[English] 日本語
Yorodumi
- EMDB-53323: Cryo-EM structure of the MMM ubiquitin ligase complex with nanobo... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-53323
TitleCryo-EM structure of the MMM ubiquitin ligase complex with nanobody 270 (Composite map)
Map dataComposite map for high-resolution MEGF8-MOSMO-nanobody 270 and low-resolution MEGF8 ICD-MGRN1. Wild-type MMM.
Sample
  • Complex: Human MEGF8-MOSMO-MGRN1 (MMM) ternary complex bound to nanobody 270
    • Complex: MOSMO
      • Protein or peptide: Modulator of smoothened protein
    • Complex: MEGF8
      • Protein or peptide: Isoform 2 of Multiple epidermal growth factor-like domains protein 8
    • Complex: Nanobody 270
      • Protein or peptide: Nanobody 270
    • Complex: MGRN1
      • Protein or peptide: Isoform 4 of E3 ubiquitin-protein ligase MGRN1
  • Ligand: ZINC ION
  • Ligand: PALMITIC ACID
  • Ligand: (1~{S},2~{S},4~{S},5'~{R},6~{R},7~{S},8~{R},9~{S},12~{S},13~{R},16~{S})-16-methoxy-5',7,9,13-tetramethyl-spiro[5-oxapentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icos-18-ene-6,2'-oxane]
  • Ligand: water
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


epiboly involved in gastrulation with mouth forming second / negative regulation of melanin biosynthetic process / determination of digestive tract left/right asymmetry / determination of heart left/right asymmetry / craniofacial suture morphogenesis / embryonic heart tube left/right pattern formation / left/right pattern formation / fasciculation of sensory neuron axon / cell migration involved in gastrulation / pharyngeal arch artery morphogenesis ...epiboly involved in gastrulation with mouth forming second / negative regulation of melanin biosynthetic process / determination of digestive tract left/right asymmetry / determination of heart left/right asymmetry / craniofacial suture morphogenesis / embryonic heart tube left/right pattern formation / left/right pattern formation / fasciculation of sensory neuron axon / cell migration involved in gastrulation / pharyngeal arch artery morphogenesis / positive regulation of eating behavior / embryonic skeletal system morphogenesis / embryonic skeletal system development / positive regulation of axon extension involved in axon guidance / limb morphogenesis / negative regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / embryonic brain development / embryonic heart tube morphogenesis / coronary vasculature development / embryonic limb morphogenesis / regulation of neuron differentiation / negative regulation of G protein-coupled receptor signaling pathway / embryonic digit morphogenesis / aorta development / ciliary membrane / smoothened signaling pathway / endosome to lysosome transport / BMP signaling pathway / protein monoubiquitination / ubiquitin ligase complex / lung development / negative regulation of smoothened signaling pathway / protein sequestering activity / regulation of protein stability / RING-type E3 ubiquitin transferase / protein polyubiquitination / ubiquitin-protein transferase activity / intracellular protein localization / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / heart development / regulation of gene expression / protein-containing complex assembly / gene expression / in utero embryonic development / early endosome / cell differentiation / protein ubiquitination / calcium ion binding / endoplasmic reticulum / Golgi apparatus / extracellular exosome / zinc ion binding / membrane / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
E3 ubiquitin-protein ligase MGRN1/RNF157-like / : / RNF157-like N-terminal domain / : / Attractin/LZTR1 beta-propeller / Modulator of smoothened protein / Attenuator of Hedgehog / EGF domain / : / Laminin/attractin EGF domain ...E3 ubiquitin-protein ligase MGRN1/RNF157-like / : / RNF157-like N-terminal domain / : / Attractin/LZTR1 beta-propeller / Modulator of smoothened protein / Attenuator of Hedgehog / EGF domain / : / Laminin/attractin EGF domain / EGF domain / Laminin-type EGF-like (LE) domain profile. / Laminin-type EGF-like (LE) domain signature. / Laminin-type epidermal growth factor-like domai / Laminin EGF domain / Laminin-type EGF domain / Plexin repeat / Plexin repeat / CUB domain / Domain first found in C1r, C1s, uEGF, and bone morphogenetic protein. / CUB domain / Spermadhesin, CUB domain superfamily / CUB domain profile. / : / Calcium-binding EGF domain / Kelch-type beta propeller / Zinc finger, C3HC4 type (RING finger) / PSI domain / domain found in Plexins, Semaphorins and Integrins / EGF-type aspartate/asparagine hydroxylation site / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Epidermal growth factor-like domain. / EGF-like domain profile. / Ring finger / EGF-like domain signature 1. / EGF-like domain signature 2. / EGF-like domain / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
E3 ubiquitin-protein ligase MGRN1 / 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: 3.03 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 N / Sarkar P / Lartey D / Gao L / Pardon E / Milenkovic L / Chalk R / Steyaert J / Bazan F / Rouse S / ...Authors: Williams C / Nocka LM / Hedger G / Carrique L / Pusapati GV / Parashara P / Latorraca N / Sarkar P / Lartey D / Gao L / Pardon E / Milenkovic L / Chalk R / Steyaert J / Bazan F / Rouse S / Marqusee S / Kong JH / Siebold C / Rohatgi R
History
DepositionApr 4, 2025-
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_53323.png

