[English] 日本語
Yorodumi
- PDB-7pbu: RuvAB branch migration motor complexed to the Holliday junction -... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7pbu
TitleRuvAB branch migration motor complexed to the Holliday junction - RuvA-HJ core [t2 dataset]
Components
  • (Holliday junction) x 2
  • Holliday junction ATP-dependent DNA helicase RuvA
KeywordsHYDROLASE / DNA recombination / DNA repair / branch migration / Holliday junction / helicase
Function / homology
Function and homology information


Holliday junction helicase complex / Holliday junction resolvase complex / four-way junction helicase activity / four-way junction DNA binding / DNA recombination / DNA repair / ATP binding / cytoplasm
Similarity search - Function
Holliday junction DNA helicase RuvA, C-terminal / DNA helicase, Holliday junction RuvA type, domain I, bacterial / RuvA, C-terminal domain superfamily / RuvA N terminal domain / RuvA, C-terminal domain / Bacterial DNA recombination protein RuvA / RuvA domain 2-like / Helix-hairpin-helix domain / Helix-hairpin-helix DNA-binding motif, class 1 / Helix-hairpin-helix DNA-binding motif class 1 / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
DNA / DNA (> 10) / Holliday junction branch migration complex subunit RuvA
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsGoessweiner-Mohr, N. / Fahrenkamp, D. / Wald, J. / Marlovits, T.C.
CitationJournal: Nature / Year: 2022
Title: Mechanism of AAA+ ATPase-mediated RuvAB-Holliday junction branch migration.
Authors: Jiri Wald / Dirk Fahrenkamp / Nikolaus Goessweiner-Mohr / Wolfgang Lugmayr / Luciano Ciccarelli / Oliver Vesper / Thomas C Marlovits /
Abstract: The Holliday junction is a key intermediate formed during DNA recombination across all kingdoms of life. In bacteria, the Holliday junction is processed by two homo-hexameric AAA+ ATPase RuvB motors, ...The Holliday junction is a key intermediate formed during DNA recombination across all kingdoms of life. In bacteria, the Holliday junction is processed by two homo-hexameric AAA+ ATPase RuvB motors, which assemble together with the RuvA-Holliday junction complex to energize the strand-exchange reaction. Despite its importance for chromosome maintenance, the structure and mechanism by which this complex facilitates branch migration are unknown. Here, using time-resolved cryo-electron microscopy, we obtained structures of the ATP-hydrolysing RuvAB complex in seven distinct conformational states, captured during assembly and processing of a Holliday junction. Five structures together resolve the complete nucleotide cycle and reveal the spatiotemporal relationship between ATP hydrolysis, nucleotide exchange and context-specific conformational changes in RuvB. Coordinated motions in a converter formed by DNA-disengaged RuvB subunits stimulate hydrolysis and nucleotide exchange. Immobilization of the converter enables RuvB to convert the ATP-contained energy into a lever motion, which generates the pulling force driving the branch migration. We show that RuvB motors rotate together with the DNA substrate, which, together with a progressing nucleotide cycle, forms the mechanistic basis for DNA recombination by continuous branch migration. Together, our data decipher the molecular principles of homologous recombination by the RuvAB complex, elucidate discrete and sequential transition-state intermediates for chemo-mechanical coupling of hexameric AAA+ motors and provide a blueprint for the design of state-specific compounds targeting AAA+ motors.
History
DepositionAug 2, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 14, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Nov 30, 2022Group: Database references / Category: citation_author / Item: _citation_author.identifier_ORCID
Revision 1.3Jan 18, 2023Group: Database references / Category: pdbx_database_related

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Holliday junction ATP-dependent DNA helicase RuvA
B: Holliday junction ATP-dependent DNA helicase RuvA
C: Holliday junction ATP-dependent DNA helicase RuvA
D: Holliday junction ATP-dependent DNA helicase RuvA
E: Holliday junction
F: Holliday junction ATP-dependent DNA helicase RuvA
G: Holliday junction
H: Holliday junction ATP-dependent DNA helicase RuvA
I: Holliday junction
J: Holliday junction ATP-dependent DNA helicase RuvA
K: Holliday junction
L: Holliday junction ATP-dependent DNA helicase RuvA


