7PBU

RuvAB branch migration motor complexed to the Holliday junction - RuvA-HJ core [t2 dataset]

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

Mechanism of AAA+ ATPase-mediated RuvAB-Holliday junction branch migration.

Wald, J., Fahrenkamp, D., Goessweiner-Mohr, N., Lugmayr, W., Ciccarelli, L., Vesper, O., Marlovits, T.C.

(2022) Nature 609: 630-639

  • DOI: https://doi.org/10.1038/s41586-022-05121-1
  • Primary Citation of Related Structures:  
    7PBL, 7PBM, 7PBN, 7PBO, 7PBP, 7PBQ, 7PBR, 7PBS, 7PBT, 7PBU

  • PubMed Abstract: 

    The Holliday junction is a key intermediate formed during DNA recombination across all kingdoms of life 1 . 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 2 . 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.

    • Organizational Affiliation: 

    Institute of Structural and Systems Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany. jiri.wald@cssb-hamburg.de.


Macromolecules

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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Holliday junction ATP-dependent DNA helicase RuvA
A, B, C, D, F
A, B, C, D, F, H, J, L
133Salmonella enterica subsp. enterica serovar TyphimuriumMutation(s): 0 
Gene Names: 
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_148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EC: 3.6.4.12
UniProt
Find proteins for A0A0M0QTS9 (Salmonella typhimurium)
Explore A0A0M0QTS9 
Go to UniProtKB:  A0A0M0QTS9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0M0QTS9
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
Holliday junction
E, G
17synthetic construct
Sequence Annotations
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 3
MoleculeChains LengthOrganismImage
Holliday junction
I, K
17synthetic construct
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONRELION3

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2022-09-14
    Type: Initial release
  • Version 1.1: 2022-09-28
    Changes: Database references
  • Version 1.2: 2022-11-30
    Changes: Database references
  • Version 1.3: 2023-01-18
    Changes: Database references