7Q5B: Transposon Ty3-G Gag-Pol polyprotein
Cryo-EM structure of Ty3 retrotransposon targeting a TFIIIB-bound tRNA gene. Determined by electron microscopy at 3.98 Å resolution. Released 26 Jan 2022.
- Method
- Electron microscopy
- Resolution
- 3.98 Å
- Organism
- Saccharomyces cerevisiae S288C
- Chains
- 13
- Atoms
- 21,746
- Mol. weight
- 927.78 kDa
- Released
- 26 Jan 2022
Explore 7Q5B in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
7Q5B contains 91 α-helices and 73 β-strands across 7 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 A: 17 helices, 14 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 30-37 | 8 | |
| α-helix | 48-59 | 12 | |
| β-strand | 66-68 | 3 | 1 |
| β-strand | 71-73 | 3 | 1 |
| β-strand | 78 | 1 | 2 |
| α-helix | 82-84 | 3 | |
| α-helix | 85-91 | 7 | |
| α-helix | 104-111 | 8 | |
| β-strand | 115 | 1 | 2 |
| α-helix | 120-128 | 9 | |
| α-helix | 132-137 | 6 | |
| β-strand | 160-165 | 6 | 3 |
| β-strand | 178-184 | 7 | 3 |
| β-strand | 193-195 | 3 | 3 |
| α-helix | 205-213 | 9 | |
| β-strand | 221-224 | 4 | 3 |
| β-strand | 225 | 1 | 4 |
| α-helix | 228-231 | 4 | |
| α-helix | 233-242 | 10 | |
| β-strand | 245-246 | 2 | 3 |
| β-strand | 249 | 1 | 4 |
| α-helix | 254-256 | 3 | |
| α-helix | 259-274 | 16 | |
| α-helix | 282-295 | 14 | |
| α-helix | 305-308 | 4 | |
| α-helix | 335-361 | 27 | |
| α-helix | 389-390 | 2 | |
| β-strand | 402-407 | 6 | 5 |
| β-strand | 410-413 | 4 | 5 |
| β-strand | 424-426 | 3 | 5 |
| α-helix | 427-429 | 3 | |
Chain B: 21 helices, 21 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 30-37 | 8 | |
| α-helix | 48-59 | 12 | |
| β-strand | 66-68 | 3 | 6 |
| β-strand | 71-73 | 3 | 6 |
| β-strand | 78 | 1 | 7 |
| α-helix | 82-84 | 3 | |
| α-helix | 85-93 | 9 | |
| α-helix | 95-97 | 3 | |
| α-helix | 104-111 | 8 | |
| β-strand | 115 | 1 | 7 |
| α-helix | 120-130 | 11 | |
| α-helix | 134-137 | 4 | |
| α-helix | 142-144 | 3 | |
| β-strand | 145 | 1 | 8 |
| β-strand | 160 | 1 | 9 |
| β-strand | 162-165 | 4 | 10 |
| α-helix | 169-171 | 3 | |
| β-strand | 180-183 | 4 | 10 |
| β-strand | 191-193 | 3 | 10 |
| α-helix | 206-214 | 9 | |
| β-strand | 221 | 1 | 9 |
| α-helix | 233-241 | 9 | |
| β-strand | 245 | 1 | 9 |
| α-helix | 254-257 | 4 | |
| α-helix | 258-274 | 17 | |
| α-helix | 285-295 | 11 | |
| α-helix | 305-310 | 6 | |
| α-helix | 325-327 | 3 | |
| α-helix | 335-361 | 27 | |
| β-strand | 366 | 1 | 8 |
| β-strand | 375-377 | 3 | 11 |
| β-strand | 400-401 | 2 | 11 |
| β-strand | 402-407 | 6 | 12 |
| β-strand | 410-413 | 4 | 12 |
| β-strand | 424-426 | 3 | 12 |
| β-strand | 431-432 | 2 | 11 |
| α-helix | 450-453 | 4 | |
| β-strand | 458-464 | 7 | 13 |
| β-strand | 471-475 | 5 | 13 |
| β-strand | 486 | 1 | 13 |
| α-helix | 488-490 | 3 | |
