7TFK: Atomic model of S. cerevisiae clamp loader RFC
Atomic model of S. cerevisiae clamp loader RFC bound to two DNA molecules, one at the 5'-recessed end and the other at the 3'-recessed end. Determined by electron microscopy at 3.25 Å resolution. Released 16 Nov 2022.
- Method
- Electron microscopy
- Resolution
- 3.25 Å
- Organisms
- Saccharomyces cerevisiae, synthetic construct
- Chains
- 9
- Atoms
- 14,363
- Mol. weight
- 288.61 kDa
- Ligands
- MG, AGS, ADP
- Released
- 16 Nov 2022
Explore 7TFK in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
7TFK contains 109 α-helices and 43 β-strands across 5 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: 25 helices, 10 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 298-301 | 4 | |
| α-helix | 314-325 | 12 | |
| α-helix | 327-332 | 6 | |
| β-strand | 348 | 1 | 1 |
| β-strand | 349-351 | 3 | 2 |
| α-helix | 359-370 | 12 | |
| β-strand | 373-375 | 3 | 2 |
| β-strand | 419-424 | 6 | 2 |
| α-helix | 426-428 | 3 | |
| α-helix | 437-445 | 9 | |
| β-strand | 451-454 | 4 | 2 |
| α-helix | 461-466 | 6 | |
| β-strand | 470 | 1 | 1 |
| α-helix | 478-479 | 2 | |
| α-helix | 482-494 | 13 | |
| β-strand | 497-498 | 2 | 3 |
| α-helix | 500-502 | 3 | |
| α-helix | 503-509 | 7 | |
| α-helix | 514-527 | 14 | |
| β-strand | 530-531 | 2 | 3 |
| α-helix | 533-542 | 10 | |
| α-helix | 548-550 | 3 | |
| α-helix | 551-558 | 8 | |
| α-helix | 566-571 | 6 | |
| α-helix | 574-583 | 10 | |
| α-helix | 588-595 | 8 | |
| β-strand | 599 | 1 | 4 |
| α-helix | 610-631 | 22 | |
| α-helix | 638-640 | 3 | |
| α-helix | 641-645 | 5 | |
| α-helix | 646-650 | 5 | |
| α-helix | 651-654 | 4 | |
| β-strand | 660 | 1 | 4 |
| α-helix | 664-667 | 4 | |
| α-helix | 669-689 | 21 | |
Chain B: 20 helices, 9 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 7-10 | 4 | |
| α-helix | 20-22 | 3 | |
| α-helix | 27-39 | 13 | |
| α-helix | 42-44 | 3 | |
| β-strand | 45-48 | 4 | 5 |
| α-helix | 57-66 | 10 | |
| β-strand | 76-79 | 4 | 5 |
| α-helix | 86-97 | 12 | |
| β-strand | 109-110 | 2 | 6 |
| β-strand | 111-114 | 4 | 5 |
| α-helix | 121-134 | 14 | |
| β-strand | 138-139 | 2 | 6 |
| β-strand | 141-144 | 4 | 5 |
| α-helix | 152-156 | 5 | |
| β-strand | 159-160 | 2 | 5 |
| α-helix | 165-167 | 3 | |
| α-helix | 168-182 | 15 | |
| β-strand | 186 | 1 | 7 |
| α-helix | 188-198 | 11 | |
| α-helix | 202-214 | 13 | |
| β-strand | 219 | 1 | 7 |
| α-helix | 221-227 | 7 | |
| α-helix | 229-231 | 3 | |
| α-helix | 232-240 | 9 | |
| α-helix | 245-252 | 8 | |
| α-helix | 253-257 | 5 | |
| α-helix | 263-275 | 13 | |
| α-helix | 282-301 | 20 | |
| α-helix | 306-320 | 15 | |
