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- PDB-7awt: E. coli NADH quinone oxidoreductase hydrophilic arm -

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Basic information

Entry
Database: PDB / ID: 7awt
TitleE. coli NADH quinone oxidoreductase hydrophilic arm
Components
  • (NADH-quinone oxidoreductase subunit ...) x 5
  • NADH-quinone oxidoreductase
KeywordsELECTRON TRANSPORT / E. coli / respiratory complex I
Function / homology
Function and homology information


NADH dehydrogenase complex / Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions / NADH:ubiquinone reductase (non-electrogenic) activity / oxidoreductase complex / molybdopterin cofactor binding / respiratory chain complex I / NADH dehydrogenase (ubiquinone) activity / ATP synthesis coupled electron transport / quinone binding / 2 iron, 2 sulfur cluster binding ...NADH dehydrogenase complex / Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions / NADH:ubiquinone reductase (non-electrogenic) activity / oxidoreductase complex / molybdopterin cofactor binding / respiratory chain complex I / NADH dehydrogenase (ubiquinone) activity / ATP synthesis coupled electron transport / quinone binding / 2 iron, 2 sulfur cluster binding / NAD binding / FMN binding / 4 iron, 4 sulfur cluster binding / iron ion binding / membrane / metal ion binding / plasma membrane
Similarity search - Function
NADH dehydrogenase, subunit CD / Molybdopterin oxidoreductase Fe4S4 domain / Molybdopterin oxidoreductase Fe4S4 domain / Molybdopterin dinucleotide-binding domain / Molydopterin dinucleotide binding domain / : / NADH-quinone oxidoreductase subunit 3, ferredoxin-like domain / Respiratory-chain NADH dehydrogenase 20 Kd subunit signature. / NADH-ubiquinone oxidoreductase, 20 Kd subunit / NADH-quinone oxidoreductase, chain I ...NADH dehydrogenase, subunit CD / Molybdopterin oxidoreductase Fe4S4 domain / Molybdopterin oxidoreductase Fe4S4 domain / Molybdopterin dinucleotide-binding domain / Molydopterin dinucleotide binding domain / : / NADH-quinone oxidoreductase subunit 3, ferredoxin-like domain / Respiratory-chain NADH dehydrogenase 20 Kd subunit signature. / NADH-ubiquinone oxidoreductase, 20 Kd subunit / NADH-quinone oxidoreductase, chain I / NAD(P)H-quinone oxidoreductase subunit D/H / NADH:ubiquinone oxidoreductase, 49kDa subunit, conserved site / Respiratory chain NADH dehydrogenase 49 Kd subunit signature. / : / NADH-quinone oxidoreductase, subunit D / Aspartate decarboxylase-like domain superfamily / NADH:ubiquinone oxidoreductase, subunit G / Respiratory-chain NADH dehydrogenase, 49 Kd subunit / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 3. / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 2. / NADH ubiquinone oxidoreductase, F subunit / NADH dehydrogenase, subunit C / NADH:ubiquinone oxidoreductase, 30kDa subunit, conserved site / Respiratory chain NADH dehydrogenase 30 Kd subunit signature. / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 1. / NADH:ubiquinone oxidoreductase, 75kDa subunit, conserved site / NADH:ubiquinone oxidoreductase, 30kDa subunit / NADH:ubiquinone oxidoreductase, 30kDa subunit superfamily / Respiratory-chain NADH dehydrogenase, 30 Kd subunit / NADH-ubiquinone oxidoreductase-G iron-sulfur binding region / NADH-ubiquinone oxidoreductase-G iron-sulfur binding region / 2Fe-2S iron-sulfur cluster binding domain / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 1. / NADH:ubiquinone oxidoreductase, subunit G, iron-sulphur binding / His(Cys)3-ligated-type [4Fe-4S] domain profile. / NADH:ubiquinone oxidoreductase, 51kDa subunit, conserved site / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 2. / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain superfamily / NADH-ubiquinone oxidoreductase-F iron-sulfur binding region / NADH-ubiquinone oxidoreductase-F iron-sulfur binding region / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain superfamily / Respiratory-chain NADH dehydrogenase 51 Kd subunit / Molybdopterin oxidoreductase, 4Fe-4S domain / Prokaryotic molybdopterin oxidoreductases 4Fe-4S domain profile. / NADH:ubiquinone oxidoreductase-like, 20kDa subunit / NADH ubiquinone oxidoreductase, 20 Kd subunit / Molybdopterin oxidoreductase / Molybdopterin oxidoreductase / [NiFe]-hydrogenase, large subunit / 4Fe-4S dicluster domain / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain
Similarity search - Domain/homology
FE2/S2 (INORGANIC) CLUSTER / FLAVIN MONONUCLEOTIDE / IRON/SULFUR CLUSTER / NADH-quinone oxidoreductase subunit C/D / NADH-quinone oxidoreductase subunit F / NADH-quinone oxidoreductase / NADH-quinone oxidoreductase subunit I / NADH-quinone oxidoreductase subunit B / NADH-quinone oxidoreductase subunit E
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.73 Å
AuthorsSchimpf, J. / Grishkovskaya, I. / Haselbach, D. / Friedrich, T.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG)278002225/RTG 2202 Germany
German Research Foundation (DFG)SPP 1927 Germany
CitationJournal: Structure / Year: 2022
Title: Structure of the peripheral arm of a minimalistic respiratory complex I.
Authors: Johannes Schimpf / Sabrina Oppermann / Tatjana Gerasimova / Ana Filipa Santos Seica / Petra Hellwig / Irina Grishkovskaya / Daniel Wohlwend / David Haselbach / Thorsten Friedrich /
Abstract: Respiratory complex I drives proton translocation across energy-transducing membranes by NADH oxidation coupled with (ubi)quinone reduction. In humans, its dysfunction is associated with ...Respiratory complex I drives proton translocation across energy-transducing membranes by NADH oxidation coupled with (ubi)quinone reduction. In humans, its dysfunction is associated with neurodegenerative diseases. The Escherichia coli complex represents the structural minimal form of an energy-converting NADH:ubiquinone oxidoreductase. Here, we report the structure of the peripheral arm of the E. coli complex I consisting of six subunits, the FMN cofactor, and nine iron-sulfur clusters at 2.7 Å resolution obtained by cryo electron microscopy. While the cofactors are in equivalent positions as in the complex from other species, individual subunits are adapted to the absence of supernumerary proteins to guarantee structural stability. The catalytically important subunits NuoC and D are fused resulting in a specific architecture of functional importance. Striking features of the E. coli complex are scrutinized by mutagenesis and biochemical characterization of the variants. Moreover, the arrangement of the subunits sheds light on the unknown assembly of the complex.
History
DepositionNov 9, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 15, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 13, 2021Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / em_admin / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update
Revision 1.2Jan 19, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.year
Revision 1.3Jul 10, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_3d_fitting_list / em_admin / pdbx_initial_refinement_model
Item: _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id ..._em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _em_admin.last_update