| α-helix | 500-503 | 4 | |
Chain C: 15 helices, 15 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 29-33 | 5 | |
| α-helix | 48-59 | 12 | |
| β-strand | 78 | 1 | 14 |
| α-helix | 85-93 | 9 | |
| α-helix | 104-111 | 8 | |
| β-strand | 115 | 1 | 14 |
| α-helix | 120-131 | 12 | |
| β-strand | 160-164 | 5 | 15 |
| β-strand | 180-184 | 5 | 15 |
| β-strand | 192-193 | 2 | 15 |
| α-helix | 205-212 | 8 | |
| β-strand | 221-222 | 2 | 15 |
| α-helix | 234-241 | 8 | |
| α-helix | 259-274 | 16 | |
| α-helix | 286-295 | 10 | |
| α-helix | 305-308 | 4 | |
| α-helix | 330-339 | 10 | |
| α-helix | 342-351 | 10 | |
| β-strand | 375-378 | 4 | 16 |
| β-strand | 399-401 | 3 | 16 |
| β-strand | 402-407 | 6 | 17 |
| β-strand | 410-413 | 4 | 17 |
| β-strand | 424-425 | 2 | 17 |
| α-helix | 427-429 | 3 | |
| β-strand | 430-431 | 2 | 16 |
| α-helix | 448-453 | 6 | |
| β-strand | 458-464 | 7 | 18 |
| β-strand | 471-475 | 5 | 18 |
| β-strand | 484-486 | 3 | 18 |
| α-helix | 497-510 | 14 | |
Chain D: 12 helices, 12 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 29-33 | 5 | |
| α-helix | 48-59 | 12 | |
| β-strand | 66-68 | 3 | 19 |
| β-strand | 71-73 | 3 | 19 |
| β-strand | 78 | 1 | 19 |
| α-helix | 85-93 | 9 | |
| α-helix | 95-97 | 3 | |
| α-helix | 104-111 | 8 | |
| β-strand | 115 | 1 | 19 |
| α-helix | 120-130 | 11 | |
| β-strand | 160-161 | 2 | 20 |
| β-strand | 162-164 | 3 | 21 |
| β-strand | 178-184 | 7 | 21 |
| β-strand | 189-195 | 7 | 21 |
| α-helix | 204-213 | 10 | |
| β-strand | 221-222 | 2 | 20 |
| α-helix | 234-241 | 8 | |
| β-strand | 247-248 | 2 | 20 |
| α-helix | 259-274 | 16 | |
| α-helix | 286-294 | 9 | |
| β-strand | 298 | 1 | 22 |
| β-strand | 302 | 1 | 22 |
| α-helix | 305-309 | 5 | |
| α-helix | 335-362 | 28 | |
Chain X: 5 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 422-434 | 13 | |
| α-helix | 439-445 | 7 | |
| α-helix | 451-464 | 14 | |
| α-helix | 466-475 | 10 | |
| α-helix | 482-488 | 7 | |
Chain Y: 5 helices, 11 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 63-65 | 3 | |
| β-strand | 66-75 | 10 | 23 |
| α-helix | 83-87 | 5 | |
| β-strand | 92-93 | 2 | 23 |
| β-strand | 102-104 | 3 | 23 |
| β-strand | 114-115 | 2 | 23 |
| β-strand | 120-126 | 7 | 23 |
| α-helix | 129-146 | 18 | |
| β-strand | 156-165 | 10 | 23 |
| α-helix | 173-178 | 6 | |
| β-strand | 183-186 | 4 | 23 |
| β-strand | 190-196 | 7 | 23 |
| β-strand | 203-206 | 4 | 23 |
| β-strand | 211-215 | 5 | 23 |
| β-strand | 217 | 1 | 23 |
| α-helix | 221-236 | 16 | |
Chain Z: 16 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 72-94 | 23 | |
| α-helix | 98-113 | 16 | |
| α-helix | 122-136 | 15 | |
| α-helix | 143-146 | 4 | |
| α-helix | 154-168 | 15 | |
| α-helix | 173-175 | 3 | |
| α-helix | 179-185 | 7 | |