Chain C: 23 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 15-18 | 4 | |
| α-helix | 24-26 | 3 | |
| α-helix | 31-43 | 13 | |
| β-strand | 49-52 | 4 | 8 |
| α-helix | 60-70 | 11 | |
| β-strand | 79-82 | 4 | 8 |
| α-helix | 90-92 | 3 | |
| α-helix | 93-97 | 5 | |
| α-helix | 98-102 | 5 | |
| α-helix | 104-105 | 2 | |
| β-strand | 112-116 | 5 | 8 |
| α-helix | 119-121 | 3 | |
| α-helix | 124-136 | 13 | |
| β-strand | 141-147 | 7 | 8 |
| α-helix | 150-152 | 3 | |
| α-helix | 155-160 | 6 | |
| β-strand | 162-165 | 4 | 8 |
| α-helix | 167-169 | 3 | |
| α-helix | 171-185 | 15 | |
| β-strand | 188-189 | 2 | 9 |
| α-helix | 191-201 | 11 | |
| α-helix | 205-218 | 14 | |
| β-strand | 226-227 | 2 | 9 |
| α-helix | 229-236 | 8 | |
| α-helix | 238-240 | 3 | |
| α-helix | 241-253 | 13 | |
| α-helix | 258-270 | 13 | |
| α-helix | 274-283 | 10 | |
| α-helix | 293-312 | 20 | |
| α-helix | 316-332 | 17 | |
Chain D: 23 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 27-29 | 3 | |
| α-helix | 46-54 | 9 | |
| β-strand | 61-64 | 4 | 10 |
| α-helix | 71-91 | 21 | |
| β-strand | 92-95 | 4 | 10 |
| α-helix | 103-105 | 3 | |
| α-helix | 106-110 | 5 | |
| α-helix | 111-115 | 5 | |
| α-helix | 117-122 | 6 | |
| α-helix | 123-128 | 6 | |
| β-strand | 135-140 | 6 | 10 |
| α-helix | 142-144 | 3 | |
| α-helix | 147-152 | 6 | |
| α-helix | 155-159 | 5 | |
| β-strand | 164-169 | 6 | 10 |
| α-helix | 178-183 | 6 | |
| β-strand | 185-188 | 4 | 10 |
| α-helix | 198-207 | 10 | |
| α-helix | 216-223 | 8 | |
| α-helix | 228-245 | 18 | |
| α-helix | 249-252 | 4 | |
| α-helix | 253-260 | 8 | |
| α-helix | 262-264 | 3 | |
| α-helix | 265-277 | 13 | |
| α-helix | 280-291 | 12 | |
| α-helix | 297-308 | 12 | |
| α-helix | 316-334 | 19 | |
| α-helix | 339-351 | 13 | |
Chain E: 18 helices, 12 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 4-7 | 4 | |
| α-helix | 21-31 | 11 | |
| α-helix | 36-38 | 3 | |
| β-strand | 39-42 | 4 | 11 |
| α-helix | 49-61 | 13 | |
| β-strand | 71-72 | 2 | 12 |
| β-strand | 75 | 1 | 13 |
| β-strand | 83 | 1 | 13 |
| β-strand | 86-87 | 2 | 12 |
| β-strand | 88 | 1 | 11 |
| β-strand | 94-95 | 2 | 11 |
| α-helix | 105-116 | 12 | |
| β-strand | 136-140 | 5 | 11 |
| α-helix | 143-145 | 3 | |
| α-helix | 150-160 | 11 | |
| β-strand | 165-170 | 6 | 11 |
| α-helix | 179-183 | 5 | |
| β-strand | 186-189 | 4 | 11 |
| α-helix | 191-193 | 3 | |
| α-helix | 195-208 | 14 | |
| β-strand | 212-213 | 2 | 14 |
| α-helix | 217-226 | 10 | |
| α-helix | 230-243 | 14 | |
| β-strand | 247-248 | 2 | 14 |
| α-helix | 253-255 | 3 | |
| α-helix | 258-272 | 15 | |
| α-helix | 276-291 | 16 | |
| α-helix | 296-307 | 12 | |
| α-helix | 315-333 | 19 | |
