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- PDB-4hyt: Na,K-ATPase in the E2P state with bound ouabain and Mg2+ in the c... -

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Basic information

Entry
Database: PDB / ID: 4hyt
TitleNa,K-ATPase in the E2P state with bound ouabain and Mg2+ in the cation-binding site
Components
  • (Sodium/potassium-transporting ATPase subunit ...) x 2
  • Na+/K+ ATPase gamma subunit transcript variant a
KeywordsHYDROLASE/MEMBRANE PROTEIN / membrane transporter / HYDROLASE-MEMBRANE PROTEIN complex
Function / homology
Function and homology information


Ion homeostasis / positive regulation of P-type sodium:potassium-exchanging transporter activity / Na+/K+-exchanging ATPase / positive regulation of sodium ion export across plasma membrane / positive regulation of potassium ion import across plasma membrane / Ion transport by P-type ATPases / P-type sodium:potassium-exchanging transporter activity / membrane repolarization / sodium ion binding / sodium:potassium-exchanging ATPase complex ...Ion homeostasis / positive regulation of P-type sodium:potassium-exchanging transporter activity / Na+/K+-exchanging ATPase / positive regulation of sodium ion export across plasma membrane / positive regulation of potassium ion import across plasma membrane / Ion transport by P-type ATPases / P-type sodium:potassium-exchanging transporter activity / membrane repolarization / sodium ion binding / sodium:potassium-exchanging ATPase complex / sodium ion export across plasma membrane / regulation of calcium ion transmembrane transport / intracellular potassium ion homeostasis / establishment or maintenance of transmembrane electrochemical gradient / intracellular sodium ion homeostasis / regulation of cardiac muscle contraction by calcium ion signaling / ion channel regulator activity / relaxation of cardiac muscle / potassium ion import across plasma membrane / ATPase activator activity / potassium ion binding / organelle membrane / intercalated disc / lateral plasma membrane / sperm flagellum / ATP metabolic process / regulation of sodium ion transport / cardiac muscle contraction / T-tubule / proton transmembrane transport / protein localization to plasma membrane / sarcolemma / transmembrane transport / intracellular calcium ion homeostasis / melanosome / protein-macromolecule adaptor activity / ATPase binding / regulation of gene expression / basolateral plasma membrane / protein stabilization / cell adhesion / apical plasma membrane / axon / innate immune response / protein kinase binding / ATP hydrolysis activity / ATP binding / membrane / plasma membrane
Similarity search - Function
Na, k-atpase alpha subunit. / : / : / Ion-transport regulator, FXYD motif / ATP1G1/PLM/MAT8 family / FXYD family signature. / Calcium-transporting ATPase, transmembrane domain / Calcium-transporting ATPase, transmembrane domain / Calcium-transporting ATPase, cytoplasmic transduction domain A / Calcium-transporting ATPase, cytoplasmic transduction domain A ...Na, k-atpase alpha subunit. / : / : / Ion-transport regulator, FXYD motif / ATP1G1/PLM/MAT8 family / FXYD family signature. / Calcium-transporting ATPase, transmembrane domain / Calcium-transporting ATPase, transmembrane domain / Calcium-transporting ATPase, cytoplasmic transduction domain A / Calcium-transporting ATPase, cytoplasmic transduction domain A / Sodium/potassium-transporting ATPase subunit beta / Sodium/potassium-transporting ATPase subunit beta superfamily / Sodium / potassium ATPase beta chain / Sodium and potassium ATPases beta subunits signature 1. / Sodium and potassium ATPases beta subunits signature 2. / Calcium-transporting ATPase, cytoplasmic domain N / Calcium-transporting ATPase, cytoplasmic domain N / P-type ATPase subfamily IIC, subunit alpha / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / Cation-transporting P-type ATPase, C-terminal / Cation transporting ATPase, C-terminus / Cation transporter/ATPase, N-terminus / Cation-transporting P-type ATPase, N-terminal / Cation transporter/ATPase, N-terminus / Cation transport ATPase (P-type) / E1-E2 ATPase / P-type ATPase, haloacid dehalogenase domain / P-type ATPase, phosphorylation site / P-type ATPase, cytoplasmic domain N / E1-E2 ATPases phosphorylation site. / P-type ATPase, A domain superfamily / P-type ATPase / P-type ATPase, transmembrane domain superfamily / haloacid dehalogenase-like hydrolase / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Distorted Sandwich / Up-down Bundle / Immunoglobulin-like / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-17F / Chem-1AT / Chem-1DS / O-DODECANYL OCTAETHYLENE GLYCOL / CHOLESTEROL / OUABAIN / Sodium/potassium-transporting ATPase subunit alpha-1 / Sodium/potassium-transporting ATPase subunit beta-1 / FXYD domain-containing ion transport regulator
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.404 Å
AuthorsLaursen, M. / Yatime, L. / Nissen, P. / Fedosova, N.U.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Crystal structure of the high-affinity Na+,K+-ATPase-ouabain complex with Mg2+ bound in the cation binding site.
Authors: Laursen, M. / Yatime, L. / Nissen, P. / Fedosova, N.U.
History
DepositionNov 14, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / 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_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.pdbx_formal_charge / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_unobs_or_zero_occ_atoms.label_asym_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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: Sodium/potassium-transporting ATPase subunit alpha-1
B: Sodium/potassium-transporting ATPase subunit beta-1
G: Na+/K+ ATPase gamma subunit transcript variant a
C: Sodium/potassium-transporting ATPase subunit alpha-1
D: Sodium/potassium-transporting ATPase subunit beta-1
E: Na+/K+ ATPase gamma subunit transcript variant a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)320,75533
Polymers310,3526
Non-polymers10,40327
Water1086
1
A: Sodium/potassium-transporting ATPase subunit alpha-1
B: Sodium/potassium-transporting ATPase subunit beta-1
G: Na+/K+ ATPase gamma subunit transcript variant a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,15819
Polymers155,1763
Non-polymers6,98216
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6020 Å2
ΔGint-40 kcal/mol
Surface area57920 Å2
MethodPISA
2
C: Sodium/potassium-transporting ATPase subunit alpha-1
D: Sodium/potassium-transporting ATPase subunit beta-1
E: Na+/K+ ATPase gamma subunit transcript variant a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,59714
Polymers155,1763
Non-polymers3,42111
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6000 Å2
ΔGint-40 kcal/mol
Surface area57580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.470, 118.080, 494.660
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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Sodium/potassium-transporting ATPase subunit ... , 2 types, 4 molecules ACBD