| α-helix | 197-210 | 14 | |
| α-helix | 220-234 | 15 | |
| α-helix | 242-246 | 5 | |
| α-helix | 252-265 | 14 | |
| α-helix | 288-293 | 6 | |
| α-helix | 449-454 | 6 | |
| α-helix | 477-479 | 3 | |
| α-helix | 480-490 | 11 | |
| α-helix | 493-496 | 4 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| DNA (56-mer) | R | DNA | 56 | Saccharomyces cerevisiae S288C | |
| DNA (31-mer) | S | DNA | 31 | Saccharomyces cerevisiae S288C | |
| DNA (34-mer) | r | DNA | 34 | Saccharomyces cerevisiae S288C | |
| DNA (9-mer) | s | DNA | 9 | Saccharomyces cerevisiae S288C | |
| Transposon Ty3-G Gag-Pol polyprotein | A, B, C, D | protein | 1547 | Saccharomyces cerevisiae S288C | Q99315 (AlphaFold model) |
| Transcription factor TFIIIB component B'' | X | protein | 594 | Saccharomyces cerevisiae S288C | P46678 (AlphaFold model) |
| TATA-box-binding protein | Y | protein | 240 | Saccharomyces cerevisiae S288C | P13393 (AlphaFold model) |
| Transcription factor IIIB 70 kDa subunit | Z | protein | 596 | Saccharomyces cerevisiae S288C | P29056 (AlphaFold model) |
| DNA (19-mer) | t, u | DNA | 19 | Saccharomyces cerevisiae S288C | |
Sequence of entity 1 (R), FASTA
>7Q5B_1 DNA (56-MER) (chains R)
GAGCCCGTAATACAACAGATTTTTTCTCTTAGTTTTAAATTTTTATATTTCGTCGA
Sequence of entity 2 (S), FASTA
>7Q5B_2 DNA (31-MER) (chains S)
GAGCCCGTAATACAACAAAATCCAACAAATA
Sequence of entity 3 (r), FASTA
>7Q5B_3 DNA (34-MER) (chains r)
TCGACGAAATATAAAAATTTAAAACTAAGAGAAA
Sequence of entity 4 (s), FASTA
>7Q5B_4 DNA (9-MER) (chains s)
TATTTGTTG
Sequence of entity 5 (A, B, C, D), FASTA
>7Q5B_5 Transposon Ty3-G Gag-Pol polyprotein (chains A, B, C, D)
MSFMDQIPGGGNYPKLPVECLPNFPIQPSLTFRGRNDSHKLKNFISEIMLNMSMISWPND
ASRIVYCRRHLLNPAAQWANDFVQEQGILEITFDTFIQGLYQHFYKPPDINKIFNAITQL
SEAKLGIERLNQRFRKIWDRMPPDFMTEKAAIMTYTRLLTKETYNIVRMHKPETLKDAME
EAYQTTALTERFFPGFELDADGDTIIGATTHLQEEYDSDYDSEDNLTQNGYVHTVRTRRS
YNKPMSNHRNRRNNNPSREECIKNRLCFYCKKEGHRLNECRARKAVLTDLELESKDQQTP
FIKTLPIVHYIAIPEMDNTAEKTIKIQNTKVKTLFDSGSPTSFIRRDIVELLKYEIYETP
PLRFRGFVATKSAVTSEAVTIDLKINDLHITLAAYILDNMDYQLLIGNPILRRYPKILHT
VLNTRESPDSLKPKTYRSETVNNVRTYSAGNRGNPRNIKLSFAPTILEATDPKSAGNRGD
SRTKTLSLATTTPAAIDPLTTLDNPGSTQSTFAQFPIPEEASILEEDGKYSNVVSTIQSV
EPNATDHSNKDTFCTLPVWLQQKYREIIRNDLPPRPADINNIPVKHDIEIKPGARLPRLQ
PYHVTEKNEQEINKIVQKLLDNKFIVPSKSPCSSPVVLVPKKDGTFRLCVDYRTLNKATI
SDPFPLPRIDNLLSRIGNAQIFTTLDLHSGYHQIPMEPKDRYKTAFVTPSGKYEYTVMPF
GLVNAPSTFARYMADTFRDLRFVNVYLDDILIFSESPEEHWKHLDTVLERLKNENLIVKK
KKCKFASEETEFLGYSIGIQKIAPLQHKCAAIRDFPTPKTVKQAQRFLGMINYYRRFIPN
CSKIAQPIQLFICDKSQWTEKQDKAIDKLKDALCNSPVLVPFNNKANYRLTTDASKDGIG
AVLEEVDNKNKLVGVVGYFSKSLESAQKNYPAGELELLGIIKALHHFRYMLHGKHFTLRT
DHISLLSLQNKNEPARRVQRWLDDLATYDFTLEYLAGPKNVVADAISRAVYTITPETSRP
IDTESWKSYYKSDPLCSAVLIHMKELTQHNVTPEDMSAFRSYQKKLELSETFRKNYSLED
