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- PDB-8hhf: The bacterial divisome protein complex FtsB-FtsL-FtsQ -

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Basic information

Entry
Database: PDB / ID: 8hhf
TitleThe bacterial divisome protein complex FtsB-FtsL-FtsQ
Components
  • Cell division protein FtsB
  • Cell division protein FtsL
  • Cell division protein FtsQ
KeywordsMEMBRANE PROTEIN / Bacterial cell division / divisome / FtsB / FtsL / FtsQ / FtsBLQ / FtsQLB / membrane protein complex / heterotrimer
Function / homology
Function and homology information


cell septum assembly / FtsZ-dependent cytokinesis / cell division site / plasma membrane
Similarity search - Function
Cell division protein FtsL / Cell division protein FtsL / Septum formation initiator FtsL/DivIC / Cell division protein FtsB / Septum formation initiator / Cell division protein FtsQ, C-terminal / Cell division protein FtsQ / Cell division protein FtsQ/DivIB, C-terminal / POTRA domain, FtsQ-type / Cell division protein FtsQ/DivIB, C-terminal ...Cell division protein FtsL / Cell division protein FtsL / Septum formation initiator FtsL/DivIC / Cell division protein FtsB / Septum formation initiator / Cell division protein FtsQ, C-terminal / Cell division protein FtsQ / Cell division protein FtsQ/DivIB, C-terminal / POTRA domain, FtsQ-type / Cell division protein FtsQ/DivIB, C-terminal / POTRA domain, FtsQ-type / POTRA domain / POTRA domain profile.
Similarity search - Domain/homology
Cell division protein FtsL / Cell division protein FtsQ / Cell division protein FtsB
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.04 Å
AuthorsNguyen, V.H.T. / Chen, X.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Academia Sinica (Taiwan) Taiwan
CitationJournal: Nat Commun / Year: 2023
Title: Structure of the heterotrimeric membrane protein complex FtsB-FtsL-FtsQ of the bacterial divisome.
Authors: Nguyen, H.T.V. / Chen, X. / Parada, C. / Luo, A.C. / Shih, O. / Jeng, U.S. / Huang, C.Y. / Shih, Y.L. / Ma, C.
History
DepositionNov 16, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 26, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Source and taxonomy / Category: chem_comp_atom / chem_comp_bond / entity_src_gen
Item: _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name
Revision 1.2Nov 29, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
Q: Cell division protein FtsQ
B: Cell division protein FtsB
L: Cell division protein FtsL


Theoretical massNumber of molelcules
Total (without water)58,5933
Polymers58,5933
Non-polymers00
Water543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7080 Å2
ΔGint-41 kcal/mol
Surface area25150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)199.610, 53.940, 101.850
Angle α, β, γ (deg.)90.000, 116.670, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Cell division protein FtsQ /


Mass: 31467.660 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K-12
Gene: ftsQ, A9X72_20810, ACU57_16060, BGM66_003029, BN17_45151, BO068_001919, BON68_06480, BON72_08970, BON73_04910, BON74_02170, BON75_16740, BON76_15060, BON77_21520, BON80_15910, BON89_27020, ...Gene: ftsQ, A9X72_20810, ACU57_16060, BGM66_003029, BN17_45151, BO068_001919, BON68_06480, BON72_08970, BON73_04910, BON74_02170, BON75_16740, BON76_15060, BON77_21520, BON80_15910, BON89_27020, BON93_20085, BON94_26730, BvCmsHHP019_03716, C5Y87_12070, CCS08_22990, CR538_21045, CTR35_001627, DAH19_13315, DAH50_07465, DS732_05370, DTL43_06330, DXT70_08670, E2119_07785, E2134_11600, E4K51_06165, E5P23_04335, E5P31_03955, E5P32_08015, E5P35_00730, E5P36_04260, E5P39_13665, E5P40_07375, E5P41_14185, E5P42_01010, E5P43_09200, E5P44_09730, E5P45_08355, E5P46_13085, E5P47_04370, E5P48_12150, E5P49_11070, E5P50_01390, E5S36_10750, E5S51_07905, EI021_04715, EIZ93_07570, EL79_3779, EL80_3726, ELT20_04095, ELT41_01600, ELX85_12445, F2N20_00540, F2N31_00540, F9V24_01135, FJQ40_06395, FOI11_013215, FOI11_22465, FV293_03270, FWK02_17275, GJO56_09885, GKF89_02115, GNW61_10395, GP944_03500, GP965_07730, GP979_06755, GRW05_06695, HMV95_04965, HX136_20990, IH768_05560, J0541_002403, JNP96_04660, NCTC11126_03516, NCTC13216_02643, NCTC8008_03748, NCTC8500_04640, NCTC9037_04264, NCTC9045_04807, NCTC9117_05152, NCTC9706_01498, SAMEA3751407_02594, SAMEA3752557_00798
Production host: Escherichia coli (E. coli) / References: UniProt: J7Q602
#2: Protein Cell division protein FtsB /


