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- PDB-9whx: Cryo-EM structure of the IS621 recombinase in complex with bridge... -

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Basic information

Entry
Database: PDB / ID: 9whx
TitleCryo-EM structure of the IS621 recombinase in complex with bridge RNA, left-half DNA, and right-half DNA in the pre-strand exchange state
Components
  • IS621 transposase
  • LH, bottom strand
  • LH, top strand
  • RH, bottom strand
  • RH, top strand
  • bridge RNA
KeywordsDNA BINDING PROTEIN / Holliday junction / RNA dependent recombinase / RECOMBINATION-DNA-RNA complex
Function / homology
Function and homology information


transposase activity / DNA transposition / DNA binding
Similarity search - Function
Transposase, IS111A/IS1328/IS1533, N-terminal / : / Transposase / Transposase, IS116/IS110/IS902 / Transposase IS116/IS110/IS902 family
Similarity search - Domain/homology
DNA / DNA (> 10) / RNA / RNA (> 10) / RNA (> 100) / IS621 transposase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.5 Å
AuthorsHiraizumi, M. / Tsujimoto, E. / Shiojiri, N. / Nagahata, N. / Yamashita, K. / Nishimasu, H.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Science and TechnologyJPMJCR23B6 Japan
Other privateInamori Foundation
CitationJournal: To Be Published
Title: Cryo-EM structure of the IS621 recombinase in complex with bridge RNA, left-half DNA, and right-half DNA in the pre-strand exchange state
Authors: Hiraizumi, M.
History
DepositionAug 27, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 12, 2026Provider: repository / Type: Initial release
Revision 1.0Aug 12, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: IS621 transposase
B: IS621 transposase
C: IS621 transposase
D: IS621 transposase
E: bridge RNA
F: bridge RNA
G: LH, top strand
H: LH, bottom strand
I: RH, top strand
J: RH, bottom strand
hetero molecules


Theoretical massNumber of molelcules
Total (without water)312,78812
Polymers312,74010
Non-polymers492
Water724
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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DNA chain , 4 types, 4 molecules GHIJ

#3: DNA chain LH, top strand


Mass: 11551.417 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
#4: DNA chain LH, bottom strand


Mass: 11809.589 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
#5: DNA chain RH, top strand


Mass: 13536.707 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
#6: DNA chain RH, bottom strand


Mass: 13562.671 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)

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Protein / RNA chain , 2 types, 6 molecules ABCDEF

#1: Protein
IS621 transposase


Mass: 36735.355 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: O3K_03330, O3K_03970, O3K_05990, O3K_07835, O3K_09380, O3K_16710, O3K_17245, O3K_20600, O3K_22425
Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A0E0Y1P1
#2: RNA chain bridge RNA


Mass: 57668.918 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: cell-free synthesis / Source: (synth.) Escherichia coli (E. coli)

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Non-polymers , 2 types, 6 molecules

