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- PDB-4hqj: Crystal structure of Na+,K+-ATPase in the Na+-bound state -

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Basic information

Entry
Database: PDB / ID: 4hqj
TitleCrystal structure of Na+,K+-ATPase in the Na+-bound state
Components
  • (Sodium/potassium-transporting ATPase subunit ...) x 2
  • Na+/K+ ATPase gamma subunit transcript variant a
KeywordsHYDROLASE/TRANSPORT PROTEIN / Membrane protein / Na+/K+ transport / HYDROLASE-TRANSPORT PROTEIN complex
Function / homology
Function and homology information


Basigin interactions / Ion homeostasis / Na+/K+-exchanging ATPase / positive regulation of sodium ion export across plasma membrane / positive regulation of potassium ion import across plasma membrane / regulation of monoatomic ion transport / Ion transport by P-type ATPases / transporter activator activity / P-type sodium:potassium-exchanging transporter activity / sodium ion binding ...Basigin interactions / Ion homeostasis / Na+/K+-exchanging ATPase / positive regulation of sodium ion export across plasma membrane / positive regulation of potassium ion import across plasma membrane / regulation of monoatomic ion transport / Ion transport by P-type ATPases / transporter activator activity / P-type sodium:potassium-exchanging transporter activity / sodium ion binding / sodium:potassium-exchanging ATPase complex / membrane repolarization / establishment or maintenance of transmembrane electrochemical gradient / sodium ion export across plasma membrane / positive regulation of potassium ion transmembrane transport / regulation of calcium ion transmembrane transport / intracellular sodium ion homeostasis / ion channel regulator activity / intracellular potassium ion homeostasis / regulation of cardiac muscle contraction by calcium ion signaling / relaxation of cardiac muscle / positive regulation of sodium ion transmembrane transport / organelle membrane / potassium ion import across plasma membrane / potassium ion binding / ATPase activator activity / sperm flagellum / intercalated disc / lateral plasma membrane / ATP metabolic process / cardiac muscle contraction / regulation of sodium ion transport / T-tubule / proton transmembrane transport / protein localization to plasma membrane / sarcolemma / transmembrane transport / intracellular calcium ion homeostasis / melanosome / ATPase binding / regulation of gene expression / protein-macromolecule adaptor activity / basolateral plasma membrane / cell adhesion / protein stabilization / apical plasma membrane / axon / innate immune response / protein kinase binding / ATP hydrolysis activity / ATP binding / membrane / plasma membrane
Similarity search - Function
: / Ion-transport regulator, FXYD motif / : / ATP1G1/PLM/MAT8 family / FXYD family signature. / 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. ...: / Ion-transport regulator, FXYD motif / : / ATP1G1/PLM/MAT8 family / FXYD family signature. / 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. / P-type ATPase subfamily IIC, subunit alpha / 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 superfamily
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / TETRAFLUOROALUMINATE ION / CHOLESTEROL / 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 / SIRAS / Resolution: 4.3 Å
AuthorsNyblom, M. / Reinhard, L. / Gourdon, P. / Nissen, P.
CitationJournal: Science / Year: 2013
Title: Crystal structure of Na+, K(+)-ATPase in the Na(+)-bound state.
Authors: Nyblom, M. / Poulsen, H. / Gourdon, P. / Reinhard, L. / Andersson, M. / Lindahl, E. / Fedosova, N. / Nissen, P.
History
DepositionOct 25, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 2, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 10, 2014Group: Database references
Revision 1.2Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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 / _struct_conn.pdbx_dist_value / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)313,25223
Polymers310,0726
Non-polymers3,18017
Water00
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)156,43311
Polymers155,0363
Non-polymers1,3978
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8490 Å2
ΔGint-78 kcal/mol
Surface area57610 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)156,81912
Polymers155,0363
Non-polymers1,7839
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8500 Å2
ΔGint-80 kcal/mol
Surface area58240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.073, 219.578, 261.958
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22
13
23

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 32:258 OR RESSEQ 273:397 OR RESSEQ 403:822 OR RESSEQ 827:1016 )
211CHAIN C AND (RESSEQ 32:258 OR RESSEQ 273:397 OR RESSEQ 403:822 OR RESSEQ 827:1016 )
112CHAIN B AND (RESSEQ 22:167 OR RESSEQ 169:193 OR RESSEQ 197:303 )
212CHAIN D AND (RESSEQ 22:167 OR RESSEQ 169:193 OR RESSEQ 197:303 )
113CHAIN G AND (RESSEQ 23:47 )
213CHAIN E AND (RESSEQ 23:47 )

NCS ensembles :
ID
1
2
3

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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: 112797.578 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: 35144.309 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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Non-polymers , 5 types, 17 molecules

#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#5: Chemical ChemComp-ALF / TETRAFLUOROALUMINATE ION


Mass: 102.975 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: AlF4
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#7: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#8: Chemical
ChemComp-CLR / CHOLESTEROL


Mass: 386.654 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C27H46O

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Details

Has protein modificationY
Sequence detailsTHE EXPERIMENTAL INFO OF UNIPROT (P05027, AT1B1_PIG) SHOWS CONFLICT AT THIS POSITION: F -> S (IN ...THE EXPERIMENTAL INFO OF UNIPROT (P05027, AT1B1_PIG) SHOWS CONFLICT AT THIS POSITION: F -> S (IN REF. 1; CAA27575).

