA WKPAGLPPPA FRRSEPFLAP LLLTGAGGPW GPMGGGCCPP AIPATTAGLR AGPITLEPTE DGMA GVATL LLQLPGGPHA PNGACLGSAL VTLRHRLHEY CGGGGGAGGS GHGTGAGRKG LLSQDNLTSM SLGTETSQVA PA

UniProtKB: Isoform 2 of Multiple epidermal growth factor-like domains protein 8

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration5 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
150.0 mMNaClsodium chloride
20.0 mMC8H19NO4SHEPES
2.0 % v/vC3H8O3glycerol
2.0 mMCaCl2calcium chloride
0.02 % w/vC19H36O10glycyl-dodecyl-beta-D-maltoside (GDN)

Details: 20 mM HEPES pH 7.5, 150 mM NaCl, 2% (v/v) glycerol, 2 mM CaCl2, 0.02% (w/v) GDN
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris X / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Number grids imaged: 1 / Number real images: 15995 / Average exposure time: 3.07 sec. / Average electron dose: 50.0 e/Å2 / Details: Images were collected in counted mode.
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.6 µm / Nominal defocus min: 1.6 µm / Nominal magnification: 165000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 3362125
Details: Particles initially picked from 2D templates (imported from EMD-53323 dataset).
CTF correctionDetails: Patch CTF estimation was performed in cryoSPARC live pre-processing.
Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

9qqs


Details: For helix-stabilized MEGF8-MOSMO-nanobody 270 sub-complex, wild-type MEGF8-MOSMO-nanobody 270 (9QQS PDB) was docked in the map using fit-in-map tool in ChimeraX. Mutated residues in the ...Details: For helix-stabilized MEGF8-MOSMO-nanobody 270 sub-complex, wild-type MEGF8-MOSMO-nanobody 270 (9QQS PDB) was docked in the map using fit-in-map tool in ChimeraX. Mutated residues in the MEGF8 cytoplasmic helix were manually changed in Coot.
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.95 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Software - details: Local refinement.
Details: Particle subtraction of the detergent micelle and cytoplasmic regions (MEGF8 ICD-MGRN1) was performed before local refinement of the MEGF8 (residues 2374-2614)-MOSMO-nanobody 270 complex.
Number images used: 120547
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationNumber classes: 3 / Avg.num./class: 109042
Details: 3D classification (without alignment) was performed in cryoSPARC using a mask around transmembrane and extracellular regions of the map (i.e. MOSMO, MEGF8 residues 2374-2580, nanobody 270).
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelPDB ID:

9qs6


Chain - Source name: PDB / Chain - Initial model type: experimental model
DetailsInitial local fitting was done using ChimeraX then manual model building in Coot was interspersed with real space refinement in Phenix.
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 98.3

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more