Theoretical massNumber of molelcules
Total (without water)139,70112
Polymers139,70112
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, D4
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area19730 Å2
ΔGint-85 kcal/mol
Surface area61350 Å2
MethodPISA

-
Components

#1: Protein
Holliday junction ATP-dependent DNA helicase RuvA


Mass: 14860.438 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria)
Gene: ruvA, A3104_04360, A3S30_12815, A3T81_10475, A3U32_08040, A3V03_15555, A3V89_15755, A3W57_12595, A3W75_09730, A3X15_16725, A3X55_18545, A3Y76_18960, A4N07_18675, A4O05_13120, A4O41_13995, A4R48_ ...Gene: ruvA, A3104_04360, A3S30_12815, A3T81_10475, A3U32_08040, A3V03_15555, A3V89_15755, A3W57_12595, A3W75_09730, A3X15_16725, A3X55_18545, A3Y76_18960, A4N07_18675, A4O05_13120, A4O41_13995, A4R48_03555, A6D61_19645, AAA76_15415, AAB27_10170, AAB79_14680, AAC35_19210, ADQ28_18925, AF497_06575, AGM99_19520, AHN93_19355, AKH62_05145, AL144_07245, AL168_13275, AL184_08575, AQ530_20325, AU613_21305, AVA38_10310, AVC05_12030, AVL16_03380, AWT30_04170, AXX99_19885, B1265_18390, B1398_11015, B1642_21005, B1P38_18570, B2E31_18735, B4V59_02030, B4W90_19900, B6362_14325, B7Q27_17415, B8Y16_02315, B8Z46_03380, B9C90_13190, B9C96_10980, B9M14_03980, B9O84_20430, BBQ66_17875, BIC00_17935, BIC13_17075, BK110_18430, BKM50_18425, BMS46_18075, BMU56_19625, BZ203_15840, BZZ88_19070, C5W43_03605, CB102_15235, CB119_08750, CB198_07280, CB380_21505, CB535_05310, CB570_17460, CB646_18010, CBM67_10595, CBM76_08005, CBZ90_18715, CC339_18485, CC403_17275, CC453_11190, CC652_13440, CC971_18400, CCP17_18835, CDZ72_17145, CE70_01895, CED07_17535, CEQ70_19855, CFF58_03605, CFF59_03410, CHN22_03380, CIX60_20020, CPS79_06290, CQO33_10550, CSG22_19025, CVR97_18235, D4361_14120, D4387_19750, D4422_17805, D5823_07645, D5N86_14490, D5N95_15345, D5O82_08895, D5P17_20720, D5X47_14425, D5Y28_10680, D6422_17850, D6J79_19635, D8S24_16890, DD95_03300, DLB93_17215, DLR28_12360, DMI89_11085, DMO92_20225, DN165_16600, DNB97_11455, DNM27_19505, DNZ37_14615, DO533_14050, DP680_14360, DPB42_24680, DPD91_17340, DPF41_06595, DPF68_18980, DPS76_09640, DQD22_15400, DQR44_15500, DRM14_19730, DRR75_15340, DRT38_23380, DRT61_20665, DRV05_09715, DSF94_18945, DSG41_09900, DTF68_19605, DU071_21865, DU223_09180, DU657_10120, DU879_19615, DUV75_00760, DWU22_13690, DY580_20770, DYM27_19865, E0935_12270, E1A11_17010, E6W45_13400, EBD14_15340, EBK21_19660, EC404_05120, EEQ30_12650, EER35_11585, EHB09_02315, EL822_20025, ELS01_11305, EPB30_16090, EQG93_20735, EVY71_15105, EW905_19450, F0D96_03330, F2P00_04425, F3Q97_16890, F3R12_16560, F9G02_08090, F9O44_06330, FE758_08635, FEM52_20865, FGZ46_12135, FJM64_21435, FQC24_03995, FQX78_16495, G0038_05370, G0040_14630, G0042_05160, G0045_04645, G0047_04425, G0048_04645, G0051_04495, G0052_04480, G0059_16270, G0061_18365, G0062_04425, G0063_04645, G0067_04490, G0069_04495, G0070_04425, G0071_02335, G0072_18060, G0074_03845, G0076_09830, G0077_04570, G0080_04495, G0084_04425, G0086_04645, G0087_04645, G0088_03845, G0089_04305, G0090_18565, G0094_06110, G0100_04645, G0101_04930, G0102_18480, G0111_04570, G0113_07905, G0117_04640, G0123_04645, G0124_04480, G0148_04570, G0157_04060, G0170_04570, G0A05_20370, G0A28_08020, G0A32_09325, G0A39_13460, G0A43_07515, G0A44_14720, G0A46_17450, G0A50_13995, G0A51_15070, G0A52_16995, G0A53_13715, G0A56_10210, G0A58_13370, G0A60_08630, G0A61_09285, G0A63_17830, G0A66_14765, G0A67_09855, G0A68_07315, G0A70_13970, G0A73_14720, G0A76_13550, G0A79_10870, G0A85_06680, G0A88_03615, G0A92_16395, G0A96_15350, G0A97_09860, G0A99_04350, G0B03_14510, G0B05_11195, G0B07_12920, G0B08_11100, G0B12_13635, G0B28_07790, G0B96_17725, G0C03_09525, G0C04_00320, G0C34_16405, G0E15_19520, G0E20_18325, G0G84_09765, G0J24_00315, G0J26_18625, G0J27_17935, G0J28_18455, G0J31_17115, G0J33_11885, G0J34_00315, G0J36_20340, G0J37_00315, G0J40_15725, G0J43_14890, G0J44_19710, G0J45_19615, G0J46_20750, G0J47_00315, G0J49_00315, G0J50_19580, G0J51_19850, G0J53_15365, G0J55_18355, G0J58_16205, G0J59_19730, G0J62_01215, G0J65_19090, G0J66_17410, G0J67_02710, G0J69_19340, G0J71_17230, G0J73_20930, G0J76_18935, G0J79_15475, G0J81_04550, G0J82_17330, G0J85_04550, G0J89_20125, G0J92_18930, G0J94_20435, G0J96_20985, G0J97_19790, G0K00_14690, G0K02_19370, G0K03_16735, G0K04_20155, G0K05_08015, G0K07_19190, G0K10_18840, G0K13_14165, G0K15_20415, G0K16_18570, G0K18_18175, G0K19_15605, G0K20_08360, G0K23_16195, G0K25_19520, G0K26_18910, G0K28_18855, G0K30_19060, G0K31_17750, G0K32_07100, G0K33_18050, G0K37_17000, G0K38_19665, G0K39_12955, G0K41_06410, G0K42_19730, G0K44_18600, G0K46_04550, G0K47_00315, G0K48_19680, G0K49_19460, G0K52_20110, G0K53_20285, G0K56_14585, G0K58_16320, G0K59_20915, G0K61_12175, G0K65_17590, G0K68_19555, G0K70_19195, G0K72_08220, G0K74_09545, G0K75_14735, G0K78_04550, G0K80_18310, G0K83_17415, G0K84_18585, G0K85_19440, G0K88_000200, G0K89_000185, G0K90_000162, G0K94_000188, G0K95_000393, G0L00_001272, G0L02_000369, G0L03_03395, G0L06_03355, G0L07_06370, G0L10_06010, G0L14_04495, G0L15_00175, G0L18_02610, G0L19_04265, G0L20_06050, G0L24_11105, G0L25_13880, G0L29_13070, G0L31_13365, G0L32_11360, G0L34_10210, G0L35_10295, G0L36_12260, G0L37_14800, G0L38_03935, G0L40_08420, G0L42_07850, G0L48_05605, G0L49_04895, G0L51_16900, G0L52_12995, G0L55_17090, G0L59_12270, G0L62_12990, G0L63_12675, G0L65_16685, G0L67_15510, G0L68_16430, G0L70_19000, G0L73_10360, G0L76_16040, G0L77_17705, G0L78_16570, G0L79_13070, G0L83_12585, G0L85_15215, G0L86_003407, G0L88_08035, G0L89_12955, G0L91_13450, G0L93_14905, G0L96_17395, G0L98_14825, G0M00_15155, G0M02_15475, G0M05_07430, G0M06_002948, G0M10_06795, G0M13_002511, G0M14_09485, G0M16_09065, G0M18_001838, G0M21_12630, G0M22_002392, G0M25_002320, G0M26_13590, G0M27_18365, G0M28_14500, G0M29_002555, G0M30_14605, G0M33_08695, G0M35_17455, G0M36_13345, G0M38_11600, G0M39_14605, G0M40_09455, G0M41_12175, G0M45_15325, G0