[English] 日本語
Yorodumi
- EMDB-21503: Structure of S. pombe Arp2/3 complex in inactive state -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-21503
TitleStructure of S. pombe Arp2/3 complex in inactive state
Map dataMap of S. pombe Arp2/3 complex in inactive state
Sample
  • Complex: Arp2/3 complex
    • Protein or peptide: Actin-related protein 3
    • Protein or peptide: Actin-related protein 2
    • Protein or peptide: Actin-related protein 2/3 complex subunit 1
    • Protein or peptide: Actin-related protein 2/3 complex subunit 2
    • Protein or peptide: Actin-related protein 2/3 complex subunit 3
    • Protein or peptide: Actin-related protein 2/3 complex subunit 4
    • Protein or peptide: Actin-related protein 2/3 complex subunit 5
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
KeywordsArp2/3 / actin / cytoskeletal protein / actin regulator / STRUCTURAL PROTEIN
Function / homology
Function and homology information


Regulation of actin dynamics for phagocytic cup formation / RHO GTPases Activate WASPs and WAVEs / actin cortical patch organization / cell cortex of cell tip / medial cortex / Neutrophil degranulation / establishment or maintenance of cell polarity regulating cell shape / actin cortical patch assembly / Arp2/3 protein complex / Arp2/3 complex-mediated actin nucleation ...Regulation of actin dynamics for phagocytic cup formation / RHO GTPases Activate WASPs and WAVEs / actin cortical patch organization / cell cortex of cell tip / medial cortex / Neutrophil degranulation / establishment or maintenance of cell polarity regulating cell shape / actin cortical patch assembly / Arp2/3 protein complex / Arp2/3 complex-mediated actin nucleation / cell tip / actin cortical patch / regulation of actin filament polymerization / mating projection tip / cortical actin cytoskeleton organization / cell division site / mitotic cytokinesis / actin filament polymerization / structural constituent of cytoskeleton / endocytosis / actin filament binding / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Actin-related protein 2/3 complex subunit 5 / Actin-related protein 2/3 complex subunit 2 / Actin-related protein 2/3 complex subunit 3 / Actin-related protein 2/3 complex subunit 4 / Actin-related protein 2/3 complex subunit 1 / Arp2/3 complex subunit 2/4 / Actin-related protein 2/3 complex subunit 5 superfamily / Actin-related protein 2/3 complex subunit 3 superfamily / Arp2/3 complex, 34 kD subunit p34-Arc / ARP2/3 complex ARPC3 (21 kDa) subunit ...Actin-related protein 2/3 complex subunit 5 / Actin-related protein 2/3 complex subunit 2 / Actin-related protein 2/3 complex subunit 3 / Actin-related protein 2/3 complex subunit 4 / Actin-related protein 2/3 complex subunit 1 / Arp2/3 complex subunit 2/4 / Actin-related protein 2/3 complex subunit 5 superfamily / Actin-related protein 2/3 complex subunit 3 superfamily / Arp2/3 complex, 34 kD subunit p34-Arc / ARP2/3 complex ARPC3 (21 kDa) subunit / ARP2/3 complex 16 kDa subunit (p16-Arc) / ARP2/3 complex 20 kDa subunit (ARPC4) / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / ATPase, nucleotide binding domain / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Actin-related protein 2/3 complex subunit 2 / Actin-related protein 3 / Actin-related protein 2/3 complex subunit 1 / Actin-related protein 2/3 complex subunit 5 / Actin-related protein 2/3 complex subunit 4 / Actin-related protein 2 / Actin-related protein 2/3 complex subunit 3
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsShaaban M / Nolen BJ / Chowdhury S
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM127440, R01GM092917, S10OD012272 United States
CitationJournal: Nat Struct Mol Biol / Year: 2020
Title: Cryo-EM reveals the transition of Arp2/3 complex from inactive to nucleation-competent state.
Authors: Mohammed Shaaban / Saikat Chowdhury / Brad J Nolen /
Abstract: Arp2/3 complex, a crucial actin filament nucleator, undergoes structural rearrangements during activation by nucleation-promoting factors (NPFs). However, the conformational pathway leading to the ...Arp2/3 complex, a crucial actin filament nucleator, undergoes structural rearrangements during activation by nucleation-promoting factors (NPFs). However, the conformational pathway leading to the nucleation-competent state is unclear due to lack of high-resolution structures of the activated state. Here we report a ~3.9 Å resolution cryo-EM structure of activated Schizosaccharomyces pombe Arp2/3 complex bound to the S. pombe NPF Dip1 and attached to the end of the nucleated actin filament. The structure reveals global and local conformational changes that allow the two actin-related proteins in Arp2/3 complex to mimic a filamentous actin dimer and template nucleation. Activation occurs through a clamp-twisting mechanism, in which Dip1 forces two core subunits in Arp2/3 complex to pivot around one another, shifting half of the complex into a new activated position. By showing how Dip1 stimulates activation, the structure reveals how NPFs can activate Arp2/3 complex in diverse cellular processes.
History
DepositionMar 3, 2020-
Header (metadata) releaseApr 1, 2020-
Map releaseAug 12, 2020-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.444
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.444
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6w18
  • Surface level: 0.444
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21503.png

