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- PDB-5k47: CryoEM structure of the human Polycystin-2/PKD2 TRP channel -

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Entry
Database: PDB / ID: 5k47
TitleCryoEM structure of the human Polycystin-2/PKD2 TRP channel
ComponentsPolycystin-2Polycystin 2
KeywordsTRANSPORT PROTEIN / ion channel / transient receptor potential channel / polycystic kidney disease / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


detection of nodal flow / metanephric smooth muscle tissue development / metanephric cortex development / metanephric cortical collecting duct development / metanephric distal tubule development / polycystin complex / mesonephric tubule development / mesonephric duct development / : / metanephric part of ureteric bud development ...detection of nodal flow / metanephric smooth muscle tissue development / metanephric cortex development / metanephric cortical collecting duct development / metanephric distal tubule development / polycystin complex / mesonephric tubule development / mesonephric duct development / : / metanephric part of ureteric bud development / determination of liver left/right asymmetry / renal tubule morphogenesis / metanephric ascending thin limb development / HLH domain binding / basal cortex / metanephric mesenchyme development / metanephric S-shaped body morphogenesis / renal artery morphogenesis / positive regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity / migrasome / cilium organization / VxPx cargo-targeting to cilium / detection of mechanical stimulus / regulation of calcium ion import / cation channel complex / calcium-induced calcium release activity / muscle alpha-actinin binding / placenta blood vessel development / voltage-gated monoatomic ion channel activity / cellular response to hydrostatic pressure / outward rectifier potassium channel activity / voltage-gated monoatomic cation channel activity / non-motile cilium / cellular response to fluid shear stress / cellular response to osmotic stress / voltage-gated sodium channel activity / transcription regulator inhibitor activity / actinin binding / motile cilium / inorganic cation transmembrane transport / determination of left/right symmetry / neural tube development / aorta development / protein heterotetramerization / ciliary membrane / branching involved in ureteric bud morphogenesis / negative regulation of G1/S transition of mitotic cell cycle / spinal cord development / heart looping / cytoplasmic side of endoplasmic reticulum membrane / voltage-gated potassium channel activity / cell surface receptor signaling pathway via JAK-STAT / potassium channel activity / centrosome duplication / sodium ion transmembrane transport / negative regulation of ryanodine-sensitive calcium-release channel activity / voltage-gated calcium channel activity / embryonic placenta development / monoatomic cation channel activity / cellular response to cAMP / release of sequestered calcium ion into cytosol / potassium ion transmembrane transport / cellular response to calcium ion / cytoskeletal protein binding / basal plasma membrane / ciliary basal body / liver development / establishment of localization in cell / lumenal side of endoplasmic reticulum membrane / calcium ion transmembrane transport / protein tetramerization / phosphoprotein binding / cytoplasmic vesicle membrane / cilium / intracellular calcium ion homeostasis / mitotic spindle / Wnt signaling pathway / cellular response to reactive oxygen species / positive regulation of nitric oxide biosynthetic process / calcium ion transport / cell-cell junction / lamellipodium / regulation of cell population proliferation / heart development / ATPase binding / positive regulation of cytosolic calcium ion concentration / protein homotetramerization / basolateral plasma membrane / transmembrane transporter binding / regulation of cell cycle / negative regulation of cell population proliferation / signaling receptor binding / calcium ion binding / endoplasmic reticulum membrane / positive regulation of gene expression / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / extracellular exosome
Similarity search - Function
