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- PDB-7kl1: Cocrystal structure of human CaMKII-alpha (CAMK2A)kinase domain a... -

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Basic information

Entry
Database: PDB / ID: 7kl1
TitleCocrystal structure of human CaMKII-alpha (CAMK2A)kinase domain and GluN2B(S1303D)
Components
  • Calcium/calmodulin-dependent protein kinase type II subunit alpha
  • Glutamate receptor ionotropic, NMDA 2B
KeywordsTRANSFERASE / CaMKII / Kinase / Human / CAMK2A
Function / homology
Function and homology information


peptidyl-threonine autophosphorylation / regulation of endocannabinoid signaling pathway / calcium- and calmodulin-dependent protein kinase complex / excitatory chemical synaptic transmission / regulation of neuron migration / Ca2+/calmodulin-dependent protein kinase / regulation of neurotransmitter secretion / Synaptic adhesion-like molecules / Activated NTRK2 signals through FYN / dendritic spine development ...peptidyl-threonine autophosphorylation / regulation of endocannabinoid signaling pathway / calcium- and calmodulin-dependent protein kinase complex / excitatory chemical synaptic transmission / regulation of neuron migration / Ca2+/calmodulin-dependent protein kinase / regulation of neurotransmitter secretion / Synaptic adhesion-like molecules / Activated NTRK2 signals through FYN / dendritic spine development / Trafficking of AMPA receptors / positive regulation of calcium ion transport / positive regulation of cysteine-type endopeptidase activity / glutamate-gated calcium ion channel activity / negative regulation of hydrolase activity / glutamate receptor signaling pathway / Assembly and cell surface presentation of NMDA receptors / regulation of monoatomic cation transmembrane transport / negative regulation of dendritic spine maintenance / Neurexins and neuroligins / calmodulin-dependent protein kinase activity / NMDA glutamate receptor activity / NMDA selective glutamate receptor complex / calcium ion transmembrane import into cytosol / protein heterotetramerization / regulation of mitochondrial membrane permeability involved in apoptotic process / glutamate binding / glycine binding / CaMK IV-mediated phosphorylation of CREB / regulation of neuronal synaptic plasticity / Negative regulation of NMDA receptor-mediated neuronal transmission / positive regulation of cardiac muscle cell apoptotic process / Unblocking of NMDA receptors, glutamate binding and activation / Phase 0 - rapid depolarisation / monoatomic cation transmembrane transport / positive regulation of excitatory postsynaptic potential / Long-term potentiation / Ion transport by P-type ATPases / Regulation of MECP2 expression and activity / HSF1-dependent transactivation / glutamate receptor binding / cellular response to interferon-beta / MECP2 regulates neuronal receptors and channels / Ion homeostasis / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / EPHB-mediated forward signaling / excitatory postsynaptic potential / ionotropic glutamate receptor signaling pathway / Ras activation upon Ca2+ influx through NMDA receptor / positive regulation of synaptic transmission, glutamatergic / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic membrane / synaptic transmission, glutamatergic / long-term synaptic potentiation / response to ischemia / angiotensin-activated signaling pathway / postsynaptic density membrane / brain development / regulation of synaptic plasticity / G1/S transition of mitotic cell cycle / RAF activation / positive regulation of receptor signaling pathway via JAK-STAT / cellular response to type II interferon / endocytic vesicle membrane / 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 / calcium ion transport / Interferon gamma signaling / Signaling by BRAF and RAF1 fusions / late endosome / Ca2+ pathway / amyloid-beta binding / positive regulation of NF-kappaB transcription factor activity / kinase activity / chemical synaptic transmission / RAF/MAP kinase cascade / postsynaptic membrane / peptidyl-serine phosphorylation / response to ethanol / dendritic spine / postsynaptic density / protein autophosphorylation / lysosome / learning or memory / cytoskeleton / calmodulin binding / neuron projection / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / endoplasmic reticulum membrane / cell surface / protein homodimerization activity / mitochondrion / zinc ion binding / nucleoplasm / ATP binding / identical protein binding
Similarity search - Function
