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- EMDB-23917: The HER2 S310F/HER3/NRG1b Heterodimer -

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Basic information

Entry
Database: EMDB / ID: EMD-23917
TitleThe HER2 S310F/HER3/NRG1b Heterodimer
Map dataFinal HER2S310F/HER3/NRG1b ectodomain reconstruction at 3.1A resolution based on 0.143FSC metric. Filtered with the FSC and sharpened with b-factor of -90.
Sample
  • Complex: NRB1b-bound HER2-S310F/HER3 Heterodimer in the context of near full-length receptors
    • Complex: HER3
      • Protein or peptide: Receptor tyrosine-protein kinase erbB-3
    • Complex: HER2-S310F, MBP Fusion
      • Protein or peptide: Receptor tyrosine-protein kinase erbB-2,Maltose/maltodextrin-binding periplasmic protein
    • Complex: Neuregulin-1
      • Protein or peptide: Isoform 6 of Pro-neuregulin-1, membrane-bound isoform
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Function / homology
Function and homology information


neuregulin binding / positive regulation of cardiac muscle tissue development / cranial nerve development / Schwann cell differentiation / neuregulin receptor activity / negative regulation of secretion / endocardial cushion development / negative regulation of immature T cell proliferation in thymus / ERBB3:ERBB2 complex / ERBB2-ERBB4 signaling pathway ...neuregulin binding / positive regulation of cardiac muscle tissue development / cranial nerve development / Schwann cell differentiation / neuregulin receptor activity / negative regulation of secretion / endocardial cushion development / negative regulation of immature T cell proliferation in thymus / ERBB3:ERBB2 complex / ERBB2-ERBB4 signaling pathway / GRB7 events in ERBB2 signaling / immature T cell proliferation in thymus / RNA polymerase I core binding / positive regulation of calcineurin-NFAT signaling cascade / peripheral nervous system development / regulation of microtubule-based process / ErbB-3 class receptor binding / negative regulation of cell adhesion / negative regulation of motor neuron apoptotic process / semaphorin receptor complex / Sema4D induced cell migration and growth-cone collapse / motor neuron axon guidance / neurotransmitter receptor localization to postsynaptic specialization membrane / motor neuron apoptotic process / PLCG1 events in ERBB2 signaling / neuromuscular junction development / ERBB2-EGFR signaling pathway / ERBB2 Activates PTK6 Signaling / positive regulation of Rho protein signal transduction / detection of maltose stimulus / Drug-mediated inhibition of ERBB2 signaling / Resistance of ERBB2 KD mutants to trastuzumab / Resistance of ERBB2 KD mutants to sapitinib / Resistance of ERBB2 KD mutants to tesevatinib / Resistance of ERBB2 KD mutants to neratinib / Resistance of ERBB2 KD mutants to osimertinib / Resistance of ERBB2 KD mutants to afatinib / Resistance of ERBB2 KD mutants to AEE788 / Resistance of ERBB2 KD mutants to lapatinib / Drug resistance in ERBB2 TMD/JMD mutants / enzyme-linked receptor protein signaling pathway / positive regulation of transcription by RNA polymerase I / maltose transport complex / ERBB2-ERBB3 signaling pathway / protein tyrosine kinase activator activity / Signaling by ERBB4 / oligodendrocyte differentiation / growth factor binding / carbohydrate transport / ERBB2 Regulates Cell Motility / semaphorin-plexin signaling pathway / PI3K events in ERBB2 signaling / carbohydrate transmembrane transporter activity / positive regulation of cell adhesion / maltose binding / lateral plasma membrane / maltose transport / maltodextrin transmembrane transport / positive regulation of protein targeting to membrane / regulation of angiogenesis / coreceptor activity / Schwann cell development / negative regulation of signal transduction / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / extrinsic apoptotic signaling pathway in absence of ligand / Signaling by ERBB2 / cellular response to epidermal growth factor stimulus / cell surface receptor protein tyrosine kinase signaling pathway / myelination / Downregulation of ERBB2:ERBB3 signaling / GRB2 events in ERBB2 signaling / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / transmembrane receptor protein tyrosine kinase activity / ATP-binding cassette (ABC) transporter complex / SHC1 events in ERBB2 signaling / Constitutive Signaling by Overexpressed ERBB2 / phosphatidylinositol 3-kinase/protein kinase B signal transduction / basal plasma membrane / neurogenesis / regulation of ERK1 and ERK2 cascade / cell chemotaxis / positive regulation of translation / positive regulation of epithelial cell proliferation / Signaling by ERBB2 TMD/JMD mutants / positive regulation of MAP kinase activity / wound healing / Signaling by ERBB2 ECD mutants / neuromuscular junction / neuron differentiation / Signaling by ERBB2 KD Mutants / receptor protein-tyrosine kinase / receptor tyrosine kinase binding / cellular response to growth factor stimulus / Downregulation of ERBB2 signaling / ruffle membrane / peptidyl-tyrosine phosphorylation / transmembrane signaling receptor activity / Constitutive Signaling by Aberrant PI3K in Cancer / PIP3 activates AKT signaling / myelin sheath