Downloads & links

-
Map

FileDownload / File: emd_21503.map.gz / Format: CCP4 / Size: 61 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap of S. pombe Arp2/3 complex in inactive state
Voxel sizeX=Y=Z: 0.8757 Å
Density
Contour LevelBy AUTHOR: 0.444 / Movie #1: 0.444
Minimum - Maximum-1.8510381 - 3.076487
Average (Standard dev.)0.009181952 (±0.09671269)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions252252252
Spacing252252252
CellA=B=C: 220.67639 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.875698412698410.875698412698410.87569841269841
M x/y/z252252252
origin x/y/z0.0000.0000.000
length x/y/z220.676220.676220.676
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ250250250
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS252252252
D min/max/mean-1.8513.0760.009

-
Supplemental data

-
Mask #1

Fileemd_21503_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Unsharpened map of S. pombe Arp2/3 complex in inactive state

Fileemd_21503_additional.map
AnnotationUnsharpened map of S. pombe Arp2/3 complex in inactive state
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map 1

Fileemd_21503_half_map_1.map
AnnotationHalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map 2

Fileemd_21503_half_map_2.map
AnnotationHalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : Arp2/3 complex

EntireName: Arp2/3 complex
Components
  • Complex: Arp2/3 complex
    • Protein or peptide: Actin-related protein 3
    • Protein or peptide: Actin-related protein 2
    • Protein or peptide: Actin-related protein 2/3 complex subunit 1
    • Protein or peptide: Actin-related protein 2/3 complex subunit 2
    • Protein or peptide: Actin-related protein 2/3 complex subunit 3
    • Protein or peptide: Actin-related protein 2/3 complex subunit 4
    • Protein or peptide: Actin-related protein 2/3 complex subunit 5
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION

+
Supramolecule #1: Arp2/3 complex

SupramoleculeName: Arp2/3 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7 / Details: Inactive state of S. pombe Arp2/3 complex
Source (natural)Organism: Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843 / Location in cell: cytoplasm
Molecular weightTheoretical: 225 KDa

+
Macromolecule #1: Actin-related protein 3

MacromoleculeName: Actin-related protein 3 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843
Molecular weightTheoretical: 47.427137 KDa
SequenceString: MASFNVPIIM DNGTGYSKLG YAGNDAPSYV FPTVIATRSA GASSGPAVSS KPSYMASKGS GHLSSKRATE DLDFFIGNDA LKKASAGYS LDYPIRHGQI ENWDHMERFW QQSLFKYLRC EPEDHYFLLT EPPLNPPENR ENTAEIMFES FNCAGLYIAV Q AVLALAAS ...String:
MASFNVPIIM DNGTGYSKLG YAGNDAPSYV FPTVIATRSA GASSGPAVSS KPSYMASKGS GHLSSKRATE DLDFFIGNDA LKKASAGYS LDYPIRHGQI ENWDHMERFW QQSLFKYLRC EPEDHYFLLT EPPLNPPENR ENTAEIMFES FNCAGLYIAV Q AVLALAAS WTSSKVTDRS LTGTVVDSGD GVTHIIPVAE GYVIGSSIKT MPLAGRDVTY FVQSLLRDRN EPDSSLKTAE RI KEECCYV CPDIVKEFSR FDREPDRYLK YASESITGHS TTIDVGFERF LAPEIFFNPE IASSDFLTPL PELVDNVVQS SPI DVRKGL YKNIVLSGGS TLFKNFGNRL QRDLKRIVDE RIHRSEMLSG AKSGGVDVNV ISHKRQRNAV WFGGSLLAQT PEFG SYCHT KADYEEYGAS IARRYQIFGN SL

