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- PDB-9y7b: Composite map of IF-3a transposase complex with paired transposon ends -

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Basic information

Entry
Database: PDB / ID: 9y7b
TitleComposite map of IF-3a transposase complex with paired transposon ends
Components
  • (IF3A Left Transposon ...) x 2
  • (IF3A Right Transposon ...) x 2
  • (Integration host factor subunit ...) x 2
  • IF3A Tn6677 TnsB
KeywordsDNA BINDING PROTEIN / Nucleic acid binding / DNA integration / Transposon / CRISPR
Function / homology
Function and homology information


positive regulation of metabolic process / structural constituent of chromatin / regulation of translation / chromosome / DNA recombination / regulation of DNA-templated transcription / DNA binding / DNA-templated transcription / cytosol
Similarity search - Function
Integration host factor, alpha subunit / Integration host factor, beta subunit / Histone-like DNA-binding protein, conserved site / Bacterial histone-like DNA-binding proteins signature. / Histone-like DNA-binding protein / Bacterial DNA-binding protein / bacterial (prokaryotic) histone like domain / Integration host factor (IHF)-like DNA-binding domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA (> 100) / Integration host factor subunit beta / Integration host factor subunit alpha
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Vibrio cholerae (bacteria)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsMiller, D.J. / Truong, V.H. / Fatma, S. / Kellogg, E.H.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)F31GM151863 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5R01GM144566 United States
CitationJournal: To Be Published
Title: Structural basis of end recognition and pairing by I-F3 CRISPR-associated transposon
Authors: Truong, V.H. / Fatma, S. / Miller, D.J. / Kellogg, E.H.
History
DepositionSep 9, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 2, 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

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Assembly

Deposited unit
G: Integration host factor subunit alpha
H: Integration host factor subunit beta
K: IF3A Right Transposon End
N: IF3A Right Transposon End Complement
E: IF3A Left Transposon End
F: IF3A Left Transposon End Complement
A: IF3A Tn6677 TnsB
B: IF3A Tn6677 TnsB
C: IF3A Tn6677 TnsB
D: IF3A Tn6677 TnsB


Theoretical massNumber of molelcules
Total (without water)472,04910
Polymers472,04910
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Integration host factor subunit ... , 2 types, 2 molecules GH

#1: Protein Integration host factor subunit alpha / IHF-alpha


Mass: 13931.625 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: ihfA, himA, A2J79_000930, A5U30_001019, ABE91_027190, ACU57_21980, AWP47_09610, B6R15_001933, B6R31_000302, BANRA_02348, BCB93_002834, BG944_000171, BGM66_002502, BK300_17630, BK383_05705, ...Gene: ihfA, himA, A2J79_000930, A5U30_001019, ABE91_027190, ACU57_21980, AWP47_09610, B6R15_001933, B6R31_000302, BANRA_02348, BCB93_002834, BG944_000171, BGM66_002502, BK300_17630, BK383_05705, BKL28_002571, BMT50_22885, BMT91_02205, BRV02_001422, BTB68_001576, BTQ06_20600, BvCmsKKP061_04247, BXT93_25240, C0P57_002919, C1Q91_000521, C2M16_14730, C2R31_000190, C3F40_02150, C719_002019, C9160_06370, C9194_02050, C9Z68_00790, CCS08_14315, CF22_000727, CG702_13450, CIG67_20500, CQ842_05605, CQ842_22860, CR538_11775, CTR35_003956, CV83915_04676, CWS33_05125, D3C88_18970, D3G36_00475, D4N09_09315, D9D43_00230, D9E49_08565, D9J61_01980, DD762_26985, DIV22_02110, DL968_11680, DNQ45_14155, DNX30_01380, DS732_14275, DTL43_16690, DU321_09120, E2863_02131, E4K51_04325, E5H86_01680, E6D34_01870, EAI46_16195, ECs2419, EIA08_08075, EIZ93_02170, EN85_001576, EPS76_06685, EPS97_04000, EWK56_01355, ExPECSC038_01685, F7F11_07925, F7N46_05290, F9413_02030, F9461_08620, F9B07_05770, FGAF848_03490, FIJ20_00925, FJQ40_22265, FKO60_10015, FOI11_004490, FOI11_15555, FPI65_10530, FPS11_12895, FTV93_04475, FV293_05140, FVB16_11840, FWK02_29490, FZU14_13175, G3V95_01990, G3W53_07370, G4A38_00705, G4A47_06120, G5603_11510, GAI89_08045, GAJ12_14850, GGB84_000795, GKF66_01325, GNW61_13630, GNZ05_11185, GOP25_00990, GP711_11840, GP944_00090, GP954_12555, GP965_17295, GP975_05575, GQM04_13795, GQM13_05005, GQM21_17620, GRW05_00660, GRW24_20085, GTP92_00710, GUC01_03600, HEP30_001115, HEP34_002146, HHH44_000863, HI055_000495, HIE29_000945, HJQ60_004734, HKA49_000256, HLX92_05360, HLZ39_02795, HLZ50_03385, HMV95_01090, HV109_10395, HV209_08075, HVV39_26000, HVW04_02115, HVW43_02430, HVY77_11865, HX136_13730, I6H02_02010, IDONEFKE_00227, IFC14_003775, IH772_05745, J0541_000503, J5U05_000743, J8F57_001073, JNA65_05935, JNA68_15365, JNP96_15140, NCTC10764_01828, NCTC7927_02514, NCTC8603_01569, NCTC8960_05068, NQD80_06010, NY836_14360, OFN31_03700, OGM49_12905, P6223_003450, PWL68_002583, Q2V20_16000, Q2V64_10395, QDW62_11940, QO046_04120, R8G00_02655, R8O40_000769, SAMEA3752557_04266, TUM18780_19850, V9Z47_14705, WR15_13865
Production host: Escherichia coli (E. coli) / References: UniProt: Q14F23
#2: Protein Integration host factor subunit beta / IHF-beta


Mass: 10671.178 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ihfB, himD, ECS88_0940 / Production host: Escherichia coli (E. coli) / References: UniProt: B7MHM1

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IF3A Right Transposon ... , 2 types, 2 molecules KN

#3: DNA chain IF3A Right Transposon End


Mass: 27972.029 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain IF3A Right Transposon End Complement


Mass: 59532.105 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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IF3A Left Transposon ... , 2 types, 2 molecules EF

#5: DNA chain IF3A Left Transposon End


Mass: 39313.316 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#6: DNA chain IF3A Left Transposon End Complement


Mass: 41028.285 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Protein , 1 types, 4 molecules ABCD

#7: Protein
IF3A Tn6677 TnsB


Mass: 69899.992 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Production host: Escherichia coli (E. coli)

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Details

Has protein modificationN

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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: 1F3A-transposase complex with paired transposon ends / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.694 MDa / Experimental value: NO
Source (natural)Organism: Vibrio cholerae (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: OTHER
Electron lensMode: OTHER / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategoryDetails (eV)
1cryoSPARC4.7.0particle selectionCryoSPARC Blob Picker and Topaz Train/Extract jobs were used to select particle images.
2PHENIX1.20.1_4487:model refinement
13cryoSPARC4.7.03D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 168668 / Algorithm: BACK PROJECTION / Num. of class averages: 1 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00222167
ELECTRON MICROSCOPYf_angle_d0.4330992
ELECTRON MICROSCOPYf_dihedral_angle_d18.9118714
ELECTRON MICROSCOPYf_chiral_restr0.0343406
ELECTRON MICROSCOPYf_plane_restr0.0033100

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