[English] 日本語
Yorodumi- PDB-7pbm: RuvAB branch migration motor complexed to the Holliday junction -... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7pbm | ||||||
---|---|---|---|---|---|---|---|
Title | RuvAB branch migration motor complexed to the Holliday junction - RuvB AAA+ state s2 [t2 dataset] | ||||||
Components |
| ||||||
Keywords | HYDROLASE / 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 helicase / DNA recombination / DNA repair / ATP hydrolysis activity / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Streptococcus thermophilus (bacteria) Salmonella typhimurium (bacteria) synthetic construct (others) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å | ||||||
Authors | Fahrenkamp, D. / Goessweiner-Mohr, N. / Wald, J. / Marlovits, T.C. | ||||||
Citation | Journal: 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7pbm.cif.gz | 667.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7pbm.ent.gz | 560.1 KB | Display | PDB format |
PDBx/mmJSON format | 7pbm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7pbm_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7pbm_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 7pbm_validation.xml.gz | 66.8 KB | Display | |
Data in CIF | 7pbm_validation.cif.gz | 99.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pb/7pbm ftp://data.pdbj.org/pub/pdb/validation_reports/pb/7pbm | HTTPS FTP |
-Related structure data
Related structure data | 13295MC 7pblC 7pbnC 7pboC 7pbpC 7pbqC 7pbrC 7pbsC 7pbtC 7pbuC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
-Holliday junction ATP-dependent DNA helicase ... , 3 types, 8 molecules ABCDEFGH
#1: Protein | Mass: 35447.508 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus thermophilus (bacteria) / Gene: ruvB, CDA68_01670, STHERMO_2112 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: A0A2U2MES7, DNA helicase #2: Protein/peptide | | Mass: 5105.734 Da / Num. of mol.: 1 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: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: A0A0M0QTS9, DNA helicase #3: Protein/peptide | | Mass: 5442.131 Da / Num. of mol.: 1 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: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) Strain (production host): ruvA / References: UniProt: A0A0M0QTS9, DNA helicase |
---|
-DNA chain , 2 types, 2 molecules UV
#4: DNA chain | Mass: 4643.037 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
---|---|
#5: DNA chain | Mass: 4535.946 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Non-polymers , 3 types, 9 molecules
#6: Chemical | #7: Chemical | #8: Chemical | |
---|
-Details
Has ligand of interest | N |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: RuvAB branch migration motor complexed to the Holliday junction - RuvB motor state s2 [t2 dataset] Type: COMPLEX / Details: RuvB helicase / Entity ID: #1-#5 / Source: RECOMBINANT |
---|---|
Molecular weight | Value: 0.220 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 solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: in-vitro reconstituted freshly before vitrification |
Specimen support | Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2 |
Vitrification | Instrument: 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 |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: 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 holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average 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 optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 10 eV |
-Processing
EM software |
| ||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 32612 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: OTHER |