7STE: Rad24-RFC ADP state
Rad24-RFC ADP state. Determined by electron microscopy at 2.73 Å resolution. Released 6 Apr 2022.
- Method
- Electron microscopy
- Resolution
- 2.73 Å
- Organism
- Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
- Chains
- 5
- Atoms
- 14,249
- Mol. weight
- 236.48 kDa
- Ligands
- ADP, ATP, MG
- Released
- 6 Apr 2022
Explore 7STE in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
7STE contains 110 α-helices and 40 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: 28 helices, 10 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 66-69 | 4 | |
| α-helix | 82-95 | 14 | |
| β-strand | 104-109 | 6 | 9 |
| α-helix | 115-130 | 16 | |
| α-helix | 131-133 | 3 | |
| β-strand | 148 | 1 | 10 |
| α-helix | 165-175 | 11 | |
| α-helix | 178-180 | 3 | |
| β-strand | 183 | 1 | 10 |
| β-strand | 184-185 | 2 | 9 |
| α-helix | 195-210 | 16 | |
| β-strand | 219-224 | 6 | 9 |
| β-strand | 227 | 1 | 11 |
| β-strand | 243 | 1 | 11 |
| α-helix | 246-249 | 4 | |
| α-helix | 252-255 | 4 | |
| β-strand | 260-264 | 5 | 9 |
| α-helix | 267-269 | 3 | |
| α-helix | 270-291 | 22 | |
| α-helix | 297-307 | 11 | |
| α-helix | 311-323 | 13 | |
| α-helix | 335-347 | 13 | |
| α-helix | 356-366 | 11 | |
| α-helix | 369-372 | 4 | |
| α-helix | 375-383 | 9 | |
| α-helix | 384-390 | 7 | |
| α-helix | 394-409 | 16 | |
| α-helix | 414-429 | 16 | |
| α-helix | 439-441 | 3 | |
| β-strand | 443 | 1 | 12 |
| α-helix | 446-471 | 26 | |
| α-helix | 477-479 | 3 | |
| α-helix | 480-484 | 5 | |
| α-helix | 487-502 | 16 | |
| α-helix | 526-528 | 3 | |
| α-helix | 538 | 1 | |
| β-strand | 549 | 1 | 12 |
| α-helix | 565-583 | 19 | |
Chain B: 18 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 8-10 | 3 | |
| α-helix | 11-14 | 4 | |
| α-helix | 27-39 | 13 | |
| β-strand | 45-48 | 4 | 1 |
| α-helix | 55-66 | 12 | |
| β-strand | 75-78 | 4 | 1 |
| α-helix | 86-98 | 13 | |
| β-strand | 109-113 | 5 | 1 |
| α-helix | 121-133 | 13 | |
| β-strand | 138-144 | 7 | 1 |
| α-helix | 152-157 | 6 | |
| β-strand | 159-162 | 4 | 1 |
| α-helix | 167-182 | 16 | |
| β-strand | 186 | 1 | 2 |
| α-helix | 188-198 | 11 | |
| α-helix | 202-215 | 14 | |
| β-strand | 219 | 1 | 2 |
| α-helix | 221-228 | 8 | |
| α-helix | 231-232 | 2 | |
| α-helix | 233-241 | 9 | |
| α-helix | 245-251 | 7 | |
| α-helix | 252-257 | 6 | |
| α-helix | 263-275 | 13 | |
| α-helix | 282-300 | 19 | |
| α-helix | 306-320 | 15 | |
Chain C: 21 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 | 3 |
| α-helix | 59-71 | 13 | |
| α-helix | 75-78 | 4 | |
| β-strand | 79-83 | 5 | 3 |
| α-helix | 90-102 | 13 | |
| α-helix | 104-105 | 2 | |
| β-strand | 112-117 | 6 | 3 |
| α-helix | 119-121 | 3 | |
| α-helix | 124-136 | 13 | |
| β-strand | 141-147 | 7 | 3 |
| α-helix | 150-152 | 3 | |
| α-helix | 155-160 | 6 | |
| β-strand | 162-165 | 4 | 3 |
| α-helix | 166-170 | 5 | |
| α-helix | 171-184 | 14 | |
| β-strand | 188-189 | 2 | 4 |
| α-helix | 191-201 | 11 | |
| α-helix | 205-218 | 14 | |
| β-strand | 226-227 | 2 | 4 |
