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- PDB-7ndg: Cryo-EM structure of the ternary complex between Netrin-1, Neogen... -

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Entry
Database: PDB / ID: 7ndg
TitleCryo-EM structure of the ternary complex between Netrin-1, Neogenin and Repulsive Guidance Molecule B
Components
  • NeogeninNEO1
  • Netrin-1
  • RGM domain family member B
  • Repulsive Guidance Molecule B (C-terminal region)
KeywordsSIGNALING PROTEIN / Signal transduction / cell surface receptors / neuron regeneration / cell migration / Netrin / Neogenin / Repulsive Guidance Molecule / complex structure / protein-protein interactions
Function / homology
Function and homology information


regulation of glial cell migration / chemorepulsion of axon / anterior/posterior axon guidance / Cdc42 protein signal transduction / Role of second messengers in netrin-1 signaling / Netrin-1 signaling / Regulation of commissural axon pathfinding by SLIT and ROBO / motor neuron migration / negative regulation of axon extension / substrate-dependent cell migration, cell extension ...regulation of glial cell migration / chemorepulsion of axon / anterior/posterior axon guidance / Cdc42 protein signal transduction / Role of second messengers in netrin-1 signaling / Netrin-1 signaling / Regulation of commissural axon pathfinding by SLIT and ROBO / motor neuron migration / negative regulation of axon extension / substrate-dependent cell migration, cell extension / Netrin mediated repulsion signals / mammary gland duct morphogenesis / positive regulation of cell motility / nuclear migration / DCC mediated attractive signaling / regulation of synapse assembly / inner ear morphogenesis / DSCAM interactions / basement membrane / endoplasmic reticulum-Golgi intermediate compartment / positive regulation of axon extension / glial cell proliferation / BMP signaling pathway / coreceptor activity / side of membrane / positive regulation of glial cell proliferation / cell-cell adhesion / actin cytoskeleton / Ras protein signal transduction / DNA-binding transcription factor activity, RNA polymerase II-specific / cell adhesion / membrane raft / RNA polymerase II cis-regulatory region sequence-specific DNA binding / apoptotic process / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / signal transduction / extracellular region / nucleoplasm / membrane / identical protein binding / plasma membrane / cytosol
Similarity search - Function
Repulsive guidance molecule, C-terminal / Repulsive guidance molecule, N-terminal / Repulsive guidance molecule / Repulsive guidance molecule (RGM) C-terminus / Repulsive guidance molecule (RGM) N-terminus / Neogenin, C-terminal / Neogenin C-terminus / Laminin, N-terminal / Laminin N-terminal (Domain VI) / Laminin N-terminal domain profile. ...Repulsive guidance molecule, C-terminal / Repulsive guidance molecule, N-terminal / Repulsive guidance molecule / Repulsive guidance molecule (RGM) C-terminus / Repulsive guidance molecule (RGM) N-terminus / Neogenin, C-terminal / Neogenin C-terminus / Laminin, N-terminal / Laminin N-terminal (Domain VI) / Laminin N-terminal domain profile. / Laminin N-terminal domain (domain VI) / 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 / Netrin C-terminal Domain / Netrin module, non-TIMP type / UNC-6/NTR/C345C module / Netrin domain / NTR domain profile. / Tissue inhibitor of metalloproteinases-like, OB-fold / Immunoglobulin domain / Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / EGF-like domain signature 1. / Fibronectin type III domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type-III domain profile. / Galactose-binding-like domain superfamily / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Netrin-1 / Repulsive guidance molecule B / Neogenin
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.98 Å
