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- EMDB-8165: Cryo-EM structure of a human cytoplasmic actomyosin complex at ne... -

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Basic information

Entry
Database: EMDB / ID: EMD-8165
TitleCryo-EM structure of a human cytoplasmic actomyosin complex at near-atomic resolution
Map dataNone
Sample
  • Complex: F-actin-myosin-tropomyosin complex
    • Complex: F-actinActin
      • Protein or peptide: Actin, cytoplasmic 2
    • Complex: Myosin
      • Protein or peptide: NON MUSCLE MYOSIN 2C, ALPHA-ACTININ
    • Complex: tropomyosin
      • Protein or peptide: Tropomyosin alpha-3 chain
Function / homology
Function and homology information


contractile vacuole / COPI-mediated anterograde transport / basal body patch / Platelet degranulation / sorocarp development / myosin II filament / tight junction assembly / Neutrophil degranulation / macropinocytic cup / : ...contractile vacuole / COPI-mediated anterograde transport / basal body patch / Platelet degranulation / sorocarp development / myosin II filament / tight junction assembly / Neutrophil degranulation / macropinocytic cup / : / actin filament-based movement / actin crosslink formation / regulation of transepithelial transport / structural constituent of postsynaptic actin cytoskeleton / protein localization to bicellular tight junction / morphogenesis of a polarized epithelium / profilin binding / Formation of annular gap junctions / vocalization behavior / Gap junction degradation / dense body / Cell-extracellular matrix interactions / actomyosin / myosin filament / actomyosin structure organization / myosin II complex / RHO GTPases Activate ROCKs / regulation of stress fiber assembly / RHO GTPases activate CIT / Adherens junctions interactions / hyperosmotic response / Sema4D induced cell migration and growth-cone collapse / Sensory processing of sound by outer hair cells of the cochlea / Sensory processing of sound by inner hair cells of the cochlea / Interaction between L1 and Ankyrins / sarcomere organization / NuA4 histone acetyltransferase complex / regulation of synaptic vesicle endocytosis / microfilament motor activity / apical junction complex / regulation of focal adhesion assembly / maintenance of blood-brain barrier / cortical actin cytoskeleton / positive regulation of wound healing / myofibril / EPHA-mediated growth cone collapse / Recycling pathway of L1 / cell leading edge / filamentous actin / RHO GTPases activate PAKs / pseudopodium / actin filament bundle assembly / brush border / neuronal action potential / calyx of Held / skeletal muscle contraction / EPH-ephrin mediated repulsion of cells / RHO GTPases Activate WASPs and WAVEs / RHO GTPases activate IQGAPs / RHOBTB2 GTPase cycle / phagocytic vesicle / phagocytosis / skeletal muscle tissue development / stress fiber / RHO GTPases activate PKNs / EPHB-mediated forward signaling / cellular response to starvation / extracellular matrix / axonogenesis / cell projection / cell motility / actin filament / RHO GTPases Activate Formins / Translocation of SLC2A4 (GLUT4) to the plasma membrane / sensory perception of sound / FCGR3A-mediated phagocytosis / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / Signaling by high-kinase activity BRAF mutants / Schaffer collateral - CA1 synapse / MAP2K and MAPK activation / structural constituent of cytoskeleton / Regulation of actin dynamics for phagocytic cup formation / platelet aggregation / VEGFA-VEGFR2 Pathway / cellular response to type II interferon / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / actin filament binding / cell-cell junction / Signaling by BRAF and RAF1 fusions / protein-macromolecule adaptor activity / cell junction / Clathrin-mediated endocytosis / cell cortex / regulation of cell shape / growth cone / actin cytoskeleton organization / angiogenesis
Similarity search - Function
EF-hand, Ca insensitive / Ca2+ insensitive EF hand / Ca2+ insensitive EF hand / Spectrin repeat / Spectrin repeat / Actinin-type actin-binding domain signature 1. / Actinin-type actin-binding domain signature 2. / Actinin-type actin-binding domain, conserved site / Myosin tail / Myosin tail ...EF-hand, Ca insensitive / Ca2+ insensitive EF hand / Ca2+ insensitive EF hand / Spectrin repeat / Spectrin repeat / Actinin-type actin-binding domain signature 1. / Actinin-type actin-binding domain signature 2. / Actinin-type actin-binding domain, conserved site / Myosin tail / Myosin tail / Myosin N-terminal SH3-like domain / Spectrin/alpha-actinin / Spectrin repeats / Myosin S1 fragment, N-terminal / Calponin homology domain / Calponin homology (CH) domain / Myosin, N-terminal, SH3-like / Myosin N-terminal SH3-like domain profile. / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / Short calmodulin-binding motif containing conserved Ile and Gln residues. / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. / Myosin. Large ATPases. / IQ motif profile. / IQ motif, EF-hand binding site / Actins signature 1. / Actin, conserved site / Actins signature 2. / Kinesin motor domain superfamily / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / EF-hand domain pair / EF-hand, calcium binding motif / ATPase, nucleotide binding domain / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Alpha-actinin A / Actin, cytoplasmic 2 / Myosin-14
Similarity search - Component
Biological speciesHomo sapiens (human) / Dictyostelium discoideum (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
Authorsvon der Ecken J / Heissler SM / Pathan-Chhatbar S / Manstein DJ / Raunser S
CitationJournal: Nature / Year: 2016
Title: Cryo-EM structure of a human cytoplasmic actomyosin complex at near-atomic resolution.
Abstract: The interaction of myosin with actin filaments is the central feature of muscle contraction and cargo movement along actin filaments of the cytoskeleton. The energy for these movements is generated ...The interaction of myosin with actin filaments is the central feature of muscle contraction and cargo movement along actin filaments of the cytoskeleton. The energy for these movements is generated during a complex mechanochemical reaction cycle. Crystal structures of myosin in different states have provided important structural insights into the myosin motor cycle when myosin is detached from F-actin. The difficulty of obtaining diffracting crystals, however, has prevented structure determination by crystallography of actomyosin complexes. Thus, although structural models exist of F-actin in complex with various myosins, a high-resolution structure of the F-actin–myosin complex is missing. Here, using electron cryomicroscopy, we present the structure of a human rigor actomyosin complex at an average resolution of 3.9 Å. The structure reveals details of the actomyosin interface, which is mainly stabilized by hydrophobic interactions. The negatively charged amino (N) terminus of actin interacts with a conserved basic motif in loop 2 of myosin, promoting cleft closure in myosin. Surprisingly, the overall structure of myosin is similar to rigor-like myosin structures in the absence of F-actin, indicating that F-actin binding induces only minimal conformational changes in myosin. A comparison with pre-powerstroke and intermediate (Pi-release) states of myosin allows us to discuss the general mechanism of myosin binding to F-actin. Our results serve as a strong foundation for the molecular understanding of cytoskeletal diseases, such as autosomal dominant hearing loss and diseases affecting skeletal and cardiac muscles, in particular nemaline myopathy and hypertrophic cardiomyopathy.
History
DepositionApr 27, 2016-
Header (metadata) releaseMay 25, 2016-
Map releaseJun 15, 2016-
UpdateNov 28, 2018-
Current statusNov 28, 2018Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.04
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  • Surface view with fitted model
  • Atomic models: PDB-5jlh
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5jlh
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-5jlh
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8165.png

