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- PDB-4hz3: MthK pore crystallized in presence of TBSb -

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Basic information

Entry
Database: PDB / ID: 4hz3
TitleMthK pore crystallized in presence of TBSb
ComponentsCalcium-gated potassium channel mthK
KeywordsMETAL TRANSPORT / transmembrane ion channel family / potassium channel
Function / homology
Function and homology information


monoatomic cation transmembrane transporter activity / potassium ion transport / identical protein binding / metal ion binding / plasma membrane
Similarity search - Function
: / Regulator of K+ conductance, N-terminal / TrkA-N domain / Regulator of K+ conductance, C-terminal / Regulator of K+ conductance, C-terminal domain superfamily / TrkA-C domain / RCK C-terminal domain profile. / RCK N-terminal domain profile. / Helix Hairpins - #70 / Potassium channel domain ...: / Regulator of K+ conductance, N-terminal / TrkA-N domain / Regulator of K+ conductance, C-terminal / Regulator of K+ conductance, C-terminal domain superfamily / TrkA-C domain / RCK C-terminal domain profile. / RCK N-terminal domain profile. / Helix Hairpins - #70 / Potassium channel domain / Ion channel / Helix Hairpins / NAD(P)-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
HEXANE-1,6-DIOL / : / Calcium-gated potassium channel MthK
Similarity search - Component
Biological speciesMethanothermobacter thermautotrophicus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsPosson, D.J. / McCoy, J.G. / Nimigean, C.M.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2013
Title: The voltage-dependent gate in MthK potassium channels is located at the selectivity filter.
Authors: Posson, D.J. / McCoy, J.G. / Nimigean, C.M.
History
DepositionNov 14, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 26, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2013Group: Database references
Revision 1.2Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.location / _software.name / _software.type / _software.version
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_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 / _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_conn.ptnr2_label_seq_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
D: Calcium-gated potassium channel mthK
C: Calcium-gated potassium channel mthK
A: Calcium-gated potassium channel mthK
B: Calcium-gated potassium channel mthK
E: Calcium-gated potassium channel mthK
F: Calcium-gated potassium channel mthK
G: Calcium-gated potassium channel mthK
H: Calcium-gated potassium channel mthK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,90036
Polymers81,2248
Non-polymers2,67628
Water3,891216
1
D: Calcium-gated potassium channel mthK
C: Calcium-gated potassium channel mthK
A: Calcium-gated potassium channel mthK
B: Calcium-gated potassium channel mthK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,18620
Polymers40,6124
Non-polymers1,57416
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7100 Å2
ΔGint-59 kcal/mol
Surface area16650 Å2
MethodPISA
2
E: Calcium-gated potassium channel mthK
F: Calcium-gated potassium channel mthK
G: Calcium-gated potassium channel mthK
H: Calcium-gated potassium channel mthK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,71416
Polymers40,6124
Non-polymers1,10212
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7030 Å2
ΔGint-59 kcal/mol
Surface area16770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.965, 63.396, 63.311
Angle α, β, γ (deg.)89.990, 89.950, 90.000
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Calcium-gated potassium channel mthK


Mass: 10152.961 Da / Num. of mol.: 8 / Fragment: unp residues 11-101 / Mutation: S68H, V77C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermobacter thermautotrophicus (archaea)
Strain: Delta H / Gene: mthK, MTH_1520 / Plasmid: pqe82 / Production host: Escherichia coli (E. coli) / References: UniProt: O27564
#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: K
#3: Chemical
ChemComp-HEZ / HEXANE-1,6-DIOL