AuthorsRobinson, R.A. / Griffiths, S.C. / van de Haar, L.L. / Malinauskas, T. / van Battum, E.Y. / Zelina, P. / Schwab, R.A. / Karia, D. / Malinauskaite, L. / Brignani, S. ...Robinson, R.A. / Griffiths, S.C. / van de Haar, L.L. / Malinauskas, T. / van Battum, E.Y. / Zelina, P. / Schwab, R.A. / Karia, D. / Malinauskaite, L. / Brignani, S. / van den Munkhof, M. / Dudukcu, O. / De Ruiter, A.A. / Van den Heuvel, D.M.A. / Bishop, B. / Elegheert, J. / Aricescu, A.R. / Pasterkamp, R.J. / Siebold, C.
Funding support United Kingdom, Netherlands, 10items
OrganizationGrant numberCountry
Cancer Research UKC20724/A14414 United Kingdom
Cancer Research UKC20724/A26752 United Kingdom
European Research Council (ERC)647278 United Kingdom
Medical Research Council (MRC, United Kingdom)MR/L017776/1 United Kingdom
Medical Research Council (MRC, United Kingdom)MR/L009609/1 United Kingdom
Medical Research Council (MRC, United Kingdom)MC_UP_1201/15 United Kingdom
Wellcome Trust099675/Z/12/Z United Kingdom
Wellcome Trust090532/Z/09/Z United Kingdom
Netherlands Organisation for Scientific Research (NWO)ALW-VICI Netherlands
H2020 Marie Curie Actions of the European Commission289581 Netherlands
CitationJournal: Cell / Year: 2021
Title: Simultaneous binding of Guidance Cues NET1 and RGM blocks extracellular NEO1 signaling.
Authors: Ross A Robinson / Samuel C Griffiths / Lieke L van de Haar / Tomas Malinauskas / Eljo Y van Battum / Pavol Zelina / Rebekka A Schwab / Dimple Karia / Lina Malinauskaite / Sara Brignani / ...Authors: Ross A Robinson / Samuel C Griffiths / Lieke L van de Haar / Tomas Malinauskas / Eljo Y van Battum / Pavol Zelina / Rebekka A Schwab / Dimple Karia / Lina Malinauskaite / Sara Brignani / Marleen H van den Munkhof / Özge Düdükcü / Anna A De Ruiter / Dianne M A Van den Heuvel / Benjamin Bishop / Jonathan Elegheert / A Radu Aricescu / R Jeroen Pasterkamp / Christian Siebold /
Abstract: During cell migration or differentiation, cell surface receptors are simultaneously exposed to different ligands. However, it is often unclear how these extracellular signals are integrated. Neogenin ...During cell migration or differentiation, cell surface receptors are simultaneously exposed to different ligands. However, it is often unclear how these extracellular signals are integrated. Neogenin (NEO1) acts as an attractive guidance receptor when the Netrin-1 (NET1) ligand binds, but it mediates repulsion via repulsive guidance molecule (RGM) ligands. Here, we show that signal integration occurs through the formation of a ternary NEO1-NET1-RGM complex, which triggers reciprocal silencing of downstream signaling. Our NEO1-NET1-RGM structures reveal a "trimer-of-trimers" super-assembly, which exists in the cell membrane. Super-assembly formation results in inhibition of RGMA-NEO1-mediated growth cone collapse and RGMA- or NET1-NEO1-mediated neuron migration, by preventing formation of signaling-compatible RGM-NEO1 complexes and NET1-induced NEO1 ectodomain clustering. These results illustrate how simultaneous binding of ligands with opposing functions, to a single receptor, does not lead to competition for binding, but to formation of a super-complex that diminishes their functional outputs.
History
DepositionFeb 1, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 31, 2021Provider: repository / Type: Initial release
Revision 2.0Apr 28, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / citation ...atom_site / citation / em_entity_assembly / em_entity_assembly_molwt / em_entity_assembly_naturalsource / em_entity_assembly_recombinant / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_gen / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_torsion / struct_asym / struct_conf / struct_conn / struct_mon_prot_cis / struct_ref / struct_ref_seq / struct_ref_seq_dif / struct_sheet / struct_sheet_order / struct_sheet_range
Item: _atom_site.auth_asym_id / _atom_site.auth_comp_id ..._atom_site.auth_asym_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _entity_poly_seq.entity_id / _entity_poly_seq.mon_id / _entity_poly_seq.num / _pdbx_entity_nonpoly.entity_id / _pdbx_nonpoly_scheme.asym_id / _pdbx_nonpoly_scheme.entity_id / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_seq_id / _struct_mon_prot_cis.label_asym_id / _struct_mon_prot_cis.pdbx_label_asym_id_2

