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- EMDB-72650: Composite map of IF-3a transposase complex with paired transposon ends -

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Basic information

Entry
Database: EMDB / ID: EMD-72650
TitleComposite map of IF-3a transposase complex with paired transposon ends
Map data
Sample
  • Complex: 1F3A-transposase complex with paired transposon ends
    • Protein or peptide: Integration host factor subunit alpha
    • Protein or peptide: Integration host factor subunit beta
    • DNA: IF3A Right Transposon End
    • DNA: IF3A Right Transposon End Complement
    • DNA: IF3A Left Transposon End
    • DNA: IF3A Left Transposon End Complement
    • Protein or peptide: IF3A Tn6677 TnsB
KeywordsNucleic acid binding / DNA integration / Transposon / CRISPR / DNA BINDING PROTEIN
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
Integration host factor subunit beta / Integration host factor subunit alpha
Similarity search - Component
Biological speciesVibrio cholerae (bacteria) / Escherichia coli (E. coli) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsTruong VH / Miller DJ / Fatma S / Kellogg EH
Funding support United States, 2 items
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 VH / Fatma S / Miller DJ / Kellogg EH
History
DepositionSep 9, 2025-
Header (metadata) releaseSep 2, 2026-
Map releaseSep 2, 2026-
UpdateSep 2, 2026-
Current statusSep 2, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72650.png

Downloads & links

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Map

FileDownload / File: emd_72650.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.26 Å/pix.
x 256 pix.
= 322.56 Å		1.26 Å/pix.
x 256 pix.
= 322.56 Å		1.26 Å/pix.
x 256 pix.
= 322.56 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.26 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 10.0
Minimum - Maximum-3.1471293 - 57.803739999999998
Average (Standard dev.)4.376846 (±1.0296232)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 322.56 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : 1F3A-transposase complex with paired transposon ends

EntireName: 1F3A-transposase complex with paired transposon ends
Components
  • Complex: 1F3A-transposase complex with paired transposon ends
    • Protein or peptide: Integration host factor subunit alpha
    • Protein or peptide: Integration host factor subunit beta
    • DNA: IF3A Right Transposon End
    • DNA: IF3A Right Transposon End Complement
    • DNA: IF3A Left Transposon End
    • DNA: IF3A Left Transposon End Complement
    • Protein or peptide: IF3A Tn6677 TnsB

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Supramolecule #1: 1F3A-transposase complex with paired transposon ends

SupramoleculeName: 1F3A-transposase complex with paired transposon ends / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7
Source (natural)Organism: Vibrio cholerae (bacteria)
Molecular weightTheoretical: 694 KDa

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Macromolecule #1: Integration host factor subunit alpha

MacromoleculeName: Integration host factor subunit alpha / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 13.931625 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MGSSHHHHHH SQDPENLYFQ GSMALTKAEM SEYLFDKLGL SKRDAKELVE LFFEEIRRAL ENGEQVKLSG FGNFDLRDKN QRPGRNPKT GEDIPITARR VVTFRPGQKL KSRVENASPK DE

UniProtKB: Integration host factor subunit alpha

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Macromolecule #2: Integration host factor subunit beta

MacromoleculeName: Integration host factor subunit beta / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 10.671178 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MTKSELIERL ATQQSHIPAK TVEDAVKEML EHMASTLAQG ERIEIRGFGS FSLHYRAPRT GRNPKTGDKV ELEGKYVPHF KPGKELRDR ANIYG

UniProtKB: Integration host factor subunit beta

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Macromolecule #7: IF3A Tn6677 TnsB