Downloads & links

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Map

FileDownload / File: emd_8165.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNone
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 256 pix.
= 281.6 Å		1.1 Å/pix.
x 256 pix.
= 281.6 Å		1.1 Å/pix.
x 256 pix.
= 281.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.049 / Movie #1: 0.04
Minimum - Maximum-0.08232533 - 0.18568054
Average (Standard dev.)0.00005229109 (±0.011984889)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-129-128-123
Dimensions256256256
Spacing256256256
CellA=B=C: 281.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.11.11.1
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z281.600281.600281.600
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-128-129-123
NC/NR/NS256256256
D min/max/mean-0.0820.1860.000

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Supplemental data

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Sample components

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Entire : F-actin-myosin-tropomyosin complex

EntireName: F-actin-myosin-tropomyosin complex
Components
  • Complex: F-actin-myosin-tropomyosin complex
    • Complex: F-actinActin
      • Protein or peptide: Actin, cytoplasmic 2
    • Complex: Myosin
      • Protein or peptide: NON MUSCLE MYOSIN 2C, ALPHA-ACTININ
    • Complex: tropomyosin
      • Protein or peptide: Tropomyosin alpha-3 chain

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Supramolecule #1: F-actin-myosin-tropomyosin complex

SupramoleculeName: F-actin-myosin-tropomyosin complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Filament
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #2: F-actin

