[English] 日本語
Yorodumi
- PDB-4hoi: Crystal structure of PAS domain from the mouse EAG1 potassium channel -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4hoi
TitleCrystal structure of PAS domain from the mouse EAG1 potassium channel
ComponentsPotassium voltage-gated channel subfamily H member 1
KeywordsTRANSPORT PROTEIN / Potassium channel domain
Function / homology
Function and homology information


Voltage gated Potassium channels / regulation of presynaptic cytosolic calcium ion concentration / voltage-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / delayed rectifier potassium channel activity / nuclear inner membrane / phosphatidylinositol bisphosphate binding / parallel fiber to Purkinje cell synapse / regulation of synaptic vesicle exocytosis / voltage-gated potassium channel complex / potassium ion transmembrane transport ...Voltage gated Potassium channels / regulation of presynaptic cytosolic calcium ion concentration / voltage-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / delayed rectifier potassium channel activity / nuclear inner membrane / phosphatidylinositol bisphosphate binding / parallel fiber to Purkinje cell synapse / regulation of synaptic vesicle exocytosis / voltage-gated potassium channel complex / potassium ion transmembrane transport / cellular response to calcium ion / postsynaptic density membrane / regulation of cell population proliferation / presynaptic membrane / early endosome membrane / perikaryon / calmodulin binding / axon / dendrite / plasma membrane
Similarity search - Function
Potassium channel, voltage-dependent, EAG / : / Potassium channel, voltage-dependent, EAG/ELK/ERG / PAS domain / PAS-associated, C-terminal / PAC domain profile. / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / PAS domain / Cyclic nucleotide-monophosphate binding domain ...Potassium channel, voltage-dependent, EAG / : / Potassium channel, voltage-dependent, EAG/ELK/ERG / PAS domain / PAS-associated, C-terminal / PAC domain profile. / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / PAS domain / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / Beta-Lactamase / PAS repeat profile. / PAS domain / RmlC-like jelly roll fold / PAS domain superfamily / Ion transport domain / Ion transport protein / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Voltage-gated delayed rectifier potassium channel KCNH1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å
AuthorsAdaixo, R. / Morais-Cabral, J.H.
Citation
Journal: Plos One / Year: 2013
Title: Structural properties of PAS domains from the KCNH potassium channels
Authors: Adaixo, R. / Harley, C.A. / Castro-Rodrigues, A.F. / Morais-Cabral, J.H.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2010
Title: Crystallization and preliminary crystallographic characterization of the PAS domains of EAG and ELK potassium channels
Authors: Adaixo, R. / Morais-Cabral, J.H.
History
DepositionOct 22, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 27, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
Revision 1.2Nov 8, 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 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Potassium voltage-gated channel subfamily H member 1
B: Potassium voltage-gated channel subfamily H member 1
C: Potassium voltage-gated channel subfamily H member 1
D: Potassium voltage-gated channel subfamily H member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,78510
Polymers53,2094
Non-polymers5766
Water7,116395
1
A: Potassium voltage-gated channel subfamily H member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,3982
Polymers13,3021
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Potassium voltage-gated channel subfamily H member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,4943
Polymers13,3021
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Potassium voltage-gated channel subfamily H member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,3982
Polymers13,3021
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Potassium voltage-gated channel subfamily H member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,4943
Polymers13,3021
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: Potassium voltage-gated channel subfamily H member 1
hetero molecules

D: Potassium voltage-gated channel subfamily H member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8935
Polymers26,6042
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_665-x+1,-x+y+1,-z+2/31
Buried area1440 Å2
ΔGint-11 kcal/mol
Surface area11440 Å2
MethodPISA
6
B: Potassium voltage-gated channel subfamily H member 1
C: Potassium voltage-gated channel subfamily H member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8935
Polymers26,6042
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1490 Å2
ΔGint-11 kcal/mol
Surface area11410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.276, 91.276, 172.521
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
DetailsThe biological unit is most likely a monomer. There are 4 biological units in the asymmetric unit

-
Components

#1: Protein
Potassium voltage-gated channel subfamily H member 1 / Ether-a-go-go potassium channel 1 / EAG channel 1 / EAG1 / m-eag / Voltage-gated potassium channel ...Ether-a-go-go potassium channel 1 / EAG channel 1 / EAG1 / m-eag / Voltage-gated potassium channel subunit Kv10.1