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 5.06 Å3/Da / Density % sol: 75.68 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 19% PEG2KMME, 150mM NaCl, 6% glycerol, 6% MPD, 25mM DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 278K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSLS X06SA11
SYNCHROTRONSLS X06SA21.1008
Detector
TypeIDDetectorDate
PSI PILATUS 6M1PIXELNov 19, 2010
PSI PILATUS 6M2PIXELAug 14, 2010
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Fixed-exit LN2 cooled Double Crystal Monochromator, Crystal type Si(111)SINGLE WAVELENGTHMx-ray1
2Fixed-exit LN2 cooled Double Crystal Monochromator, Crystal type Si(111)SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.10081
ReflectionResolution: 4.3→55 Å / Num. all: 43619 / Num. obs: 43585 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellHighest resolution: 4.3 Å / % possible all: 99.9

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Processing

Software
NameVersionClassification
remdaq.pilatusdata collection
SHARPphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: SIRAS / Resolution: 4.3→11.999 Å / SU ML: 0.62 / σ(F): 2.01 / Phase error: 31.55 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2878 2080 5.02 %RANDOM
Rwork0.2612 ---
all0.2625 ---
obs0.2626 41407 99.95 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 4.3→11.999 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20359 0 212 0 20571
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00721048
X-RAY DIFFRACTIONf_angle_d1.12528551
X-RAY DIFFRACTIONf_dihedral_angle_d15.667782
X-RAY DIFFRACTIONf_chiral_restr0.0833236
X-RAY DIFFRACTIONf_plane_restr0.0053640
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A7468X-RAY DIFFRACTIONPOSITIONAL
12C7468X-RAY DIFFRACTIONPOSITIONAL0.031
21B2271X-RAY DIFFRACTIONPOSITIONAL
22D2271X-RAY DIFFRACTIONPOSITIONAL0.028
31G188X-RAY DIFFRACTIONPOSITIONAL
32E188X-RAY DIFFRACTIONPOSITIONAL0.057
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
4.3001-4.39530.3741470.36722576
4.3953-4.49950.34741320.34092604
4.4995-4.61450.37311390.33752586
4.6145-4.74210.3391410.33132614
4.7421-4.88520.31721300.32522592
4.8852-5.04720.31461380.32362586
5.0472-5.23310.37391350.32682625
5.2331-5.44990.37341390.32522627
5.4499-5.70770.32991420.31052604
5.7077-6.02240.35821360.30222610
6.0224-6.42050.32731360.27682646
6.4205-6.95030.27841420.25332622
6.9503-7.7140.24711390.21722664
7.714-8.98490.20631420.18322663
8.9849-11.99950.20091420.1682708
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.3946-0.86990.75157.38820.40588.71640.495-0.8160.33660.6679-0.3546-0.0532-0.4799-0.0501-0.23790.9006-0.06440.11531.36360.01191.372641.668956.796922.6695
21.6902-0.93664.31936.17010.03167.39530.195-0.2356-0.13730.0475-0.310.4811-0.4343-0.35050.23150.91860.02380.20661.27310.23751.183310.493742.37215.9748
36.89641.51540.42526.58531.51774.8494-0.6511.4376-0.0117-1.09680.4692-0.4533-0.45820.65420.15181.1008-0.0574-0.01251.47230.01130.975230.739840.5525-5.433
43.20040.3623-2.06872.38861.44675.36060.0422-0.16220.26731.16540.10530.30250.4054-0.1888-0.18561.74820.19450.24151.1660.29971.07833.648643.063262.1198
58.1454-2.9524-4.53497.79826.11365.4867-1.9714-0.1144-0.2117-0.2135-1.88153.2318-0.2136-0.82961.97181.0788-0.77210.15321.3220.25442.371722.639843.67956.73
65.20890.4639-0.36292.6442-1.10296.33950.1835-0.1242-0.27190.32550.09620.13670.02881.1-0.29991.5615-0.1435-0.11811.9234-0.31181.83574.621982.537311.576
75.18072.58362.12396.749-0.2280.8341-0.20270.9386-0.5404-0.09840.5478-1.3387-0.39321.6247-0.37391.7817-0.33410.32.5435-0.66561.821727.8225105.422424.1583
