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- EMDB-34389: Structure of human phagocyte NADPH oxidase in the resting state -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-34389
TitleStructure of human phagocyte NADPH oxidase in the resting state
Map data
Sample
  • Complex: NADPH oxidase2
    • Protein or peptide: Cytochrome b-245 light chain
    • Protein or peptide: Cytochrome b-245 heavy chain
    • Protein or peptide: 7D5 Fab light chain
    • Protein or peptide: 7D5 Fab heavy chain
    • Protein or peptide: Green Fluorescent Protein, Anti-Fab (kappa) nanobody[TP1170] chimera
  • Ligand: FLAVIN-ADENINE DINUCLEOTIDE
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine
  • Ligand: water
KeywordsNOX2 / p22 / CYBA / CYBB / TP1170 / NOX / OXIDOREDUCTASE
Function / homology
Function and homology information


smooth muscle hypertrophy / superoxide-generating NADPH oxidase activity / Oxidoreductases; Acting on NADH or NADPH; With oxygen as acceptor / cellular response to L-glutamine / hypoxia-inducible factor-1alpha signaling pathway / positive regulation of toll-like receptor 2 signaling pathway / positive regulation of defense response to bacterium / mucus secretion / perinuclear endoplasmic reticulum / superoxide-generating NAD(P)H oxidase activity ...smooth muscle hypertrophy / superoxide-generating NADPH oxidase activity / Oxidoreductases; Acting on NADH or NADPH; With oxygen as acceptor / cellular response to L-glutamine / hypoxia-inducible factor-1alpha signaling pathway / positive regulation of toll-like receptor 2 signaling pathway / positive regulation of defense response to bacterium / mucus secretion / perinuclear endoplasmic reticulum / superoxide-generating NAD(P)H oxidase activity / Cross-presentation of particulate exogenous antigens (phagosomes) / NADPH oxidase complex / cytochrome complex assembly / respiratory burst / WNT5:FZD7-mediated leishmania damping / ROS and RNS production in phagocytes / regulation of release of sequestered calcium ion into cytosol / cellular response to ethanol / response to angiotensin / hydrogen peroxide biosynthetic process / superoxide anion generation / positive regulation of mucus secretion / superoxide metabolic process / cellular response to cadmium ion / positive regulation of reactive oxygen species biosynthetic process / response to aldosterone / Detoxification of Reactive Oxygen Species / tertiary granule membrane / RHO GTPases Activate NADPH Oxidases / monoatomic ion channel complex / RAC2 GTPase cycle / RAC3 GTPase cycle / NADPH binding / specific granule membrane / positive regulation of phagocytosis / RAC1 GTPase cycle / response to nutrient / FAD binding / secretory granule / establishment of localization in cell / defense response / SH3 domain binding / positive regulation of interleukin-6 production / VEGFA-VEGFR2 Pathway / phagocytic vesicle membrane / positive regulation of angiogenesis / positive regulation of tumor necrosis factor production / nuclear envelope / flavin adenine dinucleotide binding / monoatomic ion transmembrane transport / electron transfer activity / oxidoreductase activity / endosome / inflammatory response / protein heterodimerization activity / response to xenobiotic stimulus / innate immune response / neuronal cell body / heme binding / dendrite / Neutrophil degranulation / endoplasmic reticulum membrane / metal ion binding / membrane / plasma membrane
Similarity search - Function
Cytochrome b245, heavy chain / Cytochrome b558 alpha-subunit / Cytochrome Cytochrome b558 alpha-subunit / Ferric reductase, NAD binding domain / : / Ferric reductase NAD binding domain / FAD-binding 8 / FAD-binding domain / Ferric reductase transmembrane component-like domain / Ferric reductase like transmembrane component ...Cytochrome b245, heavy chain / Cytochrome b558 alpha-subunit / Cytochrome Cytochrome b558 alpha-subunit / Ferric reductase, NAD binding domain / : / Ferric reductase NAD binding domain / FAD-binding 8 / FAD-binding domain / Ferric reductase transmembrane component-like domain / Ferric reductase like transmembrane component / FAD-binding domain, ferredoxin reductase-type / Ferredoxin-NADP reductase (FNR), nucleotide-binding domain / Ferredoxin reductase-type FAD binding domain profile. / Riboflavin synthase-like beta-barrel
Similarity search - Domain/homology
NADPH oxidase 2 / Cytochrome b-245 light chain
Similarity search - Component
Biological speciesHomo sapiens (human) / Mus musculus (house mouse) / Vicugna pacos (alpaca)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsChen L / Liu R / Song K
Funding support China, 3 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)91957201 China
National Natural Science Foundation of China (NSFC)31821091 China
National Natural Science Foundation of China (NSFC)31870833 China
CitationJournal: Elife / Year: 2022
Title: Structure of human phagocyte NADPH oxidase in the resting state.
Authors: Rui Liu / Kangcheng Song / Jing-Xiang Wu / Xiao-Peng Geng / Liming Zheng / Xiaoyin Gao / Hailin Peng / Lei Chen /
Abstract: Phagocyte oxidase plays an essential role in the first line of host defense against pathogens. It oxidizes intracellular NADPH to reduce extracellular oxygen to produce superoxide anions that ...Phagocyte oxidase plays an essential role in the first line of host defense against pathogens. It oxidizes intracellular NADPH to reduce extracellular oxygen to produce superoxide anions that participate in pathogen killing. The resting phagocyte oxidase is a heterodimeric complex formed by two transmembrane proteins NOX2 and p22. Despite the physiological importance of this complex, its structure remains elusive. Here, we reported the cryo-EM structure of the functional human NOX2-p22 complex in nanodisc in the resting state. NOX2 shows a canonical 6-TM architecture of NOX and p22 has four transmembrane helices. M3, M4, and M5 of NOX2, and M1 and M4 helices of p22 are involved in the heterodimer formation. Dehydrogenase (DH) domain of NOX2 in the resting state is not optimally docked onto the transmembrane domain, leading to inefficient electron transfer and NADPH binding. Structural analysis suggests that the cytosolic factors might activate the NOX2-p22 complex by stabilizing the DH in a productive docked conformation.
History
DepositionSep 24, 2022-
Header (metadata) releaseDec 21, 2022-
Map releaseDec 21, 2022-
UpdateOct 16, 2024-
Current statusOct 16, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_34389.png