MacromoleculeName: IF3A Tn6677 TnsB / type: protein_or_peptide / ID: 7 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Vibrio cholerae (bacteria)
Molecular weightTheoretical: 69.899992 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAKKGFSSFH RKAVSSQDTL ESIELVSSAN CLESVTYQDI SAFPETIAVE INFRLSILRF LARKCETIVA KSIEPHRVEL QQNYSRKIP SAITIYRWWL AFRKSDYNPI SLAPNIKDRG NRETKVSTVV DSIMEQAVER VISGRKVNVS SAYKRVRRKV R QYNLTHGT ...String:
MAKKGFSSFH RKAVSSQDTL ESIELVSSAN CLESVTYQDI SAFPETIAVE INFRLSILRF LARKCETIVA KSIEPHRVEL QQNYSRKIP SAITIYRWWL AFRKSDYNPI SLAPNIKDRG NRETKVSTVV DSIMEQAVER VISGRKVNVS SAYKRVRRKV R QYNLTHGT KYTYPKYESV RKRVKKKTPF ELLAAGKGER VAKREFRRMG KKILTSSVLE RVEIDHTVVD LFAVHEEYRI PL GRPWLTQ LVDCYSKAVI GFYLGFEPPS YVSVSLALKN AIQRKDDLIS SYESIENEWL CYGIPDLLVT DNGKEFLSKA FDQ ACESLL INVHQNKVET PDNKPHVERN YGTINTSLLD DLPGKSFSQY LQREGYDSVG EATLTLNEIR EIYLIWLVDI YHKK PNQRG TNCPNVAWKK GCQEWEPEEF SGSKDELDFK FAIVDYKQLT KVGITVYKEL SYSNDRLAEY RGKKGNHKVQ FKYNP ECMA VIWVLDEDMN EYFTVNAIDY EYASRVSLWQ HKYNMKYQAE LNSAEYDEDK EIDAEIKIEE IADRSIVKTN KIRARR RGA RHQENSARAK SISNANPASI QKHEDEIVSA DNDDWDIDYV

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Macromolecule #3: IF3A Right Transposon End

MacromoleculeName: IF3A Right Transposon End / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 27.972029 KDa
SequenceString: (DG)(DT)(DA)(DA)(DG)(DC)(DG)(DC)(DA)(DT) (DA)(DG)(DA)(DT)(DT)(DC)(DT)(DC)(DT)(DG) (DT)(DG)(DT)(DT)(DG)(DA)(DT)(DA)(DC) (DA)(DA)(DC)(DC)(DA)(DT)(DA)(DA)(DA)(DA) (DT) (DG)(DA)(DT)(DA)(DA)(DT) ...String:
(DG)(DT)(DA)(DA)(DG)(DC)(DG)(DC)(DA)(DT) (DA)(DG)(DA)(DT)(DT)(DC)(DT)(DC)(DT)(DG) (DT)(DG)(DT)(DT)(DG)(DA)(DT)(DA)(DC) (DA)(DA)(DC)(DC)(DA)(DT)(DA)(DA)(DA)(DA) (DT) (DG)(DA)(DT)(DA)(DA)(DT)(DT)(DA) (DC)(DA)(DC)(DC)(DC)(DA)(DT)(DA)(DA)(DA) (DT)(DT) (DG)(DA)(DT)(DA)(DA)(DT)(DT) (DA)(DT)(DC)(DA)(DC)(DA)(DC)(DC)(DC)(DA) (DT)(DA)(DA) (DA)(DT)(DT)(DG)(DA)(DT) (DA)(DT)(DT)(DG)(DC)

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Macromolecule #4: IF3A Right Transposon End Complement

MacromoleculeName: IF3A Right Transposon End Complement / type: dna / ID: 4 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 59.532105 KDa
SequenceString: (DG)(DC)(DA)(DA)(DT)(DA)(DT)(DC)(DA)(DA) (DT)(DT)(DT)(DA)(DT)(DG)(DG)(DG)(DT)(DG) (DT)(DG)(DA)(DT)(DA)(DA)(DT)(DT)(DA) (DT)(DC)(DA)(DA)(DT)(DT)(DT)(DA)(DT)(DG) (DG) (DG)(DT)(DG)(DT)(DA)(DA) ...String:
(DG)(DC)(DA)(DA)(DT)(DA)(DT)(DC)(DA)(DA) (DT)(DT)(DT)(DA)(DT)(DG)(DG)(DG)(DT)(DG) (DT)(DG)(DA)(DT)(DA)(DA)(DT)(DT)(DA) (DT)(DC)(DA)(DA)(DT)(DT)(DT)(DA)(DT)(DG) (DG) (DG)(DT)(DG)(DT)(DA)(DA)(DT)(DT) (DA)(DT)(DC)(DA)(DT)(DT)(DT)(DT)(DA)(DT) (DG)(DG) (DT)(DT)(DG)(DT)(DA)(DT)(DC) (DA)(DA)(DC)(DA)(DA)(DA)(DT)(DG)(DT)(DT) (DG)(DC)(DA) (DG)(DG)(DA)(DT)(DA)(DT) (DC)(DC)(DT)(DG)(DC)(DT)(DG)(DA)(DT)(DG) (DA)(DA)(DG)(DC) (DA)(DG)(DA)(DA)(DC) (DA)(DA)(DC)(DT)(DT)(DT)(DA)(DA)(DC)(DG) (DC)(DC)(DG)(DT)(DG) (DC)(DG)(DC)(DT) (DG)(DT)(DG)(DA)(DA)(DA)(DA)(DG)(DC)(DA) (DA)(DT)(DG)(DA)(DA)(DG) (DC)(DC)(DA) (DA)(DA)(DG)(DC)(DG)(DT)(DC)(DC)(DT)(DG) (DT)(DA)(DA)(DG)(DG)(DC)(DG) (DG)(DT) (DC)(DC)(DA)(DA)(DT)(DG)(DG)(DC)(DT)(DT) (DG)(DA)(DT)(DG)(DA)(DA)(DC)(DC) (DA) (DG)(DA)(DC)(DC)(DA)(DG)(DG)(DG)(DC)(DA) (DC)