Mass: 118.174 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C6H14O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / 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: 2.17 Å3/Da / Density % sol: 43.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 3.5 4.0M 1,6-hexanediol, 100mM MES, 10mM TBSb , pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 14, 2011
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionRedundancy: 3.3 % / Av σ(I) over netI: 18.39 / Number: 238805 / Rmerge(I) obs: 0.048 / Χ2: 0.88 / D res high: 1.7 Å / D res low: 50 Å / Num. obs: 73276 / % possible obs: 96.4
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
3.66509910.0280.7983.3
2.913.6698.410.0360.8323.4
2.542.9197.810.0470.8363.3
2.312.549710.0640.853.3
2.142.3196.810.090.8693.2
2.022.1496.210.1360.963.3
1.912.0295.710.1840.9533.2
1.831.9195.410.3030.9453.2
1.761.8394.710.4690.8673.2
1.71.7693.210.6770.8893.1
ReflectionResolution: 1.7→50 Å / Num. obs: 73276 / % possible obs: 96.4 % / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Rmerge(I) obs: 0.048 / Χ2: 0.879 / Net I/σ(I): 13.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.7-1.763.10.67771440.889193.2
1.76-1.833.20.46971400.867194.7
1.83-1.913.20.30372380.945195.4
1.91-2.023.20.18472990.953195.7
2.02-2.143.30.13672730.96196.2
2.14-2.313.20.0973450.869196.8
2.31-2.543.30.06474050.85197
2.54-2.913.30.04774260.836197.8
2.91-3.663.40.03674920.832198.4
3.66-503.30.02875140.798199

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å43.96 Å
Translation2.5 Å43.96 Å