Mass: 13478.979 Da / Num. of mol.: 1 / Mutation: D59H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K-12
Gene: ygbQ, b2748, ftsB, A6592_02700, A9X72_05420, AAG43_001157, AAS29_002327, ACN68_01085, ACN81_22700, ACU57_10415, AF998_003984, AM464_05440, APX88_26425, AT335_001935, AT845_002951, AW118_02170, ...Gene: ygbQ, b2748, ftsB, A6592_02700, A9X72_05420, AAG43_001157, AAS29_002327, ACN68_01085, ACN81_22700, ACU57_10415, AF998_003984, AM464_05440, APX88_26425, AT335_001935, AT845_002951, AW118_02170, AW119_00505, B6R12_002921, B6R15_004315, B6R31_001385, B6R48_002213, B6R87_001779, BANRA_03605, BANRA_03816, BEA19_14400, BER14_04895, BF481_001551, BG944_005039, BGM66_001300, BHS81_16470, BJI68_04455, BJJ90_05425, BK292_23370, BK383_11510, BKL28_002147, BLM69_002676, BMC79_001641, BMT50_16440, BMT91_16935, BN17_26281, BO068_003238, BOH76_22505, BON63_19750, BON64_10250, BON65_10655, BON67_16550, BON68_07845, BON69_14865, BON70_14165, BON71_18350, BON72_06905, BON73_04200, BON74_11250, BON75_11915, BON76_10600, BON77_23390, BON80_04815, BON81_09700, BON82_02555, BON83_09775, BON86_17645, BON87_00170, BON89_01935, BON92_08965, BON93_21085, BON94_04190, BON95_16370, BON96_25220, BON97_25970, BON98_24845, BR331_13510, BRV02_002856, BRV34_003183, BRV41_003345, BTB68_002198, BTQ06_25695, BUO55_002741, BvCmsF30A_03976, BvCmsHHP019_05490, BvCmsHHP056_03513, BvCmsKKP036_03957, BvCmsKKP061_02287, BvCmsKSNP073_04237, BVL39_13140, BXT93_22835, BZL69_02290, C0P57_004097, C1Q91_001211, C2R31_001402, C5N07_05990, C5Y87_14880, C9114_19275, C9160_11615, C9E67_06290, C9Z68_11480, CA593_13145, CCS08_05870, CDC27_14480, CDL36_10580, CDL37_05475, CF22_001372, CG831_002442, CHM61_004550, CIG67_14820, CO706_11605, CQ986_002524, CQB02_03210, CR538_05670, CR539_18670, CTR35_002600, CV83915_03375, CWS33_18255, CX938_003723, CXJ73_001678, CY655_17660, D0X26_15425, D3822_00190, D3Y67_06265, D9D43_16505, D9D77_00530, D9E34_04515, D9H94_08045, D9J03_06940, DAH17_11780, DAH18_08090, DAH19_15820, DAH20_05945, DAH21_20810, DAH22_00530, DAH23_03755, DAH24_03765, DAH25_05315, DAH26_03760, DAH27_03345, DAH28_03335, DAH29_09130, DAH30_04850, DAH31_08600, DAH32_02190, DAH33_08870, DAH34_12005, DAH35_08065, DAH36_13970, DAH37_01500, DAH38_06765, DAH40_04515, DAH41_01770, DAH42_02270, DAH43_05505, DAH45_03780, DAH46_05500, DAH47_03040, DAH48_01310, DAH49_04735, DAH50_09730, DD762_14720, DEN86_01675, DEN87_06010, DEN88_12480, DEN89_06010, DEN90_07595, DEN91_04170, DEN92_03855, DEN93_00690, DEN94_03985, DEN95_06590, DEN96_04540, DEN97_04105, DEN98_04110, DEN99_01465, DEO00_03540, DEO01_04750, DEO02_05355, DEO03_10945, DEO04_03070, DEO05_03065, DEO06_14675, DEO07_14800, DEO08_11655, DEO09_03070, DEO10_04970, DEO11_04985, DEO12_05285, DEO13_04860, DEO14_10405, DEO15_03720, DEO17_10685, DEO18_14335, DEO19_03885, DEO20_03780, DIV22_15835, DKP82_11040, DM870_03105, DN627_19300, DNX30_08755, DRW19_11595, DS732_20520, DTL43_09190, DTL90_02495, DTM45_13710, DU321_05970, DXT69_17360, DXT70_08325, DXT71_19650, DXT73_08240, E0I42_15505, E2112_09555, E2113_09350, E2114_10320, E2115_08525, E2116_15190, E2117_09815, E2118_09245, E2119_10765, E2120_14915, E2121_02015, E2122_11735, E2123_09600, E2124_11825, E2125_14100, E2127_10965, E2128_08105, E2129_22705, E2130_14460, E2131_15845, E2132_11790, E2133_06760, E2134_08305, E2135_15680, E2136_06425, E4K51_11225, E4T14_21585, E5H86_04825, E5M02_10925, E5P22_05770, E5P23_03445, E5P24_05600, E5P25_11055, E5P26_11690, E5P27_02515, E5P28_09905, E5P29_13475, E5P30_13810, E5P31_11865, E5P32_06050, E5P33_06685, E5P34_03510, E5P35_05585, E5P36_12075, E5P37_18585, E5P39_08565, E5P40_04955, E5P41_03935, E5P42_06115, E5P43_04960, E5P44_06155, E5P45_05830, E5P46_03860, E5P47_08365, E5P48_08500, E5P49_06610, E5P50_05955, E5P51_10505, E5P52_10315, E5S34_04800, E5S35_14100, E5S36_19180, E5S37_09785, E5S38_04045, E5S39_15870, E5S42_03440, E5S43_09080, E5S44_15530, E5S45_15150, E5S46_13650, E5S47_05125, E5S48_06165, E5S51_18450, E5S52_14265, E5S53_09375, E5S54_10235, E5S55_08335, E5S56_08850, E5S57_00290, E5S58_00490, E5S61_16790, E5S62_06130, E6D34_14775, EAI46_07250, EAN77_13820, EAX79_09035, EC1094V2_948, EC95NR1_01987, ECs3602, ED648_01345, EHD79_13700, EI021_10985, EIA08_07110, EIZ93_05810, EKI52_20755, EL79_0951, EL80_0954, ELT17_12700, ELT20_17240, ELT21_23265, ELT27_11215, ELT28_05140, ELT29_12425, ELT41_08750, ELT49_08555, ELT51_15170, ELT58_07355, ELU85_05930, ELU90_11220, ELU99_13270, ELV08_08070, ELV09_15590, ELV10_02555, ELV15_03805, ELV16_00560, ELV21_04885, ELV26_12080, ELV28_12555, ELV40_02705, ELX48_08725, ELX61_07165, ELX66_15205, ELX69_11900, ELX76_04460, ELX85_04260, ELX96_07925, ELY02_14155, ELY32_16870, ELY36_13285, ELY39_04535, ELY41_01415, ELY48_08790, EN85_001469, ERS139208_02413, ExPECSC038_01238, EXX13_06030, EYV17_10490, EYV18_03170, EYX47_08185, F0L67_14180, F2N20_16730, F2N31_16335, F3N40_16780, F7N46_14340, F9461_10345, F9B07_08855, F9S83_03495, F9V24_05845, FDM60_13010, FFF58_10515, FGG80_17910, FHO90_00450, FHQ91_11950, FIJ20_09535, FJQ40_08620, FJQ51_01270, FJQ53_01475, FKO60_18855, FOI11_00770, FOI11_022410, FPJ29_02580, FPS11_13985, FQF29_08350, FV293_17625, FVB16_11015, FWK02_01495, FY127_09825, G3813_002375, G3V95_10445, G4A38_14890, G4A47_01820, G5603_07050, G7630_001935, G9448_20130, GAI66_02250, GAI89_18445, GAJ12_00705, GAJ26_13810, GF699_10330, GFY34_09225, GIB53_20945, GJ11_17855, GJO56_21000, GKF66_22940, GKF89_15865, GNW61_10135, GNZ05_06795, GOP25_06480, GP944_20765, GP954_16030, GP965_19000, GP975_18645, GQM04_19210, GQM13_06950, GQM21_22525, GQW68_02525, GQW80_08720, GRW05_19835, GRW24_26615, GRW56_12285, GRW57_13710, GSM54_10720, GSY44_11250, GTP88_14390, GUC01_18635, H0O37_18560, H0O39_10000, H0O72_12700, HEP30_016230, HEP34_003091, HHH44_000061, HJ942_003313, HJQ60_000143, HJS37_003746, HJU54_000976, HKA49_002448, HL563_12225, HL601_05720, HLV18_00605, HLX92_15920, HLZ50_16935, HMJ82_10310, HMV95_03780, HNC36_10085, HNC59_00675, HNC66_02820, HNC99_10495, HND12_16955, HV109_05095, HV146_18020, HV209_17635, HVW04_21435, HVW19_09715, HVW43_22665, HVX32_16115, HVY77_05890, HVZ29_16240, HVZ71_05535, HX136_05215, I6H00_23980, I6H01_07705, I6H02_09220, IA00_004614, IH768_16030, IH772_07675, IT029_001852, J0541_002488, J4S20_000102, J5U05_001032, JE86ST02C_32090, JE86ST05C_32140, JFD_05027, JNP96_21365, NCTC10082_03501, NCTC10090_04155, NCTC10764_00342, NCTC10865_01399, NCTC10974_01325, NCTC11126_05099, NCTC11181_03313, NCTC11341_01150, NCTC13127_01476, NCTC13216_00792, NCTC4450_03076, NCTC7922_03113, NCTC8008_00547, NCTC8179_06727, NCTC8333_01272, NCTC8450_05688, NCTC8500_01136, NCTC8960_03819, NCTC9036_01170, NCTC9037_01265, NCTC9044_00531, NCTC9045_01252, NCTC9073_04844, NCTC9077_01455, NCTC9111_01553, NCTC9117_01643, NCTC9702_01334, NCTC9706_03334, NCTC9775_04881, NCTC9777_02739, NCTC9962_05400, ND22_002843, RG28_07850, SAMEA3472044_02733, SAMEA3472056_03187, SAMEA3472147_02219, SAMEA3751407_03499, SAMEA3752557_03775, SAMEA3753106_02570, TUM18780_09890, WP4S18E07_10690, WR15_05115
Production host: Escherichia coli (E. coli) / References: UniProt: Q1JQN6
#3: Protein Cell division protein FtsL /


