7U1P: RFC:PCNA
RFC:PCNA bound to DNA with a ssDNA gap of five nucleotides. Determined by electron microscopy at 3.0 Å resolution. Released 6 Jul 2022.
- Method
- Electron microscopy
- Resolution
- 3.0 Å
- Organisms
- Saccharomyces cerevisiae, synthetic construct
- Chains
- 11
- Atoms
- 22,727
- Mol. weight
- 369.57 kDa
- Ligands
- ADP, MG, AGS
- Released
- 6 Jul 2022
Explore 7U1P in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
7U1P contains 161 α-helices and 110 β-strands across 8 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: 48 helices, 14 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 150-152 | 3 | |
| β-strand | 162-164 | 3 | 1 |
| α-helix | 174-182 | 9 | |
| β-strand | 187-188 | 2 | 1 |
| β-strand | 198-200 | 3 | 1 |
| α-helix | 207-216 | 10 | |
| β-strand | 219-221 | 3 | 1 |
| α-helix | 223-232 | 10 | |
| α-helix | 234 | 1 | |
| α-helix | 241-276 | 36 | |
| α-helix | 293-295 | 3 | |
| α-helix | 298-301 | 4 | |
| α-helix | 307-309 | 3 | |
| α-helix | 314-325 | 12 | |
| α-helix | 327-332 | 6 | |
| β-strand | 348-352 | 5 | 2 |
| α-helix | 359-370 | 12 | |
| α-helix | 372 | 1 | |
| β-strand | 373-378 | 6 | 2 |
| α-helix | 385-396 | 12 | |
| β-strand | 398 | 1 | 3 |
| α-helix | 401-405 | 5 | |
| α-helix | 414-416 | 3 | |
| β-strand | 419-424 | 6 | 2 |
| α-helix | 426-428 | 3 | |
| α-helix | 430-431 | 2 | |
| α-helix | 436-445 | 10 | |
| β-strand | 451-455 | 5 | 2 |
| α-helix | 461-466 | 6 | |
| β-strand | 470-474 | 5 | 2 |
| α-helix | 475-479 | 5 | |
| α-helix | 480-493 | 14 | |
| β-strand | 497-498 | 2 | 4 |
| α-helix | 500-502 | 3 | |
| α-helix | 503-510 | 8 | |
| α-helix | 514-524 | 11 | |
| β-strand | 530-531 | 2 | 4 |
| α-helix | 536-543 | 8 | |
| α-helix | 547-550 | 4 | |
| α-helix | 551-558 | 8 | |
| α-helix | 566-571 | 6 | |
| α-helix | 574-583 | 10 | |
| α-helix | 588-595 | 8 | |
| β-strand | 599-601 | 3 | 5 |
| α-helix | 604-605 | 2 | |
| α-helix | 610-631 | 22 | |
| α-helix | 638-640 | 3 | |
| α-helix | 641-645 | 5 | |
| α-helix | 646-650 | 5 | |
| α-helix | 651-655 | 5 | |
| β-strand | 658-660 | 3 | 5 |
| α-helix | 665-667 | 3 | |
| α-helix | 669-689 | 21 | |
| α-helix | 698-700 | 3 | |
| α-helix | 701-705 | 5 | |
| α-helix | 706-719 | 14 | |
| α-helix | 722-724 | 3 | |
| α-helix | 725-734 | 10 | |
| α-helix | 739-746 | 8 | |
| α-helix | 751-753 | 3 | |
| α-helix | 756-761 | 6 | |
| α-helix | 764-777 | 14 | |
