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Entry
Database: PDB / ID: 5jlh
TitleCryo-EM structure of a human cytoplasmic actomyosin complex at near-atomic resolution
Components
  • Actin, cytoplasmic 2
  • Myosin-14,Alpha-actinin A
  • Tropomyosin alpha-3 chain
KeywordsCONTRACTILE PROTEIN / CONTRACTILE FILAMENT / MUSCLE / THIN FILAMENT / CYTOSKELETON / STRUCTURAL PROTEIN / HYDROLASE COMPLEX / F-actin / tropomyosin / filament / myosin / protein polymers / cryo EM
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 / actin filament-based movement ...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. / ATPase, substrate binding domain, subdomain 4 / Actin; Chain A, domain 4 / 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 / ATPase, nucleotide binding domain / 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 / Nucleotidyltransferase; domain 5 / Alpha-Beta Complex / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Alpha-actinin A / Actin, cytoplasmic 2 / Myosin-14
Similarity search - Component
Biological speciesHomo sapiens (human)
Dictyostelium discoideum (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å
Authorsvon der Ecken, J. / Heissler, S.M. / Pathan-Chhatbar, S. / Manstein, D.J. / Raunser, S.
Funding support Germany, 2items
OrganizationGrant numberCountry
Max Planck Society Germany
Behrens-Weise foundation Germany
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, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 15, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 29, 2016Group: Database references
Revision 1.2Jul 13, 2016Group: Database references
Revision 1.3Aug 2, 2017Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Experimental preparation
Category: em_sample_support / em_software ...em_sample_support / em_software / pdbx_database_related / struct_conn / struct_conn_type
Item: _em_sample_support.grid_type / _em_software.name / _em_software.version
Revision 1.4Oct 17, 2018Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description / Source and taxonomy / Structure summary
Category: cell / em_entity_assembly ...cell / em_entity_assembly / em_entity_assembly_naturalsource / em_entity_assembly_recombinant / pdbx_database_related / refine / refine_hist / refine_ls_restr / refine_ls_restr_ncs / refine_ls_shell
Item: _cell.Z_PDB / _pdbx_database_related.content_type ..._cell.Z_PDB / _pdbx_database_related.content_type / _refine.pdbx_refine_id / _refine_hist.pdbx_refine_id / _refine_ls_restr.pdbx_refine_id / _refine_ls_restr_ncs.pdbx_refine_id / _refine_ls_shell.pdbx_refine_id
Revision 1.5Dec 11, 2019Group: Other / Category: atom_sites
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][1] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][2] / _atom_sites.fract_transf_matrix[3][3]
Revision 1.6Nov 9, 2022Group: Database references / Refinement description / Category: database_2 / struct_ncs_oper
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Assembly

Deposited unit
A: Actin, cytoplasmic 2
B: Actin, cytoplasmic 2
C: Actin, cytoplasmic 2
D: Actin, cytoplasmic 2
E: Actin, cytoplasmic 2
F: Myosin-14,Alpha-actinin A
G: Myosin-14,Alpha-actinin A
H: Tropomyosin alpha-3 chain
I: Tropomyosin alpha-3 chain
J: Tropomyosin alpha-3 chain
K: Tropomyosin alpha-3 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)491,96521
Polymers489,70811
Non-polymers2,25810
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
12G
22F

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A1 - 377
2111B1 - 377
3111C1 - 377
4111D1 - 377
5111E1 - 377
1121G50 - 816
2121F50 - 816

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(1), (0.891811, -0.452406, 0.001274), (0.893761, 0.448534, 0.003084)51.60482, -34.04406
2given(-0.97322, 0.229878, -6.0E-5), (-0.972932, -0.23109, 0.000652), (1)140.9939, 184.70058
3given(-0.973697, -0.227845, -0.000584), (0.227845, -0.973697, -0.00012), (-0.000541, -0.00025, 1)184.48206, 168.14206, -27.37182

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Components

#1: Protein
Actin, cytoplasmic 2 / / Gamma-actin


Mass: 41707.570 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACTG1, ACTG / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P63261
#2: Protein Myosin-14,Alpha-actinin A / Myosin heavy chain 14 / Myosin heavy chain / non-muscle IIc / Non-muscle myosin heavy chain IIc / ...Myosin heavy chain 14 / Myosin heavy chain / non-muscle IIc / Non-muscle myosin heavy chain IIc / NMHC II-C / ALPHA-ACTININ / Actin-binding protein A / F-actin cross-linking protein


Mass: 117570.633 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
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
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Dictyostelium discoideum (eukaryote)
Gene: MYH14, KIAA2034, FP17425, abpA, actnA, DDB_G0268632 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q7Z406, UniProt: P05095
#3: Protein
Tropomyosin alpha-3 chain


Mass: 11507.176 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
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).
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#4: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
Sequence detailsHuman TROPOMYSIN WAS USED (UNP P06753-2,TPM3_HUMAN, RESIDUES 62-196) DUE TO THE LIMITED RESOLUTION ...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).