Mass: 13646.827 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K-12 / Gene: ftsL / Production host: Escherichia coli (E. coli) / References: UniProt: D6II44
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 4.29 Å3/Da / Density % sol: 71.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.1M Tris ph 8.0, 20-35% PEG400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 22, 2020
RadiationMonochromator: LN2 cooled Si(111) double crystal monochromator (DCM)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→49.85 Å / Num. obs: 21882 / % possible obs: 99.7 % / Redundancy: 10.024 % / Biso Wilson estimate: 105.427 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.126 / Rrim(I) all: 0.133 / Χ2: 0.834 / Net I/σ(I): 9.25 / Num. measured all: 219340 / Scaling rejects: 281
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.9-2.9810.3693.1920.8416798162616200.7453.34899.6
2.98-3.0610.3482.5391.1115936154515400.8342.66599.7
3.06-3.1510.0661.761.5515301152315200.871.84999.8
3.15-3.249.5051.382.0314068148114800.9111.45699.9
3.24-3.3510.3120.7893.0714828144014380.9690.82799.9
3.35-3.4710.6860.564.3114586136713650.980.58599.9
3.47-3.610.5560.4415.5214472137213710.990.46299.9
3.6-3.7410.3130.3047.113015126512620.9940.31899.8
3.74-3.9110.3570.2379.313081126812630.9960.24899.6
3.91-4.110.3060.20211.6312109117611750.9950.21299.9
4.1-4.3210.0280.16514.0311211112411180.9940.17399.5
4.32-4.599.5410.14215.210323108610820.9940.1599.6
4.59-4.98.750.12216.188846101510110.9960.1399.6
4.9-5.2910.0880.11917.7694229389340.9950.12599.6
5.29-5.810.1230.10918.0688278768720.9960.11599.5
5.8-6.489.9370.10719.3377617857810.9960.11299.5
6.48-7.499.4420.08520.3266667077060.9980.0999.9
7.49-9.178.7180.07122.2752836106060.9970.07699.3
9.17-12.979.3580.06224.2443614714660.9980.06598.9
12.97-49.858.9930.06624.424462802720.9970.0797.1

