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- PDB-7jy9: Structure of a 9 base pair RecA-D loop complex -

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Basic information

Entry
Database: PDB / ID: 7jy9
TitleStructure of a 9 base pair RecA-D loop complex
Components
  • (DNA (42-MER)) x 2
  • DNA (27-MER)
  • Protein RecA
KeywordsDNA BINDING PROTEIN/DNA / Recombination / DNA repair / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


DNA polymerase V complex / homologous recombination / SOS response / recombinational repair / ATP-dependent DNA damage sensor activity / response to ionizing radiation / translesion synthesis / ATP-dependent activity, acting on DNA / cell motility / single-stranded DNA binding ...DNA polymerase V complex / homologous recombination / SOS response / recombinational repair / ATP-dependent DNA damage sensor activity / response to ionizing radiation / translesion synthesis / ATP-dependent activity, acting on DNA / cell motility / single-stranded DNA binding / DNA-binding transcription factor binding / DNA recombination / damaged DNA binding / DNA repair / DNA damage response / ATP hydrolysis activity / ATP binding / cytosol / cytoplasm
Similarity search - Function
DNA recombination/repair protein RecA, conserved site / DNA recombination and repair protein RecA, C-terminal / : / RecA C-terminal domain / recA signature. / DNA recombination and repair protein RecA / : / recA bacterial DNA recombination protein / DNA recombination and repair protein RecA, monomer-monomer interface / RecA family profile 2. ...DNA recombination/repair protein RecA, conserved site / DNA recombination and repair protein RecA, C-terminal / : / RecA C-terminal domain / recA signature. / DNA recombination and repair protein RecA / : / recA bacterial DNA recombination protein / DNA recombination and repair protein RecA, monomer-monomer interface / RecA family profile 2. / DNA recombination and repair protein RecA-like, ATP-binding domain / RecA family profile 1. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / DNA / DNA (> 10) / Protein RecA / Protein RecA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsPavletich, N.P.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Nature / Year: 2020
Title: Mechanism of strand exchange from RecA-DNA synaptic and D-loop structures.
Authors: Haijuan Yang / Chun Zhou / Ankita Dhar / Nikola P Pavletich /
Abstract: The strand-exchange reaction is central to homologous recombination. It is catalysed by the RecA family of ATPases, which form a helical filament with single-stranded DNA (ssDNA) and ATP. This ...The strand-exchange reaction is central to homologous recombination. It is catalysed by the RecA family of ATPases, which form a helical filament with single-stranded DNA (ssDNA) and ATP. This filament binds to a donor double-stranded DNA (dsDNA) to form synaptic filaments, which search for homology and then catalyse the exchange of the complementary strand, forming either a new heteroduplex or-if homology is limited-a D-loop. How synaptic filaments form, search for homology and catalyse strand exchange is poorly understood. Here we report the cryo-electron microscopy analysis of synaptic mini-filaments with both non-complementary and partially complementary dsDNA, and structures of RecA-D-loop complexes containing a 10- or a 12-base-pair heteroduplex. The C-terminal domain of RecA binds to dsDNA and directs it to the RecA L2 loop, which inserts into and opens up the duplex. The opening propagates through RecA sequestering the homologous strand at a secondary DNA-binding site, which frees the complementary strand to sample pairing with the ssDNA. At each RecA step, there is a roughly 20% probability that duplex opening will terminate and the as-yet-unopened dsDNA portion will bind to another C-terminal domain. Homology suppresses this process, through the cooperation of heteroduplex pairing with the binding of ssDNA to the secondary site, to extend dsDNA opening. This mechanism locally limits the length of ssDNA sampled for pairing if homology is not encountered, and could allow for the formation of multiple, widely separated synapses on the donor dsDNA, which would increase the likelihood of encountering homology. These findings provide key mechanistic insights into homologous recombination.
History
DepositionAug 29, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 11, 2020Group: 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 1.2Mar 6, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model / refine
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 / _refine.ls_d_res_high / _refine.ls_d_res_low

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Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
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  • Superimposition on EM map
  • EMDB-22525
  • Imaged by UCSF Chimera
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Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein RecA
B: Protein RecA
C: Protein RecA
D: Protein RecA
E: Protein RecA
F: Protein RecA
G: Protein RecA
H: Protein RecA
I: Protein RecA
T: DNA (42-MER)
U: DNA (42-MER)
S: DNA (27-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)364,09030
Polymers359,16212
Non-polymers4,92818
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: scanning transmission electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 1 types, 9 molecules ABCDEFGHI

#1: Protein
Protein RecA / Recombinase A


Mass: 35960.281 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: recA, NCTC11341_01072 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A376NU07, UniProt: P0A7G6*PLUS

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DNA chain , 3 types, 3 molecules TUS

#2: DNA chain DNA (42-MER)


Mass: 13804.859 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
#3: DNA chain DNA (42-MER)


Mass: 13687.785 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
#4: DNA chain DNA (27-MER)


Mass: 8027.228 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)

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Non-polymers , 2 types, 18 molecules

#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Mg
#6: Chemical
ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM

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Details

Has ligand of interestN

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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: RecA-D loop complex / Type: COMPLEX / Entity ID: #1-#4 / Source: MULTIPLE SOURCES
Source (natural)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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
Image recordingElectron dose: 57 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: REFMAC / Version: 5.8.0258 / Classification: refinement
EM software
IDNameCategory
1RELIONparticle selection
4RELIONCTF correction
7Omodel fitting
13REFMACmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 399184 / Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: RECIPROCAL
Atomic model buildingPDB-ID: 3CMW

3cmw


Accession code: 3CMW / Source name: PDB / Type: experimental model
RefinementResolution: 2.7→2.7 Å / Cor.coef. Fo:Fc: 0.879 / SU B: 16.801 / SU ML: 0.144 / ESU R: 0.262
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rwork0.26507 --
obs0.26507 299081 100 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.77 Å2
Baniso -1Baniso -2Baniso -3
1--1.09 Å2-0.16 Å20.26 Å2
2---0.61 Å20.65 Å2
3---1.7 Å2
Refinement stepCycle: 1 / Total: 24849
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0060.01325408
ELECTRON MICROSCOPYr_bond_other_d0.0350.01723408
ELECTRON MICROSCOPYr_angle_refined_deg1.5381.60434697
ELECTRON MICROSCOPYr_angle_other_deg2.3691.66354433
ELECTRON MICROSCOPYr_dihedral_angle_1_deg6.50752955
ELECTRON MICROSCOPYr_dihedral_angle_2_deg33.61523.591039
ELECTRON MICROSCOPYr_dihedral_angle_3_deg18.149154248
ELECTRON MICROSCOPYr_dihedral_angle_4_deg21.68515124
ELECTRON MICROSCOPYr_chiral_restr0.0620.23406
ELECTRON MICROSCOPYr_gen_planes_refined0.0040.0226695
ELECTRON MICROSCOPYr_gen_planes_other0.0050.024853
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it2.4564.37411847
ELECTRON MICROSCOPYr_mcbond_other2.4554.37311846
ELECTRON MICROSCOPYr_mcangle_it4.4521.80914793
ELECTRON MICROSCOPYr_mcangle_other4.4521.81214794
ELECTRON MICROSCOPYr_scbond_it2.5645.96613561
ELECTRON MICROSCOPYr_scbond_other2.5645.96613562
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other4.76429.68319905
ELECTRON MICROSCOPYr_long_range_B_refined7.95268.18125450
ELECTRON MICROSCOPYr_long_range_B_other7.95168.17925451
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork0.633 22082 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: ELECTRON MICROSCOPY