#1: Protein Sodium/potassium-transporting ATPase subunit alpha-1 / Na(+)/K(+) ATPase alpha-1 subunit / Sodium pump subunit alpha-1


Mass: 112877.562 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: P05024, EC: 3.6.3.9
#2: Protein Sodium/potassium-transporting ATPase subunit beta-1 / Sodium/potassium-dependent ATPase subunit beta-1


Mass: 35204.402 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: P05027

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Protein , 1 types, 2 molecules GE

#3: Protein Na+/K+ ATPase gamma subunit transcript variant a


Mass: 7094.115 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: Q58K79

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Sugars , 2 types, 6 molecules

#4: 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-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
#12: 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.: 5
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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Non-polymers , 8 types, 27 molecules

#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-OBN / OUABAIN / Ouabain


Mass: 584.652 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C29H44O12
#7: Chemical
ChemComp-CLR / CHOLESTEROL / Cholesterol


Mass: 386.654 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H46O
#8: Chemical ChemComp-1AT / beta-D-fructofuranosyl 6-O-decanoyl-alpha-D-glucopyranoside


Mass: 496.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H40O12
#9: Chemical ChemComp-1DS / 1-O-decanoyl-beta-D-tagatofuranosyl beta-D-allopyranoside


Mass: 496.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H40O12
#10: Chemical
ChemComp-17F / O-[(S)-({(2R)-2,3-bis[(9Z)-octadec-9-enoyloxy]propyl}oxy)(hydroxy)phosphoryl]-L-serine / 1,2-Dioleoyl-sn-glycero-3-phospho-L-serine


