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- PDB-8bwc: E. coli BAM complex (BamABCDE) wild-type -

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Basic information

Entry
Database: PDB / ID: 8bwc
TitleE. coli BAM complex (BamABCDE) wild-type
Components
  • Outer membrane protein assembly factor BamA
  • Outer membrane protein assembly factor BamB
  • Outer membrane protein assembly factor BamC
  • Outer membrane protein assembly factor BamD
  • Outer membrane protein assembly factor BamE
KeywordsMEMBRANE PROTEIN / Outer Membrane Protein / Protein Folding / beta barrel
Function / homology
Function and homology information


Bam protein complex / Gram-negative-bacterium-type cell outer membrane assembly / protein insertion into membrane / cell outer membrane / membrane / identical protein binding
Similarity search - Function
Outer membrane protein assembly factor BamB / NlpB/DapX lipoprotein / Outer membrane protein assembly factor BamC / Outer membrane protein assembly factor BamC, C-terminal / NlpB/DapX lipoprotein / Outer membrane protein assembly factor BamD / Outer membrane protein assembly factor BamE / Lipoprotein SmpA/OmlA / Outer membrane lipoprotein BamD-like / SmpA / OmlA family ...Outer membrane protein assembly factor BamB / NlpB/DapX lipoprotein / Outer membrane protein assembly factor BamC / Outer membrane protein assembly factor BamC, C-terminal / NlpB/DapX lipoprotein / Outer membrane protein assembly factor BamD / Outer membrane protein assembly factor BamE / Lipoprotein SmpA/OmlA / Outer membrane lipoprotein BamD-like / SmpA / OmlA family / Outer membrane lipoprotein / BamE-like / Outer membrane protein assembly factor BamA / Pyrrolo-quinoline quinone repeat / PQQ-like domain / POTRA domain, BamA/TamA-like / Surface antigen variable number repeat / POTRA domain / POTRA domain profile. / Pyrrolo-quinoline quinone beta-propeller repeat / beta-propeller repeat / Surface antigen D15-like / Bacterial surface antigen (D15) / Omp85 superfamily domain / Quinoprotein alcohol dehydrogenase-like superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / Tetratricopeptide-like helical domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Outer membrane protein assembly factor BamE / Outer membrane protein assembly factor BamD / Outer membrane protein assembly factor BamC / Outer membrane protein assembly factor BamA / Outer membrane protein assembly factor BamB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Escherichia coli BL21 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsMachin, J.M. / Radford, S.E. / Ranson, N.A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust222373/Z/21/Z United Kingdom
CitationJournal: Angew Chem Int Ed Engl / Year: 2023
Title: Darobactin B Stabilises a Lateral-Closed Conformation of the BAM Complex in E. coli Cells.
Authors: Samuel F Haysom / Jonathan Machin / James M Whitehouse / Jim E Horne / Katherine Fenn / Yue Ma / Hassane El Mkami / Nils Böhringer / Till F Schäberle / Neil A Ranson / Sheena E Radford / Christos Pliotas /
Abstract: The β-barrel assembly machinery (BAM complex) is essential for outer membrane protein (OMP) folding in Gram-negative bacteria, and represents a promising antimicrobial target. Several conformational ...The β-barrel assembly machinery (BAM complex) is essential for outer membrane protein (OMP) folding in Gram-negative bacteria, and represents a promising antimicrobial target. Several conformational states of BAM have been reported, but all have been obtained under conditions which lack the unique features and complexity of the outer membrane (OM). Here, we use Pulsed Electron-Electron Double Resonance (PELDOR, or DEER) spectroscopy distance measurements to interrogate the conformational ensemble of the BAM complex in E. coli cells. We show that BAM adopts a broad ensemble of conformations in the OM, while in the presence of the antibiotic darobactin B (DAR-B), BAM's conformational equilibrium shifts to a restricted ensemble consistent with the lateral closed state. Our in-cell PELDOR findings are supported by new cryoEM structures of BAM in the presence and absence of DAR-B. This work demonstrates the utility of PELDOR to map conformational changes in BAM within its native cellular environment.
History
DepositionDec 6, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 24, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Sep 6, 2023Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Outer membrane protein assembly factor BamA
B: Outer membrane protein assembly factor BamB
C: Outer membrane protein assembly factor BamC
D: Outer membrane protein assembly factor BamD
E: Outer membrane protein assembly factor BamE


Theoretical massNumber of molelcules
Total (without water)200,2265
Polymers200,2265
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Outer membrane protein assembly factor BamA