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Structure visualization

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  • Deposited structure unit
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Assembly

Deposited unit
B: NADH-quinone oxidoreductase subunit B
D: NADH-quinone oxidoreductase subunit C/D
E: NADH-quinone oxidoreductase subunit E
F: NADH-quinone oxidoreductase subunit F
G: NADH-quinone oxidoreductase
I: NADH-quinone oxidoreductase subunit I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)285,81624
Polymers282,3526
Non-polymers3,46418
Water2,252125
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area31880 Å2
ΔGint-369 kcal/mol
Surface area76740 Å2

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Components

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NADH-quinone oxidoreductase subunit ... , 5 types, 5 molecules BDEFI

#1: Protein NADH-quinone oxidoreductase subunit B / NADH dehydrogenase I subunit B / NDH-1 subunit B


Mass: 25081.809 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: nuoB, EJC75_10485 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A4P6IQ32, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#2: Protein NADH-quinone oxidoreductase subunit C/D / NADH dehydrogenase I subunit C/D / NDH-1 subunit C/D


Mass: 68321.945 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: nuoD, nuoC, nuoCD, A9R57_03750, ACU57_26515, AUQ13_04755, BHS87_13060, BJJ90_07840, EL75_1346, EL79_1355, EL80_1377, PGD_00936
Production host: Escherichia coli (E. coli)
References: UniProt: A0A024L1E0, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#3: Protein NADH-quinone oxidoreductase subunit E


Mass: 18614.049 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A5A4T568
#4: Protein NADH-quinone oxidoreductase subunit F