UniProtKB: Actin-related protein 3

+
Macromolecule #2: Actin-related protein 2

MacromoleculeName: Actin-related protein 2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843
Molecular weightTheoretical: 44.286758 KDa
SequenceString: MESAPIVLDN GTGFVKVGYA KDNFPRFQFP SIVGRPILRA EEKTGNVQIK DVMVGDEAEA VRSLLQVKYP MENGIIRDFE EMNQLWDYT FFEKLKIDPR GRKILLTEPP MNPVANREKM CETMFERYGF GGVYVAIQAV LSLYAQGLSS GVVVDSGDGV T HIVPVYES ...String:
MESAPIVLDN GTGFVKVGYA KDNFPRFQFP SIVGRPILRA EEKTGNVQIK DVMVGDEAEA VRSLLQVKYP MENGIIRDFE EMNQLWDYT FFEKLKIDPR GRKILLTEPP MNPVANREKM CETMFERYGF GGVYVAIQAV LSLYAQGLSS GVVVDSGDGV T HIVPVYES VVLNHLVGRL DVAGRDATRY LISLLLRKGY AFNRTADFET VREMKEKLCY VSYDLELDHK LSEETTVLMR NY TLPDGRV IKVGSERYEC PECLFQPHLV GSEQPGLSEF IFDTIQAADV DIRKYLYRAI VLSGGSSMYA GLPSRLEKEI KQL WFERVL HGDPARLPNF KVKIEDAPRR RHAVFIGGAV LADIMAQNDH MWVSKAEWEE YGVRALDKLG PRTT

UniProtKB: Actin-related protein 2

+
Macromolecule #3: Actin-related protein 2/3 complex subunit 1

MacromoleculeName: Actin-related protein 2/3 complex subunit 1 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843
Molecular weightTheoretical: 41.643465 KDa
SequenceString: MATSQVLHIL PKPSYEHAFN SQRTEFVTTT ATNQVELYEQ DGNGWKHART FSDHDKIVTC VDWAPKSNRI VTCSQDRNAY VYEKRPDGT WKQTLVLLRL NRAATFVRWS PNEDKFAVGS GARVISVCYF EQENDWWVSK HLKRPLRSTI LSLDWHPNNV L LAAGCADR ...String:
MATSQVLHIL PKPSYEHAFN SQRTEFVTTT ATNQVELYEQ DGNGWKHART FSDHDKIVTC VDWAPKSNRI VTCSQDRNAY VYEKRPDGT WKQTLVLLRL NRAATFVRWS PNEDKFAVGS GARVISVCYF EQENDWWVSK HLKRPLRSTI LSLDWHPNNV L LAAGCADR KAYVLSAYVR DVDAKPEASV WGSRLPFNTV CAEYPSGGWV HAVGFSPSGN ALAYAGHDSS VTIAYPSAPE QP PRALITV KLSQLPLRSL LWANESAIVA AGYNYSPILL QGNESGWAHT RDLDAGTSKT SFTHTGNTGE GREEEGPVSF TAL RSTFRN MDLKGSSQSI SSLPTVHQNM IATLRPYAGT PGNITAFTSS GTDGRVVLWT L

UniProtKB: Actin-related protein 2/3 complex subunit 1

+
Macromolecule #4: Actin-related protein 2/3 complex subunit 2

MacromoleculeName: Actin-related protein 2/3 complex subunit 2 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843
Molecular weightTheoretical: 37.02523 KDa
SequenceString: MLSLDYNNIF IYELLTERFS SENPSSIDQV VTDFDGVTFH ISTPEEKTKI LISLSMKCYP ELVNYGTLDL LKQIYGAYVH EPEMGYNFS ILIDLQQLPA TDEEKEQLAM SISMLKRNVL AAPFHRAFTK QAELADLARK DPENAPMLDK QATSQELMAI H YRDEETIV ...String:
MLSLDYNNIF IYELLTERFS SENPSSIDQV VTDFDGVTFH ISTPEEKTKI LISLSMKCYP ELVNYGTLDL LKQIYGAYVH EPEMGYNFS ILIDLQQLPA TDEEKEQLAM SISMLKRNVL AAPFHRAFTK QAELADLARK DPENAPMLDK QATSQELMAI H YRDEETIV LWPEHDRVTV VFSTKFREET DRIFGKVFLQ EFVDARRRPA IQTAPQVLFS YRDPPLEIRD IQGIQKGDDF GF VTFVLFE RHFTPQNRED CISHIQVFRN TLHFHIKASK AYMHQRMRKR VADFQKVLNR AKPDVELERK TATGRSFVRA