M46_002381, G0M48_002696, G0M51_10065, G0M53_11890, G0M55_12775, G0M56_13160, G0M58_13240, G0M63_12835, G0M65_12830, G0M67_12515, G0N45_03845, G0N48_13640, G0N51_02015, G0N53_12220, G0N55_03845, G0N57_13985, G0N58_03520, G0N59_04430, G0N60_03940, G0N61_04425, G0N62_02335, G0N64_03100, G0N65_20220, G0N66_03920, G0N67_14845, G0N71_17705, G0N75_04425, G0N78_15235, G0N82_20135, G0N84_04425, G0N85_21475, G0N86_03845, G0N88_00310, G0N89_04490, G0N90_19470, G0N92_13355, G0N94_13260, G0N95_12725, G0N98_18690, G0N99_19505, G0O00_17175, G0O03_13255, G0O10_03990, G0O14_11750, G0O15_19700, G0O18_03490, G0O19_04930, G0O20_08065, G0O22_16685, G0O25_17080, G0O27_03845, G0O31_03845, G0O32_09420, G0O36_02935, G0O37_17135, G0O39_04425, G0O40_04425, G0O41_16585, G0O42_18080, G0O43_04495, G0O44_02930, G0O47_03845, G0O52_03915, G0O55_03560, G0O57_17310, G0O58_04495, G0O59_04990, G0O60_03845, G0O63_03835, G0O66_19795, G0O68_03990, G0O70_04495, G0O71_04495, G0O74_19245, G0O75_04495, G0O77_04420, G0O78_03850, G0O80_03845, G0O81_18455, G0O82_04565, G0O84_04495, G0O85_04625, G0O86_20270, G0O87_02405, G0O88_03010, G0O89_04865, G0O92_04565, G0O93_11855, G0O94_19860, G0O97_21615, G0O99_16570, G0P00_02015, G0P01_14125, G0P02_18125, G0P05_20035, G0P06_04565, G0P08_18610, G0P12_02030, G0P13_04495, G0P17_18155, G0P18_20530, G0P19_11030, G0P24_14340, G0P26_04495, G0P28_04565, G0P30_04425, G0P31_04495, G0P36_10425, G0P37_21480, G0P41_15675, G0P44_15565, G0P45_15940, G0P48_04495, G0P49_12000, G0P52_04495, G0P53_12915, G0P56_03845, G0P57_04495, G0P58_03845, G0P63_02240, G0P65_03730, G0P67_18480, G0P68_10080, G0P69_06340, G0P73_15995, G0P75_14890, G0P76_22875, G1N61_16005, G1N64_15925, G1N66_15920, G1N68_15615, G1N71_15905, G1N72_15920, G1N86_16200, G1N87_15945, G1N91_16925, G1O00_16210, G1O02_16210, G1O04_15925, G1O05_15920, G1O08_17675, G1O10_10745, G1O12_16215, G1O16_16210, G1O17_15695, G1O18_16215, G1O20_16205, G1O23_15245, G1O25_16200, G1O26_16205, G1O27_16005, G1O28_15965, G1O29_15985, G1O32_16195, G1O34_16275, G1O38_16615, G1O40_16210, G1O43_16195, G1O46_15905, G1O48_15980, G1O49_16055, G1O51_16200, G1O53_16270, G1O62_16210, G1O63_16190, G1O65_15980, G1O67_15525, G1O68_16210, G1O69_15765, G1O71_15760, G1O72_16280, G1O76_16285, G1O77_16200, G1O80_16295, G1O81_15930, G1O83_16790, G1O84_16285, G1O87_16290, G1O88_16275, G1O89_16210, G1O90_16280, G1O93_16280, G1O94_16275, G1O96_16280, G1P02_16270, G1P03_17125, G1P06_15950, G1P09_16175, G1P10_16225, G1P12_16280, G1P14_14670, G1P15_16740, G1P17_16290, G1P19_16280, G1P23_16285, G1P24_16200, G1P25_17765, G1P26_16200, G1P29_17110, G1P31_16270, G1P35_16205, G1P36_16200, G1P37_17055, G1P40_16275, G1P44_16205, G1P45_16285, G1P47_16000, G1P48_16285, G1P51_16285, G1P52_17055, G1P53_17000, G1P54_16295, G1P55_15975, G1P56_16260, G1P57_16010, G1P58_16275, G1P59_16285, G1P61_15020, G1P64_15975, G1P67_16275, G1P69_16195, G1P72_12865, G1P75_15530, G1P76_15870, G1P78_19040, G1P83_18150, G1P84_16210, G1P87_16280, G1P90_21160, G1P91