#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: Cryo-EM structure of the IS621 recombinase in complex with bridge RNA, left-half DNA, and right-half DNA in the pre-strand exchange state
Type: COMPLEX / Entity ID: #1-#6 / Source: RECOMBINANT
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.5
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 / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
4cryoSPARCCTF correction
9Servalcatmodel refinement
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
12cryoSPARCclassification
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 558374 / Symmetry type: POINT
RefinementResolution: 2.5→2.5 Å / Num. reflection obs: 2838426 / Average fsc work: 0.7997
Displacement parametersBiso mean: 105.01 Å2
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
ELECTRON MICROSCOPYs_bond_nonh_d0.0064154400.0115
ELECTRON MICROSCOPYs_angle_nonh_deg1.6592218881.8438
ELECTRON MICROSCOPYs_dihedral_angle_1_deg5.669512485
ELECTRON MICROSCOPYs_dihedral_angle_2_deg1.28995584.3925
ELECTRON MICROSCOPYs_dihedral_angle_3_deg12.9302269110
ELECTRON MICROSCOPYs_dihedral_angle_6_deg14.444253110
ELECTRON MICROSCOPYs_chiral_restr0.062325240.123
ELECTRON MICROSCOPYs_planes0.0079179000.02
ELECTRON MICROSCOPYs_nbd0.2091171560.2
ELECTRON MICROSCOPYs_nbtor0.2157220260.2
ELECTRON MICROSCOPYs_hbond_nbd0.15684010.2
LS refinement shell
Resolution (Å)Refine-IDNum. reflection obsFsc work
2.4-2.425ELECTRON MICROSCOPY878370.3855
2.426-2.448ELECTRON MICROSCOPY753250.417
2.448-2.471ELECTRON MICROSCOPY731550.4514
2.471-2.494ELECTRON MICROSCOPY717970.4821
2.494-2.517ELECTRON MICROSCOPY702970.5127
2.518-2.542ELECTRON MICROSCOPY702690.539
2.542-2.566ELECTRON MICROSCOPY669430.5653
2.566-2.591ELECTRON MICROSCOPY668610.5943
2.591-2.617ELECTRON MICROSCOPY654970.6283
2.617-2.643ELECTRON MICROSCOPY640950.6516
2.643-2.669ELECTRON MICROSCOPY629050.6735
2.669-2.696ELECTRON MICROSCOPY610450.6935
2.696-2.724ELECTRON MICROSCOPY611490.7133
2.724-2.752ELECTRON MICROSCOPY593830.7376
2.752-2.781ELECTRON MICROSCOPY579450.7695
2.781-2.81ELECTRON MICROSCOPY561610.7999
2.811-2.84ELECTRON MICROSCOPY553630.8229
2.841-2.871ELECTRON MICROSCOPY542730.838
2.871-2.903ELECTRON MICROSCOPY531730.8491
2.903-2.934ELECTRON MICROSCOPY518850.8657
2.935-2.967ELECTRON MICROSCOPY512950.8854
2.968-3.001ELECTRON MICROSCOPY498450.9019
3.001-3.035ELECTRON MICROSCOPY486370.914
3.035-3.07ELECTRON MICROSCOPY472390.9213
3.071-3.106ELECTRON MICROSCOPY465690.929
3.106-3.143ELECTRON MICROSCOPY457690.9359
3.143-3.181ELECTRON MICROSCOPY440670.9405
3.181-3.219ELECTRON MICROSCOPY432730.9437
3.219-3.259ELECTRON MICROSCOPY423330.9479
3.259-3.299ELECTRON MICROSCOPY415930.9514
3.299-3.341ELECTRON MICROSCOPY400150.9555
3.341-3.383ELECTRON MICROSCOPY391890.9587
3.384-3.427ELECTRON MICROSCOPY378610.961
3.427-3.472ELECTRON MICROSCOPY374550.963
3.472-3.518ELECTRON MICROSCOPY363730.9643
3.518-3.565ELECTRON MICROSCOPY350130.9647
3.565-3.613ELECTRON MICROSCOPY348490.9644
3.614-3.663ELECTRON MICROSCOPY333430.9634