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
Aimlessdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5Z2W

5z2w


Resolution: 3.04→49.85 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 37.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2939 948 5 %
Rwork0.2701 18002 -
obs0.2712 18950 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 351.32 Å2 / Biso mean: 137.0097 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 3.04→49.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3283 0 0 3 3286
Biso mean---95.29 -
Num. residues----409
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.04-3.20030.35041350.32312547100
3.2003-3.40070.34551320.3006253599
3.4007-3.66320.3161340.2784254399
3.6632-4.03170.30631340.2618254899
4.0317-4.61480.30021350.24592571100
4.6148-5.81270.33771370.29282587100
5.8127-49.850.25161410.26012671100
Refinement TLS params.Method: refined / Origin x: -22.3138 Å / Origin y: 23.3915 Å / Origin z: 8.8716 Å
111213212223313233
T0.7649 Å20.1057 Å2-0.1875 Å2-1.4062 Å20.0256 Å2--0.8342 Å2
L0.6298 °20.069 °20.3947 °2-0.9764 °2-1.3201 °2--2.8398 °2
S0.0758 Å °0.2163 Å °0.3662 Å °0.0338 Å °-0.1273 Å °0.086 Å °-0.0252 Å °0.4046 Å °0.1303 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allQ22 - 260
2X-RAY DIFFRACTION1allB1 - 89
3X-RAY DIFFRACTION1allL39 - 119
4X-RAY DIFFRACTION1allC1 - 3

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