86.7841.3599-2.36961.95530.90162.47070.01251.26530.0997-1.50960.6327-0.9597-1.00390.859-0.78143.0817-0.60010.63043.5248-0.50412.365728.022101.4099-5.1586
92.4133-0.4184-1.3672.3617-0.08019.04130.3173-0.00580.07330.52590.21070.1749-0.22670.2513-0.37851.6534-0.18960.24251.4026-0.37911.37971.0401106.644662.3371
103.55163.3526-0.04354.01322.10115.59140.0313-3.9711.93820.9981-2.8350.0205-1.52480.3433.3522.5668-0.7683-0.40832.6552-0.43532.541225.9662100.81369.7959
116.22820.05893.72823.5383-2.46585.31730.27311.81910.56410.3067-2.2126-0.327-0.29131.37041.85082.04660.57040.57031.90580.05531.8909-18.655641.558458.6032
123.20170.13-0.28041.46641.83593.740.2567-1.0636-0.1181.2226-0.3616-0.04160.47590.06020.04674.105-0.26510.68192.64430.16292.3057-11.041247.444107.7523
130.0887-0.3211-0.2350.9521-0.15136.71150.29550.260.0955-0.237-0.23390.3805-0.1319-0.05240.012.8932-0.2546-0.0218-0.25932.88364.27623.394225.829370.3844
141.9923-0.973-0.520.6852.40079.3429-1.65222.64911.17270.31340.8018-1.65420.4235-1.09470.67064.6915-0.94330.39041.73690.85622.9158-12.111127.52772.1966
155.7241-0.8363-2.38325.61474.67324.227-0.30510.29050.87020.0474-0.30060.82973.0004-0.49060.35512.2388-0.013-0.08131.28880.26841.60112.026326.48574.6818
164.6097-4.2183-2.76337.44251.99379.04380.7857-0.5588-0.82250.0231-1.1560.4138-0.74221.58630.15122.0163-0.4523-0.01042.2491-0.19771.362518.5523114.211474.0821
172.35930.021-0.88893.9618-0.64352.5494-0.0042-0.6307-0.08030.8923-0.28511.11740.3018-0.2460.23593.4353-0.11620.78472.5624-0.19362.4163-19.2097105.8178105.8344
184.06171.4825-4.43890.9819-0.91566.00520.50680.08540.435-0.0987-1.89852.94050.81310.45210.75723.7763-0.4911-1.4742.6607-0.05174.31819.2441105.329667.8827
194.7785-1.9144-5.92411.14012.24747.31321.00840.05110.02840.9055-0.61410.28410.90140.50250.63153.94851.572-0.4271.4279-2.14471.5147-8.8666123.287365.3669
202.98-0.99461.21363.7443-4.12314.48470.03520.45561.84340.0553-1.1838-1.47590.21220.0980.22944.72371.4672-1.37482.4703-0.78674.36711.0979127.086674.706
212.84652.15651.9393.6475-1.83455.3010.49880.0891-0.42630.6014-0.15971.23850.9322-0.9362-0.72132.60750.19940.26031.7139-0.00442.0159-17.7531119.718365.0498
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 32:91 OR RESID 158:274)
2X-RAY DIFFRACTION2CHAIN A AND (RESID 348:376 OR RESID 590:747)
3X-RAY DIFFRACTION3CHAIN A AND (RESID 377:589)
4X-RAY DIFFRACTION4CHAIN A AND (RESID 92:157 OR RESID 275:347 OR RESID 748:1016 OR RESID 1104:1106)
5X-RAY DIFFRACTION5CHAIN A AND (RESID 1101:1103)
6X-RAY DIFFRACTION6CHAIN C AND (RESID 30:91 OR RESID 158:274)
7X-RAY DIFFRACTION7CHAIN C AND (RESID 348:376 OR RESID 590:747)
8X-RAY DIFFRACTION8CHAIN C AND (RESID 377:589)
9X-RAY DIFFRACTION9CHAIN C AND (RESID 92:157 OR RESID 275:347 OR RESID 748:1016 OR RESID 1104:1106)
10X-RAY DIFFRACTION10CHAIN C AND (RESID 1101:1103)
11X-RAY DIFFRACTION11CHAIN B AND (RESID 22:64)
12X-RAY DIFFRACTION12CHAIN B AND (RESID 65:303)
13X-RAY DIFFRACTION13CHAIN A AND (RESID 1107:1107)
14X-RAY DIFFRACTION14CHAIN A AND (RESID 1108:1108)
15X-RAY DIFFRACTION15CHAIN G
16X-RAY DIFFRACTION16CHAIN D AND (RESID 22:64)
17X-RAY DIFFRACTION17CHAIN D AND (RESID 65:303)
18X-RAY DIFFRACTION18CHAIN D AND (RESID 400:400)
19X-RAY DIFFRACTION19CHAIN C AND (RESID 1107:1107)
20X-RAY DIFFRACTION20CHAIN C AND (RESID 1108:1108)
21X-RAY DIFFRACTION21CHAIN E

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  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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