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Processing

Software
NameVersionClassificationNB
PHENIX1.7.3_928refinement
SCALEPACKdata scaling
PHASER2.4.0phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LDC
Resolution: 1.7→36.128 Å / Occupancy max: 1 / Occupancy min: 0.22 / SU ML: 0.19 / σ(F): 1.96 / Phase error: 16.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1916 3661 5 %
Rwork0.1726 --
obs0.1736 73246 95.84 %
Solvent computationShrinkage radii: 1.24 Å / VDW probe radii: 1.4 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 81.234 Å2 / ksol: 0.442 e/Å3
Displacement parametersBiso max: 95.19 Å2 / Biso mean: 30.982 Å2 / Biso min: 13.18 Å2
Baniso -1Baniso -2Baniso -3
1--4.0256 Å20.2579 Å20.6536 Å2
2--2.2494 Å20.2386 Å2
3---1.7763 Å2
Refinement stepCycle: LAST / Resolution: 1.7→36.128 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5120 0 168 216 5504
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d1.1
X-RAY DIFFRACTIONf_angle_d0.009
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
16.8158-1.4529-4.96335.81871.3416.4727-0.16890.2886-0.012-0.2030.26110.45910.055-0.5717-0.08950.1843-0.0273-0.01630.22540.08140.2253-3.2332-18.489639.1781
22.45380.6107-0.32863.0516-1.75742.2056-0.0837-0.2441-0.44230.015-0.0446-0.17240.19830.15460.1380.15440.01690.02390.15560.02080.201913.6853-13.875936.5273
39.1314-0.8193-2.86453.04860.33163.2062-0.18730.298-0.4871-0.13950.11440.10160.299-0.13420.07580.2023-0.03360.02060.1237-0.01190.20836.8681-14.612128.9366
45.8715-3.85821.01873.66022.20137.74230.298-0.7511-0.65150.41240.31162.1122-0.2152-1.76940.51730.39330.08980.38170.4909-0.00810.8709-8.3924-6.476344.3497
56.88460.96535.03795.66090.92336.5572-0.179-0.25440.05410.20890.2550.47620.0166-0.4531-0.09460.19160.01630.0150.21460.07690.2194-3.254215.867424.054
62.7161-0.74140.25473.8295-1.57051.9522-0.06660.18370.4801-0.0376-0.0817-0.173-0.20450.16830.14790.1605-0.0233-0.03180.16490.02210.206713.957811.243427.0156
78.94470.74563.21382.80870.5593.6653-0.262-0.33840.47880.05640.13190.0934-0.4164-0.2180.16770.20180.0327-0.02050.1242-0.00770.20085.997912.078734.2392
85.33484.0135-1.20684.73661.92365.0370.42040.89850.3739-0.61580.26462.0710.4842-1.87960.13280.4435-0.0575-0.32570.54630.00810.7773-8.40743.867818.8879
98.315-5.85160.82916.6178-1.06095.3608-0.1708-0.0157-0.24-0.0126-0.07870.4560.1854-0.38640.20050.2144-0.01760.02180.247-0.07990.2316-3.22926.262348.7859
102.9296-0.17-0.52431.86231.41622.5638-0.0864-0.47830.10380.17990.1676-0.19260.00950.1749-0.07020.15150.0296-0.02320.2099-0.01990.147414.19932.700144.3632
112.7168-3.3020.81244.6832-0.59912.8531-0.1559-0.3662-0.22990.35650.01950.32410.0833-0.23530.10060.2080.02120.03920.23960.01290.1734.8667-3.447844.677
124.8427-0.92733.87119.6499-3.04643.6693-0.0941-0.54670.7029-0.2315-0.24691.862-0.7916-2.299-0.16080.44650.3327-0.08170.75280.01670.4934-8.407511.391236.7918
136.86824.8926-1.30976.5088-1.27035.9339-0.192-0.07120.28830.0058-0.0790.5627-0.2557-0.44630.20170.19520.019-0.01810.2545-0.08710.2396-3.2696-8.88414.4504
143.00280.09570.37541.72161.21182.6774-0.08050.4871-0.0883-0.22430.1409-0.1639-0.00390.1553-0.06310.1504-0.03340.01810.1951-0.01950.139314.1768-5.308618.8658
158.4373.2717-1.07053.7669-0.42832.5815-0.15370.37890.2193-0.30150.01280.2386-0.1027-0.1760.110.1831-0.0174-0.04460.2167-0.00410.1224.84480.835518.5551
163.750.0253-2.75624.2063-0.70842.1571-0.01990.7644-0.71290.068-0.43771.9210.9029-2.134-0.15920.4535-0.34090.07280.7671-0.03850.516-8.4072-14.042526.4137
177.088-4.8793-1.78936.74671.34756.2639-0.14870.00230.0843-0.026-0.0978-0.4723-0.25220.46160.18120.183-0.0245-0.01520.22650.08380.21086.5121-40.576680.4225
182.6979-0.16370.90272.0432-1.69923.8321-0.0969-0.4297-0.20340.1920.12420.1209-0.0044-0.1614-0.04140.15370.02810.02030.19920.0210.1549-10.7124-37.602375.827
192.6546-3.1601-0.62475.00880.98182.8859-0.2095-0.31450.08880.40510.044-0.1892-0.07270.15840.13750.20630.0199-0.03590.2304-0.00610.1649-2.7429-30.369676.6369