Downloads & links

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Map

FileDownload / File: emd_34389.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 280 pix.
= 295.56 Å		1.06 Å/pix.
x 280 pix.
= 295.56 Å		1.06 Å/pix.
x 280 pix.
= 295.56 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.05557 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.3
Minimum - Maximum-7.8497906 - 11.910914999999999
Average (Standard dev.)-0.007216034 (±0.19130883)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 295.56 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : NADPH oxidase2

EntireName: NADPH oxidase2
Components
  • Complex: NADPH oxidase2
    • Protein or peptide: Cytochrome b-245 light chain
    • Protein or peptide: Cytochrome b-245 heavy chain
    • Protein or peptide: 7D5 Fab light chain
    • Protein or peptide: 7D5 Fab heavy chain
    • Protein or peptide: Green Fluorescent Protein, Anti-Fab (kappa) nanobody[TP1170] chimera
  • Ligand: FLAVIN-ADENINE DINUCLEOTIDE
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine
  • Ligand: water

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Supramolecule #1: NADPH oxidase2

SupramoleculeName: NADPH oxidase2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5

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Macromolecule #1: Cytochrome b-245 light chain

MacromoleculeName: Cytochrome b-245 light chain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 21.005398 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGQIEWAMWA NEQALASGLI LITGGIVATA GRFTQWYFGA YSIVAGVFVC LLEYPRGKRK KGSTMERWGQ KYMTAVVKLF GPFTRNYYV RAVLHLLLSV PAGFLLATIL GTACLAIASG IYLLAAVRGE QWTPIEPKPR ERPQIGGTIK QPPSNPPPRP P AEARKKPS ...String:
MGQIEWAMWA NEQALASGLI LITGGIVATA GRFTQWYFGA YSIVAGVFVC LLEYPRGKRK KGSTMERWGQ KYMTAVVKLF GPFTRNYYV RAVLHLLLSV PAGFLLATIL GTACLAIASG IYLLAAVRGE QWTPIEPKPR ERPQIGGTIK QPPSNPPPRP P AEARKKPS EEEAAAAAGG PPGGPQVNPI PVTDEVV

UniProtKB: Cytochrome b-245 light chain

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Macromolecule #2: Cytochrome b-245 heavy chain