Mass: 49352.332 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: nuoF, A6V01_13755, ACU57_26505, AMK83_13840, AML07_04350, AUQ13_04765, AUS26_02240, AW106_12795, AWB10_08250, AZZ83_002438, B7C53_18940, B9T59_22345, BANRA_00851, BANRA_03072, BANRA_04773, ...Gene: nuoF, A6V01_13755, ACU57_26505, AMK83_13840, AML07_04350, AUQ13_04765, AUS26_02240, AW106_12795, AWB10_08250, AZZ83_002438, B7C53_18940, B9T59_22345, BANRA_00851, BANRA_03072, BANRA_04773, BEN53_14595, BHF03_03880, BHF46_01730, BHS81_14175, BK248_00860, BK292_05290, BK296_01020, BK383_00250, BMA87_02945, BMT91_07775, BON65_13640, BON86_24430, BON92_12680, BON95_09120, BUE81_22605, BvCms2454_00746, BvCms28BK_03198, BvCmsHHP001_03303, BvCmsKSP026_02101, BvCmsNSP006_01096, BW690_09740, BXT93_03430, BZL31_15150, C4M78_17025, C5715_07070, C5F72_08640, C5F73_19840, C5N07_04185, C5P44_06790, C9306_02040, C9Z28_02725, C9Z39_01460, C9Z69_00815, C9Z89_04315, CDL37_03605, CI641_004330, CI693_06855, CIG45_06055, COD30_04005, CQP61_09520, CRD98_00870, D2185_05400, D3821_01640, D4628_04120, D4636_00545, D4638_01305, D4718_06850, D4V08_02555, D5H35_06205, D6004_05690, D6T98_01170, D6X36_03890, D7Z75_03825, D9610_02990, D9D44_01275, D9E49_01010, D9E73_00855, D9G11_07710, D9G69_03910, D9H10_04150, D9H53_15420, D9H70_02345, D9I18_14220, D9I87_13725, D9J03_10045, D9J11_03345, D9J52_03020, D9S45_09510, DAH32_13110, DEO04_00250, DIV22_21085, DJ492_03390, DJ503_11040, DL257_04580, DL326_06740, DL530_07780, DL705_09630, DL800_17430, DLU50_00840, DLW60_04875, DM129_02235, DM155_04030, DM267_09550, DM820_00550, DN660_04080, DN700_00545, DND79_04995, DNW42_02440, DNX30_06170, DOY67_08465, DQF71_03220, DQO13_04220, DQP61_00840, DRW19_09495, DS143_05695, DT034_07530, DTL43_00370, DTL90_13100, DTZ20_01245, DVB38_04835, DWB25_08295, E0K84_03605, E2112_03890, E2114_09530, E2115_04905, E2119_16160, E2127_14390, E2128_10460, E2129_15075, E2135_02805, E2855_02915, E2863_02877, E4K61_01395, E5S42_01460, E5S61_00535, E5S62_17345, EA184_09115, EAI52_04445, EAM59_07165, EAN70_08340, EAX79_05190, EB525_RS07480, EBM08_06425, EC1094V2_1394, EC3234A_175c00630, EC95NR1_01387, ECTO6_01644, ED178_07115, ED307_03840, ED600_10345, EEP23_07145, EG599_02320, EG796_14640, EH412_08495, EHD79_00530, EHJ36_09560, EI021_18270, EI028_02610, EI041_16810, EIA21_10570, EIZ93_06525, EKI52_23705, EL75_1348, EL79_1357, EL80_1379, ELT20_15430, ELT22_11130, ELT23_05195, ELT49_05605, ELT58_04715, ELV05_03045, ELV08_10065, EPS91_10180, EPT01_05120, EPU41_13385, ERS085379_00188, ERS085386_00208, ERS150876_02659, ExPECSC019_02995, ExPECSC038_02313, EXX06_13115, EXX24_00205, EXX55_12575, EXX71_01510, EXX87_07270, EYD11_07465, EYY27_07830, F1E13_01775, F1E19_11420, F7F00_07635, F7F18_03770, F7F23_12415, F7F26_06575, F7F29_01405, F7F56_01340, F9059_05310, F9225_15495, F9Z74_15180, FORC82_1552, FQ022_16920, FQ915_15315, FV293_06770, FV295_04395, FWK02_17585, FZ043_16850, FZN06_04430, G3V64_01355, G5616_08820, G5668_05175, G5670_05315, G5680_07940, GHR40_12060, GII67_01480, GII91_07865, GIJ01_18890, GKF21_10745, GKF28_09910, GKF34_10195, GKF39_02500, GKF47_10255, GKF52_10320, GKF74_02415, GKF86_02460, GKF89_15750, GKG08_04525, GKG09_03430, GKG11_03430, GKG12_06425, GKG22_03430, GKG29_03430, GP654_10525, GP662_01335, GP664_02125, GP666_01245, GP678_01495, GP689_04555, GP700_00840, GP727_18600, GP892_00660, GP912_01620, GP935_11155, GQA23_00845, GQE30_00240, GQE34_00275, GQE51_04055, GQE64_02710, GQM17_00600, GQM18_11425, GRW05_01905, GRW12_05105, GRW27_13850, GRW42_12615, GRW81_01585, HmCmsJML079_03904, NCTC10082_04010, NCTC10766_00211, NCTC12650_01901, NCTC13846_01677, NCTC7927_01818, NCTC8450_03934, NCTC8500_01767, NCTC8622_03891, NCTC8960_04372, NCTC9007_03395, NCTC9045_01880, NCTC9062_01542, NCTC9111_05438, NCTC9117_02186, NCTC9119_01758, NCTC9703_00796, NCTC9706_04854, NCTC9777_05069, NCTC9962_07097, NCTC9969_01783, PGD_00938, RK56_005495, SAMEA3472047_02540, SAMEA3472055_03856, SAMEA3472056_00576, SAMEA3472110_03603, SAMEA3472112_03618, SAMEA3472147_01543, SAMEA3484427_04453, SAMEA3484429_04478, SAMEA3485101_03070, SAMEA3752372_03727, SAMEA3752557_00624, SAMEA3752559_01734, SAMEA3753300_00090, UN86_09935
Production host: Escherichia coli (E. coli)
References: UniProt: A0A037YNA7, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#6: Protein NADH-quinone oxidoreductase subunit I