Chain B: 27 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 8-10 | 3 | |
| α-helix | 11-14 | 4 | |
| α-helix | 20-22 | 3 | |
| α-helix | 27-39 | 13 | |
| α-helix | 42-44 | 3 | |
| β-strand | 45-48 | 4 | 6 |
| α-helix | 56-67 | 12 | |
| α-helix | 68-70 | 3 | |
| α-helix | 71-74 | 4 | |
| β-strand | 75-77 | 3 | 6 |
| α-helix | 86-87 | 2 | |
| α-helix | 88-93 | 6 | |
| α-helix | 94-98 | 5 | |
| β-strand | 99 | 1 | 7 |
| β-strand | 109-113 | 5 | 6 |
| α-helix | 116-118 | 3 | |
| α-helix | 121-133 | 13 | |
| β-strand | 138-144 | 7 | 6 |
| α-helix | 147-149 | 3 | |
| α-helix | 152-156 | 5 | |
| β-strand | 159-162 | 4 | 6 |
| α-helix | 165-167 | 3 | |
| α-helix | 168-182 | 15 | |
| β-strand | 186 | 1 | 8 |
| α-helix | 188-198 | 11 | |
| α-helix | 202-215 | 14 | |
| β-strand | 219 | 1 | 8 |
| α-helix | 221-227 | 7 | |
| α-helix | 229-231 | 3 | |
| α-helix | 232-240 | 9 | |
| α-helix | 245-251 | 7 | |
| α-helix | 252-257 | 6 | |
| α-helix | 263-276 | 14 | |
| α-helix | 282-301 | 20 | |
| α-helix | 306-320 | 15 | |
Chain C: 20 helices, 8 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 | 9 |
| α-helix | 59-71 | 13 | |
| β-strand | 79-83 | 5 | 9 |
| α-helix | 90-92 | 3 | |
| α-helix | 93-97 | 5 | |
| α-helix | 98-102 | 5 | |
| β-strand | 103 | 1 | 10 |
| β-strand | 112-117 | 6 | 9 |
| α-helix | 119-121 | 3 | |
| α-helix | 124-136 | 13 | |
| β-strand | 141-146 | 6 | 9 |
| β-strand | 162-165 | 4 | 9 |
| α-helix | 167-169 | 3 | |
| α-helix | 171-184 | 14 | |
| β-strand | 189 | 1 | 11 |
| α-helix | 191-201 | 11 | |
| α-helix | 205-218 | 14 | |
| β-strand | 227 | 1 | 11 |
| α-helix | 229-236 | 8 | |
| α-helix | 238-240 | 3 | |
| α-helix | 241-253 | 13 | |
| α-helix | 256-270 | 15 | |
| α-helix | 274-287 | 14 | |
| α-helix | 293-311 | 19 | |
| α-helix | 316-332 | 17 | |
Chain D: 24 helices, 10 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 15-23 | 9 | |
| α-helix | 27-30 | 4 | |
| α-helix | 36-38 | 3 | |
| α-helix | 43-54 | 12 | |
| α-helix | 58-60 | 3 | |
| β-strand | 61-64 | 4 | 12 |
| α-helix | 71-83 | 13 | |
| α-helix | 85-91 | 7 | |
| β-strand | 92-95 | 4 | 12 |
| α-helix | 103-104 | 2 | |
| α-helix | 105-110 | 6 | |
| α-helix | 111-115 | 5 | |
| β-strand | 116 | 1 | 13 |
| α-helix | 117-122 | 6 | |
| α-helix | 123-128 | 6 | |
| β-strand | 135-140 | 6 | 12 |
| α-helix | 142-144 | 3 | |
| α-helix | 147-159 | 13 | |
| β-strand | 164-170 | 7 | 12 |
| α-helix | 178-183 | 6 | |