Downloads & links

-
Map

FileDownload / File: emd_53323.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationComposite map for high-resolution MEGF8-MOSMO-nanobody 270 and low-resolution MEGF8 ICD-MGRN1. Wild-type MMM.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (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: 5.9
Minimum - Maximum-55.129562 - 70.9602
Average (Standard dev.)0.0010343497 (±0.9343732)
SymmetrySpace group: 1
Details

EMDB XML:

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

-
Supplemental data

-
Sample components

+
Entire : Human MEGF8-MOSMO-MGRN1 (MMM) ternary complex bound to nanobody 270

EntireName: Human MEGF8-MOSMO-MGRN1 (MMM) ternary complex bound to nanobody 270
Components
  • Complex: Human MEGF8-MOSMO-MGRN1 (MMM) ternary complex bound to nanobody 270
    • Complex: MOSMO
      • Protein or peptide: Modulator of smoothened protein
    • Complex: MEGF8
      • Protein or peptide: Isoform 2 of Multiple epidermal growth factor-like domains protein 8
    • Complex: Nanobody 270
      • Protein or peptide: Nanobody 270
    • Complex: MGRN1
      • Protein or peptide: Isoform 4 of E3 ubiquitin-protein ligase MGRN1
  • Ligand: ZINC ION
  • Ligand: PALMITIC ACID
  • Ligand: (1~{S},2~{S},4~{S},5'~{R},6~{R},7~{S},8~{R},9~{S},12~{S},13~{R},16~{S})-16-methoxy-5',7,9,13-tetramethyl-spiro[5-oxapentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icos-18-ene-6,2'-oxane]
  • Ligand: water

+
Supramolecule #1: Human MEGF8-MOSMO-MGRN1 (MMM) ternary complex bound to nanobody 270

SupramoleculeName: Human MEGF8-MOSMO-MGRN1 (MMM) ternary complex bound to nanobody 270
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
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.
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 MEGF8, MOSMO and MGRN1 to form the MMM complex.
Source (natural)Organism: Homo sapiens (human)

+
Supramolecule #3: MEGF8

SupramoleculeName: MEGF8 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3
Details: MEGF8 was co-expressed with MOSMO and MGRN1 to form the MMM complex.
Source (natural)Organism: Homo sapiens (human)

+
Supramolecule #4: Nanobody 270

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

+
Supramolecule #5: MGRN1

SupramoleculeName: MGRN1 / type: complex / ID: 5 / Parent: 1 / Macromolecule list: #1
Details: MGRN1 was co-expressed with MEGF8 and MOSMO to form the MMM complex.
Source (natural)Organism: Homo sapiens (human)