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeDetailsEntity IDParent-IDSource
1F-actin-myosin-tropomyosin complexCOMPLEXFilament#1-#30MULTIPLE SOURCES
2actin, myosinCOMPLEX#1-#21RECOMBINANT
3tropomyosinCOMPLEX#31RECOMBINANT
Molecular weightValue: 0.44 MDa / Experimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Homo sapiens (human)9606
23Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
12Spodoptera frugiperda (fall armyworm)7108
23Escherichia coli (E. coli)562
Buffer solutionpH: 7.5
Details: 5 mM Tris-HCl pH 7.5, 1 mM DTT, 100 mM KCl, and 2 mM MgCl2
Buffer component
IDConc.FormulaBuffer-ID
15 mMTris-HClTris1
21 mMDTT1
3100 mMKCl1
42 mMMgCl21
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: C-flat-2/1
EM embeddingMaterial: I
VitrificationInstrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE / Humidity: 90 %
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 imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS / Details: Cs corrected microscope
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 59000 X / Calibrated defocus min: 700 nm / Calibrated defocus max: 2800 nm
Image recordingAverage exposure time: 0.475 sec. / Electron dose: 16 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON II (4k x 4k) / Num. of real images: 6300
Image scansMovie frames/image: 8 / Used frames/image: 2-8

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Processing

SoftwareName: REFMAC / Version: 5.8.0088 / Classification: refinement
EM software
IDNameVersionCategoryDetails
1SPARXparticle selectionsxhelixboxer.py
2EPUimage acquisition
4CTFFIND4CTF correction
5RELION1.3CTF correction
8MODELLERmodel fittinghomology modelling
9UCSF Chimeramodel fittingrigid-body fitting
10iMODFITmodel fittingflexible fitting
11Cootmodel refinementmanual building, refinement
12REFMACmodel refinementrefinement
13RELION1.3initial Euler assignment
14RELION1.3final Euler assignment
15RELION1.3classification2D classification
16SPARXclassificationsorting out of outliers within the same filament
17RELION1.33D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 166.9 ° / Axial rise/subunit: 27.5 Å / Axial symmetry: C1
Particle selectionNum. of particles selected: 138000
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 118000
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.
Symmetry type: HELICAL
Atomic model building
IDB valueProtocolDetails
1180BACKBONE TRACE
2RIGID BODY FITtropomyosin fitting
Atomic model building
IDPDB-IDPdb chain-ID 3D fitting-ID
13J8A

3j8a

A1
24PD3

4pd3

A1
34A7F

4a7f

B2
43J8A

3j8a

B1
53J8A

3j8a

C1
63J8A

3j8a

D1
73J8A

3j8a

E1
84A7F

4a7f

H2
RefinementResolution: 3.9→211.2 Å / Cor.coef. Fo:Fc: 0.907 / SU B: 27.204 / SU ML: 0.36 / ESU R: 0.558
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS MERGED WITH THE FINAL F-ACTIN-MUYOSIN MAP (3.9 ANGSTROM) TO OBTAIN MAP OF THE ENTIRE F-ACTIN TROPOMYOSIN COMPLEX.
RfactorNum. reflection% reflection
Rwork0.33844 --
obs0.33844 254196 100 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 180.474 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å22.15 Å2-0.05 Å2
2--1.8 Å2-0.18 Å2
3----1.95 Å2
Refinement stepCycle: 1 / Total: 26477
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
ELECTRON MICROSCOPYr_bond_refined_d0.015270250.019
ELECTRON MICROSCOPYr_bond_other_d0.003256190.02
ELECTRON MICROSCOPYr_angle_refined_deg1.833365781.972
ELECTRON MICROSCOPYr_angle_other_deg1.155589723
ELECTRON MICROSCOPYr_dihedral_angle_1_deg7.11933335
ELECTRON MICROSCOPYr_dihedral_angle_2_deg27.036124723.865
ELECTRON MICROSCOPYr_dihedral_angle_3_deg13.084470615
ELECTRON MICROSCOPYr_dihedral_angle_4_deg11.79320015
ELECTRON MICROSCOPYr_chiral_restr0.11740210.2
ELECTRON MICROSCOPYr_gen_planes_refined0.01304900.021
ELECTRON MICROSCOPYr_gen_planes_other0.00361670.02
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it11.4511336517.257
ELECTRON MICROSCOPYr_mcbond_other11.4441336417.256
ELECTRON MICROSCOPYr_mcangle_it18.9211668725.859
ELECTRON MICROSCOPYr_mcangle_other18.9221668825.86
ELECTRON MICROSCOPYr_scbond_it13.2061366018.783
ELECTRON MICROSCOPYr_scbond_other13.2041366018.784
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other22.841989127.541
ELECTRON MICROSCOPYr_long_range_B_refined37.635109964
ELECTRON MICROSCOPYr_long_range_B_other37.636109965
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: ELECTRON MICROSCOPY / Type: tight thermal / Weight position: 0.5

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A578639.27
11B578672.44
11C578648.46
11D578630.16
11E578633.98
22G1158312.57
LS refinement shellResolution: 3.9→4.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.485 18797 -
Rfree-0 -
obs--100 %

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