9F12: Integration host factor subunit alpha
CryoEM structure of the F plasmid relaxosome with oriT DNA ss-27_-3ds-2_+143 and TraI its TE mode, derived from ss-27_-3ds-2_+143-R Locally-refined 3.42 A Map. Determined by electron microscopy at 3.42 Å resolution. Released 4 Jun 2025.
- Method
- Electron microscopy
- Resolution
- 3.42 Å
- Organism
- Escherichia coli K-12
- Chains
- 8
- Atoms
- 12,171
- Mol. weight
- 358 kDa
- Ligands
- MG
- Released
- 4 Jun 2025
Explore 9F12 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
9F12 contains 46 α-helices and 61 β-strands across 6 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.
Chain C: 3 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3 | 1 | 1 |
| α-helix | 5-15 | 11 | |
| α-helix | 20-39 | 20 | |
| β-strand | 44-46 | 3 | 2 |
| β-strand | 50-57 | 8 | 2 |
| β-strand | 60 | 1 | 3 |
| β-strand | 63 | 1 | 4 |
| β-strand | 70 | 1 | 4 |
| β-strand | 73 | 1 | 3 |
| β-strand | 76-83 | 8 | 2 |
| α-helix | 85-91 | 7 | |
Chain D: 4 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2 | 1 | 2 |
| α-helix | 3-13 | 11 | |
| α-helix | 19-38 | 20 | |
| β-strand | 43-45 | 3 | 1 |
| β-strand | 49-56 | 8 | 1 |
| α-helix | 57-58 | 2 | |
| β-strand | 59-62 | 4 | 5 |
| β-strand | 69-72 | 4 | 5 |
| β-strand | 75-82 | 8 | 1 |
| α-helix | 84-90 | 7 | |
Chain E: 4 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 13-19 | 7 | 12 |
| α-helix | 20-31 | 12 | |
| β-strand | 35 | 1 | 6 |
| α-helix | 37-51 | 15 | |
| β-strand | 67-73 | 7 | 12 |
| α-helix | 76-89 | 14 | |
| α-helix | 93-107 | 15 | |
Chain F: 6 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2 | 1 | 6 |
| α-helix | 3 | 1 | |
| β-strand | 4 | 1 | 7 |
| β-strand | 13-19 | 7 | 8 |
| α-helix | 23-33 | 11 | |
| α-helix | 37-51 | 15 | |
| α-helix | 56-58 | 3 | |
| β-strand | 67-73 | 7 | 8 |
| α-helix | 76-89 | 14 | |
| β-strand | 91 | 1 | 7 |
| α-helix | 93-107 | 15 | |
| β-strand | 112 | 1 | 9 |
| β-strand | 116 | 1 | 9 |
Chain G: 4 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 13-19 | 7 | 10 |
| α-helix | 20-33 | 14 | |
| α-helix | 37-51 | 15 | |
| β-strand | 67-73 | 7 | 10 |
| α-helix | 76-89 | 14 | |
| α-helix | 93-107 | 15 | |
| β-strand | 113 | 1 | 11 |
| β-strand | 116 | 1 | 11 |
Chain H: 25 helices, 33 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-7 | 6 | 13 |
| α-helix | 10-17 | 8 | |
| β-strand | 32-34 | 3 | 13 |
| α-helix | 36-40 | 5 | |
| α-helix | 49-57 | 9 | |
| β-strand | 59 | 1 | 14 |
| β-strand | 65 | 1 | 14 |
| β-strand | 69-70 | 2 | 15 |
| β-strand | 73-74 | 2 | 15 |
| β-strand | 79-85 | 7 | 13 |
| α-helix | 88-97 | 10 | |
| α-helix | 100-117 | 18 | |
| α-helix | 118-120 | 3 | |
| β-strand | 122-126 | 5 | 16 |
| β-strand | 131-135 | 5 | 16 |
| β-strand | 141-148 | 8 | 13 |
| β-strand | 154-163 | 10 | 13 |
| β-strand | 166-167 | 2 | 17 |
| β-strand | 172-173 | 2 | 17 |
| α-helix | 174-176 | 3 | |
| α-helix | 185-191 | 7 | |
| α-helix | 193-210 | 18 | |
| β-strand | 216-217 | 2 | 18 |
| α-helix | 220-222 | 3 | |
| β-strand | 224-225 | 2 | 18 |
| α-helix | 230-232 | 3 | |
| α-helix | 236-245 | 10 | |
| α-helix | 251-260 | 10 | |