| β-strand | 185-188 | 4 | 12 |
| β-strand | 192 | 1 | 14 |
| α-helix | 194-207 | 14 | |
| β-strand | 212 | 1 | 15 |
| α-helix | 216-224 | 9 | |
| β-strand | 226 | 1 | 14 |
| α-helix | 228-245 | 18 | |
| β-strand | 251 | 1 | 15 |
| α-helix | 253-259 | 7 | |
| α-helix | 265-276 | 12 | |
| α-helix | 280-290 | 11 | |
| α-helix | 297-310 | 14 | |
| α-helix | 316-333 | 18 | |
| α-helix | 339-352 | 14 | |
Chain E: 19 helices, 9 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 13-15 | 3 | |
| α-helix | 20-31 | 12 | |
| β-strand | 39-42 | 4 | 16 |
| α-helix | 49-60 | 12 | |
| α-helix | 63-66 | 4 | |
| β-strand | 69-76 | 8 | 16 |
| β-strand | 82-89 | 8 | 16 |
| β-strand | 93-96 | 4 | 16 |
| α-helix | 105-108 | 4 | |
| α-helix | 109-113 | 5 | |
| α-helix | 114-119 | 6 | |
| β-strand | 136-140 | 5 | 16 |
| α-helix | 148-160 | 13 | |
| β-strand | 165-170 | 6 | 16 |
| α-helix | 179-184 | 6 | |
| β-strand | 186-189 | 4 | 16 |
| α-helix | 191-194 | 4 | |
| α-helix | 195-209 | 15 | |
| β-strand | 212-213 | 2 | 17 |
| α-helix | 217-224 | 8 | |
| α-helix | 230-243 | 14 | |
| β-strand | 247-248 | 2 | 17 |
| α-helix | 252-254 | 3 | |
| α-helix | 258-272 | 15 | |
| α-helix | 276-290 | 15 | |
| α-helix | 296-308 | 13 | |
| α-helix | 315-333 | 19 | |
| α-helix | 339-352 | 14 | |
Chain F: 8 helices, 21 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-6 | 5 | 18 |
| α-helix | 9-19 | 11 | |
| β-strand | 25-30 | 6 | 19 |
| β-strand | 35-40 | 6 | 19 |
| β-strand | 46-51 | 6 | 19 |
| β-strand | 57-59 | 3 | 18 |
| β-strand | 62 | 1 | 18 |
| β-strand | 66-71 | 6 | 19 |
| α-helix | 72-79 | 8 | |
| β-strand | 87-92 | 6 | 18 |
| β-strand | 99-105 | 7 | 18 |
| β-strand | 110-116 | 7 | 18 |
| β-strand | 119 | 1 | 13 |
| β-strand | 135-140 | 6 | 19 |
| α-helix | 141-151 | 11 | |
| β-strand | 157-163 | 7 | 20 |
| β-strand | 166-172 | 7 | 20 |
| β-strand | 176-182 | 7 | 20 |
| α-helix | 191-193 | 3 | |
| β-strand | 196-199 | 4 | 19 |
| β-strand | 203-208 | 6 | 20 |
| α-helix | 209-215 | 7 | |
| α-helix | 216-220 | 5 | |
| β-strand | 224-229 | 6 | 19 |
| β-strand | 235-240 | 6 | 19 |
| β-strand | 245-250 | 6 | 19 |
| α-helix | 252 | 1 | |
| β-strand | 253 | 1 | 10 |
| α-helix | 254 | 1 | |
Chain G: 9 helices, 22 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-6 | 5 | 20 |
| α-helix | 9-18 | 10 | |
| β-strand | 25-31 | 7 | 21 |
| β-strand | 34-40 | 7 | 21 |
| β-strand | 46-53 | 8 | 21 |