Mass: 88514.742 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: bamA, yaeT, A5U30_000296, A6592_02945, A8499_001882, A9X72_20365, AAG43_001505, ACN68_08270, ACN81_28495, ACU57_18535, AF998_001683, AM464_17685, APX88_24870, AT335_002559, AT845_002198, AW118_ ...Gene: bamA, yaeT, A5U30_000296, A6592_02945, A8499_001882, A9X72_20365, AAG43_001505, ACN68_08270, ACN81_28495, ACU57_18535, AF998_001683, AM464_17685, APX88_24870, AT335_002559, AT845_002198, AW118_17900, AWP47_05630, B6R12_000956, B6R15_000220, B6R31_002460, B6R48_000717, B6R87_000718, BANRA_00651, BANRA_01136, BEA19_03425, BER14_07740, BF481_003681, BG944_001864, BGM66_002013, BHS81_00690, BJI68_15680, BJJ90_21320, BK292_13710, BK383_20200, BKL28_001074, BLM69_001467, BMT49_02215, BMT50_03970, BMT91_01325, BN17_46001, BO068_002867, BOH76_17675, BON63_15405, BON64_03425, BON65_09470, BON66_02910, BON67_09950, BON68_19005, BON69_16435, BON70_27195, BON71_14840, BON72_09420, BON73_05360, BON74_02620, BON75_17190, BON76_15510, BON77_21970, BON78_08335, BON79_15615, BON80_16360, BON81_06815, BON82_14505, BON83_24810, BON84_04065, BON87_26650, BON88_11825, BON89_11070, BON90_22375, BON92_02795, BON93_03895, BON94_19435, BON95_12990, BON96_17170, BON98_18140, BR158_000492, BRV02_001577, BTB68_000231, BTQ06_06530, BvCmsF30A_01249, BvCmsHHP056_04085, BvCmsKKP061_01626, BVL39_02145, BXT93_00750, C0P57_001486, C1Q91_003240, C2121_002944, C2M16_10840, C2R31_000619, C2U48_09565, C3F40_12200, C5N07_08620, C5Y87_12615, C9114_06985, C9160_13545, C9E67_25165, C9Z68_04825, CA593_02825, CCS08_22545, CCV12_001992, CDC27_24730, CDL36_07950, CF22_003987, CG831_000812, CIG67_16620, CO706_23095, CQ986_003586, CR538_20600, CR628_003260, CTR35_003026, CV83915_01397, CWS33_09660, CX938_000225, CXJ73_002511, CY655_00940, D0X26_09375, D1912_21110, D1H34_004224, D3G36_16715, D3Y67_16445, D4N09_06760, D4U49_05910, D9D77_16570, D9E34_01065, D9E49_02105, D9J61_11550, DAH17_03105, DAH18_22205, DAH19_12870, DAH20_13860, DAH21_22225, DAH22_03605, DAH23_11155, DAH24_11225, DAH25_12780, DAH26_11170, DAH27_18735, DAH28_17975, DAH29_14730, DAH30_10570, DAH31_15650, DAH32_15150, DAH33_22250, DAH34_04145, DAH35_21475, DAH36_21050, DAH37_16290, DAH38_20975, DAH40_22075, DAH41_15665, DAH42_01610, DAH43_04070, DAH45_06290, DAH46_02585, DAH47_00130, DAH48_03820, DAH49_04075, DAH50_07015, DD762_01135, DEN86_04025, DEN87_21110, DEN88_17015, DEN89_20325, DEN90_18665, DEN91_15525, DEN92_14715, DEN93_18270, DEN94_16145, DEN95_12205, DEN96_06230, DEN97_04385, DEN98_04390, DEN99_03155, DEO00_05230, DEO01_06055, DEO02_09495, DEO03_16425, DEO04_22130, DEO05_22000, DEO06_22645, DEO07_22470, DEO08_20705, DEO09_21855, DEO10_22115, DEO11_22010, DEO13_08600, DEO14_11200, DEO15_08380, DEO17_19865, DEO18_03450, DEO19_04170, DEO20_19760, DIV22_06310, DM870_23205, DN627_10205, DNQ45_10075, DNX30_02230, DRW19_04885, DS732_05815, DTL43_05880, DTL90_09775, DTM45_12675, DU321_03690, DXT69_01430, DXT70_16970, DXT71_01950, DXT73_18965, E0I42_19020, E2112_01200, E2113_05810, E2114_18200, E2115_17415, E2116_17440, E2117_05485, E2118_15330, E2119_15620, E2120_18160, E2121_14045, E2122_04495, E2123_15040, E2124_16725, E2125_18030, E2127_15050, E2128_01390, E2129_02820, E2130_17625, E2131_12100, E2132_15165, E2133_09940, E2134_12015, E2135_11675, E2136_14045, E2646_16120, E3O05_11515, E4K51_05750, E4T14_02285, E4T84_08860, E5H86_15850, E5M02_17400, E5P22_04130, E5P23_04750, E5P24_16165, E5P25_12900, E5P26_03475, E5P27_14125, E5P28_14015, E5P29_07840, E5P30_07230, E5P31_13525, E5P32_01600, E5P33_01100, E5P34_12070, E5P35_01145, E5P36_00555, E5P37_21230, E5P39_14350, E5P40_06990, E5P41_07170, E5P42_02575, E5P43_09410, E5P44_10415, E5P45_09040, E5P46_08190, E5P47_11175, E5P48_06230, E5P49_11800, E5P50_17540, E5P51_06990, E5P52_06800, E5S34_18420, E5S35_00130, E5S36_11165, E5S37_18815, E5S38_07550, E5S39_17385, E5S42_18205, E5S43_01760, E5S44_09