| α-helix | 229-236 | 8 | |
| α-helix | 241-253 | 13 | |
| α-helix | 256-270 | 15 | |
| α-helix | 274-285 | 12 | |
| α-helix | 294-311 | 18 | |
| α-helix | 316-332 | 17 | |
Chain D: 23 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 27-30 | 4 | |
| α-helix | 36-38 | 3 | |
| α-helix | 43-55 | 13 | |
| β-strand | 61-64 | 4 | 5 |
| α-helix | 71-80 | 10 | |
| α-helix | 88-91 | 4 | |
| β-strand | 92-95 | 4 | 5 |
| α-helix | 104-115 | 12 | |
| α-helix | 117-122 | 6 | |
| α-helix | 123-128 | 6 | |
| β-strand | 135-139 | 5 | 5 |
| α-helix | 142-144 | 3 | |
| α-helix | 147-159 | 13 | |
| β-strand | 164-170 | 7 | 5 |
| α-helix | 173-175 | 3 | |
| α-helix | 178-181 | 4 | |
| β-strand | 185-188 | 4 | 5 |
| α-helix | 190-193 | 4 | |
| α-helix | 194-208 | 15 | |
| β-strand | 212 | 1 | 6 |
| α-helix | 216-224 | 9 | |
| α-helix | 228-245 | 18 | |
| β-strand | 251 | 1 | 6 |
| α-helix | 253-260 | 8 | |
| α-helix | 262-264 | 3 | |
| α-helix | 265-277 | 13 | |
| α-helix | 280-291 | 12 | |
| α-helix | 297-309 | 13 | |
| α-helix | 316-334 | 19 | |
| α-helix | 339-351 | 13 | |
Chain E: 20 helices, 9 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 4-7 | 4 | |
| α-helix | 13-15 | 3 | |
| α-helix | 20-30 | 11 | |
| α-helix | 33-35 | 3 | |
| β-strand | 39-42 | 4 | 7 |
| α-helix | 49-61 | 13 | |
| β-strand | 69-76 | 8 | 7 |
| β-strand | 82-89 | 8 | 7 |
| β-strand | 93-96 | 4 | 7 |
| α-helix | 98-100 | 3 | |
| α-helix | 106-118 | 13 | |
| β-strand | 136-141 | 6 | 7 |
| α-helix | 143-145 | 3 | |
| α-helix | 148-160 | 13 | |
| β-strand | 165-171 | 7 | 7 |
| α-helix | 179-184 | 6 | |
| β-strand | 186-189 | 4 | 7 |
| α-helix | 191-194 | 4 | |
| α-helix | 195-209 | 15 | |
| β-strand | 212-213 | 2 | 8 |
| α-helix | 217-226 | 10 | |
| α-helix | 230-243 | 14 | |
| β-strand | 247-248 | 2 | 8 |
| α-helix | 252-254 | 3 | |
| α-helix | 258-272 | 15 | |
| α-helix | 276-291 | 16 | |
| α-helix | 296-308 | 13 | |
| α-helix | 315-334 | 20 | |
| α-helix | 338-353 | 16 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Replication factor C subunit 4 | B | protein | 323 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P40339 (AlphaFold model) |
| Replication factor C subunit 3 | C | protein | 339 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P38629 (AlphaFold model) |
| Replication factor C subunit 2 | D | protein | 353 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P40348 (AlphaFold model) |
| Replication factor C subunit 5 | E | protein | 354 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P38251 (AlphaFold model) |
| Checkpoint protein RAD24 | A | protein | 696 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P32641 |
Sequence of entity 1 (B), FASTA
>7STE_1 Replication factor C subunit 4 (chains B)
MSKTLSLQLPWVEKYRPQVLSDIVGNKETIDRLQQIAKDGNMPHMIISGMPGIGKTTSVH
CLAHELLGRSYADGVLELNASDDRGIDVVRNQIKHFAQKKLHLPPGKHKIVILDEADSMT
AGAQQALRRTMELYSNSTRFAFACNQSNKIIEPLQSRCAILRYSKLSDEDVLKRLLQIIK
LEDVKYTNDGLEAIIFTAEGDMRQAINNLQSTVAGHGLVNADNVFKIVDSPHPLIVKKML
LASNLEDSIQILRTDLWKKGYSSIDIVTTSFRVTKNLAQVKESVRLEMIKEIGLTHMRIL