UniProtKB: Actin-related protein 2/3 complex subunit 2

+
Macromolecule #5: Actin-related protein 2/3 complex subunit 3

MacromoleculeName: Actin-related protein 2/3 complex subunit 3 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843
Molecular weightTheoretical: 19.865746 KDa
SequenceString:
MPAYHSSFLS LTDVPTTGNI AMLPLKTKFR GPAYPADESQ MDIIDECIGL FRANCFFRNF EIKGPADRTL IYGTLFISEC LGRVNGLNY RDAERQLNSL ALENFSIPGS AGFPLNALYA PPLSPQDAEI MRTYLTQFRQ ELAYRLLSHV YATEKDHPSK W WTCFSKRR FMNKAL

UniProtKB: Actin-related protein 2/3 complex subunit 3

+
Macromolecule #6: Actin-related protein 2/3 complex subunit 4

MacromoleculeName: Actin-related protein 2/3 complex subunit 4 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843
Molecular weightTheoretical: 19.637695 KDa
SequenceString:
MSNTLRPYLN AVRSTLTASL ALEEFSSEIV ERQSQPEVEV GRSPEILLKP LVVSRNEQEQ CLIESSVNSV RFSIRIKQVD EIERILVRK FMQFLMGRAE SFFILRRKPV QGYDISFLIT NYHTEEMLKH KLVDFIIEFM EEVDAEISEM KLFLNGRARL V AETYLSCF

UniProtKB: Actin-related protein 2/3 complex subunit 4

+
Macromolecule #7: Actin-related protein 2/3 complex subunit 5

MacromoleculeName: Actin-related protein 2/3 complex subunit 5 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843
Molecular weightTheoretical: 16.922059 KDa
SequenceString:
MTFRTLDVDS ITEPVLTEQD IFPIRNETAE QVQAAVSQLI PQARSAIQTG NALQGLKTLL SYVPYGNDVQ EVRTQYLNAF VDVLSNIRA ADIPAFVKEC STEEIDNIVN FIYRGLANPQ AYNSSVLLNW HEKVVEISGI GCIVRVLNSR PDL

UniProtKB: Actin-related protein 2/3 complex subunit 5

+
Macromolecule #8: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 8 / Number of copies: 2 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM / Adenosine triphosphate

+
Macromolecule #9: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 9 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration2.5 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
50.0 mMNaClSodium chloridesodium chloride
1.0 mMMgCl2magnesium chloride
1.0 mMC10H16N5O13P3adenosine triphosphate
10.0 mMC4H11NO3tris(hydroxymethyl)aminomethane
1.0 mMC4H10O2S2dithiothreitol
GridModel: Quantifoil, UltrAuFoil, R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Support film - Film thickness: 50 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 120 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.019 kPa / Details: 20mA current
VitrificationCryogen name: ETHANE / Chamber humidity: 98 % / Chamber temperature: 277.15 K / Instrument: HOMEMADE PLUNGER
Details: 4 uL of sample was applied to freshly glow-discharged grid. Excess sample was manually blotted off with a dry Whatman No.1 filter paper for 5-7 seconds. Immediately after the blotting step ...Details: 4 uL of sample was applied to freshly glow-discharged grid. Excess sample was manually blotted off with a dry Whatman No.1 filter paper for 5-7 seconds. Immediately after the blotting step the sample containing grid was rapidly vitrified by plunge freezing into liquid ethane..

-
Electron microscopy

MicroscopeFEI TALOS ARCTICA
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: -1.3 µm / Nominal defocus min: -0.7000000000000001 µm / Nominal magnification: 120000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
DetailsData were collected by combining untilted and tilted (20, 30 and 40 degrees) images. Stage shifting to the targeted exposure position was used for navigation during data acquisition.
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 4000 pixel / Digitization - Dimensions - Height: 4000 pixel / Number grids imaged: 3 / Number real images: 5309 / Average exposure time: 40.0 sec. / Average electron dose: 44.34 e/Å2
Details: Each micrograph was collected as dose-fractionated movies consisting of 62 fractions per movie.
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

-
Image processing

Particle selectionNumber selected: 3336981 / Details: Automated Gaussian-based blob picker was used.
Startup modelType of model: INSILICO MODEL
In silico model: Ab initio models were reconstructed from the dataset
Initial angle assignmentType: NOT APPLICABLE
Final 3D classificationNumber classes: 2 / Software - Name: cryoSPARC (ver. 2.12.4)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC (ver. 2.12.4)
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.12.4) / Number images used: 112170
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelPDB ID:

3dwl


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-6w18:
Structure of S. pombe Arp2/3 complex in inactive state

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more