| α-helix | 54-56 | 3 | |
| β-strand | 57-59 | 3 | 20 |
| β-strand | 62 | 1 | 20 |
| β-strand | 66-71 | 6 | 21 |
| α-helix | 72-81 | 10 | |
| β-strand | 87-92 | 6 | 20 |
| β-strand | 98-104 | 7 | 20 |
| β-strand | 111-117 | 7 | 20 |
| α-helix | 118 | 1 | |
| β-strand | 119 | 1 | 7 |
| β-strand | 135-140 | 6 | 21 |
| α-helix | 141-154 | 14 | |
| β-strand | 157-162 | 6 | 22 |
| β-strand | 167-172 | 6 | 22 |
| β-strand | 177-182 | 6 | 22 |
| β-strand | 196-199 | 4 | 21 |
| β-strand | 203-208 | 6 | 22 |
| α-helix | 209-216 | 8 | |
| β-strand | 224-229 | 6 | 21 |
| α-helix | 234 | 1 | |
| β-strand | 235-240 | 6 | 21 |
| β-strand | 244-250 | 7 | 21 |
| α-helix | 251 | 1 | |
| β-strand | 252 | 1 | 22 |
| β-strand | 253 | 1 | 3 |
| α-helix | 254 | 1 | |
Chain H: 6 helices, 18 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-5 | 4 | 22 |
| α-helix | 9-17 | 9 | |
| β-strand | 25-30 | 6 | 23 |
| β-strand | 35-40 | 6 | 23 |
| β-strand | 46-52 | 7 | 23 |
| α-helix | 54-56 | 3 | |
| β-strand | 59-62 | 4 | 22 |
| β-strand | 66-71 | 6 | 23 |
| α-helix | 72-79 | 8 | |
| β-strand | 87-92 | 6 | 22 |
| β-strand | 98-104 | 7 | 22 |
| β-strand | 110-117 | 8 | 22 |
| β-strand | 135-140 | 6 | 23 |
| α-helix | 141-151 | 11 | |
| β-strand | 157-162 | 6 | 18 |
| β-strand | 167-170 | 4 | 18 |
| β-strand | 176-182 | 7 | 18 |
| β-strand | 196-199 | 4 | 23 |
| β-strand | 203-208 | 6 | 18 |
| α-helix | 209-215 | 7 | |
| α-helix | 216-220 | 5 | |
| β-strand | 224-229 | 6 | 23 |
| β-strand | 235-240 | 6 | 23 |
| β-strand | 244-250 | 7 | 23 |
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 |
| Proliferating cell nuclear antigen | F, G, H | protein | 264 | Saccharomyces cerevisiae | P15873 |
| DNA - Primer | I | DNA | 25 | synthetic construct | |
| DNA - Template | J | DNA | 50 | synthetic construct | |
| DNA - non primer | K | DNA | 20 | synthetic construct | |
Sequence of entity 1 (A), FASTA
>7U1P_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
>7U1P_2 Replication factor C subunit 4 (chains B)
MSKTLSLQLPWVEKYRPQVLSDIVGNKETIDRLQQIAKDGNMPHMIISGMPGIGKTTSVH
CLAHELLGRSYADGVLELNASDDRGIDVVRNQIKHFAQKKLHLPPGKHKIVILDEADSMT
AGAQQALRRTMELYSNSTRFAFACNQSNKIIEPLQSRCAILRYSKLSDEDVLKRLLQIIK
LEDVKYTNDGLEAIIFTAEGDMRQAINNLQSTVAGHGLVNADNVFKIVDSPHPLIVKKML
LASNLEDSIQILRTDLWKKGYSSIDIVTTSFRVTKNLAQVKESVRLEMIKEIGLTHMRIL
EGVGTYLQLASMLAKIHKLNNKA
Sequence of entity 3 (C), FASTA
>7U1P_3 Replication factor C subunit 3 (chains C)