EGVGTYLQLASMLAKIHKLNNKA
Sequence of entity 2 (C), FASTA
>7STE_2 Replication factor C subunit 3 (chains C)
MSTSTEKRSKENLPWVEKYRPETLDEVYGQNEVITTVRKFVDEGKLPHLLFYGPPGTGKT
STIVALAREIYGKNYSNMVLELNASDDRGIDVVRNQIKDFASTRQIFSKGFKLIILDEAD
AMTNAAQNALRRVIERYTKNTRFCVLANYAHKLTPALLSRCTRFRFQPLPQEAIERRIAN
VLVHEKLKLSPNAEKALIELSNGDMRRVLNVLQSCKATLDNPDEDEISDDVIYECCGAPR
PSDLKAVLKSILEDDWGTAHYTLNKVRSAKGLALIDLIEGIVKILEDYELQNEETRVHLL
TKLADIEYSISKGGNDQIQGSAVIGAIKASFENETVKAN
Sequence of entity 3 (D), FASTA
>7STE_3 Replication factor C subunit 2 (chains D)
MFEGFGPNKKRKISKLAAEQSLAQQPWVEKYRPKNLDEVTAQDHAVTVLKKTLKSANLPH
MLFYGPPGTGKTSTILALTKELYGPDLMKSRILELNASDERGISIVREKVKNFARLTVSK
PSKHDLENYPCPPYKIIILDEADSMTADAQSALRRTMETYSGVTRFCLICNYVTRIIDPL
ASRCSKFRFKALDASNAIDRLRFISEQENVKCDDGVLERILDISAGDLRRGITLLQSASK
GAQYLGDGKNITSTQVEELAGVVPHDILIEIVEKVKSGDFDEIKKYVNTFMKSGWSAASV
VNQLHEYYITNDNFDTNFKNQISWLLFTTDSRLNNGTNEHIQLLNLLVKISQL
Sequence of entity 4 (E), FASTA
>7STE_4 Replication factor C subunit 5 (chains E)
MSLWVDKYRPKSLNALSHNEELTNFLKSLSDQPRDLPHLLLYGPNGTGKKTRCMALLESI
FGPGVYRLKIDVRQFVTASNRKLELNVVSSPYHLEITPSDMGNNDRIVIQELLKEVAQME
QVDFQDSKDGLAHRYKCVIINEANSLTKDAQAALRRTMEKYSKNIRLIMVCDSMSPIIAP
IKSRCLLIRCPAPSDSEISTILSDVVTNERIQLETKDILKRIAQASNGNLRVSLLMLESM
ALNNELALKSSSPIIKPDWIIVIHKLTRKIVKERSVNSLIECRAVLYDLLAHCIPANIIL
KELTFSLLDVETLNTTNKSSIIEYSSVFDERLSLGNKAIFHLEGFIAKVMCCLD
Sequence of entity 5 (A), FASTA
>7STE_5 Checkpoint protein RAD24 (chains A)
MDSTNLNKRPLLQYSLSSLGSQITKWSSSRPTSPVRKARSTENDFLSKQDTSSILPSIND
DGGEQWYEKFKPNCLEQVAIHKRKLKDVQEALDAMFLPNAKHRILLLSGPSGCSKSTVIK
ELSKILVPKYRQNSNGTSFRSTPNEHKVTEFRGDCIVNDLPQMESFSEFLKGARYLVMSN
LSLILIEDLPNVFHIDTRRRFQQLILQWLYSSEPLLPPLVICITECEIPENDNNYRKFGI
DYTFSAETIMNKEILMHPRLKRIKFNPINSTLLKKHLKFICVQNMKMLKEKNKWNKRQEV
IDYIAQETGDIRSAITTLQFWATSSGSLPISTRESTISYFHAIGKVIHGSHSTNNDNEMI
NNLFENSNNLLSKEDFKLGILENYNTFNKGEFSISDASSIVDCLSECDNMNGLPESNEYG
LREVRKTFRNISKQGHNHGTVYFPREWKVRKLQNSFKVQAEDWLNVSLYKYNAVHSFRNI
TLEFGYYAPLIRKCQSYKKKYILYYLKNLPSGSSGPKQTMDKFSDIMKVENGIDVVDRIG
GPIEALSVEDGLAPLMDNDSNNCDHLEDQKKERDRRLRMLIDQYERNVMMANDDLEDEET
SFNDDPIVDSDSDNSNNIGNETFGRSDEDESLCEILSQRQPRKAPVISESLSDSDLEILG
LNLEVLFQGPGGDYKDDDDKDYKDDDDKDYKDDDDK
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ADP | Adenosine-5'-diphosphate | C10 H15 N5 O10 P2 | 4 |
| ATP | Adenosine-5'-triphosphate | C10 H16 N5 O13 P3 | 1 |
| MG | Magnesium ion | Mg | 1 |
Primary citation
Mechanisms of loading and release of the 9-1-1 checkpoint clamp. Castaneda, J.C., Schrecker, M., Remus, D. et al. Nat Struct Mol Biol (2022) 29:369-375. DOI 10.1038/s41594-022-00741-7 · PubMed
Other PDB entries of the same protein (UniProt P40339 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 8DQW 2.1 Å, Open state of Rad24-RFC:9-1-1 bound to a 5' ss/dsDNA junction
- 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)
- 7ST9 2.2 Å, Open state of Rad24-RFC:9-1-1 bound to a 5' ss/dsDNA junction
- 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…
Browse structure collections
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