MacromoleculeName: Cytochrome b-245 heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: Oxidoreductases
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 65.412727 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGNWAVNEGL SIFVILVWLG LNVFLFVWYY RVYDIPPKFF YTRKLLGSAL ALARAPAACL NFNCMLILLP VCRNLLSFLR GSSACCSTR VRRQLDRNLT FHKMVAWMIA LHSAIHTIAH LFNVEWCVNA RVNNSDPYSV ALSELGDRQN ESYLNFARKR I KNPEGGLY ...String:
MGNWAVNEGL SIFVILVWLG LNVFLFVWYY RVYDIPPKFF YTRKLLGSAL ALARAPAACL NFNCMLILLP VCRNLLSFLR GSSACCSTR VRRQLDRNLT FHKMVAWMIA LHSAIHTIAH LFNVEWCVNA RVNNSDPYSV ALSELGDRQN ESYLNFARKR I KNPEGGLY LAVTLLAGIT GVVITLCLIL IITSSTKTIR RSYFEVFWYT HHLFVIFFIG LAIHGAERIV RGQTAESLAV HN ITVCEQK ISEWGKIKEC PIPQFAGNPP MTWKWIVGPM FLYLCERLVR FWRSQQKVVI TKVVTHPFKT IELQMKKKGF KME VGQYIF VKCPKVSKLE WHPFTLTSAP EEDFFSIHIR IVGDWTEGLF NACGCDKQEF QDAWKLPKIA VDGPFGTASE DVFS YEVVM LVGAGIGVTP FASILKSVWY KYCNNATNLK LKKIYFYWLC RDTHAFEWFA DLLQLLESQM QERNNAGFLS YNIYL TGWD ESQANHFAVH HDEEKDVITG LKQKTLYGRP NWDNEFKTIA SQHPNTRIGV FLCGPEALAE TLSKQSISNS ESGPRG VHF IFNKENF

UniProtKB: NADPH oxidase 2

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Macromolecule #3: 7D5 Fab light chain

MacromoleculeName: 7D5 Fab light chain / type: protein_or_peptide / ID: 3
Details: Fab cleaved from monoclonal antibody purchased from commercial supplier. The expression system is not known.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 17.9751 KDa
SequenceString: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) ...String:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)

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Macromolecule #4: 7D5 Fab heavy chain

MacromoleculeName: 7D5 Fab heavy chain / type: protein_or_peptide / ID: 4
Details: Fab cleaved from monoclonal antibody purchased from commercial supplier. The expression system is not known.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 18.315516 KDa
SequenceString: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) ...String:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)

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Macromolecule #5: Green Fluorescent Protein, Anti-Fab (kappa) nanobody[TP1170] chimera

MacromoleculeName: Green Fluorescent Protein, Anti-Fab (kappa) nanobody[TP1170] chimera
type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Vicugna pacos (alpaca)
Molecular weightTheoretical: 46.217344 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSKGEELFTG VVPILVELDG DVNGHKFSVR GEGEGDATIG KLTLKFICTT GKLPVPWPTL VTTLTYGVQC FSRYPDHMKR HDFFKSAMP EGYVQERTIS FKDDGKYKTR AVVKFEGDTL VNRIELKGTD FKEDGNILGH KLEYNFNSHN VYITADKQKN G IKANFTVR ...String:
MSKGEELFTG VVPILVELDG DVNGHKFSVR GEGEGDATIG KLTLKFICTT GKLPVPWPTL VTTLTYGVQC FSRYPDHMKR HDFFKSAMP EGYVQERTIS FKDDGKYKTR AVVKFEGDTL VNRIELKGTD FKEDGNILGH KLEYNFNSHN VYITADKQKN G IKANFTVR HNVEDGSVQL ADHYQQNTPI GDGPVLLPDN HYLSTQTKLS KDPNEKRDHM VLHEYVNAAG ITHHHHHHHH SS GLVPRGS GWSHPQFEKG SGDYKDDDDK GSGWSHPQFE KLEVLFQGPE FQVQLVESGG GWVQPGGSLR LSCAASGFTF SDT AMMWVR QAPGKGREWV AAIDTGGGYT YYADSVKGRF TISRDNAKNT LYLQMNSLKP EDTARYYCAK TYSGNYYSNY TVAN YGTTG RGTLVTVSS

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Macromolecule #7: FLAVIN-ADENINE DINUCLEOTIDE

MacromoleculeName: FLAVIN-ADENINE DINUCLEOTIDE / type: ligand / ID: 7 / Number of copies: 1 / Formula: FAD
Molecular weightTheoretical: 785.55 Da
Chemical component information

ChemComp-FAD:
FLAVIN-ADENINE DINUCLEOTIDE / FAD*YM

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Macromolecule #8: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 8 / Number of copies: 2 / Formula: HEM
Molecular weightTheoretical: 616.487 Da
Chemical component information

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE

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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: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine

MacromoleculeName: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine / type: ligand / ID: 10 / Number of copies: 1 / Formula: LBN
Molecular weightTheoretical: 760.076 Da
Chemical component information

ChemComp-LBN:
1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine / phospholipid*YM

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Macromolecule #11: water

MacromoleculeName: water / type: ligand / ID: 11 / Number of copies: 1 / 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

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 37.6 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 84035
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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