EMIYYQDRLVVPIKQQNAVMRLYHDHTLFGGHFGVTVTLAKISPIYYWPKLQHSIIQYIR
TCVQCQLIKSHRPRLHGLLQPLPIAEGRWLDISMDFVTGLPPTSNNLNMILVVVDRFSKR
AHFIATRKTLDATQLIDLLFRYIFSYHGFPRTITSDRDVRMTADKYQELTKRLGIKSTMS
SANHPQTDGQSERTIQTLNRLLRAYASTNIQNWHVYLPQIEFVYNSTPTRTLGKSPFEID
LGYLPNTPAIKSDDEVNARSFTAVELAKHLKALTIQTKEQLEHAQIEMETNNNQRRKPLL
LNIGDHVLVHRDAYFKKGAYMKVQQIYVGPFRVVKKINDNAYELDLNSHKKKHRVINVQF
LKKFVYRPDAYPKNKPISSTERIKRAHEVTALIGIDTTHKTYLCHMQDVDPTLSVEYSEA
EFCQIPERTRRSILANFRQLYETQDNPEREEDVVSQNEICQYDNTSP
Sequence of entity 6 (X), FASTA
>7Q5B_6 Transcription factor TFIIIB component B'' (chains X)
MSSIVNKSGTRFAPKVRQRRAATGGTPTPKPRTPQLFIPESKEIEEDNSDNDKGVDENET
AIVEKPSLVGERSLEGFTLTGTNGHDNEIGDEGPIDASTQNPKADVIEDNVTLKPAPLQT
HRDQKVPRSSRLASLSKDNESRPSFKPSFLDSSSNSNGTARRLSTISNKLPKKIRLGSIT
ENDMNLKTFKRHRVLGKPSSAKKPAGAHRISIVSKISPPTAMTDSLDRNEFSSETSTSRE
ADENENYVISKVKDIPKKVRDGESAKYFIDEENFTMAELCKPNFPIGQISENFEKSKMAK
KAKLEKRRHLRELRMRARQEFKPLHSLTKEEQEEEEEKRKEERDKLLNADIPESDRKAHT
AIQLKLNPDGTMAIDEETMVVDRHKNASIENEYKEKVDENPFANLYNYGSYGRGSYTDPW
TVEEMIKFYKALSMWGTDFNLISQLYPYRSRKQVKAKFVNEEKKRPILIELALRSKLPPN
FDEYCCEIKKNIGTVADFNEKLIELQNEHKHHMKEIEEAKNTAKEEDQTAQRLNDANLNK
KGSGGIMTNDLKVYRKTEVVLGTIDDLKRKKLKERNNDDNEDNEGSEEEPEIDQ
Sequence of entity 7 (Y), FASTA
>7Q5B_7 TATA-box-binding protein (chains Y)
MADEERLKEFKEANKIVFDPNTRQVWENQNRDGTKPATTFQSEEDIKRAAPESEKDTSAT
SGIVPTLQNIVATVTLGCRLDLKTVALHARNAEYNPKRFAAVIMRIREPKTTALIFASGK
MVVTGAKSEDDSKLASRKYARIIQKIGFAAKFTDFKIQNIVGSCDVKFPIRLEGLAFSHG
TFSSYEPELFPGLIYRMVKPKIVLLIFVSGKIVLTGAKQREEIYQAFEAIYPVLSEFRKM
Sequence of entity 8 (Z), FASTA
>7Q5B_8 Transcription factor IIIB 70 kDa subunit (chains Z)
MPVCKNCHGTEFERDLSNANNDLVCKACGVVSEDNPIVSEVTFGETSAGAAVVQGSFIGA
GQSHAAFGGSSALESREATLNNARRKLRAVSYALHIPEYITDAAFQWYKLALANNFVQGR
RSQNVIASCLYVACRKEKTHHMLIDFSSRLQVSVYSIGATFLKMVKKLHITELPLADPSL
FIQHFAEKLDLADKKIKVVKDAVKLAQRMSKDWMFEGRRPAGIAGACILLACRMNNLRRT
HTEIVAVSHVAEETLQQRLNEFKNTKAAKLSVQKFRENDVEDGEARPPSFVKNRKKERKI
KDSLDKEEMFQTSEEALNKNPILTQVLGEQELSSKEVLFYLKQFSERRARVVERIKATNG
IDGENIYHEGSENETRKRKLSEVSIQNEHVEGEDKETEGTEEKVKKVKTKTSEEKKENES
GHFQDAIDGYSLETDPYCPRNLHLLPTTDTYLSKVSDDPDNLEDVDDEELNAHLLNEEAS
KLKERIWIGLNADFLLEQESKRLKQEADIATGNTSVKKKRTRRRNNTRSDEPTKTVDAAA
AIGLMSDLQDKSGLHAALKAAEESGDFTTADSVKNMLQKASFSKKINYDAIDGLFR
Sequence of entity 9 (t, u), FASTA
>7Q5B_9 DNA (19-MER) (chains t, u)
GGTGTTGTATTACGGGCTC
Primary citation
Structural basis of Ty3 retrotransposon integration at RNA Polymerase III-transcribed genes. Abascal-Palacios, G., Jochem, L., Pla-Prats, C. et al. Nat Commun (2021) 12:6992-6992. DOI 10.1038/s41467-021-27338-w · PubMed
Other PDB entries of the same protein (UniProt Q99315 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 4OL8 3.1 Å, Ty3 reverse transcriptase bound to DNA/RNA
Browse structure collections
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