Ferredoxin I 4Fe-4S cluster domain / Polycystin domain / Polycystin domain / Polycystic kidney disease type 2 protein / Polycystin cation channel, PKD1/PKD2 / Polycystin cation channel / Voltage-dependent channel domain superfamily / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.22 Å
AuthorsPike, A.C.W. / Grieben, M. / Shintre, C.A. / Tessitore, A. / Shrestha, L. / Mukhopadhyay, S. / Mahajan, P. / Chalk, R. / Burgess-Brown, N.A. / Huiskonen, J.T. ...Pike, A.C.W. / Grieben, M. / Shintre, C.A. / Tessitore, A. / Shrestha, L. / Mukhopadhyay, S. / Mahajan, P. / Chalk, R. / Burgess-Brown, N.A. / Huiskonen, J.T. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Carpenter, E.P. / Structural Genomics Consortium (SGC)
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust092809/Z/10/Z United Kingdom
CitationJournal: Nat Struct Mol Biol / Year: 2017
Title: Structure of the polycystic kidney disease TRP channel Polycystin-2 (PC2).
Authors: Mariana Grieben / Ashley C W Pike / Chitra A Shintre / Elisa Venturi / Sam El-Ajouz / Annamaria Tessitore / Leela Shrestha / Shubhashish Mukhopadhyay / Pravin Mahajan / Rod Chalk / Nicola A ...Authors: Mariana Grieben / Ashley C W Pike / Chitra A Shintre / Elisa Venturi / Sam El-Ajouz / Annamaria Tessitore / Leela Shrestha / Shubhashish Mukhopadhyay / Pravin Mahajan / Rod Chalk / Nicola A Burgess-Brown / Rebecca Sitsapesan / Juha T Huiskonen / Elisabeth P Carpenter /
Abstract: Mutations in either polycystin-1 (PC1 or PKD1) or polycystin-2 (PC2, PKD2 or TRPP1) cause autosomal-dominant polycystic kidney disease (ADPKD) through unknown mechanisms. Here we present the ...Mutations in either polycystin-1 (PC1 or PKD1) or polycystin-2 (PC2, PKD2 or TRPP1) cause autosomal-dominant polycystic kidney disease (ADPKD) through unknown mechanisms. Here we present the structure of human PC2 in a closed conformation, solved by electron cryomicroscopy at 4.2-Å resolution. The structure reveals a novel polycystin-specific 'tetragonal opening for polycystins' (TOP) domain tightly bound to the top of a classic transient receptor potential (TRP) channel structure. The TOP domain is formed from two extensions to the voltage-sensor-like domain (VSLD); it covers the channel's endoplasmic reticulum lumen or extracellular surface and encloses an upper vestibule, above the pore filter, without blocking the ion-conduction pathway. The TOP-domain fold is conserved among the polycystins, including the homologous channel-like region of PC1, and is the site of a cluster of ADPKD-associated missense variants. Extensive contacts among the TOP-domain subunits, the pore and the VSLD provide ample scope for regulation through physical and chemical stimuli.
History
DepositionMay 20, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 24, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2016Group: Database references
Revision 1.2Jan 11, 2017Group: Database references
Revision 1.3Feb 15, 2017Group: Database references
Revision 1.4Aug 30, 2017Group: Data collection / Experimental preparation
Category: em_imaging_optics / em_sample_support / em_software
Item: _em_imaging_optics.energyfilter_name / _em_sample_support.grid_type ..._em_imaging_optics.energyfilter_name / _em_sample_support.grid_type / _em_software.fitting_id / _em_software.name / _em_software.version
Revision 1.5Oct 3, 2018Group: Data collection / Refinement description
Category: refine / refine_hist ...refine / refine_hist / refine_ls_restr / refine_ls_shell
Item: _refine_hist.pdbx_refine_id / _refine_ls_restr.pdbx_refine_id / _refine_ls_shell.pdbx_refine_id
Revision 1.6Oct 10, 2018Group: Data collection / Refinement description / Structure summary
Category: entity / refine / refine_ls_restr_ncs
Item: _entity.formula_weight / _refine_ls_restr_ncs.pdbx_refine_id
Revision 1.7Dec 11, 2019Group: Other / Structure summary / Category: atom_sites / cell / entity
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] / _cell.Z_PDB / _entity.formula_weight
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 21, 2020Group: Data collection / Structure summary / Category: chem_comp / em_imaging_optics
Item: _chem_comp.pdbx_synonyms / _em_imaging_optics.chr_aberration_corrector ..._chem_comp.pdbx_synonyms / _em_imaging_optics.chr_aberration_corrector / _em_imaging_optics.phase_plate / _em_imaging_optics.sph_aberration_corrector