Similarity search - Function
: / Epidermal growth factor receptor transmembrane-juxtamembrane segment / Tyrosine protein kinase, EGF/ERB/XmrK receptor / Growth factor receptor domain 4 / Growth factor receptor domain IV / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Receptor L-domain / Furin-like cysteine-rich domain / Receptor L-domain superfamily / Furin-like cysteine rich region ...: / Epidermal growth factor receptor transmembrane-juxtamembrane segment / Tyrosine protein kinase, EGF/ERB/XmrK receptor / Growth factor receptor domain 4 / Growth factor receptor domain IV / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Receptor L-domain / Furin-like cysteine-rich domain / Receptor L-domain superfamily / Furin-like cysteine rich region / Receptor L domain / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Furin-like repeat / Furin-like repeats / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Growth factor receptor cysteine-rich domain superfamily / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Receptor tyrosine-protein kinase erbB-2 / Maltose/maltodextrin-binding periplasmic protein / Receptor tyrosine-protein kinase erbB-3 / Isoform 6 of Pro-neuregulin-1, membrane-bound isoform
Similarity search - Component
Biological speciesHomo sapiens (human) / Escherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.09 Å
AuthorsDiwanji D / Trenker R / Verba KA / Jura N
Funding support United States, Germany, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM139635 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)1F30CA247147 United States
German Research Foundation (DFG)TR 1668/1-1 Germany
CitationJournal: Nature / Year: 2021
Title: Structures of the HER2-HER3-NRG1β complex reveal a dynamic dimer interface.
Authors: Devan Diwanji / Raphael Trenker / Tarjani M Thaker / Feng Wang / David A Agard / Kliment A Verba / Natalia Jura /
Abstract: Human epidermal growth factor receptor 2 (HER2) and HER3 form a potent pro-oncogenic heterocomplex upon binding of growth factor neuregulin-1β (NRG1β). The mechanism by which HER2 and HER3 interact ...Human epidermal growth factor receptor 2 (HER2) and HER3 form a potent pro-oncogenic heterocomplex upon binding of growth factor neuregulin-1β (NRG1β). The mechanism by which HER2 and HER3 interact remains unknown in the absence of any structures of the complex. Here we isolated the NRG1β-bound near full-length HER2-HER3 dimer and, using cryo-electron microscopy, reconstructed the extracellulardomain module, revealing unexpected dynamics at the HER2-HER3 dimerization interface. We show that the dimerization arm of NRG1β-bound HER3 is unresolved because the apo HER2 monomer does not undergo a ligand-induced conformational change needed to establish a HER3 dimerization arm-binding pocket. In a structure of the oncogenic extracellular domain mutant HER2(S310F), we observe a compensatory interaction with the HER3 dimerization arm that stabilizes the dimerization interface. Both HER2-HER3 and HER2(S310F)-HER3 retain the capacity to bind to the HER2-directed therapeutic antibody trastuzumab, but the mutant complex does not bind to pertuzumab. Our structure of the HER2(S310F)-HER3-NRG1β-trastuzumab Fab complex reveals that the receptor dimer undergoes a conformational change to accommodate trastuzumab. Thus, similar to oncogenic mutations, therapeutic agents exploit the intrinsic dynamics of the HER2-HER3 heterodimer. The unique features of a singly liganded HER2-HER3 heterodimer underscore the allosteric sensing of ligand occupancy by the dimerization interface and explain why extracellular domains of HER2 do not homo-associate via a canonical active dimer interface.
History
DepositionApr 30, 2021-
Header (metadata) releaseOct 27, 2021-
Map releaseOct 27, 2021-
UpdateDec 22, 2021-
Current statusDec 22, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.35
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.35
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7mn6
  • Surface level: 0.35
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23917.png

