7PBT

RuvAB branch migration motor complexed to the Holliday junction - RuvB AAA+ state s1 [t1 dataset]

PDB DOI: https://doi.org/10.2210/pdb7PBT/pdb
EM Map EMD-13302: EMDB EMDataResource
NAKB: 7PBT

Classification: HYDROLASE
Organism(s): Streptococcus thermophilus, Salmonella enterica subsp. enterica serovar Typhimurium, synthetic construct
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2021-08-02 Released: 2022-09-14
Deposition Author(s): Wald, J., Fahrenkamp, D., Goessweiner-Mohr, N., Marlovits, T.C.

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

PubMed: 36002576 Search on PubMedSearch on PubMed Central
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.

Macromolecule Content

Total Structure Weight: 229.89 kDa
Atom Count: 15,879
Modelled Residue Count: 1,948
Deposited Residue Count: 1,968
Unique protein chains: 2
Unique nucleic acid chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Holliday junction ATP-dependent DNA helicase RuvB	A, B, C, D, E A, B, C, D, E, F	315	Streptococcus thermophilus	Mutation(s): 0 Gene Names: ruvB, CDA68_01670, STHERMO_2112 EC: 3.6.4.12 (PDB Primary Data), 3.6.4 (UniProt)
UniProt
Find proteins for Q5M2B1 (Streptococcus thermophilus (strain ATCC BAA-250 / LMG 18311)) Explore Q5M2B1 Go to UniProtKB: Q5M2B1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5M2B1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Holliday junction ATP-dependent DNA helicase RuvA	G	48	Salmonella enterica subsp. enterica serovar Typhimurium	Mutation(s): 0 Gene Names: ruvA, A3104_04360, A3S30_12815, A3T81_10475, A3U32_08040, A3V03_15555, A3V89_15755, A3W57_12595, A3W75_09730, A3X15_16725... 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, 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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 EC: 3.6.4.12
UniProt
Find proteins for P66746 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore P66746 Go to UniProtKB: P66746
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P66746
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence | 3D Structure

Entity ID: 3
Molecule	Chains	Length	Organism	Image
random DNA	H [auth U]	15	synthetic construct
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence | 3D Structure

Entity ID: 4
Molecule	Chains	Length	Organism	Image
random DNA	I [auth V]	15	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AGS Query on AGS Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain L [auth B] SDF format, chain N [auth C] MOL2 format, chain J [auth A] MOL2 format, chain L [auth B] MOL2 format, chain N [auth C] mmCIF format, chain J [auth A] mmCIF format, chain L [auth B] mmCIF format, chain N [auth C]	J [auth A], L [auth B], N [auth C]	PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER C₁₀ H₁₆ N₅ O₁₂ P₃ S NLTUCYMLOPLUHL-KQYNXXCUSA-N		Interactions Focus chain J [auth A] Focus chain L [auth B] Focus chain N [auth C] Interactions & Density Focus chain J [auth A] Focus chain L [auth B] Focus chain N [auth C]
ADP Query on ADP Download Ideal Coordinates CCD File SDF format, chain P [auth D] SDF format, chain Q [auth E] SDF format, chain R [auth F] MOL2 format, chain P [auth D] MOL2 format, chain Q [auth E] MOL2 format, chain R [auth F] mmCIF format, chain P [auth D] mmCIF format, chain Q [auth E] mmCIF format, chain R [auth F]	P [auth D], Q [auth E], R [auth F]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain P [auth D] Focus chain Q [auth E] Focus chain R [auth F] Interactions & Density Focus chain P [auth D] Focus chain Q [auth E] Focus chain R [auth F]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain M [auth B] SDF format, chain O [auth C] MOL2 format, chain K [auth A] MOL2 format, chain M [auth B] MOL2 format, chain O [auth C] mmCIF format, chain K [auth A] mmCIF format, chain M [auth B] mmCIF format, chain O [auth C]	K [auth A], M [auth B], O [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain M [auth B] Focus chain O [auth C] Interactions & Density Focus chain K [auth A] Focus chain M [auth B] Focus chain O [auth C]