Mass: 788.043 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C42H78NO10P / Comment: phospholipid*YM
#11: Chemical ChemComp-CE1 / O-DODECANYL OCTAETHYLENE GLYCOL / THESIT / Octaethylene glycol monododecyl ether


Mass: 538.755 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H58O9
#13: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O

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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: 5.53 Å3/Da / Density % sol: 77.75 %
Crystal growTemperature: 292 K / Method: hanging drop / pH: 6.2
Details: 16-17% PEG 2000 mme, 10% Glycerol, 200 mM MgCl2, 100 mM MES-NMDG pH 6.2, 100 mM Urea, 5% tert-Butanol, 5mM DTT, 1.6 mM Sucrose monodecanoate, hanging drop, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Aug 14, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.4→54 Å / Num. all: 95443 / Num. obs: 72261 / % possible obs: 75.7 % / Observed criterion σ(F): 1.4 / Observed criterion σ(I): 1.4 / Redundancy: 6.7 % / Biso Wilson estimate: 111.5 Å2 / Rsym value: 0.072 / Net I/σ(I): 15.96
Reflection shellResolution: 3.4→3.49 Å / Redundancy: 6.7 % / Mean I/σ(I) obs: 1.41 / Rsym value: 1.512 / % possible all: 4.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
RemDAqdata collection
XDSdata reduction
diffractionanisotropy serverdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb ID 3N23

3n23


Resolution: 3.404→49.829 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.38 / σ(F): 1.99 / Phase error: 26.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2444 3602 4.99 %
Rwork0.2255 --
obs0.2265 72218 75.71 %
all-95443 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 128.844 Å2
Refinement stepCycle: LAST / Resolution: 3.404→49.829 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20687 0 527 6 21220
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00621669
X-RAY DIFFRACTIONf_angle_d1.19229397
X-RAY DIFFRACTIONf_dihedral_angle_d17.9378166
X-RAY DIFFRACTIONf_chiral_restr0.083352
X-RAY DIFFRACTIONf_plane_restr0.0063701
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4043-3.44910.443290.392889X-RAY DIFFRACTION3
3.4491-3.49630.3971220.3832244X-RAY DIFFRACTION8
3.4963-3.54620.3897230.3732419X-RAY DIFFRACTION12
3.5462-3.59920.365410.3615599X-RAY DIFFRACTION18
3.5992-3.65540.28440.3526825X-RAY DIFFRACTION24
3.6554-3.71530.363460.33921097X-RAY DIFFRACTION32
3.7153-3.77930.3668640.31351433X-RAY DIFFRACTION41
3.7793-3.8480.3424940.31751834X-RAY DIFFRACTION54
3.848-3.9220.37261380.31722525X-RAY DIFFRACTION72
3.922-4.0020.3171680.30183414X-RAY DIFFRACTION100
4.002-4.0890.32171750.2863455X-RAY DIFFRACTION100
4.089-4.18410.27981820.26023470X-RAY DIFFRACTION100
4.1841-4.28870.28181600.24673446X-RAY DIFFRACTION100
4.2887-4.40460.26021920.22893455X-RAY DIFFRACTION100
4.4046-4.53410.2672020.21263485X-RAY DIFFRACTION100
4.5341-4.68030.21061700.20563457X-RAY DIFFRACTION100
4.6803-4.84750.22691890.19233447X-RAY DIFFRACTION100
4.8475-5.04140.24271890.20063487X-RAY DIFFRACTION100
5.0414-5.27060.21811720.19663481X-RAY DIFFRACTION100
5.2706-5.54810.22661780.21363526X-RAY DIFFRACTION100
5.5481-5.89520.24381980.22893514X-RAY DIFFRACTION100
5.8952-6.34960.25881810.22853479X-RAY DIFFRACTION100
6.3496-6.9870.22511910.20943553X-RAY DIFFRACTION100
6.987-7.99440.21771800.19853558X-RAY DIFFRACTION100
7.9944-10.05850.17422030.16153577X-RAY DIFFRACTION100
10.0585-49.83410.23421910.2423747X-RAY DIFFRACTION99

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