+
Macromolecule #1: Isoform 4 of E3 ubiquitin-protein ligase MGRN1

MacromoleculeName: Isoform 4 of E3 ubiquitin-protein ligase MGRN1 / type: protein_or_peptide / ID: 1
Details: Full-length human MGRN1 R317E with C-terminal His-6 tag.
Number of copies: 1 / Enantiomer: LEVO / EC number: RING-type E3 ubiquitin transferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 59.454988 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGSILSRRIA GVEDIDIQAN SAYRYPPKSG NYFASHFFMG GEKFDTPHPE GYLFGENMDL NFLGSRPVQF PYVTPAPHEP VKTLRSLVN IRKDSLRLVR YKDDADSPTE DGDKPRVLYS LEFTFDADAR VAITIYCQAS EEFLNGRAVY SPKSPSLQSE T VHYKRGVS ...String:
MGSILSRRIA GVEDIDIQAN SAYRYPPKSG NYFASHFFMG GEKFDTPHPE GYLFGENMDL NFLGSRPVQF PYVTPAPHEP VKTLRSLVN IRKDSLRLVR YKDDADSPTE DGDKPRVLYS LEFTFDADAR VAITIYCQAS EEFLNGRAVY SPKSPSLQSE T VHYKRGVS QQFSLPSFKI DFSEWKDDEL NFDLDRGVFP VVIQAVVDEG DVVEVTGHAH VLLAAFEKHM DGSFSVKPLK QK QIVDRVS YLLQEIYGIE NKNNQETKPS DDENSDNSNE CVVCLSDLRD TLILPCRHLC LCTSCADTLR YQANNCPICE LPF RALLQI RAVRKKPGAL SPVSFSPVLA QSLEHDEHSN SDSVPPGYEP ISLLEALNGL RAVSPAIPSA PLYEEITYSG ISDG LSQAS CPLAAIDHIL DSSRQKGRPQ SKAPDSTLRS PSSPIHEEDE EKLSEDVDAP PPLGGAELAL RESSSPESFI TEEVD ESSS PQQGTRAASI ENVLQDSSPE HCGRGPPADI YLPALGPDSC SVGIDEGTKH HHHHH

UniProtKB: E3 ubiquitin-protein ligase MGRN1

+
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 cleavage site-TwinStrep tags. C164 is palmitoylated (PLM).
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.594246 KDa
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: 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: 3
Details: Human MEGF8 (residues 2312-2778) with C-terminal 1D4 epitope tag.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 50.352977 KDa
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 CVLLWKAKQA LDQRQEQRRH LQEMTKMASR PFA KVTVCF PPDPTAPASA WKPAGLPPPA FRRSEPFLAP LLLTGAGGPW GPMGGGCCPP AIPATTAGLR AGPITLEPTE DGMA GVATL LLQLPGGPHA PNGACLGSAL VTLRHRLHEY CGGGGGAGGS GHGTGAGRKG LLSQDNLTSM SLGTETSQVA PA

UniProtKB: Multiple epidermal growth factor-like domains protein 8

+
Macromolecule #4: Nanobody 270

MacromoleculeName: Nanobody 270 / type: protein_or_peptide / ID: 4 / Details: Nanobody 270 with C-terminal His6-EPEA tag. / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Lama glama (llama)
Molecular weightTheoretical: 14.378924 KDa
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)
SequenceString:
QVQLVESGGG LVQAGGSLRL SCAASGSIFS YDDMGWYRQA PGKQRELVAT FTNVGSTNYV DSVKGRFTIS RDNAKNTVYL QMNSLKPED TAVYYCHAYT VRRFQGMEYW GKGTQVTVSS HHHHHHEPEA

+
Macromolecule #5: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 5 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

+
Macromolecule #6: PALMITIC ACID

MacromoleculeName: PALMITIC ACID / type: ligand / ID: 6
Details: Human MOSMO with C-terminal 3C protease cleavage site-TwinStrep tags. C164 is palmitoylated (PLM).
Number of copies: 1 / Formula: PLM
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 256.424 Da
Chemical component information

ChemComp-PLM:
PALMITIC ACID

+
Macromolecule #7: (1~{S},2~{S},4~{S},5'~{R},6~{R},7~{S},8~{R},9~{S},12~{S},13~{R},1...

MacromoleculeName: (1~{S},2~{S},4~{S},5'~{R},6~{R},7~{S},8~{R},9~{S},12~{S},13~{R},16~{S})-16-methoxy-5',7,9,13-tetramethyl-spiro[5-oxapentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icos-18-ene-6,2'-oxane]
type: ligand / ID: 7 / Number of copies: 1 / Formula: A1JAX
Molecular weightTheoretical: 428.647 Da

+
Macromolecule #8: water

MacromoleculeName: water / type: ligand / ID: 8 / Number of copies: 26 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

-
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: 12956 / Average exposure time: 3.1 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: 4203652
Details: 2D classes from a Glacios screening dataset facilitated template particle picking
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: The high-resolution binary MEGF8-MOSMO complex (PDB 9QQS) and an AlphaFold3 model of MMM complex (with two Zn2+ ions) were merged and docked in the map using fit-in-map tool in ChimeraX.
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.03 Å / Resolution method: OTHER / Software - Name: cryoSPARC
Details: Using map alone (d99), resolution was estimated in Phenix real-space refinement of the composite map.
Number images used: 223808
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

-
Atomic model buiding 1

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

9qqs

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
Output model

PDB-9qru:
Cryo-EM structure of the MMM ubiquitin ligase complex with nanobody 270 (Composite map)

+
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