Mass: 20562.771 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1X3LLK1

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Protein , 1 types, 1 molecules G

#5: Protein NADH-quinone oxidoreductase


Mass: 100419.211 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: nuoG, ACU57_26500, AUQ13_04770, BMA87_02940, BON75_03580, BON98_08405, BUE81_22600, BvCms2454_00747, BvCmsHHP001_03304, BvCmsHHP019_02167, BvCmsKSP026_02100, BvCmsSINP011_02783, BZL31_15145, ...Gene: nuoG, ACU57_26500, AUQ13_04770, BMA87_02940, BON75_03580, BON98_08405, BUE81_22600, BvCms2454_00747, BvCmsHHP001_03304, BvCmsHHP019_02167, BvCmsKSP026_02100, BvCmsSINP011_02783, BZL31_15145, C5F72_08645, C5F73_19835, C5N07_04190, C9Z39_01455, CG692_14695, CI693_06850, CIG45_06060, D2185_05395, D3821_01645, D4638_01300, D4718_06845, DJ503_11035, DL326_06735, DT034_07525, DTL43_00365, E2119_16155, E2134_04090, E2135_02800, E4K61_01390, EAI52_04450, ECTO6_01645, EI021_18275, EI028_02615, EI041_16815, EIZ93_06530, ELT20_15435, EPT01_05125, EXX71_01505, EYD11_07470, F1E19_11415, FV293_06765, GHR40_12065, GKF39_02495, GKF74_02420, GKF86_02455, GKF89_15755, GP671_02435, GP689_04560, GQE33_01795, GQE34_00280, GQM17_00605, GRW05_01910, GRW27_13855, GRW80_02440, GRW81_01580, NCTC10963_01653, NCTC11022_02277, NCTC12650_01902, NCTC9045_01881, NCTC9062_01541, NCTC9117_02187, PGD_00939, RK56_005500, SAMEA3472047_02539, SAMEA3484427_04454, SAMEA3484429_04477, SAMEA3752559_01733, SAMEA3753300_00091
Production host: Escherichia coli (E. coli)
References: UniProt: A0A037YPU0, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions

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Non-polymers , 5 types, 143 molecules

#7: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Fe4S4
#8: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
#9: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: Mg
#10: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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

ComponentName: NADH quinone oxidoreductase hydrophilic arm / Type: COMPLEX / Entity ID: #1-#6 / Source: RECOMBINANT
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 6
Buffer component
IDConc.NameFormulaBuffer-ID
150 mM2-Morpholinoethanesulfonic acid (MES)C6H13NO4S1
250 mMsodium chlorideNaCl1
35 mMmagnesium chlorideMgCl21
40.005 % (w/v)Lauryl Maltose Neopentyl GlycolC47H88O221
SpecimenConc.: 0.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 85 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 81000 X / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: ZEMLIN TABLEAU
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 1 sec. / Electron dose: 67 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1
Image scansSampling size: 14 µm / Width: 4096 / Height: 4096

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Processing

SoftwareName: PHENIX / Version: 1.17_3644: / Classification: refinement
EM software
IDNameVersionCategory
2EPUimage acquisition
4CTFFIND4CTF correction
7UCSF Chimera1.13model fitting
9PHENIX1.7.3644model refinement
10Coot0.89model refinement
11cryoSPARC2.42initial Euler assignment
12cryoSPARC2.42final Euler assignment
13cryoSPARC2.42classification
14cryoSPARC2.423D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.73 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 223751 / Symmetry type: POINT
Atomic model buildingPDB-ID: 4HEA

4hea


Accession code: 4HEA / Source name: PDB / Type: experimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00519083
ELECTRON MICROSCOPYf_angle_d0.59725920
ELECTRON MICROSCOPYf_dihedral_angle_d27.5042594
ELECTRON MICROSCOPYf_chiral_restr0.0442757
ELECTRON MICROSCOPYf_plane_restr0.0053416

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  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
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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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