Downloads & links

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Map

FileDownload / File: emd_23917.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFinal HER2S310F/HER3/NRG1b ectodomain reconstruction at 3.1A resolution based on 0.143FSC metric. Filtered with the FSC and sharpened with b-factor of -90.
Voxel sizeX=Y=Z: 0.835 Å
Density
Contour LevelBy AUTHOR: 0.3 / Movie #1: 0.35
Minimum - Maximum-1.0249598 - 2.2039132
Average (Standard dev.)0.00040447412 (±0.04506169)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 334.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8350.8350.835
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z334.000334.000334.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-1.0252.2040.000

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Supplemental data

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Mask #1

Fileemd_23917_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Unfiltered and unsharpened half map 2

Fileemd_23917_half_map_1.map
AnnotationUnfiltered and unsharpened half map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Unfiltered and unsharpened half map 1

Fileemd_23917_half_map_2.map
AnnotationUnfiltered and unsharpened half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : NRB1b-bound HER2-S310F/HER3 Heterodimer in the context of near fu...

EntireName: NRB1b-bound HER2-S310F/HER3 Heterodimer in the context of near full-length receptors
Components
  • Complex: NRB1b-bound HER2-S310F/HER3 Heterodimer in the context of near full-length receptors
    • Complex: HER3
      • Protein or peptide: Receptor tyrosine-protein kinase erbB-3
    • Complex: HER2-S310F, MBP Fusion
      • Protein or peptide: Receptor tyrosine-protein kinase erbB-2,Maltose/maltodextrin-binding periplasmic protein
    • Complex: Neuregulin-1
      • Protein or peptide: Isoform 6 of Pro-neuregulin-1, membrane-bound isoform
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: NRB1b-bound HER2-S310F/HER3 Heterodimer in the context of near fu...

SupramoleculeName: NRB1b-bound HER2-S310F/HER3 Heterodimer in the context of near full-length receptors
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3

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Supramolecule #2: HER3

SupramoleculeName: HER3 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)

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Supramolecule #3: HER2-S310F, MBP Fusion

SupramoleculeName: HER2-S310F, MBP Fusion / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)

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Supramolecule #4: Neuregulin-1

SupramoleculeName: Neuregulin-1 / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Macromolecule #1: Receptor tyrosine-protein kinase erbB-3