SupramoleculeName: F-actin / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Dictyostelium discoideum (eukaryote)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)

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Supramolecule #3: Myosin

SupramoleculeName: Myosin / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Supramolecule #4: tropomyosin

SupramoleculeName: tropomyosin / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #3

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Macromolecule #1: Actin, cytoplasmic 2

MacromoleculeName: Actin, cytoplasmic 2 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Dictyostelium discoideum (eukaryote)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: EEEIAALVID NGSGMCKAGF AGDDAPRAVF PSIVGRPRHQ GVMVGMGQKD SYVGDEAQSK RGILTLKYPI EHGIVTNWDD MEKIWHHTF YNELRVAPEE HPVLLTEAPL NPKANREKMT QIMFETFNTP AMYVAIQAVL SLYASGRTTG IVMDSGDGVT H TVPIYEGY ...String:
EEEIAALVID NGSGMCKAGF AGDDAPRAVF PSIVGRPRHQ GVMVGMGQKD SYVGDEAQSK RGILTLKYPI EHGIVTNWDD MEKIWHHTF YNELRVAPEE HPVLLTEAPL NPKANREKMT QIMFETFNTP AMYVAIQAVL SLYASGRTTG IVMDSGDGVT H TVPIYEGY ALPHAILRLD LAGRDLTDYL MKILTERGYS FTTTAEREIV RDIKEKLCYV ALDFEQEMAT AASSSSLEKS YE LPDGQVI TIGNERFRCP EALFQPSFLG MESCGIHETT FNSIMKCDVD IRKDLYANTV LSGGTTMYPG IADRMQKEIT ALA PSTMKI KIIAPPERKY SVWIGGSILA SLSTFQQMWI SKQEYDESGP SIVHRKCF

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Macromolecule #2: NON MUSCLE MYOSIN 2C, ALPHA-ACTININ

MacromoleculeName: NON MUSCLE MYOSIN 2C, ALPHA-ACTININ / type: protein_or_peptide / ID: 2
Details: NON MUSCLE MYOSIN 2C HEAVY CHAIN, MOTOR DOMAIN RESIDUES 1-799 LINKED TO ALPHA-ACTININ 3, REPEATS 1 AND 2 RESIDUES 800-1039 FRAGMENT: UNP Q7Z406-1 RESIDUES 1-799, UNP P05095 RESIDUES 265-502
Enantiomer: LEVO / EC number: ec: 3.6.4.1
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAAVTMSVPG RKAPPRPGPV PEAAQPFLFT PRGPSAGGGP GSGTSPQVEW TARRLVWVPS ELHGFEAAAL RDEGEEEAEV ELAESGRRL RLPRDQIQRM NPPKFSKAED MAELTCLNEA SVLHNLRERY YSGLIYTYSG LFCVVINPYK QLPIYTEAIV E MYRGKKRH ...String:
MAAVTMSVPG RKAPPRPGPV PEAAQPFLFT PRGPSAGGGP GSGTSPQVEW TARRLVWVPS ELHGFEAAAL RDEGEEEAEV ELAESGRRL RLPRDQIQRM NPPKFSKAED MAELTCLNEA SVLHNLRERY YSGLIYTYSG LFCVVINPYK QLPIYTEAIV E MYRGKKRH EVPPHVYAVT EGAYRSMLQD REDQSILCTG ESGAGKTENT KKVIQYLAHV ASSPKGRKEP GVPGELERQL LQ ANPILEA FGNAKTVKND NSSRFGKFIR INFDVAGYIV GANIETYLLE KSRAIRQAKD ECSFHIFYQL LGGAGEQLKA DLL LEPCSH YRFLTNGPSS SPGQERELFQ ETLESLRVLG FSHEEIISML RMVSAVLQFG NIALKRERNT DQATMPDNTA AQKL CRLLG LGVTDFSRAL LTPRIKVGRD YVQKAQTKEQ ADFALEALAK ATYERLFRWL VLRLNRALDR SPRQGASFLG ILDIA GFEI FQLNSFEQLC INYTNEKLQQ LFNHTMFVLE QEEYQREGIP WTFLDFGLDL QPCIDLIERP ANPPGLLALL DEECWF PKA TDKSFVEKVA QEQGGHPKFQ RPRHLRDQAD FSVLHYAGKV DYKANEWLMK NMDPLNDNVA ALLHQSTDRL TAEIWKD VE GIVGLEQVSS LGDGPPGGRP RRGMFRTVGQ LYKESLSRLM ATLSNTNPSF VRCIVPNHEK RAGKLEPRLV LDQLRCNG V LEGIRICRQG FPNRILFQEF RQRYEILTPN AIPKGFMDGK QACEKMIQAL ELDPNLYRVG QSKIFFRAGV LAQLEEERA SEQTKSDYLK RANELVQWIN DKQASLESRD FGDSIESVQS FMNAHKEYKK TEKPPKGQEV SELEAIYNSL QTKLRLIKRE PFVAPAGLT PNEIDSTWSA LEKAEQEHAE ALRIELKRQK KIAVLLQKYN RILKKLENWA TTKSVYLGSN ETGDSITAVQ A KLKNLEAF DGECQSLEGQ SNSDLLSILA QLTELNYNGV PELTERKDTF FAQQWTGVKS SAETYKNTLL AELERLQKIE D