Mass: 13302.239 Da / Num. of mol.: 4 / Fragment: PAS domain of KCNH1 channel, UNP residues 28-137
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Eag, Kcnh1 / Plasmid: pet15b / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3) / References: UniProt: Q60603
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 395 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.9 Å3/Da / Density % sol: 68.45 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 1.3M ammonium sulfate, 0.25M lithium sulfate, 0.1M Tris-HCl, pH 8.5, vapor diffusion, sitting drop, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 24, 2008
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.85→79.06 Å / Num. all: 71849 / Num. obs: 71849 / % possible obs: 100 % / Observed criterion σ(F): 2.1 / Observed criterion σ(I): 1.3 / Redundancy: 7.8 % / Rmerge(I) obs: 0.07 / Rsym value: 0.07 / Net I/σ(I): 7.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRsym valueDiffraction-ID% possible all
1.85-1.955.50.5631.30.5631100
1.95-2.075.50.3432.20.3431100
2.07-2.215.50.2122.30.2121100
2.21-2.395.50.1534.70.1531100
2.39-2.629.30.1564.50.1561100
2.62-2.9311.10.116.40.111100
2.93-3.38110.077.70.071100
3.38-4.1410.90.0512.60.051100
4.14-5.8510.70.04213.60.0421100
5.85-43.1539.60.03913.70.039199.7

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.25data scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
PHENIX1.8.1_1168refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BYW