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.1287-0.0847-0.07941.6187-0.8661.1176-0.07930.07540.1265-0.0831-0.0089-0.0529-0.05420.16520.08820.2362-0.05830.00180.26340.00530.260153.431783.68342.2663
26.06650.9595-0.83012.7048-3.08036.20830.11520.34431.5227-0.18580.2110.74520.0812-0.6105-0.32620.1389-0.0671-0.11530.35220.20.65832.348296.271924.1616
30.83370.1150.46721.0388-0.48480.7032-0.0781-0.0010.04610.06270.08590.2183-0.06250.0248-0.00780.31080.0148-0.00230.2145-0.01490.267238.786966.140359.8169
44.4609-0.12223.65074.2817-1.70155.82730.11120.23780.1012-0.13810.08131.260.4295-0.3546-0.19250.2776-0.1718-0.13020.19340.01930.499718.237352.5640.2572
51.2949-0.05060.79471.50930.04621.19030.0218-0.1577-0.1075-0.04590.0010.2385-0.0375-0.1021-0.02280.19850.04-0.00810.2627-0.00890.14548.150843.06475.7246
64.03011.92683.18642.51192.2437.11930.09720.2099-0.8568-0.0870.21240.49640.39230.3817-0.30960.34290.1679-0.12310.1329-0.00780.705448.408418.049256.6219
71.47880.15250.87831.04350.59181.41170.1498-0.0683-0.10990.1595-0.0731-0.16740.0548-0.1392-0.07670.2782-0.0093-0.0250.2315-0.01340.162272.552438.742891.0946
82.15310.61080.33713.80061.77768.62760.13990.2038-0.5121-0.12310.0574-0.25460.22670.5833-0.19730.13790.1865-0.01260.3494-0.1650.36193.714426.094571.6113
91.10510.3002-0.22911.02590.69381.4184-0.0343-0.00520.03710.08890.0892-0.08470.02860.0494-0.05490.36-0.0038-0.01770.1501-0.03290.201489.134458.1419105.8049
103.0344-0.3463-2.6254.322.29986.4260.09390.3716-0.048-0.12610.1778-1.1577-0.48540.3531-0.27170.3489-0.17710.1670.233-0.06630.4368110.454568.958586.8117
111.6843-0.6194-1.06951.42770.29241.47540.028-0.06140.0588-0.09850.0381-0.13930.02760.1328-0.06610.27540.06390.00570.2532-0.01320.136681.683782.2738121.3394
126.5773-2.0424-4.52123.7062-0.7944.68931.01980.35612.16490.03040.1479-1.1415-1.0366-0.4107-1.16770.8454-0.0830.34880.29050.20090.890482.0707105.5756100.9141
131.4792-0.2154-0.5230.867-0.37991.56430.0665-0.09980.00690.0273-0.03340.0417-0.1193-0.0782-0.03310.24380.00780.00410.27180.01740.161656.933388.8929137.1333
147.2032-1.0036-1.86132.3906-2.41876.08680.02140.10241.4663-0.0980.28830.20960.1224-0.6036-0.30980.10740.0752-0.0190.4210.08670.519736.0768101.5449119.0257
151.02550.46110.04071.1537-0.51131.1879-0.0150.022500.0230.05550.10830.0552-0.1079-0.04050.2042-0.04920.00080.34330.02010.189639.232771.1752153.7095
163.05380.40461.83474.7668-3.24167.96140.25020.31310.2922-0.25260.03571.10510.5992-0.3412-0.28590.2549-0.2006-0.14740.39450.07440.379317.526559.9475134.9012
170.86240.53360.34642.1811-0.85431.55390.0959-0.1697-0.38190.0111-0.0936-0.15230.0326-0.0606-0.00240.23740.0586-0.01630.21080.01990.277145.817546.4118170.0157
186.63571.79033.03081.87480.42075.7660.2491-0.1298-1.0486-0.42920.3940.52160.9660.0237-0.64310.5080.0073-0.30330.29840.00430.895243.585822.2398151.1009
190.64750.9904-0.0111.5606-0.12251.405-0.2680.37890.192-0.28920.38250.2803-0.15010.1665-0.11450.46290.1939-0.07870.65040.11210.096287.682933.86748.328
200.72440.37550.20810.27950.64513.7373-0.11750.2942-0.0320.0230.147-0.0880.4638-0.4416-0.02950.40480.0555-0.23720.41010.0620.827244.951596.629993.3884
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1ELECTRON MICROSCOPY1A37 - 269
2ELECTRON MICROSCOPY1A500 - 502
3ELECTRON MICROSCOPY1S24 - 27
4ELECTRON MICROSCOPY1T18 - 19
5ELECTRON MICROSCOPY2A270 - 333
6ELECTRON MICROSCOPY3A1 - 36
7ELECTRON MICROSCOPY3B37 - 269
8ELECTRON MICROSCOPY3B500 - 502
9ELECTRON MICROSCOPY3S21 - 23
10ELECTRON MICROSCOPY3T20 - 22
11ELECTRON MICROSCOPY4B270 - 333
12ELECTRON MICROSCOPY5B1 - 36
13ELECTRON MICROSCOPY5C37 - 269
14ELECTRON MICROSCOPY5C500 - 502
15ELECTRON MICROSCOPY5S18 - 20
16ELECTRON MICROSCOPY5T23 - 25
17ELECTRON MICROSCOPY5U27 - 28
18ELECTRON MICROSCOPY6C270 - 333
19ELECTRON MICROSCOPY7C1 - 36
20ELECTRON MICROSCOPY7D37 - 269
21ELECTRON MICROSCOPY7D500 - 502
22ELECTRON MICROSCOPY7S15 - 17
23ELECTRON MICROSCOPY7T26 - 27
24ELECTRON MICROSCOPY7U25 - 26
25ELECTRON MICROSCOPY8D270 - 333
26ELECTRON MICROSCOPY9D1 - 36
27ELECTRON MICROSCOPY9E37 - 269
28ELECTRON MICROSCOPY9E500 - 502
29ELECTRON MICROSCOPY9S12 - 14
30ELECTRON MICROSCOPY9U19 - 24
31ELECTRON MICROSCOPY10E270 - 333
32ELECTRON MICROSCOPY11E1 - 36
33ELECTRON MICROSCOPY11F37 - 269
34ELECTRON MICROSCOPY11F500 - 502
35ELECTRON MICROSCOPY11S9 - 11
36ELECTRON MICROSCOPY12F270 - 333
37ELECTRON MICROSCOPY13F1 - 36
38ELECTRON MICROSCOPY13G37 - 269
39ELECTRON MICROSCOPY13G500 - 502
40ELECTRON MICROSCOPY13S6 - 8
41ELECTRON MICROSCOPY14G270 - 333
42ELECTRON MICROSCOPY15G1 - 36
43ELECTRON MICROSCOPY15H37 - 269
44ELECTRON MICROSCOPY15H500 - 502
45ELECTRON MICROSCOPY15S3 - 5
46ELECTRON MICROSCOPY16H270 - 333
47ELECTRON MICROSCOPY17H1 - 36
48ELECTRON MICROSCOPY17I34 - 269
49ELECTRON MICROSCOPY17I500 - 502
50ELECTRON MICROSCOPY17S1 - 2
51ELECTRON MICROSCOPY18I270 - 333
52ELECTRON MICROSCOPY19T3 - 17
53ELECTRON MICROSCOPY19U29 - 43
54ELECTRON MICROSCOPY20T28 - 44
55ELECTRON MICROSCOPY20U2 - 18

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