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Macromolecule #3: Tropomyosin alpha-3 chain

MacromoleculeName: Tropomyosin alpha-3 chain / type: protein_or_peptide / ID: 3
Details: Human TROPOMYSIN WAS USED (UNP P06753-2,TPM3_HUMAN, RESIDUES 62-196). DUE TO THE LIMITED RESOLUTION OF THE CRYO-EM DENSITY IN THE REGION OF TROPOMYOSIN, TROPOMYOSIN HAS BEEN REPRESENTED AS POLY(UNK).
Enantiomer: LEVO
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)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7.5
Component:
ConcentrationFormula
5.0 mMTris-HClTris
1.0 mMDTT
100.0 mMKCl
2.0 mMMgCl2

Details: 5 mM Tris-HCl pH 7.5, 1 mM DTT, 100 mM KCl, and 2 mM MgCl2
Sugar embeddingMaterial: I
GridModel: C-flat-2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Instrument: GATAN CRYOPLUNGE 3
Details: Sample (2 uL of F-actin-tropomyosin solution) was applied to a glow-discharged holey carbon grid, incubated for 20 s and manually blotted from the backside for less than a second with filter ...Details: Sample (2 uL of F-actin-tropomyosin solution) was applied to a glow-discharged holey carbon grid, incubated for 20 s and manually blotted from the backside for less than a second with filter paper. Afterwards 1.5 uL of myosin solution (3 uM without nucleotide) were added directly on the grid, incubated for 10 s and then manually blotted for 5 s from the backside with filter paper..

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus max: 2.8 µm / Calibrated defocus min: 0.7 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 59000
DetailsCs corrected microscope
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 2-8 / Number real images: 6300 / Average exposure time: 0.475 sec. / Average electron dose: 16.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 138000
CTF correctionSoftware: (Name: CTFFIND (ver. 4), RELION (ver. 1.3))
Startup modelType of model: EMDB MAP
EMDB ID:

6124

Initial angle assignmentType: NOT APPLICABLE / Software - Name: RELION (ver. 1.3)
Final angle assignmentType: NOT APPLICABLE / Software - Name: RELION (ver. 1.3)
Final reconstructionApplied symmetry - Helical parameters - Δz: 27.5 Å
Applied symmetry - Helical parameters - Δ&Phi: 166.9 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.3)
Details: THE TROPOMYOSIN MAP FILTERED TO 7.0 ANGSTROM WAS MERGED WITH THE FINAL F-ACTIN-MYOSIN MAP (3.9 ANGSTROM) TO OBTAIN A MAP OF THE ENTIRE F-ACTIN-MYOSIN-TROPOMYOSIN COMPLEX.
Number images used: 118000

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Atomic model buiding 1

Initial model
PDB IDChain

3j8a

chain_id: A, B, C, D, E

4pd3

chain_id: A
RefinementProtocol: BACKBONE TRACE / Overall B value: 180
Output model

PDB-5jlh:
Cryo-EM structure of a human cytoplasmic actomyosin complex at near-atomic resolution

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Atomic model buiding 2

Initial modelPDB ID:

4a7f


Chain - Chain ID -:

db-b


Chain - Chain ID - 1: H
Detailstropomyosin fitting
RefinementProtocol: RIGID BODY FIT
Output model

PDB-5jlh:
Cryo-EM structure of a human cytoplasmic actomyosin complex at near-atomic resolution

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