206.5768-1.1093-3.42365.0553.21623.2343-0.1928-0.4602-0.9668-0.2454-0.2155-1.67860.91142.2343-0.18670.52820.3330.12240.75250.02710.489111.6608-45.699368.4576
217.08925.07371.46836.5571.19625.9104-0.17720.0407-0.1306-0.033-0.0976-0.48570.21280.45580.22040.1850.01630.0220.22110.08060.23136.4766-25.429946.1136
222.31440.2165-0.45861.7237-1.87453.9962-0.04370.41310.1815-0.19520.15510.16360.0308-0.1718-0.11240.1705-0.0294-0.02290.20180.02630.1514-10.3601-27.865150.6955
239.24472.83521.21963.82780.58593.1484-0.14490.4008-0.3239-0.32610.0573-0.17480.0990.0380.08250.1888-0.02710.03750.1835-0.00750.1027-4.0137-35.706450.0252
244.35921.55353.6984.8733.9374.7696-0.1677-0.23840.96030.0927-0.3865-1.4953-0.6291.67690.04670.4912-0.305-0.0620.6478-0.02880.556911.6395-20.296658.0838
256.93471.654-4.61516.4393-1.32936.6706-0.15590.0384-0.13290.2290.2708-0.49280.06790.4781-0.12660.16660.0166-0.0130.2153-0.08070.21096.4785-50.182655.7038
262.9107-0.59990.03622.64291.31321.6879-0.09280.1055-0.469-0.0388-0.04450.18260.203-0.16760.15510.1454-0.0230.02960.1447-0.01870.1895-10.9549-45.761559.2871
278.59641.2821-3.52883.2057-0.7134.3123-0.1391-0.251-0.31240.08970.1315-0.11990.34770.30430.07230.1890.04210.01390.12450.00330.2062-1.6175-46.07465.427
286.09355.1709-2.59365.2322-4.55627.81080.40890.473-0.2897-0.48030.3657-1.7466-0.71831.3298-0.00180.4576-0.08910.34030.5066-0.03970.690911.6322-38.202650.5742
297.0643-1.44295.11726.2693-1.34356.9966-0.09280.02660.085-0.25730.2202-0.4776-0.03670.4689-0.12510.1901-0.0220.01890.211-0.07730.21046.4973-15.828270.8295
302.5290.45250.17263.96591.86962.0688-0.0488-0.15320.4641-0.0072-0.08050.1548-0.2008-0.19020.12470.15490.0195-0.02510.1543-0.02010.1942-10.7161-20.44467.8705
312.6328-0.66172.93483.2056-0.88494.9662-0.17350.15620.2699-0.09950.1531-0.1042-0.37370.19490.09640.1912-0.0384-0.02270.16570.01060.2189-2.7638-19.621860.6442
327.0953-4.26431.93653.4722-3.07454.69190.1563-0.78080.16080.69550.4593-1.7950.2481.5870.29280.44990.1055-0.33990.5059-0.02550.660611.6857-27.844775.9641
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 18:33)A18 - 33
2X-RAY DIFFRACTION2(chain A and resid 34:67)A34 - 67
3X-RAY DIFFRACTION3(chain A and resid 68:90)A68 - 90
4X-RAY DIFFRACTION4(chain A and resid 91:99)A91 - 99
5X-RAY DIFFRACTION5(chain B and resid 18:33)B18 - 33
6X-RAY DIFFRACTION6(chain B and resid 34:68)B34 - 68
7X-RAY DIFFRACTION7(chain B and resid 69:90)B69 - 90
8X-RAY DIFFRACTION8(chain B and resid 91:99)B91 - 99
9X-RAY DIFFRACTION9(chain C and resid 18:33)C18 - 33
10X-RAY DIFFRACTION10(chain C and resid 34:70)C34 - 70
11X-RAY DIFFRACTION11(chain C and resid 71:90)C71 - 90
12X-RAY DIFFRACTION12(chain C and resid 91:99)C91 - 99
13X-RAY DIFFRACTION13(chain D and resid 18:33)D18 - 33
14X-RAY DIFFRACTION14(chain D and resid 34:70)D34 - 70
15X-RAY DIFFRACTION15(chain D and resid 71:90)D71 - 90
16X-RAY DIFFRACTION16(chain D and resid 91:99)D91 - 99
17X-RAY DIFFRACTION17(chain E and resid 18:33)E18 - 33
18X-RAY DIFFRACTION18(chain E and resid 34:68)E34 - 68
19X-RAY DIFFRACTION19(chain E and resid 69:90)E69 - 90
20X-RAY DIFFRACTION20(chain E and resid 91:99)E91 - 99
21X-RAY DIFFRACTION21(chain F and resid 18:33)F18 - 33
22X-RAY DIFFRACTION22(chain F and resid 34:66)F34 - 66
23X-RAY DIFFRACTION23(chain F and resid 67:90)F67 - 90
24X-RAY DIFFRACTION24(chain F and resid 91:99)F91 - 99
25X-RAY DIFFRACTION25(chain G and resid 18:33)G18 - 33
26X-RAY DIFFRACTION26(chain G and resid 34:70)G34 - 70
27X-RAY DIFFRACTION27(chain G and resid 71:90)G71 - 90
28X-RAY DIFFRACTION28(chain G and resid 91:99)G91 - 99
29X-RAY DIFFRACTION29(chain H and resid 18:33)H18 - 33
30X-RAY DIFFRACTION30(chain H and resid 34:68)H34 - 68
31X-RAY DIFFRACTION31(chain H and resid 69:90)H69 - 90
32X-RAY DIFFRACTION32(chain H and resid 91:99)H91 - 99

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Jul 12, 2017. Major update of PDB

Major update of PDB

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

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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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