1byw


Resolution: 1.85→40.34 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.947 / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.15 / SU R Cruickshank DPI: 0.0996 / σ(F): 1.36 / Phase error: 18.01 / Stereochemistry target values: ML / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.1924 3629 5.06 %
Rwork0.1664 --
obs0.1677 71734 99.97 %
all-71743 -
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.8497 Å2
Baniso -1Baniso -2Baniso -3
1-0.34 Å20.17 Å2-0 Å2
2--0.34 Å2-0 Å2
3----0.51 Å2
Refinement stepCycle: LAST / Resolution: 1.85→40.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3675 0 30 395 4100
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113924
X-RAY DIFFRACTIONf_angle_d1.2145335
X-RAY DIFFRACTIONf_dihedral_angle_d13.0361458
X-RAY DIFFRACTIONf_chiral_restr0.081576
X-RAY DIFFRACTIONf_plane_restr0.005672
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 26 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.85-1.87430.23871430.24282591
1.8743-1.90.23661390.2192613
1.9-1.92720.2815980.2082587
1.9272-1.95590.22051170.19852597
1.9559-1.98650.23681390.20382626
1.9865-2.01910.21351330.1952590
2.0191-2.05390.20561460.17632568
2.0539-2.09120.20051280.17452567
2.0912-2.13140.19971460.16762593
2.1314-2.17490.21811430.16612607
2.1749-2.22220.2081500.16552599
2.2222-2.27390.22271190.1622608
2.2739-2.33080.18981510.15892576
2.3308-2.39380.18191610.15682613
2.3938-2.46420.19171290.16292621
2.4642-2.54370.22721380.17212596
2.5437-2.63460.19351370.17622593
2.6346-2.74010.21341600.17652586
2.7401-2.86480.20841490.18062630
2.8648-3.01580.20051410.18212608
3.0158-3.20470.20711250.17772654
3.2047-3.4520.19741350.16662662
3.452-3.79910.17581630.14872628
3.7991-4.34830.1631620.13212650
4.3483-5.47620.14651430.12372702
5.4762-40.34970.19331340.20152840
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)
14.92381.2639-2.38115.1257-1.37754.6739-0.09190.1640.2918-0.01990.12850.1207-0.0137-0.0895-0.03270.19360.1183-0.02410.2005-0.04070.239910.496656.923547.4411
25.0537-3.0978-2.3123.01112.26712.0825-0.2271-0.4507-0.26880.54160.3325-0.29870.67040.6061-0.09780.35990.1781-0.04610.3229-0.03830.246416.406547.852250.266
33.6227-2.673-1.20883.51260.90312.19690.41520.14210.3671-0.8973-0.132-0.3821-0.9001-0.1682-0.15380.48540.18440.03230.23690.01670.277415.277455.686536.1101
43.1371-2.2968-0.96464.3060.83341.63810.07090.0914-0.1884-0.2325-0.07220.2081-0.4137-0.3043-0.01740.42810.2292-0.06390.3048-0.05760.245312.079150.923337.2675
51.1302-2.0145-1.50024.00692.75081.90540.33610.3023-0.1402-0.1865-0.52880.17190.013-0.33490.05990.22660.3629-0.06510.1667-0.14640.3026.984551.486940.6348
62.8539-1.5309-0.82745.70913.54423.8715-0.01370.1864-0.15640.1305-0.16360.2860.1088-0.11120.1530.19550.0853-0.02970.2282-0.05740.21815.161154.911644.4888
76.28160.06594.59234.35440.54555.994-0.00380.43460.0622-0.2664-0.13260.22010.03350.21020.08520.28820.09820.02990.2374-0.06890.239222.993721.223217.3985
85.8258-2.7365-1.66815.32013.31934.3553-0.2668-0.3353-0.23120.5823-0.29540.90020.3424-0.60790.53120.31560.0310.10770.2454-0.08040.33316.637319.627826.6603
93.5617-2.4065-1.38825.62251.38481.92110.03970.35780.1094-0.9776-0.23850.2764-0.5623-0.69990.17230.47360.2114-0.10840.3037-0.07070.241417.60732.089516.4887
103.9797-1.0991-1.64163.92732.66345.2421-0.01530.25760.1457-1.0158-0.1553-0.1422-0.5092-0.23490.16070.47720.120.03310.20820.00080.245524.690232.300117.3888
110.7776-0.591-0.80313.77561.35832.8869-0.14050.0149-0.00440.0155-0.07510.125-0.0958-0.33890.22670.25990.09070.00380.2071-0.05440.235521.972429.154623.7651
122.001-4.5539-5.03174.80820.23023.73120.30990.9743-0.34-1.5266-0.6767-0.36530.2095-0.27980.23580.5390.08650.13540.2464-0.03970.300332.846113.48324.9215
131.4203-2.1301-1.79965.73895.09126.7341-0.1564-0.10340.1315-0.0176-0.0414-0.1316-0.1125-0.0650.16660.29940.0749-0.00010.1541-0.02060.231326.190128.179423.3167
143.37060.72931.83912.44931.1941.82080.0599-0.113-0.05040.2019-0.0827-0.0071-0.67140.06460.06040.3095-0.03490.03520.1301-0.02050.192330.73899.046220.8696
154.3553-0.1741-1.00995.53861.89878.5689-0.01510.1651-0.14720.0057-0.21381.14920.1596-0.84110.26320.23260.00070.02050.2211-0.08950.395721.38453.081714.8721