| α-helix | 338-353 | 16 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Replication factor C subunit 1 | A | protein | 861 | Saccharomyces cerevisiae | P38630 (AlphaFold model) |
| Replication factor C subunit 4 | B | protein | 323 | Saccharomyces cerevisiae | P40339 (AlphaFold model) |
| Replication factor C subunit 3 | C | protein | 340 | Saccharomyces cerevisiae | P38629 (AlphaFold model) |
| Replication factor C subunit 2 | D | protein | 353 | Saccharomyces cerevisiae | P40348 (AlphaFold model) |
| Replication factor C subunit 5 | E | protein | 354 | Saccharomyces cerevisiae | P38251 |
| Template strand | I, K | DNA | 40 | synthetic construct | |
| Primer strand | J, L | DNA | 20 | synthetic construct | |
Sequence of entity 1 (A), FASTA
>7TFK_1 Replication factor C subunit 1 (chains A)
MVNISDFFGKNKKSVRSSTSRPTRQVGSSKPEVIDLDTESDQESTNKTPKKMPVSNVIDV
SETPEGEKKLPLPAKRKASSPTVKPASSKKTKPSSKSSDSASNITAQDVLDKIPSLDLSN
VHVKENAKFDFKSANSNADPDEIVSEIGSFPEGKPNCLLGLTIVFTGVLPTLERGASEAL
AKRYGARVTKSISSKTSVVVLGDEAGPKKLEKIKQLKIKAIDEEGFKQLIAGMPAEGGDG
EAAEKARRKLEEQHNIATKEAELLVKKEEERSKKLAATRVSGGHLERDNVVREEDKLWTV
KYAPTNLQQVCGNKGSVMKLKNWLANWENSKKNSFKHAGKDGSGVFRAAMLYGPPGIGKT
TAAHLVAQELGYDILEQNASDVRSKTLLNAGVKNALDNMSVVGYFKHNEEAQNLNGKHFV
IIMDEVDGMSGGDRGGVGQLAQFCRKTSTPLILICNERNLPKMRPFDRVCLDIQFRRPDA
NSIKSRLMTIAIREKFKLDPNVIDRLIQTTRGDIRQVINLLSTISTTTKTINHENINEIS
KAWEKNIALKPFDIAHKMLDGQIYSDIGSRNFTLNDKIALYFDDFDFTPLMIQENYLSTR
PSVLKPGQSHLEAVAEAANCISLGDIVEKKIRSSEQLWSLLPLHAVLSSVYPASKVAGHM
AGRINFTAWLGQNSKSAKYYRLLQEIHYHTRLGTSTDKIGLRLDYLPTFRKRLLDPFLKQ
GADAISSVIEVMDDYYLTKEDWDSIMEFFVGPDVTTAIIKKIPATVKSGFTRKYNSMTHP
VAIYRTGSTIGGGGVGTSTSTPDFEDVVDADDNPVPADDEETQDSSTDLKKDKLIKQKAK
PTKRKTATSKPGGSKKRKTKA
Sequence of entity 2 (B), FASTA
>7TFK_2 Replication factor C subunit 4 (chains B)
MSKTLSLQLPWVEKYRPQVLSDIVGNKETIDRLQQIAKDGNMPHMIISGMPGIGKTTSVH
CLAHELLGRSYADGVLELNASDDRGIDVVRNQIKHFAQKKLHLPPGKHKIVILDEADSMT
AGAQQALRRTMELYSNSTRFAFACNQSNKIIEPLQSRCAILRYSKLSDEDVLKRLLQIIK
LEDVKYTNDGLEAIIFTAEGDMRQAINNLQSTVAGHGLVNADNVFKIVDSPHPLIVKKML
LASNLEDSIQILRTDLWKKGYSSIDIVTTSFRVTKNLAQVKESVRLEMIKEIGLTHMRIL
EGVGTYLQLASMLAKIHKLNNKA
Sequence of entity 3 (C), FASTA
>7TFK_3 Replication factor C subunit 3 (chains C)
MSTSTEKRSKENLPWVEKYRPETLDEVYGQNEVITTVRKFVDEGKLPHLLFYGPPGTGKT
STIVALAREIYGKNYSNMVLELNASDDRGIDVVRNQIKDFASTRQIFSKGFKLIILDEAD
AMTNAAQNALRRVIERYTKNTRFCVLANYAHKLTPALLSRCTRFRFQPLPQEAIERRIAN
VLVHEKLKLSPNAEKALIELSNGDMRRVLNVLQSCKATLDNPDEDEISDDVIYECCGAPR
PSDLKAVLKSILEDDWGTAHYTLNKVRSAKGLALIDLIEGIVKILEDYELQNEETRVHLL
TKLADIEYSISKGGNDQIQGSAVIGAIKASFENETVKANV
Sequence of entity 4 (D), FASTA
>7TFK_4 Replication factor C subunit 2 (chains D)
MFEGFGPNKKRKISKLAAEQSLAQQPWVEKYRPKNLDEVTAQDHAVTVLKKTLKSANLPH