525, E5S45_04825, E5S46_19575, E5S47_12360, E5S48_12815, E5S51_08320, E5S52_09495, E5S53_16295, E5S54_18365, E5S55_16285, E5S57_07225, E5S58_05565, E5S59_11205, E5S61_20105, E5S62_13815, E6C80_03245, E6D34_00950, EA239_13380, EA435_20340, EAI46_03605, EAN77_17385, EAX79_05520, EC1094V2_3674, EC95NR1_04363, ECs0179, ED648_00125, EHD79_10695, EI021_19885, EIA08_06365, EIZ93_07885, EKI52_10395, EL79_3697, EL80_3644, ELT16_21295, ELT17_01290, ELT20_04510, ELT21_15085, ELT22_08915, ELT23_12135, ELT24_18765, ELT25_21005, ELT26_05540, ELT27_04430, ELT28_17160, ELT29_02955, ELT30_18480, ELT31_08735, ELT32_04825, ELT33_15830, ELT34_19930, ELT35_06860, ELT36_13995, ELT38_13410, ELT39_20820, ELT40_02090, ELT41_02015, ELT44_21565, ELT45_20755, ELT46_21905, ELT48_12220, ELT49_18515, ELT50_04880, ELT52_04095, ELT55_19355, ELT56_04900, ELT58_11855, ELT59_17805, ELT60_20990, ELT61_17455, ELT63_15940, ELT72_19860, ELU07_12965, ELU82_16735, ELU83_06320, ELU85_21230, ELU88_20065, ELU89_12480, ELU90_03595, ELU91_18160, ELU94_15850, ELU95_07310, ELU97_22235, ELU98_09250, ELU99_07115, ELV00_10965, ELV01_05815, ELV02_21170, ELV03_21745, ELV04_21635, ELV07_04635, ELV08_10240, ELV09_11020, ELV10_05925, ELV11_07255, ELV12_07985, ELV13_13185, ELV15_10235, ELV16_14945, ELV20_03255, ELV21_07945, ELV22_16495, ELV23_20045, ELV26_20265, ELV28_04145, ELV29_15990, ELV40_17675, ELX48_04100, ELX61_13270, ELX66_06770, ELX68_15925, ELX69_11295, ELX76_14590, ELX79_12450, ELX85_10405, ELX96_04985, ELY02_13720, ELY31_21175, ELY32_08495, ELY39_01365, ELY41_06580, ELY48_16875, EN85_001940, EPS76_09925, ERS085406_00578, ERS139208_01237, EWK56_14925, EYV17_16485, EYV18_21785, F0L67_09105, F2N20_00125, F2N31_00125, F3N40_16060, F7F11_02035, F7N46_12575, F9413_16900, F9461_04780, F9B07_03480, F9V24_09540, F9X20_09395, FDM60_08780, FE584_15725, FE587_16410, FEJ01_15100, FFF58_06145, FHO90_19930, FIJ20_13935, FJQ40_14175, FKO60_12300, FOI11_012800, FOI11_22880, FPI65_00965, FPJ29_11720, FPS11_04890, FQF29_01490, FV293_02855, FVB16_04485, FWK02_04400, FY127_02905, FZC17_23605, FZN31_19945, FZU14_18300, G3565_18205, G3813_000507, G3V95_02420, G3W53_17975, G4A38_19380, G4A47_18815, G5603_21720, G7630_000814, G9448_10075, GAI66_14365, GAI89_16125, GAJ12_05920, GAJ26_21420, GF147_13240, GF699_14310, GFY34_15765, GIB53_10160, GJ11_00925, GJO56_09475, GKF66_15225, GKF89_14740, GNW61_11420, GNZ05_09785, GOP25_07210, GP711_09570, GP944_03110, GQM04_14355, GQM21_02740, GQN34_16145, GQW80_13555, GRC73_19630, GRW05_07735, GSM54_14470, GTP88_05365, GUC01_17920, GUI33_00125, H0O37_03390, H0O39_04955, H0O72_10145, H6Y26_004466, HEP30_016645, HEP34_000941, HHH44_003655, HI055_000768, HIE29_003111, HJQ60_000684, HJS37_001619, HJU54_003394, HKA49_001644, HL563_02695, HL601_07740, HLV18_20665, HLX92_18930, HLZ50_06920, HmCms169_00369, HMJ82_00130, HMU06_10015, HMV95_04545, HMW38_10535, HNC36_16200, HNC59_20385, HNC66_11645, HNC99_17465, HND12_10395, HV109_19340, HV209_01580, HVV39_17670, HVW04_10185, HVW19_15015, HVW43_11715, HVY77_20925, HVZ71_20360, HX136_20560, I6H01_17735, I6H02_18690, IFB95_000535, IH768_15425, IT029_001934, J0541_003907, J4S20_003219, JE86ST02C_01710, JE86ST05C_01740, JFD_01263, JNP96_05075, NCTC10082_01374, NCTC10089_04067, NCTC10090_02151, NCTC10429_04185, NCTC10865_05056, NCTC11112_03444, NCTC11181_01353, NCTC12950_04415, NCTC13127_05445, NCTC13148_05206, NCTC13216_02723, NCTC4450_07390, NCTC8008_03664, NCTC8009_07311, NCTC8621_04193, NCTC8959_04852, NCTC8960_01553, NCTC9037_04180, NCTC9073_03384, NCTC9111_04256, NCTC9706_01328, NCTC9775_02319, NCTC9777_00463, ND22_002541, RG28_03870, SAMEA3472044_04148, SAMEA3472056_00964, SAMEA3472147_00389, SAMEA3751407_04805, SAMEA3752557_00883, SAMEA3753106_03559, TUM18780_35950, WP4S18E07_36860, WR15_02370, XU56_000257
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C3TPJ2
#2: Protein Outer membrane protein assembly factor BamB