| α-helix | 262-264 | 3 | |
| α-helix | 270-282 | 13 | |
| α-helix | 288-301 | 14 | |
| β-strand | 567-570 | 4 | 19 |
| α-helix | 576-592 | 17 | |
| β-strand | 597-600 | 4 | 19 |
| α-helix | 604-620 | 17 | |
| β-strand | 629-636 | 8 | 20 |
| α-helix | 647-649 | 3 | |
| β-strand | 655-660 | 6 | 20 |
| β-strand | 665-675 | 11 | 20 |
| β-strand | 680-685 | 6 | 20 |
| β-strand | 690-694 | 5 | 20 |
| α-helix | 695-697 | 3 | |
| β-strand | 702-712 | 11 | 20 |
| β-strand | 717-720 | 4 | 21 |
| β-strand | 734-740 | 7 | 21 |
| β-strand | 744-748 | 5 | 21 |
| β-strand | 755-759 | 5 | 21 |
| α-helix | 760-761 | 2 | |
| α-helix | 764-766 | 3 | |
| β-strand | 768 | 1 | 20 |
| β-strand | 770-772 | 3 | 21 |
| β-strand | 775-776 | 2 | 19 |
| β-strand | 787-792 | 6 | 19 |
| α-helix | 799-805 | 7 | |
| β-strand | 812-816 | 5 | 19 |
| α-helix | 819 | 1 | |
| α-helix | 823-826 | 4 | |
| β-strand | 832-833 | 2 | 19 |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| T-strand DNA (96-MER) | A | DNA | 170 | Escherichia coli K-12 | |
| R-strand DNA (85-MER) | B | DNA | 145 | Escherichia coli K-12 | |
| Integration host factor subunit alpha | C | protein | 99 | Escherichia coli K-12 | P0A6X7 (AlphaFold model) |
| Integration host factor subunit beta | D | protein | 94 | Escherichia coli K-12 | P0A6Y1 (AlphaFold model) |
| Relaxosome protein TraY | E, F, G | protein | 131 | Escherichia coli K-12 | P06627 (AlphaFold model) |
| Multifunctional conjugation protein TraI | H | protein | 1763 | Escherichia coli K-12 | P14565 (AlphaFold model) |
Sequence of entity 1 (A), FASTA
>9F12_1 T-strand DNA (96-MER) (chains A)
CCTACAAAACGGTGTCGGCGCGTTGTTGTAGCCGCGCCGACACCGCTTTTTTAAATATCA
TAAAGAGAGTAAGAGAAACTAATTTTTCATAACACTCTATTTATAAAGAAAAATCAGCAA
AAACTTGTTTTTGCGTGGGGTGTGGTGCTTTTGGTGGTGAGAACCACCAA
Sequence of entity 2 (B), FASTA
>9F12_2 R-strand DNA (85-MER) (chains B)
CCACACCCCACGCAAAAACAAGTTTTTGCTGATTTTTCTTTATAAATAGAGTGTTATGAA
AAATTAGTTTCTCTTACTCTCTTTATGATATTTAAAAAAGCGGTGTCGGCGCGGCTACAA
CAACGCGCCGACACCGTTTTGTAGG
Sequence of entity 3 (C), FASTA
>9F12_3 Integration host factor subunit alpha (chains C)
MALTKAEMSEYLFDKLGLSKRDAKELVELFFEEIRRALENGEQVKLSGFGNFDLRDKNQR
PGRNPKTGEDIPITARRVVTFRPGQKLKSRVENASPKDE
Sequence of entity 4 (D), FASTA
>9F12_4 Integration host factor subunit beta (chains D)
MTKSELIERLATQQSHIPAKTVEDAVKEMLEHMASTLAQGERIEIRGFGSFSLHYRAPRT
GRNPKTGDKVELEGKYVPHFKPGKELRDRANIYG
Sequence of entity 5 (E, F, G), FASTA
>9F12_5 Relaxosome protein TraY (chains E, F, G)
MKRFGTRSATGKMVKLKLPVDVESLLIEASNRSGRSRSFEAVIRLKDHLHRYPKFNRAGN
IYGKSLVKYLTMRLDDETNQLLIAAKNRSGWCKTDEAADRVIDHLIKFPDFYNSEIFREA
DKEEDITFNTL
Sequence of entity 6 (H), FASTA
>9F12_6 Multifunctional conjugation protein TraI (chains H)
MEFELGTMMSIAQVRSAGSAGNFYTDKDNYYVLGSMGERWAGRGAEQLGLQGSVDKDVFT
RLLEGRLPDGADLSRMQDGSNRHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFA
VRQVEALASTRVMTDGQSETVLTGNLVMALFNHDTSRDQEPQLHTHAVVANVTQHNGEWK
TLSSDKVGKTGFIENVYANQIAFGRLYREKLKEQVEALGYETEVVGKHGMWEMPGVPVEA
FSGRSQTIREAVGEDASLKSRDVAALDTRKSKQHVDPEIKMAEWMQTLKETGFDIRAYRD
AADQRADLRTLTPGPASQDGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPENGV
IERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSV
PRTAGYSDAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMAREQGREVQIIAADRRSQ
MNMKQDERLSGELITGRRQLLEGMAFTPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVL
ITDSGQRTGTGSALMAMKDAGVNTYRWQGGEQRPATIISEPDRNVRYARLAGDFAASVKA
GEESVAQVSGVREQAILTQAIRSELKTQGVLGLPEVTMTALSPVWLDSRSRYLRDMYRPG
MVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDAQGETQVVRISSLDSSWSLFRPEKMPVA
DGERLRVTGKIPGLRVSGGDRLQVASVSEDAMTVVVPGRAEPATLPVSDSPFTALKLENG
WVETPGHSVSDSATVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSF
TVVSEQIKTRAGETSLETAISHQKSALHTPAQQAIHLALPVVESKKLAFSMVDLLTEAKS
FAAEGTGFTELGGEINAQIKRGDLLYVDVAKGYGTGLLVSRASYEAEKSILRHILEGKEA
VMPLMERVPGELMEKLTSGQRAATRMILETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLP
ESERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDTQLQQRSGETPDFSNTLFLLDESS
MVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSAADVAIMKEIVRQT
PELREAVYSLINRDVERALSGLESVKPSQVPRQEGAWAPEHSVTEFSHSQEAKLAEAQQK
AMLKGEAFPDVPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDVREKAGE
LGKEQVMVPVLNTANIRDGELRRLSTWETHRDALVLVDNVYHRIAGISKDDGLITLQDAE
GNTRLISPREAVAEGVTLYTPDTIRVGTGDRMRFTKSDRERGYVANSVWTVTAVSGDSVT
LSDGQQTREIRPGQEQAEQHIDLAYAITAHGAQGASETFAIALEGTEGNRKLMAGFESAY
VALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVFEPKPDREVMNAERLFSTARELRD
VAAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGKSAGIWLNPLTTDDGNG
LRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGEGRP
WNPGAITGGRVWGDIPDNSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMA
ENKPDLPDGKTEQAVREIAGQERDRAAITEREAALPEGVLREPQRVREAVREIARENLLQ
ERLQQMERDMVRDLQKEKTLGGD
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| MG | Magnesium ion | Mg | 1 |
Primary citation
Cryo-EM Structure of the relaxosome, a complex essential for bacterial mating and the spread of antibiotic resistance genes. Williams, S.M., Raffl, S., Kienesberger, S. et al. Nat Commun (2025) 16:4906-4906. DOI 10.1038/s41467-025-60116-6 · PubMed
Other PDB entries of the same protein (UniProt P0A6X7 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 1OWF 1.95 Å, Crystal structure of a mutant IHF (BetaE44A) complexed with the native H' Site
- 2HT0 2.0 Å, IHF bound to doubly nicked DNA
- 1OWG 2.1 Å, Crystal structure of WT IHF complexed with an altered H' site (T44A)
- 1OUZ 2.41 Å, Crystal structure of a mutant IHF (BetaE44A) complexed with a variant H' Site (T44A)
- 2IIE 2.41 Å, single chain Integration Host Factor protein (scIHF2) in complex with DNA
- 1IHF 2.5 Å, Integration host factor/dna complex
- 2IIF 2.72 Å, single chain Integration Host Factor mutant protein (scIHF2-K45aE) in complex with DNA
- 9F10 2.94 Å, CryoEM structure of the F plasmid relaxosome with TraI in its TE mode, without accessory…
- 9F0Z 3.42 Å, CryoEM structure of the F plasmid relaxosome with truncated TraI1-863 in its TE mode,…
- 9F0Y 3.45 Å, CryoEM structure of the F plasmid relaxosome with TraI in its TE mode, derived from the…
- 5WFE 3.64 Å, Cas1-Cas2-IHF-DNA holo-complex
- 9F11 3.68 Å, CryoEM structure of the F plasmid relaxosome with oriT DNA ss-27_+3ds+4_+143 and TraI…
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