MLFYGPPGTGKTSTILALTKELYGPDLMKSRILELNASDERGISIVREKVKNFARLTVSK
PSKHDLENYPCPPYKIIILDEADSMTADAQSALRRTMETYSGVTRFCLICNYVTRIIDPL
ASRCSKFRFKALDASNAIDRLRFISEQENVKCDDGVLERILDISAGDLRRGITLLQSASK
GAQYLGDGKNITSTQVEELAGVVPHDILIEIVEKVKSGDFDEIKKYVNTFMKSGWSAASV
VNQLHEYYITNDNFDTNFKNQISWLLFTTDSRLNNGTNEHIQLLNLLVKISQL
Sequence of entity 5 (E), FASTA
>7TFK_5 Replication factor C subunit 5 (chains E)
MSLWVDKYRPKSLNALSHNEELTNFLKSLSDQPRDLPHLLLYGPNGTGKKTRCMALLESI
FGPGVYRLKIDVRQFVTASNRKLELNVVSSPYHLEITPSDMGNNDRIVIQELLKEVAQME
QVDFQDSKDGLAHRYKCVIINEANSLTKDAQAALRRTMEKYSKNIRLIMVCDSMSPIIAP
IKSRCLLIRCPAPSDSEISTILSDVVTNERIQLETKDILKRIAQASNGNLRVSLLMLESM
ALNNELALKSSSPIIKPDWIIVIHKLTRKIVKERSVNSLIECRAVLYDLLAHCIPANIIL
KELTFSLLDVETLNTTNKSSIIEYSSVFDERLSLGNKAIFHLEGFIAKVMCCLD
Sequence of entity 6 (I, K), FASTA
>7TFK_6 Template strand (chains I, K)
TTTTTTTTTTTATGTACTCGTAGTGTCTGCTTTTTTTTTT
Sequence of entity 7 (J, L), FASTA
>7TFK_7 Primer strand (chains J, L)
GCAGACACTACGAGTACATA
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| MG | Magnesium ion | Mg | 4 |
| AGS | Phosphothiophosphoric acid-adenylate ester | C10 H16 N5 O12 P3 S | 4 |
| ADP | Adenosine-5'-diphosphate | C10 H15 N5 O10 P2 | 1 |
Primary citation
Cryo-EM structures reveal that RFC recognizes both the 3'- and 5'-DNA ends to load PCNA onto gaps for DNA repair. Zheng, F., Georgescu, R., Yao, N.Y. et al. Elife (2022) 11. DOI 10.7554/eLife.77469 · PubMed
Other PDB entries of the same protein (UniProt P38630 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 8DQX 2.1 Å, Open state of RFC:PCNA bound to a 3' ss/dsDNA junction
- 8DR1 2.14 Å, Consensus closed state of RFC:PCNA bound to a 3' ss/dsDNA junction (DNA2)
- 8DR3 2.2 Å, Closed state of RFC:PCNA bound to a 3' ss/dsDNA junction (DNA2) with NTD
- 8DR6 2.39 Å, Closed state of RFC:PCNA bound to a nicked dsDNA
- 8DR0 2.42 Å, Closed state of RFC:PCNA bound to a 3' ss/dsDNA junction
- 8DR4 2.45 Å, Open state of RFC:PCNA bound to a 3' ss/dsDNA junction (DNA2) without NTD
- 9PEO 2.57 Å, Structure of the S. cerevisiae clamp loader Replication Factor C (RFC) with mixed…
- 9PER 2.57 Å, Structure of the S. cerevisiae clamp loader Replication Factor C (RFC) with mixed…
- 9PET 2.57 Å, Structure of the S. cerevisiae clamp loader Replication Factor C (RFC) with mixed…
- 9PES 2.59 Å, Structure of the S. cerevisiae clamp loader Replication Factor C (RFC) with mixed…
- 9PEU 2.62 Å, Structure of the S. cerevisiae clamp loader Replication Factor C (RFC) with mixed…
- 9PEV 2.63 Å, Structure of the S. cerevisiae clamp loader Replication Factor C (RFC) with mixed…
Browse structure collections
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