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Structure visualization

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Assembly

Deposited unit
A: Netrin-1
B: Neogenin
F: Repulsive Guidance Molecule B (C-terminal region)
N: RGM domain family member B
C: Repulsive Guidance Molecule B (C-terminal region)
G: Netrin-1
H: Neogenin
M: RGM domain family member B
D: Netrin-1
E: Neogenin
I: Repulsive Guidance Molecule B (C-terminal region)
O: RGM domain family member B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)391,64227
Polymers388,86712
Non-polymers2,77515
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance, Surface plasmon resonance-based experimental evidence for the assembly will be described by Robinson, Griffiths, van de Haar, Malinauskas et al., Cell, 2021., ...Evidence: surface plasmon resonance, Surface plasmon resonance-based experimental evidence for the assembly will be described by Robinson, Griffiths, van de Haar, Malinauskas et al., Cell, 2021., assay for oligomerization, Cellular assay-based experimental evidence for the assembly will be described by Robinson, Griffiths, van de Haar, Malinauskas et al., Cell, 2021., equilibrium centrifugation, Analytical ultracentrifugation (AUC)-based experimental evidence for the assembly will be described by Robinson, Griffiths, van de Haar, Malinauskas et al., Cell, 2021., gel filtration, Gel filtration/size-exclusion chromatography (SEC)-based experimental evidence for the assembly will be described by Robinson, Griffiths, van de Haar, Malinauskas et al., Cell, 2021., light scattering, Multi angle light scattering (MALS)-based experimental evidence for the assembly will be described by Robinson, Griffiths, van de Haar, Malinauskas et al., Cell, 2021.
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area26560 Å2
ΔGint-110 kcal/mol
Surface area139350 Å2
MethodPISA

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Components

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Protein , 4 types, 12 molecules AGDBHEFCINMO

#1: Protein Netrin-1 / / Epididymis tissue protein Li 131P / Netrin-1


Mass: 49227.402 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NTN1, NTN1L / Plasmid: pHLsec
Details (production host): Aricescu et al., Acta Crystallogr D Biol Crystallogr, 2006, PMID 17001101
Cell line (production host): HEK293T / Organ (production host): Kidney / Production host: Homo sapiens (human) / References: UniProt: O95631
#2: Protein Neogenin / NEO1


Mass: 39268.199 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Neo1 / Plasmid: pHLsec
Details (production host): Aricescu et al., Acta Crystallogr D Biol Crystallogr, 2006, PMID 17001101
Cell line (production host): HEK293T / Organ (production host): Kidney / Production host: Homo sapiens (human) / References: UniProt: Q7TQG5
#3: Protein Repulsive Guidance Molecule B (C-terminal region) / DRG11-responsive axonal guidance and outgrowth of neurite / DRAGON


Mass: 28104.494 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: Repulsive Guidance Molecule B / Source: (gene. exp.) Homo sapiens (human) / Gene: RGMB / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: Q6NW40
#4: Protein RGM domain family member B / DRG11-responsive axonal guidance and outgrowth of neurite / DRAGON


Mass: 13022.377 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: Repulsive Guidance Molecule B / Source: (gene. exp.) Homo sapiens (human) / Gene: RGMB / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: Q6NW40

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Non-polymers / Sugars , 2 types, 15 molecules

#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: Ca / Details: Repulsive Guidance Molecule B
#6: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Details

Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Cryo-EM structure of the ternary Netrin 1-Neogenin 1-Repulsive Guidance Molecule B complexCOMPLEX#1-#30MULTIPLE SOURCES
2Netrin 1COMPLEX#11RECOMBINANT
3NeogeninNEO1COMPLEX#21RECOMBINANT
4Repulsive Guidance Molecule BCOMPLEX#31RECOMBINANT
5Repulsive Guidance Molecule B C-terminal region (chain D)COMPLEX#51RECOMBINANT
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
110.50 MDaNO
220.39 MDaNO
330.039 MDaNO
440.18 MDaNO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
11Homo sapiens (human)9606
22Mus musculus (house mouse)10090
33Homo sapiens (human)9606
44Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
11Homo sapiens (human)9606
22Homo sapiens (human)9606
33Homo sapiens (human)9606
44Homo sapiens (human)9606
Buffer solutionpH: 7.5
Details: 10 mM HEPES pH 7.5, 150 mM NaCl, 2 mM CaCl2, 1 mM sucrose octasulfate, 0.01% NaN3
Buffer component
IDConc.NameFormulaBuffer-ID
110 mMHEPESC8H18N2O4S1
2150 mMSodium chlorideNaClSodium chloride1
32 mMCalcium chlorideCaCl21
41 mMSucrose octasulfate, sodium saltC12H14Na8O27S81
50.01 % (w/v)Sodium azideNaN31
SpecimenConc.: 0.07 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: The ternary NEO1-NET1-RGMB complex was purified by SEC on a S200 10/300 Increase column with a running buffer of 10 mM HEPES pH 7.5, 150 mM NaCl, 2 mM CaCl2, 1 mM sucrose octasulfate, 0.01% ...Details: The ternary NEO1-NET1-RGMB complex was purified by SEC on a S200 10/300 Increase column with a running buffer of 10 mM HEPES pH 7.5, 150 mM NaCl, 2 mM CaCl2, 1 mM sucrose octasulfate, 0.01% NaN3 at 4 degrees C . The peak fraction containing the ternary complex was diluted to 0.07 mg per ml in SEC buffer.
Specimen supportDetails: Agar Scientific Ultra-thin carbon support film, 3 nm - on lacey carbon. https://www.agarscientific.com/ultra-thin-carbon-support-film-3-nm-on-holey-carbon
Grid material: COPPER / Grid type: PELCO Ultrathin Carbon with Lacey Carbon
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277.15 K
Details: Lacey carbon grids with 3 nm ultrathin carbon support film were glow discharged for 30 seconds at high RF level using Harrick Plasma Cleaner, model PDC-002-CE, and then 3.5 microl of the ...Details: Lacey carbon grids with 3 nm ultrathin carbon support film were glow discharged for 30 seconds at high RF level using Harrick Plasma Cleaner, model PDC-002-CE, and then 3.5 microl of the sample was pipetted per grid. Excess protein was blotted away for 3 seconds using filter paper (round filter paper for Vitrobot from Agar Scientific, catalogue number 47000-100) and Vitrobot Mark IV (Thermo Fisher Scientific) (relative force -15) at 95-100% humidity. Grids were plunge frozen in liquid ethane.