MacromoleculeName: Receptor tyrosine-protein kinase erbB-3 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: receptor protein-tyrosine kinase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 117.852719 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MRANDALQVL GLLFSLARGS EVGNSQAVCP GTLNGLSVTG DAENQYQTLY KLYERCEVVM GNLEIVLTGH NADLSFLQWI REVTGYVLV AMNEFSTLPL PNLRVVRGTQ VYDGKFAIFV MLNYNTNSSH ALRQLRLTQL TEILSGGVYI EKNDKLCHMD T IDWRDIVR ...String:
MRANDALQVL GLLFSLARGS EVGNSQAVCP GTLNGLSVTG DAENQYQTLY KLYERCEVVM GNLEIVLTGH NADLSFLQWI REVTGYVLV AMNEFSTLPL PNLRVVRGTQ VYDGKFAIFV MLNYNTNSSH ALRQLRLTQL TEILSGGVYI EKNDKLCHMD T IDWRDIVR DRDAEIVVKD NGRSCPPCHE VCKGRCWGPG SEDCQTLTKT ICAPQCNGHC FGPNPNQCCH DECAGGCSGP QD TDCFACR HFNDSGACVP RCPQPLVYNK LTFQLEPNPH TKYQYGGVCV ASCPHNFVVD QTSCVRACPP DKMEVDKNGL KMC EPCGGL CPKACEGTGS GSRFQTVDSS NIDGFVNCTK ILGNLDFLIT GLNGDPWHKI PALDPEKLNV FRTVREITGY LNIQ SWPPH MHNFSVFSNL TTIGGRSLYN RGFSLLIMKN LNVTSLGFRS LKEISAGRIY ISANRQLCYH HSLNWTKVLR GPTEE RLDI KHNRPRRDCV AEGKVCDPLC SSGGCWGPGP GQCLSCRNYS RGGVCVTHCN FLNGEPREFA HEAECFSCHP ECQPME GTA TCNGSGSDTC AQCAHFRDGP HCVSSCPHGV LGAKGPIYKY PDVQNECRPC HENCTQGCKG PELQDCLGQT LVLIGKT HL TMALTVIAGL VVIFMMLGGT FLYWRGRRIQ NKRAMRRYLE RGESIEPLDP SEKANKVLAR IFKETELRKL KVLGSGVF G TVHKGVWIPE GESIKIPVCI KVIEDKSGRQ SFQAVTDHML AIGSLDHAHI VRLLGLCPGS SLQLVTQYLP LGSLLDHVR QHRGALGPRL LLNWGVQIAK GMYYLEEHGM VHRNLAARNV LLKSPSQVQV ADFGVADLLP PDDKQLLYSE AKTPIKWMAL ESIHFGKYT HQSDVWSYGV TVWELMTFGA EPYAGLRLAE VPDLLEKGGR LAQPQICTID VYMVMVKCWM IDENIRPTFK E LANEFTRM ARDPPRYLVI KRESGPGIAP GPEPHGLTNK KLEEVELEPE LDLDLDLEAE EDNGGSLEVL FQGPSSPSAW SH PQFEKGG GSGGGSGGSS AWSHPQFEK

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Macromolecule #2: Receptor tyrosine-protein kinase erbB-2,Maltose/maltodextrin-bind...

