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- PDB-6kd5: Crystal structure of the extracellular domain of MSPL/TMPRSS13 in... -

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Basic information

Entry
Database: PDB / ID: 6kd5
TitleCrystal structure of the extracellular domain of MSPL/TMPRSS13 in complex with dec-RVKR-cmk inhibitor
Components
  • (Transmembrane protease serine ...) x 2
  • DECANOYL-ARG-VAL-LYS-ARG-CHLOROMETHYLKETONE INHIBITOR
KeywordsSTRUCTURAL PROTEIN/INHIBITOR / HYDROLASE / STRUCTURAL PROTEIN-INHIBITOR complex
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / blood microparticle / serine-type endopeptidase activity / proteolysis / membrane / plasma membrane / cytoplasm
Similarity search - Function
Peptidase S1A, TMPRSS13 / SRCR-like domain / Scavenger receptor cysteine-rich domain / SRCR domain profile. / SRCR-like domain superfamily / Scavenger receptor Cys-rich / SRCR domain / Low-density lipoprotein (LDL) receptor class A repeat / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site ...Peptidase S1A, TMPRSS13 / SRCR-like domain / Scavenger receptor cysteine-rich domain / SRCR domain profile. / SRCR-like domain superfamily / Scavenger receptor Cys-rich / SRCR domain / Low-density lipoprotein (LDL) receptor class A repeat / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Transmembrane protease serine 13
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsOhno, A. / Maita, N. / Okumura, Y. / Nikawa, T.
Funding support Japan, 8items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)15K13747 Japan
Japan Society for the Promotion of Science (JSPS)19K05696 Japan
Japan Society for the Promotion of Science (JSPS)15K09585 Japan
Japan Society for the Promotion of Science (JSPS)18K08453 Japan
Japan Society for the Promotion of Science (JSPS)15J40096 Japan
Japan Society for the Promotion of Science (JSPS)18H04981 Japan
Japan Society for the Promotion of Science (JSPS)19H04054 Japan
Japan Agency for Medical Research and Development (AMED)JP19gm0810009 Japan
CitationJournal: Life Sci Alliance / Year: 2021
Title: Crystal structure of inhibitor-bound human MSPL that can activate high pathogenic avian influenza.
Authors: Ohno, A. / Maita, N. / Tabata, T. / Nagano, H. / Arita, K. / Ariyoshi, M. / Uchida, T. / Nakao, R. / Ulla, A. / Sugiura, K. / Kishimoto, K. / Teshima-Kondo, S. / Okumura, Y. / Nikawa, T.
History
DepositionJun 30, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 24, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 1, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ASTM ..._citation.journal_abbrev / _citation.journal_id_ASTM / _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
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_conn_type / 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_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.0Nov 25, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / citation / entity / pdbx_audit_support / pdbx_branch_scheme / pdbx_entity_branch_descriptor / pdbx_entity_instance_feature / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_peptide_omega / pdbx_validate_rmsd_bond / pdbx_validate_symm_contact / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / software / struct / struct_conf / struct_conn / struct_mon_prot_cis / struct_ref_seq / struct_ref_seq_dif / struct_sheet_range
Item: _chem_comp.pdbx_synonyms / _citation.title ..._chem_comp.pdbx_synonyms / _citation.title / _entity.details / _entity.pdbx_description / _entity.pdbx_fragment / _entity.pdbx_number_of_molecules / _pdbx_branch_scheme.auth_asym_id / _pdbx_entity_branch_descriptor.descriptor / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.pdb_seq_num / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.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 / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_residues.auth_seq_id / _refine.B_iso_mean / _refine.aniso_B[1][1] / _refine.aniso_B[2][2] / _refine.aniso_B[2][3] / _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.ls_d_res_low / _refine.overall_SU_B / _refine.overall_SU_ML / _refine.pdbx_overall_ESU_R / _refine.pdbx_overall_ESU_R_Free / _refine_hist.d_res_low / _refine_hist.number_atoms_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.name / _software.version / _struct.title / _struct_conf.beg_auth_comp_id / _struct_conf.beg_auth_seq_id / _struct_conf.beg_label_comp_id / _struct_conf.beg_label_seq_id / _struct_conf.end_auth_seq_id / _struct_conf.pdbx_PDB_helix_length / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_mon_prot_cis.auth_seq_id / _struct_mon_prot_cis.pdbx_auth_seq_id_2 / _struct_mon_prot_cis.pdbx_omega_angle / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq_dif.pdbx_auth_seq_num / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.end_auth_seq_id
Description: Ligand geometry
Details: The conformation of the peptide bond between the chain C ARG2 and DKA1 was fixed.
Provider: author / Type: Coordinate replacement
Revision 3.1Apr 14, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 3.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transmembrane protease serine 13
B: Transmembrane protease serine 13
C: DECANOYL-ARG-VAL-LYS-ARG-CHLOROMETHYLKETONE INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,19013
Polymers47,6863
Non-polymers1,50410
Water1,45981
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6990 Å2
ΔGint-93 kcal/mol
Surface area17440 Å2
Unit cell
Length a, b, c (Å)55.840, 62.400, 171.630
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Transmembrane protease serine ... , 2 types, 2 molecules AB