Mass: 39882.375 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli BL21(DE3) (bacteria) / Gene: bamB, yfgL, b2512, JW2496
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P77774
#3: Protein Outer membrane protein assembly factor BamC


Mass: 34401.250 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: bamC / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C3T0D3
#4: Protein Outer membrane protein assembly factor BamD


Mass: 25816.818 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: bamD / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C3SYV7
#5: Protein Outer membrane protein assembly factor BamE


Mass: 11610.833 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: smpA, bamE, SAMEA3752557_04545 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2X7FA24

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1E. coli BAM complex (BamABCDE) wild-typeCOMPLEXall0RECOMBINANT
2Outer membrane protein assembly factor BamA, BamC, BamD and BamECOMPLEX#1, #3-#51RECOMBINANT
3Outer membrane protein assembly factor BamBCOMPLEX#21RECOMBINANT
Molecular weightValue: 0.20098298 MDa / Experimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Escherichia coli (E. coli)562
33Escherichia coli BL21(DE3) (bacteria)469008
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
22Escherichia coli BL21(DE3) (bacteria)469008
33Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)866768
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMTris1
2150 mMSodium ChlorideNaClSodium chloride1
30.025 % w/vDDM1
SpecimenConc.: 3.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 165000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1500 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 3.58 sec. / Electron dose: 44.8 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 6063
EM imaging opticsEnergyfilter name: TFS Selectris / Energyfilter slit width: 10 eV

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Processing

Software
NameVersionClassificationNB
phenix.real_space_refine1.20.1_4487refinement
PHENIX1.20.1_4487refinement
EM software
IDNameVersionCategoryDetails
1crYOLO1.8.0particle selectionParticles picked using a trained model
2EPU3image acquisition
4CTFFIND4.1.14CTF correction
9RELION4initial Euler assignment
13PHENIX1.20.1-4487model refinement
14ISOLDE1.4model refinement
CTF correctionType: NONE
Particle selectionNum. of particles selected: 656080
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 169599 / Symmetry type: POINT
Atomic model buildingB value: 82 / Protocol: FLEXIBLE FIT / Space: REAL
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 27.29 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.003511586
ELECTRON MICROSCOPYf_angle_d0.685115755
ELECTRON MICROSCOPYf_chiral_restr0.04521711
ELECTRON MICROSCOPYf_plane_restr0.01152080
ELECTRON MICROSCOPYf_dihedral_angle_d13.43624193

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