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- EMDB-57361: The complex of A1AT-NHK with the ERAD misfolded glycoprotein chec... -

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Basic information

Entry
Database: EMDB / ID: EMD-57361
TitleThe complex of A1AT-NHK with the ERAD misfolded glycoprotein checkpoint complex from Chaetomium thermophilum (EDEM:PDI heterodimer).
Map data
Sample
  • Complex: Ternary complex of human A1AT-NH and Chaetomium thermophilum Endoplasmic reticulum degradation enhancing mannosidase (CtEDEM) plus Endoplasmic reticulum degradation enhancing protein disulfide isomerase (CtPDI)
    • Complex: Green fluorescent protein N-terminally fused to alpha-1,2-Mannosidase
      • Protein or peptide: Green fluorescent protein,alpha-1,2-Mannosidase
    • Complex: Protein disulfide isomerase
      • Protein or peptide: Protein disulfide-isomerase
    • Complex: Human Alpha1-antitrypsin Null Hong Kong mutant. Sequence: MPSSVSWGILLLAGLCCLVPVSLAEDPQGDAAQKTDTSHHDQDHPTFNKITPNLAEFAFSLYRQLAHQSNSTNIFFSPVSIATAFAMLSLGTKADTHDEILEGLNFNLTEIPEAQIHEGFQELLRTLNQPDSQLQLTTGNGLFLSEGLKLVDKFLEDVKKLYHSEAFTVNFGDTEEAKKQINDYVEKGTQGKIVDLVKELDRDTVFALVNYIFFKGKWERPFEVKDTEEEDFHVDQVTTVKVPMMKRLGMFNIQHCKKLSSWVLLMKYLGNATAIFFLPDEGKLQHLENELTHDIITKFLENEDRRSASLHLPKLSITGTYDLKSVLGQLGITKVFSNGADLRGHRGGTPEALQGRA
  • Ligand: alpha-D-mannopyranose
  • Ligand: CALCIUM ION
  • Ligand: KIFUNENSINE
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: beta-D-mannopyranose
Keywordsmannosidase / disulfide isomerase / glycoprotein degradation / erad / misfolding / OXIDOREDUCTASE / serpin / Alpha1 antitrypsin / null Hong Kong / A1AT / HYDROLASE
Function / homology
Function and homology information