#1: Protein Transmembrane protease serine 13 / Membrane-type mosaic serine protease / Mosaic serine protease


Mass: 18165.039 Da / Num. of mol.: 1 / Fragment: UNP residues 192-325
Source method: isolated from a genetically manipulated source
Details: Non-catalytic chain / Source: (gene. exp.) Homo sapiens (human) / Gene: TMPRSS13, MSP, TMPRSS11 / Cell line (production host): ECV304-MSPLdTM / Production host: Homo sapiens (human)
References: UniProt: Q9BYE2, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Protein Transmembrane protease serine 13 / Membrane-type mosaic serine protease / Mosaic serine protease


Mass: 28771.436 Da / Num. of mol.: 1 / Fragment: UNP residues 326-586
Source method: isolated from a genetically manipulated source
Details: Catalytic chain / Source: (gene. exp.) Homo sapiens (human) / Gene: TMPRSS13, MSP, TMPRSS11 / Cell line (production host): ECV304-MSPLdTM / Production host: Homo sapiens (human)
References: UniProt: Q9BYE2, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases

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Protein/peptide , 1 types, 1 molecules C

#3: Protein/peptide DECANOYL-ARG-VAL-LYS-ARG-CHLOROMETHYLKETONE INHIBITOR


Mass: 749.452 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Sugars , 2 types, 2 molecules

#4: Polysaccharide alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-6DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#5: 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.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE

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Non-polymers , 3 types, 89 molecules

#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Sequence detailsThis protein is cleaved at between Arg320-Ile321, then turns into a mature form.

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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: 3.14 Å3/Da / Density % sol: 64.9 %
Crystal growTemperature: 288 K / Method: vapor diffusion / pH: 7.5 / Details: 0.1M HEPES(pH7.5), 2.4M Ammonium Sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 10, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→40 Å / Num. obs: 19249 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / CC1/2: 0.995 / Rmerge(I) obs: 0.151 / Rpim(I) all: 0.088 / Rrim(I) all: 0.175 / Net I/σ(I): 9.5
Reflection shellResolution: 2.6→2.72 Å / Redundancy: 7.3 % / Rmerge(I) obs: 1.012 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2303 / CC1/2: 0.729 / Rpim(I) all: 0.593 / Rrim(I) all: 1.174 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
iMOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ANY

2any


Resolution: 2.6→39.99 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.902 / SU B: 9.564 / SU ML: 0.194 / Cross valid method: THROUGHOUT / ESU R: 0.388 / ESU R Free: 0.266 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23567 1493 7.8 %RANDOM
Rwork0.18395 ---
obs0.18801 17570 99.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.142 Å2
Baniso -1Baniso -2Baniso -3
1-2.63 Å20 Å20 Å2
2---0.05 Å20 Å2
3----2.58 Å2
Refinement stepCycle: 1 / Resolution: 2.6→39.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2949 0 100 81 3130
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0133125
X-RAY DIFFRACTIONr_bond_other_d00.0182758
X-RAY DIFFRACTIONr_angle_refined_deg1.1911.6734247
X-RAY DIFFRACTIONr_angle_other_deg1.1211.6186416
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.7075369
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.44121.835158
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.08815506
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2141520
X-RAY DIFFRACTIONr_chiral_restr0.0460.2409
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.023416
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02675
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.6763.2411486
X-RAY DIFFRACTIONr_mcbond_other3.6763.2411486
X-RAY DIFFRACTIONr_mcangle_it5.5624.8571851
X-RAY DIFFRACTIONr_mcangle_other5.5614.8561852
X-RAY DIFFRACTIONr_scbond_it4.5713.8131639
X-RAY DIFFRACTIONr_scbond_other4.5183.7761612
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.8485.4482355
X-RAY DIFFRACTIONr_long_range_B_refined9.93260.61312215
X-RAY DIFFRACTIONr_long_range_B_other9.9360.63612201
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.414 108 -
Rwork0.334 1258 -
obs--99.56 %

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