MacromoleculeName: Receptor tyrosine-protein kinase erbB-2,Maltose/maltodextrin-binding periplasmic protein
type: protein_or_peptide / ID: 2 / Details: This mutation is oncogenic / Number of copies: 1 / Enantiomer: LEVO / EC number: receptor protein-tyrosine kinase
Source (natural)Organism: Escherichia coli (E. coli) / Strain: K12
Molecular weightTheoretical: 160.556562 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MELAALCRWG LLLALLPPGA ASTQVCTGTD MKLRLPASPE THLDMLRHLY QGCQVVQGNL ELTYLPTNAS LSFLQDIQEV QGYVLIAHN QVRQVPLQRL RIVRGTQLFE DNYALAVLDN GDPLNNTTPV TGASPGGLRE LQLRSLTEIL KGGVLIQRNP Q LCYQDTIL ...String:
MELAALCRWG LLLALLPPGA ASTQVCTGTD MKLRLPASPE THLDMLRHLY QGCQVVQGNL ELTYLPTNAS LSFLQDIQEV QGYVLIAHN QVRQVPLQRL RIVRGTQLFE DNYALAVLDN GDPLNNTTPV TGASPGGLRE LQLRSLTEIL KGGVLIQRNP Q LCYQDTIL WKDIFHKNNQ LALTLIDTNR SRACHPCSPM CKGSRCWGES SEDCQSLTRT VCAGGCARCK GPLPTDCCHE QC AAGCTGP KHSDCLACLH FNHSGICELH CPALVTYNTD TFESMPNPEG RYTFGASCVT ACPYNYLSTD VGFCTLVCPL HNQ EVTAED GTQRCEKCSK PCARVCYGLG MEHLREVRAV TSANIQEFAG CKKIFGSLAF LPESFDGDPA SNTAPLQPEQ LQVF ETLEE ITGYLYISAW PDSLPDLSVF QNLQVIRGRI LHNGAYSLTL QGLGISWLGL RSLRELGSGL ALIHHNTHLC FVHTV PWDQ LFRNPHQALL HTANRPEDEC VGEGLACHQL CARGHCWGPG PTQCVNCSQF LRGQECVEEC RVLQGLPREY VNARHC LPC HPECQPQNGS VTCFGPEADQ CVACAHYKDP PFCVARCPSG VKPDLSYMPI WKFPDEEGAC QPCPINCTHS CVDLDDK GC PAEQRASPLT SIISAVVGIL LVVVLGVVFG ILIKRRQQKI RKYTMRRLLQ ETELVEPLTP SGAMPNQAQM RILKETEL R KVKVLGSGAF GTVYKGIWIP DGENVKIPVA IKVLRENTSP KANKEILDEA YVMAGVDSPY VSRLLGICLT STVQLVTQL MPYGCLLDHV RENRGRLGSQ DLLNWCMQIA KGMSYLEDVR LVHRDLAARN VLVKSPNHVK ITDFGLARLL DIDETEYHAD GGKVPIKWM ALESILRRRF THQSDVWSYG VTVWELMTFG AKPYDGIPAR EIPDLLEKGE RLPQPPICTI DVYMIMVKCW M IDSECRPR FRELVSEFSR MARDPQRFVV IQNEDLGPAS PLDSTFYRSL LEDDDMGDLV DAEEYLVPQQ GGGSLEVLFQ GP SSPSGSS MKIEEGKLVI WINGDKGYNG LAEVGKKFEK DTGIKVTVEH PDKLEEKFPQ VAATGDGPDI IFWAHDRFGG YAQ SGLLAE ITPDKAFQDK LYPFTWDAVR YNGKLIAYPI AVEALSLIYN KDLLPNPPKT WEEIPALDKE LKAKGKSALM FNLQ EPYFT WPLIAADGGY AFKYENGKYD IKDVGVDNAG AKAGLTFLVD LIKNKHMNAD TDYSIAEAAF NKGETAMTIN GPWAW SNID TSKVNYGVTV LPTFKGQPSK PFVGVLSAGI NAASPNKELA KEFLENYLLT DEGLEAVNKD KPLGAVALKS YEEELA KDP RIAATMENAQ KGEIMPNIPQ MSAFWYAVRT AVINAASGRQ TVDEALKDAQ TNSSSSGPSS PSAWSHPQFE KGGGSGG GS GGSSAWSHPQ FEK

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Macromolecule #3: Isoform 6 of Pro-neuregulin-1, membrane-bound isoform

MacromoleculeName: Isoform 6 of Pro-neuregulin-1, membrane-bound isoform / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 9.748859 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GPSHLVKCAE KEKTFCVNGG ECFMVKDLSN PSRYLCKCPN EFTGDRCQNY VMASFYKHLG IEGSGSGSDY KDDDDKAAAL EHHHHHH

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Macromolecule #6: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / Number of copies: 5 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

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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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 67.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.09 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.15.0) / Number images used: 99755
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model(PDB ID:

3u7u

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1m6b

,

1n8z

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Output model

PDB-7mn6:
Structure of the HER2 S310F/HER3/NRG1b Heterodimer Extracellular Domain

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