mannosyl-oligosaccharide 1,2-alpha-mannosidase activity / endoplasmic reticulum mannose trimming / protein disulfide-isomerase / endoplasmic reticulum quality control compartment / Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / protein disulfide isomerase activity / protein-disulfide reductase activity / ERAD pathway / response to endoplasmic reticulum stress / bioluminescence ...mannosyl-oligosaccharide 1,2-alpha-mannosidase activity / endoplasmic reticulum mannose trimming / protein disulfide-isomerase / endoplasmic reticulum quality control compartment / Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / protein disulfide isomerase activity / protein-disulfide reductase activity / ERAD pathway / response to endoplasmic reticulum stress / bioluminescence / generation of precursor metabolites and energy / : / protein folding / carbohydrate metabolic process / endoplasmic reticulum lumen / calcium ion binding / membrane
Similarity search - Function
ER degradation-enhancing alpha-mannosidase-like protein 1/2/3 / Glycoside hydrolase family 47 / Seven-hairpin glycosidases / Glycosyl hydrolase family 47 / Protein disulphide isomerase / Thioredoxin-like domain / Disulphide isomerase / Thioredoxin / Six-hairpin glycosidase-like superfamily / Thioredoxin family active site. ...ER degradation-enhancing alpha-mannosidase-like protein 1/2/3 / Glycoside hydrolase family 47 / Seven-hairpin glycosidases / Glycosyl hydrolase family 47 / Protein disulphide isomerase / Thioredoxin-like domain / Disulphide isomerase / Thioredoxin / Six-hairpin glycosidase-like superfamily / Thioredoxin family active site. / Thioredoxin, conserved site / Thioredoxin domain profile. / Thioredoxin domain / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Thioredoxin-like superfamily
Similarity search - Domain/homology
alpha-1,2-Mannosidase / Protein disulfide-isomerase / Green fluorescent protein
Similarity search - Component
Biological speciesThermochaetoides thermophila (fungus) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.46 Å
AuthorsRoversi P / Hitchman CJ / Gooptu B / Bhogadia M / Lia A
Funding support United Kingdom, Italy, 4 items
OrganizationGrant numberCountry
Wellcome Trust204801/Z/16/Z United Kingdom
Wellcome Trust214090/Z/18/Z United Kingdom
Italian National Research Council (CNR)Plant_EDEM Italy
Italian National Research Council (CNR)B53C22009060005 Italy
CitationJournal: Biorxiv / Year: 2025
Title: Structure and function of the EDEM:PDI ERAD checkpoint complex
Authors: Hitchman CJ / Lia A / Chiritoiu GN / Munteanu CVA / Ortigosa JR / Ghenea S / Savva C / Wada I / De Benedictis M / Tax G / Bayo Y / Crescioli I / Alonzi DL / Quigley A / Modenutti CP / ...Authors: Hitchman CJ / Lia A / Chiritoiu GN / Munteanu CVA / Ortigosa JR / Ghenea S / Savva C / Wada I / De Benedictis M / Tax G / Bayo Y / Crescioli I / Alonzi DL / Quigley A / Modenutti CP / Petrescu SM / Santino A / Gooptu B / Hosokawa N / Roversi P
History
DepositionApr 7, 2026-
Header (metadata) releaseJun 24, 2026-
Map releaseJun 24, 2026-
UpdateJun 24, 2026-
Current statusJun 24, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_57361.png

Downloads & links

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Map

FileDownload / File: emd_57361.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.67 Å/pix.
x 180 pix.
= 300.6 Å		1.67 Å/pix.
x 180 pix.
= 300.6 Å		1.67 Å/pix.
x 180 pix.
= 300.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.67 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.09
Minimum - Maximum-0.46766698 - 1.060998
Average (Standard dev.)0.003058681 (±0.023645235)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions180180180
Spacing180180180
CellA=B=C: 300.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_57361_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_57361_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Ternary complex of human A1AT-NH and Chaetomium thermophilum Endo...

EntireName: Ternary complex of human A1AT-NH and Chaetomium thermophilum Endoplasmic reticulum degradation enhancing mannosidase (CtEDEM) plus Endoplasmic reticulum degradation enhancing protein disulfide isomerase (CtPDI)
Components
  • Complex: Ternary complex of human A1AT-NH and Chaetomium thermophilum Endoplasmic reticulum degradation enhancing mannosidase (CtEDEM) plus Endoplasmic reticulum degradation enhancing protein disulfide isomerase (CtPDI)
    • Complex: Green fluorescent protein N-terminally fused to alpha-1,2-Mannosidase
      • Protein or peptide: Green fluorescent protein,alpha-1,2-Mannosidase
    • Complex: Protein disulfide isomerase
      • Protein or peptide: Protein disulfide-isomerase
    • Complex: Human Alpha1-antitrypsin Null Hong Kong mutant. Sequence: MPSSVSWGILLLAGLCCLVPVSLAEDPQGDAAQKTDTSHHDQDHPTFNKITPNLAEFAFSLYRQLAHQSNSTNIFFSPVSIATAFAMLSLGTKADTHDEILEGLNFNLTEIPEAQIHEGFQELLRTLNQPDSQLQLTTGNGLFLSEGLKLVDKFLEDVKKLYHSEAFTVNFGDTEEAKKQINDYVEKGTQGKIVDLVKELDRDTVFALVNYIFFKGKWERPFEVKDTEEEDFHVDQVTTVKVPMMKRLGMFNIQHCKKLSSWVLLMKYLGNATAIFFLPDEGKLQHLENELTHDIITKFLENEDRRSASLHLPKLSITGTYDLKSVLGQLGITKVFSNGADLRGHRGGTPEALQGRA
  • Ligand: alpha-D-mannopyranose
  • Ligand: CALCIUM ION
  • Ligand: KIFUNENSINE
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: beta-D-mannopyranose

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Supramolecule #1: Ternary complex of human A1AT-NH and Chaetomium thermophilum Endo...