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 96000 X / Nominal defocus max: -700 nm / Nominal defocus min: -500 nm / C2 aperture diameter: 50 µm / Alignment procedure: BASIC
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 77 K / Temperature (min): 77 K
Image recordingAverage exposure time: 37.26 sec. / Electron dose: 40 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 1635
Details: Cryo-EM data were collected on a Titan Krios G3i microscope (Thermo Fisher Scientific) operating at 300 kV with a 50 microm C2 aperture and Volta phase plate (Thermo Fisher Scientific), at ...Details: Cryo-EM data were collected on a Titan Krios G3i microscope (Thermo Fisher Scientific) operating at 300 kV with a 50 microm C2 aperture and Volta phase plate (Thermo Fisher Scientific), at the Division of Structural Biology, University of Oxford. Movies were recorded using a FEI Falcon III direct electron detector in electron counting mode using EPU software at a nominal magnification of 96000x, corresponding to a physical pixel size of 0.85 angstrom/pixel. A total dose of 40 electrons per square angstrom was used at a dose rate of 0.77 electrons/pix/sec.
EM imaging opticsPhase plate: VOLTA PHASE PLATE

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Processing

EM software
IDNameVersionCategory
2EPUimage acquisition
4CTFFIND4.1CTF correction
7UCSF Chimera1.13.1.model fitting
9RELION3initial Euler assignment
10RELION3final Euler assignment
11RELION3classification
12RELION33D reconstruction
13PHENIX1.18.2.model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 280158
SymmetryPoint symmetry: C3 (3 fold cyclic)
3D reconstructionResolution: 5.98 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 68541
Details: In total 1635 movies were collected and drift correction, beam-induced motion and dose-weighting were performed with MotionCor2 RELION 3.1 (Zivanov et al., 2018) for 1635 movies. Contrast ...Details: In total 1635 movies were collected and drift correction, beam-induced motion and dose-weighting were performed with MotionCor2 RELION 3.1 (Zivanov et al., 2018) for 1635 movies. Contrast transfer function (CTF) was estimated using CTFFIND 4.1 (Rohou and Grigorieff, 2015) implemented in RELION. 280158 particles were picked using Warp (Tegunov and Cramer, 2019). 2D classification in cryoSPARC v2 (Punjani et al., 2017) were performed for these particles and best 2D class averaged with 100674 particles were used to generate ab-initio 3D model with C3 symmetry. C1 symmetry did not generate reasonable 3D model. All Warp picked particles were used for 3D classification in cryoSPARC v2 and the best class with 177056 particles was used for refinement in RELION 3.1 with initial model generated in cryoSPARC v2. Byesian particle polishing improved the resolution to 5.44 angstrom, however the map for RGMB was very weak. Last step of 3D classification without alignment with T regularisation parameter set to 16 was performed and gave one class with more continuous map for RGMB, which was refined to 5.98 angstrom resolution, as estimated using the Fourier shell correlation (FSC) = 0.143 criterion.
Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Target criteria: Correlation coefficient
Details: Crystal structure used as a model for fitting and rigid body refinement will be described by Robinson, Griffiths, van de Haar, Malinauskas et al., Cell, 2021.

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