168.7311-3.2557-0.3242.71481.68793.34230.0493-0.3387-0.64690.48570.09210.36950.6616-0.0539-0.08960.3881-0.02820.04010.1150.01960.280930.4846-3.520720.7263
173.2629-3.08910.77983.41780.35672.60390.0438-0.5707-0.62851.2320.193-1.36920.47710.4443-0.2070.41870.0908-0.1150.21620.0010.478341.8048-1.10621.7314
185.83115.20460.53448.9921-1.10792.3363-0.0577-0.0213-0.1823-0.02620.043-1.16730.1120.19870.02970.28290.01710.02280.1881-0.06180.370639.12560.83215.4136
190.85770.49850.02033.35261.50862.7415-0.07930.0129-0.02930.01560.1102-0.01130.00820.0547-0.0610.27810.01510.04610.1355-0.05030.262333.51874.875414.8458
201.83821.40070.79776.30182.5873.9887-0.06530.2386-0.2326-0.4552-0.0215-0.07890.34890.03110.02760.36470.02240.08480.1528-0.04180.25933.70162.542110.3669
218.728-4.6389-0.76856.56741.31752.7903-0.0945-0.11260.2256-0.31250.1852-0.3860.22570.2633-0.04060.3380.0616-0.0320.1479-0.00960.220142.273125.407954.8277
223.7276-2.94940.96736.1296-1.69327.42880.06540.0087-0.2716-0.431-0.09680.55350.4034-0.49350.05910.34030.0115-0.10410.1059-0.02730.263530.551123.528152.085
233.7025-0.75230.71343.4232-0.36631.8920.25040.005-0.2849-0.4375-0.00790.1405-0.4269-0.1333-0.17960.4950.0548-0.10280.1404-0.03230.244732.329518.479247.9613
244.98576.2606-4.74067.8559-5.95034.50480.0090.1488-0.4042-0.67630.0114-0.27940.08420.0870.10040.41180.0487-0.02010.1764-0.03170.240440.874321.831649.1955
256.78431.5821-1.30933.5471-4.70016.3253-0.15430.58650.0246-0.94420.19610.2578-0.20040.0969-0.02880.65760.0730.03170.27560.01760.192338.713730.09338.199
263.9567-0.36473.77982.9493-1.39773.9822-0.14621.05840.1641-1.0443-0.0112-0.6201-0.23991.06650.16790.4593-0.02330.07970.35530.01820.276447.081935.298345.4673
274.49251.16233.67092.72680.99513.0214-0.26150.36690.3577-0.7010.02280.1501-0.38570.40840.27350.4095-0.005-0.0510.20270.03080.243540.464536.378148.2394
285.5443-1.28263.32944.2426-6.55822.00230.1440.1823-0.07110.34450.011-0.74280.4339-0.20160.06220.56430.079-0.13070.2183-0.09550.313829.089424.878137.5595
293.7698-1.58333.53831.2408-1.43275.6932-0.3881-0.02660.2296-0.31750.04610.0756-0.5695-0.16380.24680.43440.0086-0.13380.1338-0.010.247736.264834.968550.2498
303.43313.5767-4.10843.7273-4.27964.922-0.293-1.0255-0.03070.81650.2651-1.1822-0.85291.72710.15720.34950.0294-0.12920.40230.00870.317249.659531.538469.1171
313.8409-1.36031.16984.7501-1.4283.3781-0.4043-0.18480.5711-0.20450.1990.3353-0.445-0.51360.12040.34170.0859-0.10040.1966-0.02480.273735.199734.484453.7677
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and (resseq 25:41)
2X-RAY DIFFRACTION2chain A and (resseq 42:60)
3X-RAY DIFFRACTION3chain A and (resseq 61:88)
4X-RAY DIFFRACTION4chain A and (resseq 89:105)
5X-RAY DIFFRACTION5chain A and (resseq 106:117)
6X-RAY DIFFRACTION6chain A and (resseq 118:137)
7X-RAY DIFFRACTION7chain B and (resseq 24:41)
8X-RAY DIFFRACTION8chain B and (resseq 42:60)
9X-RAY DIFFRACTION9chain B and (resseq 61:88)
10X-RAY DIFFRACTION10chain B and (resseq 89:100)
11X-RAY DIFFRACTION11chain B and (resseq 101:117)
12X-RAY DIFFRACTION12chain B and (resseq 118:122)
13X-RAY DIFFRACTION13chain B and (resseq 123:137)
14X-RAY DIFFRACTION14chain C and (resseq 28:41)
15X-RAY DIFFRACTION15chain C and (resseq 42:60)
16X-RAY DIFFRACTION16chain C and (resseq 61:76)
17X-RAY DIFFRACTION17chain C and (resseq 77:88)
18X-RAY DIFFRACTION18chain C and (resseq 89:100)
19X-RAY DIFFRACTION19chain C and (resseq 101:122)
20X-RAY DIFFRACTION20chain C and (resseq 123:137)
21X-RAY DIFFRACTION21chain D and (resseq 28:41)
22X-RAY DIFFRACTION22chain D and (resseq 42:53)
23X-RAY DIFFRACTION23chain D and (resseq 54:60)
24X-RAY DIFFRACTION24chain D and (resseq 61:67)
25X-RAY DIFFRACTION25chain D and (resseq 68:76)
26X-RAY DIFFRACTION26chain D and (resseq 77:88)
27X-RAY DIFFRACTION27chain D and (resseq 89:100)
28X-RAY DIFFRACTION28chain D and (resseq 101:105)
29X-RAY DIFFRACTION29chain D and (resseq 106:117)
30X-RAY DIFFRACTION30chain D and (resseq 118:122)
31X-RAY DIFFRACTION31chain D and (resseq 123:137)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • 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

-
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

Read more