SupramoleculeName: Ternary complex of human A1AT-NH and Chaetomium thermophilum Endoplasmic reticulum degradation enhancing mannosidase (CtEDEM) plus Endoplasmic reticulum degradation enhancing protein disulfide isomerase (CtPDI)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Details: Coexpressed by transient co-transfection of three plasmids. A1AT is in the map but was not modelled
Source (natural)Organism: Thermochaetoides thermophila (fungus) / Organelle: Endoplasmic reticulum
Molecular weightTheoretical: 55 KDa

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Supramolecule #2: Green fluorescent protein N-terminally fused to alpha-1,2-Mannosidase

SupramoleculeName: Green fluorescent protein N-terminally fused to alpha-1,2-Mannosidase
type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Thermochaetoides thermophila (fungus) / Organelle: Endoplasmic reticulum

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Supramolecule #3: Protein disulfide isomerase

SupramoleculeName: Protein disulfide isomerase / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Thermochaetoides thermophila (fungus) / Organelle: Endoplasmic reticulum

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Supramolecule #4: Human Alpha1-antitrypsin Null Hong Kong mutant. Sequence: MPSSVSW...

SupramoleculeName: Human Alpha1-antitrypsin Null Hong Kong mutant. Sequence: ...Name: Human Alpha1-antitrypsin Null Hong Kong mutant. Sequence: MPSSVSWGILLLAGLCCLVPVSLAEDPQGDAAQKTDTSHHDQDHPTFNKITPNLAEFAFSLYRQLAHQSNSTNIFFSPVSIATAFAMLSLGTKADTHDEILEGLNFNLTEIPEAQIHEGFQELLRTLNQPDSQLQLTTGNGLFLSEGLKLVDKFLEDVKKLYHSEAFTVNFGDTEEAKKQINDYVEKGTQGKIVDLVKELDRDTVFALVNYIFFKGKWERPFEVKDTEEEDFHVDQVTTVKVPMMKRLGMFNIQHCKKLSSWVLLMKYLGNATAIFFLPDEGKLQHLENELTHDIITKFLENEDRRSASLHLPKLSITGTYDLKSVLGQLGITKVFSNGADLRGHRGGTPEALQGRA
type: complex / ID: 4 / Parent: 1
Details: The protein is in the sample and appears as a low resolution volume in the map - but no atomic model for it was built.
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Green fluorescent protein,alpha-1,2-Mannosidase