Calcium/calmodulin-dependent protein kinase II, association-domain / Calcium/calmodulin dependent protein kinase II association domain / Glutamate [NMDA] receptor, epsilon subunit, C-terminal / N-methyl D-aspartate receptor 2B3 C-terminus / NTF2-like domain superfamily / Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / : ...Calcium/calmodulin-dependent protein kinase II, association-domain / Calcium/calmodulin dependent protein kinase II association domain / Glutamate [NMDA] receptor, epsilon subunit, C-terminal / N-methyl D-aspartate receptor 2B3 C-terminus / NTF2-like domain superfamily / Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / : / Ligand-gated ion channel / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / Ionotropic glutamate receptor / Eukaryotic homologues of bacterial periplasmic substrate binding proteins. / Receptor, ligand binding region / Receptor family ligand binding region / Periplasmic binding protein-like I / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, 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
ADENOSINE-5'-TRIPHOSPHATE / Glutamate receptor ionotropic, NMDA 2B / Calcium/calmodulin-dependent protein kinase type II subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsOzden, C. / Stratton, M.M. / Garman, S.C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Cell Rep / Year: 2022
Title: CaMKII binds both substrates and activators at the active site.
Authors: Ozden, C. / Sloutsky, R. / Mitsugi, T. / Santos, N. / Agnello, E. / Gaubitz, C. / Foster, J. / Lapinskas, E. / Esposito, E.A. / Saneyoshi, T. / Kelch, B.A. / Garman, S.C. / Hayashi, Y. / Stratton, M.M.
History
DepositionOct 28, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2020Provider: repository / Type: Initial release
Revision 2.0Apr 6, 2022Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Experimental preparation / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / database_2 ...atom_site / database_2 / entity / entity_src_gen / exptl_crystal_grow / pdbx_audit_support / pdbx_contact_author / pdbx_entity_nonpoly / pdbx_entity_src_syn / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_validate_close_contact / pdbx_validate_rmsd_angle / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_restr_ncs / refine_ls_shell / software / struct / struct_asym / struct_conf / struct_conn / struct_conn_type / struct_mon_prot_cis / struct_ncs_dom / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity_src_gen.gene_src_common_name / _exptl_crystal_grow.pdbx_details / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_entity_src_syn.organism_common_name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.value / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _refine.B_iso_max / _refine.B_iso_mean / _refine.B_iso_min / _refine.aniso_B[1][1] / _refine.aniso_B[2][2] / _refine.aniso_B[3][3] / _refine.correlation_coeff_Fo_to_Fc / _refine.correlation_coeff_Fo_to_Fc_free / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.overall_SU_B / _refine.overall_SU_ML / _refine.pdbx_overall_ESU_R / _refine.pdbx_overall_ESU_R_Free / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_B_iso_mean_ligand / _refine_hist.pdbx_B_iso_mean_solvent / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_protein / _refine_ls_restr.dev_ideal / _refine_ls_restr.dev_ideal_target / _refine_ls_restr.number / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct.title / _struct_mon_prot_cis.pdbx_omega_angle
Description: Atoms with unrealistic or zero occupancies
Details: We have gotten rid of some water and ligand molecules and introduce two covalent links which were missing previously.
Provider: author / Type: Coordinate replacement
Revision 2.1Aug 10, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 2.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Calcium/calmodulin-dependent protein kinase type II subunit alpha
B: Calcium/calmodulin-dependent protein kinase type II subunit alpha
C: Glutamate receptor ionotropic, NMDA 2B
D: Glutamate receptor ionotropic, NMDA 2B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,91011
Polymers66,6614
Non-polymers1,2497
Water2,126118
1
A: Calcium/calmodulin-dependent protein kinase type II subunit alpha
C: Glutamate receptor ionotropic, NMDA 2B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9245
Polymers33,3302
Non-polymers5943
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3200 Å2
ΔGint-13 kcal/mol
Surface area13360 Å2
MethodPISA
2
B: Calcium/calmodulin-dependent protein kinase type II subunit alpha
D: Glutamate receptor ionotropic, NMDA 2B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9866
Polymers33,3302
Non-polymers6564
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3370 Å2
ΔGint-11 kcal/mol
Surface area13130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.893, 92.133, 91.338
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: 0 / Auth seq-ID: 7 - 274 / Label seq-ID: 1 - 268

