9Y7B | pdb_00009y7b

Composite map of IF-3a transposase complex with paired transposon ends

• PDB DOI: https://doi.org/10.2210/pdb9Y7B/pdb
• EM Map EMD-72650: EMDB EMDataResource

• Classification: DNA BINDING PROTEIN
• Organism(s): Escherichia coli, synthetic construct, Vibrio cholerae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2025-09-09 Released: 2026-09-02 
• Deposition Author(s): Miller, D.J., Truong, V.H., Fatma, S., Kellogg, E.H.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.90 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural basis of end recognition and pairing by I-F3 CRISPR-associated transposon

Truong, V.H., Fatma, S., Miller, D.J., Kellogg, E.H.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 6-mer - A4B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 6-mer - A3B2C1 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 472.05 kDa 
• Atom Count: 21,225 
• Modeled Residue Count: 2,225 
• Deposited Residue Count: 3,171 
• Unique protein chains: 3
• Unique nucleic acid chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Integration host factor subunit alpha	A [auth G]	121	Escherichia coli	Mutation(s): 0  Gene Names:  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
UniProt
Find proteins for Q14F23 (Escherichia coli) Explore Q14F23  Go to UniProtKB:  Q14F23

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Integration host factor subunit beta	B [auth H]	94	Escherichia coli	Mutation(s): 0  Gene Names: ihfB, himD, ECS88_0940
UniProt
Find proteins for B7MHM1 (Escherichia coli O45:K1 (strain S88 / ExPEC)) Explore B7MHM1  Go to UniProtKB:  B7MHM1

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
IF3A Tn6677 TnsB	G [auth A], H [auth B], I [auth C], J [auth D]	603	Vibrio cholerae	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Length	Organism	Image
IF3A Right Transposon End	C [auth K]	91	synthetic construct

Entity ID: 4
Molecule	Chains	Length	Organism	Image
IF3A Right Transposon End Complement	D [auth N]	192	synthetic construct

Entity ID: 5
Molecule	Chains	Length	Organism	Image
IF3A Left Transposon End	E	128	synthetic construct

Entity ID: 6
Molecule	Chains	Length	Organism	Image
IF3A Left Transposon End Complement	F	133	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.90 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1_4487:
RECONSTRUCTION	cryoSPARC	4.7.0

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-09-02 
Deposition Author(s): Miller, D.J., Truong, V.H., Fatma, S., Kellogg, E.H.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	F31GM151863
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	5R01GM144566

Revision History  

• Version 1.0: 2026-09-02
  Type: Initial release