MacromoleculeName: Green fluorescent protein,alpha-1,2-Mannosidase / type: protein_or_peptide / ID: 1
Details: N-terminal GFP-fuson of the Chaetomium thermophilum Endoplasmic reticulum degradation enhancing mannosidase (CtEDEM),Green fluorescent protein N-terminally fused to alpha-1,2-Mannosidase
Number of copies: 1 / Enantiomer: LEVO
EC number: Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds
Source (natural)Organism: Thermochaetoides thermophila (fungus)
Molecular weightTheoretical: 142.162812 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MVSKGELFTG VVPILVELDG DVNGHKFSVS GEGEGDATYG KLTLKFICTT GKLPVPWPTL VTTLTYGVQC FSRYPDHMKQ HDFFKSAMP EGYVQERTIF FKDDGNYKTR AEVKFEGDTL VNRIELKGID FKEDGNILGH KLEYNYNSHN VYIMADKQKN G IKVNFKIR ...String:
MVSKGELFTG VVPILVELDG DVNGHKFSVS GEGEGDATYG KLTLKFICTT GKLPVPWPTL VTTLTYGVQC FSRYPDHMKQ HDFFKSAMP EGYVQERTIF FKDDGNYKTR AEVKFEGDTL VNRIELKGID FKEDGNILGH KLEYNYNSHN VYIMADKQKN G IKVNFKIR HNIEDGSVQL ADHYQQNTPI GDGPVLLPDN HYLSTQSALS KDPNEKRDHM VLLEFVTAAG ITLGMDELYK LE VLFQGPD RVRALRRETV EMFYYGFDNY MKVAFPEDEL RPVSCTPLTR DLKNPRNFEL NDVLGNYSLT LIDSLSTLAI LAS APAEDS GTGPKALRDF QDGVAALVEQ YGDGRPGPSG VGRRARGFDL DSKVQVFETV IRGVGGLLSA HLFAIGALPI TGYQ PLRQE DDLFNPPPIP WPNGFTYDGQ LLRLALDLAQ RLLPAFYTKT GLPYPRVNLR HGIPFYVNSP LHEDPPAKGT TEGPP EITE TCSAGAGSLV LEFTVLSRLT GDPRFEQAAK RAFWAVWYRK SQIGLIGAGV DAEQGHWIGT YSVIGAGADS FFEYAL KSH ILLSGHALPN QTHPSPLHKD VNWMDPNTLF EPLSDAENSA ESFLEAWHHA HAAIKRHLYS EREHPHYDNV NLWTGSL VS HWVDSLGAYY SGLLVLAGEV DEAIETNLLY AAIWTRYAAL PERWSLREKT VEGGLGWWPL RPEFIESTYH LYRATKDP W YLYVGEMVLR DITRRCWTPC GWAGLQNVLS GEKSDRMESF FLGETTKYMY LLFDDDHPLN KLDASFVFTT EGHPLILPK PKSARRSRNS PRSSQKALTV YQGEGFTNSC PPRPSITPLS GSVIAARDDI YHPARMVDLH LLTTSKHALD GGQMSGQHMA KSNYTLYPW TLPPELLPSN GTCAKVYQPH EVTLEFASNT QQVLGGSAFN FMLSGQNLER LSTDRIRVLS LSGLKITLQL V EEGEREWR VTKLNGIPLG RDEYVVINRA ILGDVSDPRF NLVRDPVIAK LQQLHQVNLL DDTTTEEHPD NLDTLDTASA ID LPQDQSS DSEVPDPANL SALLPDLSSF VKSLFARLSN LTSPSPDPSS NLPLNVVINQ TAILPTGIGA APLPPAASNS PSG APIPVF GPVPESLFPW KTIYAAGEAC AGPLPDSAPR ENQVILIRRG GCSFSDKLAN IPAFTPSEES LQLVVVVSDD EHEG QSGLV RPLLDEIQHT PGGMPRRHPI AMVMVGGGET VYQQLSVASA IGIQRRYYIE SSGVKVKNII VDDGDGGVDG GTKHH HHHH

UniProtKB: Green fluorescent protein, alpha-1,2-Mannosidase

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Macromolecule #2: Protein disulfide-isomerase