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Macromolecule #5: IF3A Left Transposon End

MacromoleculeName: IF3A Left Transposon End / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 39.313316 KDa
SequenceString: (DC)(DA)(DC)(DA)(DG)(DC)(DG)(DG)(DC)(DT) (DC)(DT)(DT)(DT)(DT)(DT)(DG)(DA)(DT)(DT) (DT)(DG)(DT)(DT)(DG)(DA)(DT)(DG)(DC) (DA)(DA)(DC)(DC)(DA)(DT)(DA)(DA)(DA)(DG) (DT) (DG)(DA)(DT)(DA)(DT)(DT) ...String:
(DC)(DA)(DC)(DA)(DG)(DC)(DG)(DG)(DC)(DT) (DC)(DT)(DT)(DT)(DT)(DT)(DG)(DA)(DT)(DT) (DT)(DG)(DT)(DT)(DG)(DA)(DT)(DG)(DC) (DA)(DA)(DC)(DC)(DA)(DT)(DA)(DA)(DA)(DG) (DT) (DG)(DA)(DT)(DA)(DT)(DT)(DT)(DA) (DA)(DT)(DA)(DA)(DT)(DT)(DA)(DT)(DT)(DT) (DA)(DT) (DA)(DA)(DT)(DC)(DA)(DG)(DC) (DA)(DA)(DC)(DT)(DT)(DA)(DA)(DC)(DC)(DA) (DC)(DA)(DA) (DA)(DA)(DC)(DA)(DA)(DC) (DC)(DA)(DT)(DA)(DT)(DA)(DT)(DT)(DG)(DA) (DT)(DA)(DT)(DC) (DT)(DC)(DA)(DC)(DA) (DA)(DA)(DA)(DC)(DA)(DA)(DC)(DC)(DA)(DT) (DA)(DA)(DG)(DT)(DT) (DG)(DA)(DT)(DA) (DT)(DT)(DT)(DT)

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Macromolecule #6: IF3A Left Transposon End Complement

MacromoleculeName: IF3A Left Transposon End Complement / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 41.028285 KDa
SequenceString: (DA)(DA)(DA)(DA)(DT)(DA)(DT)(DC)(DA)(DA) (DC)(DT)(DT)(DA)(DT)(DG)(DG)(DT)(DT)(DG) (DT)(DT)(DT)(DT)(DG)(DT)(DG)(DA)(DG) (DA)(DT)(DA)(DT)(DC)(DA)(DA)(DT)(DA)(DT) (DA) (DT)(DG)(DG)(DT)(DT)(DG) ...String:
(DA)(DA)(DA)(DA)(DT)(DA)(DT)(DC)(DA)(DA) (DC)(DT)(DT)(DA)(DT)(DG)(DG)(DT)(DT)(DG) (DT)(DT)(DT)(DT)(DG)(DT)(DG)(DA)(DG) (DA)(DT)(DA)(DT)(DC)(DA)(DA)(DT)(DA)(DT) (DA) (DT)(DG)(DG)(DT)(DT)(DG)(DT)(DT) (DT)(DT)(DG)(DT)(DG)(DG)(DT)(DT)(DA)(DA) (DG)(DT) (DT)(DG)(DC)(DT)(DG)(DA)(DT) (DT)(DA)(DT)(DA)(DA)(DA)(DT)(DA)(DA)(DT) (DT)(DA)(DT) (DT)(DA)(DA)(DA)(DT)(DA) (DT)(DC)(DA)(DC)(DT)(DT)(DT)(DA)(DT)(DG) (DG)(DT)(DT)(DG) (DC)(DA)(DT)(DC)(DA) (DA)(DC)(DA)(DA)(DC)(DA)(DT)(DT)(DC)(DC) (DA)(DT)(DC)(DG)(DT) (DC)(DT)(DG)(DC) (DT)(DC)(DA)(DT)(DC)(DC)(DA)(DT)(DG)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7.0) / Number images used: 168668
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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