_16275, G1Q03_15890, G1Q08_16110, G1Q67_16285, G1Q78_14435, G1Q81_15765, G1Q83_16705, G1Q84_13315, G1Q85_15410, G1Q86_15380, G1Q88_15185, G1Q90_15690, G1Q91_15935, G1Q93_14530, G1Q96_15910, G1Q98_15430, G1Q99_11585, G1R01_17130, G1R02_16210, G1R03_16275, G1R04_16220, G1R08_13440, G1R13_15440, G1R15_13765, G1R20_17000, G1R21_15000, G1R22_15960, G1R23_13795, G1R27_15530, G1R28_15725, G1R29_16290, G1R30_15980, G1R31_15765, G1R36_17220, G1R38_14700, G1R40_15810, G1R42_16465, G1R44_16900, G1R45_15115, G1R47_15505, G1R48_13140, G1R51_15915, G1R52_13725, G1R53_17220, G1R63_16285, G1R69_13750, G1R87_16410, G1R93_15885, G1S02_16000, G2203_04570, G2212_12800, G2218_16175, G2221_09750, G2279_18630, G2290_14370, G2793_06395, G2918_19985, G2951_12275, G3221_002782, G3230_003711, G3231_003749, G3247_004406, G3248_003599, G3254_002478, G3263_003866, G3270_003535, G3275_002809, G3312_003088, G3336_004410, G3357_003961, G3369_002611, G3433_004280, G3460_003233, G3464_002156, G3593_002164, G3A35_17745, G3V06_002183, G3V14_004002, G3V17_003067, G3V21_003509, G3V56_002760, G3V57_004253, G3X03_002022, G4189_001963, G4190_002081, G4192_001775, G4198_002082, G4201_003454, G4202_003501, G4A01_004164, G4A73_002546, G4A83_001993, G4A85_003926, G4A87_002824, G4B68_002372, G4B72_002617, G4B74_002882, G4C74_003033, G4D32_000606, G4D46_001658, G4F88_13855, G4F89_10185, G4F91_09845, G4F92_14185, G4G47_003967, G4G62_001511, G4G67_002717, G4G68_002791, G4G75_002761, G4G76_002705, G4G79_003827, G4G97_002596, G4H00_003504, G4H04_001947, G4H07_003183, G4H08_003105, G4H18_002082, G4H21_003380, G4H24_003550, G4H63_003212, G4I66_003129, G4J07_003742, G4J08_004887, G4J11_001114, G4J12_002149, G4J18_000635, G4J20_003985, G4J37_003448, G4J39_003265, G4J41_000446, G4J45_002836, G4J90_003265, G4K02_003015, G4K03_002122, G4O54_002196, G4O56_001176, G4O59_002242, G4O60_002083, G4O67_002842, G4O69_000062, G4P29_004139, G4P83_003605, G4P85_003558, G4P89_003099, G4P91_003170, G4P93_003182, G4Q12_003157, G4Q28_002813, G4Q31_003329, G4Q50_001749, G4Q52_001957, G4Q59_003578, G4Q60_003633, G4Q63_004176, G4Q67_002937, G4Q94_002160, G4R01_003504, G4R02_003669, G4R15_002080, G4R16_003122, G4W68_002287, G4W73_002067, G4W86_002681, G4W87_003507, G4W88_003344, G4W91_003086, G4Y10_000342, G9269_003303, G9302_003971, G9304_003425, G9305_003122, G9309_001865, G9313_002530, G9314_002446, G9367_003273, G9381_002894, G9C24_004023, G9C41_001900, G9C46_002876, G9C47_001859, G9C49_002192, G9C57_003668, G9C64_003704, G9G03_002459, G9G04_000697, G9G34_003490, G9G36_002899, G9G45_003700, G9G50_002140, G9G62_004102, G9W19_004088, G9W28_003744, G9W45_001593, G9W52_003809, G9W63_003831, G9W65_003419, G9W79_003403, G9W95_002945, G9W96_002938, G9X40_003683, GB021_04425, GB040_15420, GB055_16785, GB076_20415, GB106_17280, GB114_20125, GB120_04410, GB122_20510, GB131_13210, GB139_16080, GB171_17175, GB209_03045, GB221_18125, GB224_14215, GB238_12855, GB280_04495, GB321_04495, GB331_20715, GB339_09370, GB342_19550, GB368_14700, GB372_17490, GB416_15465, GB452_14590, GB459_20995, GB466_20710, GB505_20505, GB510_11225, GB551_03055, GB567_19780, GB645_17180, GBS44_09110, GBS58_08305, GBV53_12830, GBV54_19265, GBV60_17435, GBW03_16075, GBW44_11995, GBW52_16250, GBW76_03040, GBX12_12465, GBX20_21570, GBX46_15100, GBX55_11165, GBX64_18390, GBY13_17555, GBY23_02020, GBY73_19470, GBZ51_23005, GBZ55_11025, GCZ80_03970, GEZ01_20335, GJE27_04470, GJE28_16295, GNA59_000161, GNA88_003884, GNA97_004062, GNA99_004226, GNB28_003525, GNB36_003216, GNB86_003069, GNB92_001265, GNC11_002998, GNC19_001983, GNC45_003243, GNC75_003299, GNC95_002454, GT380_17915, GTH60_10565, GTH62_16360, GTH63_03995, GTH66_01790, GTH67_13230, GTH68_05260, GTH70_11300, GTH72_02930, GTH73_04425, GTH75_04500, GTH77_15795, GTH78_16995, GTH79_16050, GTH81_13965, GTH85_04425, GTH87_03845, GTH89_13210, GTH90_11240, GTH91_20750, GTH93_04495, GTH94_02805, GTH99_12385, GXC51_17360, GXC56_17270, GXG40_17095, GYI58_17910, GYI62_002360, GYI77_20460, GYJ04_12525, GYJ24_04505, GYJ27_13680, GYJ28_001987, GYJ30_04425, GYJ32_04570, GYJ53_16290, GYJ59_13110, GYJ60_16265, H8S97_09740, KP44_16705, NG06_22005, R035_13700, SE14_02039, STMLT2P22_CBEKMEGD_02701, Z700_11380, ZV33_15625, ZX03_07070, ZY40_16825
Production host: Streptococcus thermophilus (bacteria) / References: UniProt: A0A0M0QTS9, DNA helicase
#2: DNA chain Holliday junction


Mass: 5224.434 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain Holliday junction


Mass: 5184.410 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: RuvAB branch migration motor complexed to the Holliday junction - RuvA-HJ core [t2 dataset]
Type: COMPLEX / Details: RuvA helicase / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.2 MDa / Experimental value: NO
Source (natural)Organism: Streptococcus thermophilus (bacteria)
Source (recombinant)Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Plasmid: pProEX HTB
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: in-vitro reconstituted freshly before vitrification
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 100 % / Chamber temperature: 277 K

-
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 FIELD / Nominal defocus max: 4000 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 5 sec. / Electron dose: 30.7 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Num. of real images: 30083
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 10 eV

-
Processing

EM software
IDNameVersionCategory
1Gautomatchparticle selection
2crYOLOparticle selection
3RELIONparticle selection
4EPUimage acquisition
6CTFFINDCTF correction
9Rosettamodel fitting
10ISOLDEmodel fitting
12PHENIXmodel refinement
14RELION3final Euler assignment
16RELION33D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 229000 / Symmetry type: POINT
Atomic model buildingProtocol: OTHER

+
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://pdbjlvh1.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