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Structure visualization

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  • Deposited structure unit
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Structure viewerMolecule:
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Assembly

Deposited unit
A: Polycystin-2
B: Polycystin-2
C: Polycystin-2
D: Polycystin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)259,41416
Polymers255,9474
Non-polymers3,46712
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area30740 Å2
ΔGint-232 kcal/mol
Surface area90740 Å2
MethodPISA
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A213 - 702
2010B213 - 702
1020A213 - 702
2020C213 - 702
1030A213 - 702
2030D213 - 702
1040B213 - 702
2040C213 - 702
1050B213 - 702
2050D213 - 702
1060C213 - 702
2060D213 - 702

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Polycystin-2 / Polycystin 2 / Autosomal dominant polycystic kidney disease type II protein / Polycystic kidney disease 2 protein ...Autosomal dominant polycystic kidney disease type II protein / Polycystic kidney disease 2 protein / Polycystwin / R48321 / Transient receptor potential cation channel subfamily P member 2


Mass: 63986.668 Da / Num. of mol.: 4 / Fragment: UNP residues 185-723
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PKD2, TRPP2 / Plasmid: pFB-CT10HF-LIC / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q13563
#2: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Polycystin-2 channel tetramer (residues 185-723) / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.256 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm) / Plasmid: pFB-CT10HF-LIC
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
1200 mMsodium chlorideNaClSodium chloride1
220 mMHEPESC8H18N2O4S1
320 mMcalcium chlorideCaCl21
40.035 % (w/v)undecyl-b-D-maltopyranosideC23H44O111
SpecimenConc.: 4.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Sample was monodisperse after size exclusion chromatography
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: C-flat
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 85 K
Details: 3 microlitres were applied to the grid and blotted for 3secs prior to plunge in liquid ethane

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 37037 X / Nominal defocus max: 4500 nm / Nominal defocus min: 1100 nm / Cs: 2 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: SIDE ENTRY, EUCENTRIC
Image recordingAverage exposure time: 8.8 sec. / Electron dose: 45.1 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 758
Details: Images were collected in movie-mode at 2.5 frames per second for a duration of 8.8secs
EM imaging opticsEnergyfilter name: GIF Quantum / Energyfilter upper: 20 eV / Energyfilter lower: 0 eV
Image scansMovie frames/image: 22 / Used frames/image: 1-22

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Processing

SoftwareName: REFMAC / Version: 5.8.0135 / Classification: refinement
EM software
IDNameVersionCategory
1RELION1.3particle selection
2SerialEMimage acquisition
4CTFFIND4.0.8CTF correction
5RELION1.3CTF correction
8Cootmodel fitting
10REFMAC5.8.0135model refinement
11RELION1.3initial Euler assignment
12RELION1.3final Euler assignment
13RELION1.3classification
14RELION1.33D reconstruction
15RELION1.3model refinement
16CTFFIND4model refinement
CTF correctionDetails: CTF correction as implemented in CTTFIND4/RELION / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 161965
Details: Particles were autopicked using CTF-corrected template based picking algorithm in RELION using selected 2D class averages based on manually picked particles.
SymmetryPoint symmetry: C4 (4 fold cyclic)
3D reconstructionResolution: 4.22 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 19546
Details: Resolution determined by gold-standard FSC procedure as implemented in RELION
Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: RECIPROCAL / Details: Model was built directly into map de novo
RefinementResolution: 4.2→108 Å / Cor.coef. Fo:Fc: 0.863 / SU B: 52.839 / SU ML: 0.629
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rwork0.29561 --
obs0.29561 35621 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: 118.923 Å2
Baniso -1Baniso -2Baniso -3
1--1.13 Å20.01 Å2-0.04 Å2
2---1.13 Å20.03 Å2
3---2.25 Å2
Refinement stepCycle: 1 / Total: 15680
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0070.0216116
ELECTRON MICROSCOPYr_bond_other_d0.0010.0215000
ELECTRON MICROSCOPYr_angle_refined_deg1.0371.94721952
ELECTRON MICROSCOPYr_angle_other_deg0.848334024
ELECTRON MICROSCOPYr_dihedral_angle_1_deg5.87551928
ELECTRON MICROSCOPYr_dihedral_angle_2_deg30.75922.356696
ELECTRON MICROSCOPYr_dihedral_angle_3_deg13.272152428
ELECTRON MICROSCOPYr_dihedral_angle_4_deg15.6781592
ELECTRON MICROSCOPYr_chiral_restr0.0530.22544
ELECTRON MICROSCOPYr_gen_planes_refined0.0030.0218096
ELECTRON MICROSCOPYr_gen_planes_other0.0010.024244
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_it4.26612.2057736
ELECTRON MICROSCOPYr_mcbond_other4.26312.2047735
ELECTRON MICROSCOPYr_mcangle_it7.74818.2889656
ELECTRON MICROSCOPYr_mcangle_other7.74918.299657
ELECTRON MICROSCOPYr_scbond_it3.42212.4438380
ELECTRON MICROSCOPYr_scbond_other3.42212.4448381
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other6.48618.56512297
ELECTRON MICROSCOPYr_long_range_B_refined12.00197.30917933
ELECTRON MICROSCOPYr_long_range_B_other1297.31517934
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: ELECTRON MICROSCOPY / Type: interatomic distance / Rms dev position: 0 Å / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumber
11A53244
12B53244
21A53244
22C53244
31A53246
32D53246
41B53244
42C53244
51B53244
52D53244
61C53246
62D53246
LS refinement shellResolution: 4.2→4.309 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.447 2688 -
Rfree-0 -
obs--100 %

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