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- EMDB-53340: Cryo-EM structure of the MMM ubiquitin ligase complex with nanobo... -

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Basic information

Entry
Database: EMDB / ID: EMD-53340
TitleCryo-EM structure of the MMM ubiquitin ligase complex with nanobody 992 (Composite map)
Map data
Sample
  • Complex: Human MEGF8-MOSMO-MGRN1 (MMM) ternary complex bound to nanobody 992
    • 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 992
      • Protein or peptide: Nanobody 992
    • 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: 3.5 Å
AuthorsWilliams C / Carrique L / Pardon E / Nocka LM / Hedger G / Pusapati GV / Parashara P / Sarkar P / Latorraca NR / Lartey D ...Williams C / Carrique L / Pardon E / Nocka LM / Hedger G / Pusapati GV / Parashara P / Sarkar P / Latorraca NR / Lartey D / Gao L / Milenkovic L / 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 / Steyaert J / Bazan F / Rouse SL / Marqusee ...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 / Steyaert J / Bazan F / Rouse SL / 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

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Structure visualization

Supplemental images

emd_53340.png

Downloads & links

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Map

FileDownload / File: emd_53340.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
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: 9.699999999999999
Minimum - Maximum-58.741549999999997 - 84.653540000000007
Average (Standard dev.)-0.0018576882 (±0.9369021)
SymmetrySpace group: 1
Details

EMDB XML:

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

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Supplemental data

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Sample components

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Entire : Human MEGF8-MOSMO-MGRN1 (MMM) ternary complex bound to nanobody 992

EntireName: Human MEGF8-MOSMO-MGRN1 (MMM) ternary complex bound to nanobody 992
Components
  • Complex: Human MEGF8-MOSMO-MGRN1 (MMM) ternary complex bound to nanobody 992
    • 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 992
      • Protein or peptide: Nanobody 992
    • 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

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Supramolecule #1: Human MEGF8-MOSMO-MGRN1 (MMM) ternary complex bound to nanobody 992

SupramoleculeName: Human MEGF8-MOSMO-MGRN1 (MMM) ternary complex bound to nanobody 992
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 992, from E. coli WK6 cells, was added to MMM complex and the MMM-nanobody 992 complex formed on size-exclusion chromatography.
Source (natural)Organism: Homo sapiens (human)

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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)

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Supramolecule #3: MEGF8

SupramoleculeName: MEGF8 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3
Details: MEGF8 was co-expressed with MOSMO and MGRN1, then the complex was purified on size-exclusion chromatography with nanobody 992.
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #4: Nanobody 992

SupramoleculeName: Nanobody 992 / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #4
Source (natural)Organism: Lama glama (llama)

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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)

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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

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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. Cys164 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

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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

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Macromolecule #4: Nanobody 992

MacromoleculeName: Nanobody 992 / type: protein_or_peptide / ID: 4 / Details: Nanobody 992 with C-terminal His6-EPEA tags. / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Lama glama (llama)
Molecular weightTheoretical: 13.833139 KDa
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)
SequenceString:
QVQLVESGGG LVQVGGSLTL SCAASGRIFN IDGMGWFRQA AGKQSEWVAG VSKDGSRNYE DFAKGRFTVS RDNAKNTVYL QMNNLKPED TAVYYCAVRI DNGDDYWGQG TQVTVSSHHH HHHEPEA

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Macromolecule #5: ZINC ION

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

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Macromolecule #6: PALMITIC ACID

MacromoleculeName: PALMITIC ACID / type: ligand / ID: 6 / Number of copies: 1 / Formula: PLM
Molecular weightTheoretical: 256.424 Da
Chemical component information

ChemComp-PLM:
PALMITIC ACID

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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

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Macromolecule #8: water

MacromoleculeName: water / type: ligand / ID: 8 / Number of copies: 6 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

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

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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: 11391 / 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

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Image processing

Particle selectionNumber selected: 1959769
Details: Blob picker initially was used to pick particles containing a detergent micelle.
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:

9qru


Details: MMM model (9QRU PDB) and an AlphaFold2 model of nanobody 992 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: 3.5 Å / Resolution method: OTHER / Software - Name: cryoSPARC (ver. 4.5.1) / Software - details: Local refinement
Details: Using map alone (d99), resolution was estimated in Phenix real-space refinement of the composite map.
Number images used: 187459
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

Initial model
PDB IDChainDetails

9qru

source_name: PDB, initial_model_type: experimental modelThe initial model consisted of chains A, B, D, F, G, H for PDB entry 9QRU.
source_name: AlphaFold, initial_model_type: in silico modelNanobody 992
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-9qsh:
Cryo-EM structure of the MMM ubiquitin ligase complex with nanobody 992 (Composite map)

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