3.664-3.714ELECTRON MICROSCOPY328650.964
3.715-3.767ELECTRON MICROSCOPY312850.9644
3.767-3.821ELECTRON MICROSCOPY306030.9629
3.822-3.877ELECTRON MICROSCOPY303130.9604
3.877-3.934ELECTRON MICROSCOPY287410.9579
3.935-3.993ELECTRON MICROSCOPY284550.9564
3.994-4.055ELECTRON MICROSCOPY271570.9565
4.055-4.117ELECTRON MICROSCOPY270450.9564
4.118-4.182ELECTRON MICROSCOPY257770.9551
4.184-4.249ELECTRON MICROSCOPY244350.9552
4.25-4.318ELECTRON MICROSCOPY242770.9558
4.319-4.39ELECTRON MICROSCOPY233170.9565
4.39-4.463ELECTRON MICROSCOPY228510.9554
4.464-4.539ELECTRON MICROSCOPY217450.954
4.54-4.619ELECTRON MICROSCOPY210330.953
4.619-4.7ELECTRON MICROSCOPY207130.9526
4.701-4.785ELECTRON MICROSCOPY196470.9519
4.786-4.873ELECTRON MICROSCOPY188410.948
4.874-4.963ELECTRON MICROSCOPY182170.9423
4.965-5.058ELECTRON MICROSCOPY177270.9357
5.059-5.157ELECTRON MICROSCOPY171250.9308
5.158-5.258ELECTRON MICROSCOPY161250.924
5.26-5.365ELECTRON MICROSCOPY158710.9224
5.366-5.475ELECTRON MICROSCOPY152250.9237
5.477-5.591ELECTRON MICROSCOPY145330.9213
5.592-5.711ELECTRON MICROSCOPY137530.915
5.712-5.835ELECTRON MICROSCOPY130590.9091
5.838-5.967ELECTRON MICROSCOPY129730.9085
5.97-6.105ELECTRON MICROSCOPY120210.9083
6.106-6.246ELECTRON MICROSCOPY117310.9021
6.25-6.399ELECTRON MICROSCOPY109810.9
6.4-6.557ELECTRON MICROSCOPY107250.9051
6.559-6.722ELECTRON MICROSCOPY101170.9073
6.725-6.897ELECTRON MICROSCOPY93750.8985
6.899-7.078ELECTRON MICROSCOPY91330.894
7.083-7.275ELECTRON MICROSCOPY85770.8958
7.277-7.479ELECTRON MICROSCOPY82270.8995
7.482-7.693ELECTRON MICROSCOPY75970.8965
7.699-7.926ELECTRON MICROSCOPY73770.8901
7.929-8.169ELECTRON MICROSCOPY69010.8876
8.173-8.429ELECTRON MICROSCOPY63030.8978
8.433-8.705ELECTRON MICROSCOPY60730.9106
8.709-8.994ELECTRON MICROSCOPY56130.9171
9.005-9.315ELECTRON MICROSCOPY52750.9192
9.321-9.653ELECTRON MICROSCOPY49810.9274
9.66-10.01ELECTRON MICROSCOPY45330.938
10.024-10.41ELECTRON MICROSCOPY43030.9383
10.418-10.834ELECTRON MICROSCOPY40170.9322
10.843-11.294ELECTRON MICROSCOPY35650.9259
11.305-11.796ELECTRON MICROSCOPY33010.9295
11.807-12.33ELECTRON MICROSCOPY29910.9339
12.357-12.945ELECTRON MICROSCOPY28570.9379
12.96-13.607ELECTRON MICROSCOPY25170.9395
13.643-14.32ELECTRON MICROSCOPY21790.9407
14.362-15.159ELECTRON MICROSCOPY20850.9518
15.183-16.075ELECTRON MICROSCOPY18610.963
16.104-17.109ELECTRON MICROSCOPY16690.9664
17.216-18.285ELECTRON MICROSCOPY13110.9661
18.328-19.58ELECTRON MICROSCOPY12490.9688
19.688-21.197ELECTRON MICROSCOPY10890.9692
21.334-23.03ELECTRON MICROSCOPY9070.9603
23.118-24.986ELECTRON MICROSCOPY7290.9479
25.324-27.842ELECTRON MICROSCOPY6250.9334
27.997-31.086ELECTRON MICROSCOPY5710.9311
31.301-35.18ELECTRON MICROSCOPY3810.9442
35.492-40.504ELECTRON MICROSCOPY3010.9605
40.983-46.952ELECTRON MICROSCOPY2250.9828
48.492-57.959ELECTRON MICROSCOPY1750.9886
59.39-73.664ELECTRON MICROSCOPY1050.9739
76.672-93.904ELECTRON MICROSCOPY490.9973
108.431-265.6ELECTRON MICROSCOPY400.9413

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