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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Protein / Protein/peptide , 2 types, 4 molecules ABCD

#1: Protein Calcium/calmodulin-dependent protein kinase type II subunit alpha / / CaMK-II subunit alpha


Mass: 30548.086 Da / Num. of mol.: 2 / Mutation: D135N, Q223K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CAMK2A, CAMKA, KIAA0968 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9UQM7, Ca2+/calmodulin-dependent protein kinase
#2: Protein/peptide Glutamate receptor ionotropic, NMDA 2B / GluN2B / Glutamate [NMDA] receptor subunit epsilon-2 / N-methyl D-aspartate receptor subtype 2B / ...GluN2B / Glutamate [NMDA] receptor subunit epsilon-2 / N-methyl D-aspartate receptor subtype 2B / NR2B / N-methyl-D-aspartate receptor subunit 3 / hNR3


Mass: 2782.165 Da / Num. of mol.: 2 / Mutation: S1303D / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q13224

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Non-polymers , 4 types, 125 molecules

#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 118 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.53 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M 1,3-bis(tris(hydroxymethyl)methylamino)propane, 0.1 M Ammonium sulfate, 20% PEG 6000, 19mM HECAMEG

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: 100 K thorughout the collection / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: DECTRIS PILATUS3 R 200K-A / Detector: PIXEL / Date: Jun 25, 2019 / Details: Rigaku VariMax HF
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 24724 / % possible obs: 99.9 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.183 / Rpim(I) all: 0.083 / Rrim(I) all: 0.201 / Χ2: 2.569 / Net I/σ(I): 5.9 / Num. measured all: 141803
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.4-2.4450.52711950.8160.260.591.59798.8
2.44-2.495.30.49612110.8730.2350.5511.398100
2.49-2.535.40.46712160.8710.220.5181.50399.9
2.53-2.595.50.44812020.8980.2090.4961.464100
2.59-2.645.60.4112150.910.1890.4521.501100
2.64-2.75.60.38212400.9220.1740.4211.672100
2.7-2.775.80.32712030.9370.1480.3591.65899.9
2.77-2.855.80.31312150.9470.1420.3441.682100
2.85-2.935.90.26812410.9550.120.2951.791100
2.93-3.0260.24912250.9640.110.2731.777100
3.02-3.136.10.2112080.9710.0920.232.002100
3.13-3.266.10.27812450.9790.1170.3023.08499.9
3.26-3.416.10.20212170.9790.0940.2233.0199.9
3.41-3.586.10.15212430.9820.0660.1663.107100
3.58-3.816.10.14212550.980.0620.1553.373100
3.81-4.160.1312260.9860.0580.1433.596100
4.1-4.525.90.12512650.9820.0560.1374.242100
4.52-5.175.80.12212630.9830.0550.1353.771100
5.17-6.515.70.14112840.9830.0640.1563.04999.8
6.51-5050.12113550.9790.0590.1355.44699.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0258refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6VZK

6vzk


Resolution: 2.4→48.5 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.89 / SU B: 8.901 / SU ML: 0.203 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.508 / ESU R Free: 0.282 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2575 1177 4.8 %RANDOM
Rwork0.206 ---
obs0.2084 23497 99.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 100.31 Å2 / Biso mean: 25.653 Å2 / Biso min: 8.62 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å20 Å20 Å2
2--0.85 Å2-0 Å2
3----0.69 Å2
Refinement stepCycle: final / Resolution: 2.4→48.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4516 0 76 118 4710
Biso mean--32.4 20.96 -
Num. residues----564
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0134716
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174314
X-RAY DIFFRACTIONr_angle_refined_deg1.4851.6446399
X-RAY DIFFRACTIONr_angle_other_deg1.2321.5769979
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8275562
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.37721.797256
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.8715777
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4751532
X-RAY DIFFRACTIONr_chiral_restr0.0680.2597
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025220
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021018
Refine LS restraints NCS

Ens-ID: 1 / Number: 8288 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.11 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.4→2.46 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.313 68 -
Rwork0.253 1650 -
obs--95.82 %

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