MSTSTEKRSKENLPWVEKYRPETLDEVYGQNEVITTVRKFVDEGKLPHLLFYGPPGTGKT
STIVALAREIYGKNYSNMVLELNASDDRGIDVVRNQIKDFASTRQIFSKGFKLIILDEAD
AMTNAAQNALRRVIERYTKNTRFCVLANYAHKLTPALLSRCTRFRFQPLPQEAIERRIAN
VLVHEKLKLSPNAEKALIELSNGDMRRVLNVLQSCKATLDNPDEDEISDDVIYECCGAPR
PSDLKAVLKSILEDDWGTAHYTLNKVRSAKGLALIDLIEGIVKILEDYELQNEETRVHLL
TKLADIEYSISKGGNDQIQGSAVIGAIKASFENETVKANV
Sequence of entity 4 (D), FASTA
>7U1P_4 Replication factor C subunit 2 (chains D)
MFEGFGPNKKRKISKLAAEQSLAQQPWVEKYRPKNLDEVTAQDHAVTVLKKTLKSANLPH
MLFYGPPGTGKTSTILALTKELYGPDLMKSRILELNASDERGISIVREKVKNFARLTVSK
PSKHDLENYPCPPYKIIILDEADSMTADAQSALRRTMETYSGVTRFCLICNYVTRIIDPL
ASRCSKFRFKALDASNAIDRLRFISEQENVKCDDGVLERILDISAGDLRRGITLLQSASK
GAQYLGDGKNITSTQVEELAGVVPHDILIEIVEKVKSGDFDEIKKYVNTFMKSGWSAASV
VNQLHEYYITNDNFDTNFKNQISWLLFTTDSRLNNGTNEHIQLLNLLVKISQL
Sequence of entity 5 (E), FASTA
>7U1P_5 Replication factor C subunit 5 (chains E)
MSLWVDKYRPKSLNALSHNEELTNFLKSLSDQPRDLPHLLLYGPNGTGKKTRCMALLESI
FGPGVYRLKIDVRQFVTASNRKLELNVVSSPYHLEITPSDMGNNDRIVIQELLKEVAQME
QVDFQDSKDGLAHRYKCVIINEANSLTKDAQAALRRTMEKYSKNIRLIMVCDSMSPIIAP
IKSRCLLIRCPAPSDSEISTILSDVVTNERIQLETKDILKRIAQASNGNLRVSLLMLESM
ALNNELALKSSSPIIKPDWIIVIHKLTRKIVKERSVNSLIECRAVLYDLLAHCIPANIIL
KELTFSLLDVETLNTTNKSSIIEYSSVFDERLSLGNKAIFHLEGFIAKVMCCLD
Sequence of entity 6 (F, G, H), FASTA
>7U1P_6 Proliferating cell nuclear antigen (chains F, G, H)
GPHMASMLEAKFEEASLFKRIIDGFKDCVQLVNFQCKEDGIIAQAVDDSRVLLVSLEIGV
EAFQEYRCDHPVTLGMDLTSLSKILRCGNNTDTLTLIADNTPDSIILLFEDTKKDRIAEY
SLKLMDIDADFLKIEELQYDSTLSLPSSEFSKIVRDLSQLSDSINIMITKETIKFVADGD
IGSGSVIIKPFVDMEHPETSIKLEMDQPVDLTFGAKYLLDIIKGSSLSDRVGIRLSSEAP
ALFQFDLKSGFLQFFLAPKFNDEE
Sequence of entity 7 (I), FASTA
>7U1P_7 DNA - Primer (chains I)
GGGACGCACGCGGCATTCAAGGACT
Sequence of entity 8 (J), FASTA
>7U1P_8 DNA - Template (chains J)
TTGTGGGTAGATAAATACAGACCTAAGTCCTTGAATGCCGCGTGCGTCCC
Sequence of entity 9 (K), FASTA
>7U1P_9 DNA - non primer (chains K)
CTGTATTTATCTACCCACAA
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ADP | Adenosine-5'-diphosphate | C10 H15 N5 O10 P2 | 2 |
| MG | Magnesium ion | Mg | 4 |
| AGS | Phosphothiophosphoric acid-adenylate ester | C10 H16 N5 O12 P3 S | 3 |
Primary citation
A second DNA binding site on RFC facilitates clamp loading at gapped or nicked DNA. Liu, X., Gaubitz, C., Pajak, J. et al. Elife (2022) 11. DOI 10.7554/eLife.77483 · 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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