MacromoleculeName: Protein disulfide-isomerase / type: protein_or_peptide / ID: 2
Details: Chaetomium thermophilum Endoplasmic reticulum degradation enhancing protein disulfide isomerase (CtPDI)
Number of copies: 1 / Enantiomer: LEVO / EC number: protein disulfide-isomerase
Source (natural)Organism: Thermochaetoides thermophila (fungus)
Molecular weightTheoretical: 55.936445 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: ETGSDVIQLK KDTFDDFIKS NDLVLAEFFA PWCGHCKALA PEYEEAATNL KDKNIKLVKV DCTEETELCQ EHGVEGYPTL KVFRGLDNV TPYKGQRKAA AITSYMIKQS LPAVSDVTKD TLEEFKKADK VVLVAYVDAS DKASAEVFKK VAEKLRDNYP F GSSSDAEL ...String:
ETGSDVIQLK KDTFDDFIKS NDLVLAEFFA PWCGHCKALA PEYEEAATNL KDKNIKLVKV DCTEETELCQ EHGVEGYPTL KVFRGLDNV TPYKGQRKAA AITSYMIKQS LPAVSDVTKD TLEEFKKADK VVLVAYVDAS DKASAEVFKK VAEKLRDNYP F GSSSDAEL AEAEGVKAPA IVLYKDFDEG KAVFTEKFDE EAIQKWAKVA ATPLIGEIGP ETYGEYMAAG IPLAYIFAET PE ERKELSE KLKPIAEATR GKINFGTIDA KAYGAHAGNL NLKTDKFPAF AIQETTKNQK FPYDQDKEIT HDSIKQFVDD YLA GKIEPS IKSEPIPEKQ EGPVTVVVAK TYNDIVLDDT KDVLIEFYAP WCGHCKALAP KYEELGRLYS NSEFKDRVVI AKID ATAND VPDDIMGFPT IKMYPAGAKD KPVTYSGNRS VEDMIKFVAE NGKYKALISE NEEENATAAS SSSETSATPT STAAS EETA ASETASAEEG KETAHDKHHH HHH

UniProtKB: Protein disulfide-isomerase

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Macromolecule #6: alpha-D-mannopyranose

MacromoleculeName: alpha-D-mannopyranose / type: ligand / ID: 6 / Number of copies: 5 / Formula: MAN
Molecular weightTheoretical: 180.156 Da
Chemical component information

ChemComp-MAN:
alpha-D-mannopyranose

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Macromolecule #7: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 7 / Number of copies: 1 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #8: KIFUNENSINE

MacromoleculeName: KIFUNENSINE / type: ligand / ID: 8 / Number of copies: 1 / Formula: KIF
Molecular weightTheoretical: 232.191 Da
Chemical component information

ChemComp-KIF:
KIFUNENSINE / inhibitor, alkaloid*YM

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Macromolecule #9: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 9 / Number of copies: 2 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Macromolecule #10: beta-D-mannopyranose

MacromoleculeName: beta-D-mannopyranose / type: ligand / ID: 10 / Number of copies: 1 / Formula: BMA
Molecular weightTheoretical: 180.156 Da
Chemical component information

ChemComp-BMA:
beta-D-mannopyranose

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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

Concentration1.0 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
100.0 mMNaClSodium Chloride
20.0 mMC8H17N2NaO4SSodium HEPES

Details: 20 mM HEPES pH 7.5, 100 mM NaCl
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 75 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.02 kPa / Details: 50 mA
VitrificationCryogen name: PROPANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
Details: 3 uL of protein were added to the grid for 1 minute, at 4 degrees C with 100% humidity, before blotting with Whatman No1 filter paper (Sigma-aldrich, Germany) and washing three times with 20 ...Details: 3 uL of protein were added to the grid for 1 minute, at 4 degrees C with 100% humidity, before blotting with Whatman No1 filter paper (Sigma-aldrich, Germany) and washing three times with 20 uL drops of ultrapure water. Blot force 10 for 3 s before plunge freezing immediately into liquid ethane. A 30 second wait time after sample application before plunge freezing..
Details0.5 mL of sample was purified on a Superdex 200 Increase 10/300 GL (SEC, Cytiva - 28990944, USA) equilibrated against SEC buffer. Fractions containing the complex were identified from the SEC chromatogram and SDS-PAGE and taken forward for Cryo-EM. Concentration of each fraction was measured using the A280 nm reading.

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Electron microscopy

MicroscopeTFS KRIOS
SoftwareName: EPU
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average exposure time: 3.0 sec. / Average electron dose: 11.15 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated magnification: 105000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
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: 123770
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

9tpa
PDB Unreleased entry

Final reconstructionNumber classes used: 4 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.46 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 765
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationNumber classes: 4 / Avg.num./class: 22690 / Software - Name: cryoSPARC

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