7ZR1: Chaetomium thermophilum Mre11-Rad50-Nbs1 complex
Chaetomium thermophilum Mre11-Rad50-Nbs1 complex bound to ATPyS (composite structure). Determined by electron microscopy at 4.0 Å resolution. Released 11 Jan 2023.
- Method
- Electron microscopy
- Resolution
- 4.0 Å
- Organism
- Thermochaetoides thermophila
- Chains
- 5
- Atoms
- 21,793
- Mol. weight
- 577.83 kDa
- Ligands
- MN, MG, AGS
- Released
- 11 Jan 2023
Explore 7ZR1 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
7ZR1 contains 90 α-helices and 93 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: 23 helices, 28 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 10-15 | 6 | 1 |
| β-strand | 20 | 1 | 2 |
| α-helix | 32-47 | 16 | |
| β-strand | 51-54 | 4 | 1 |
| β-strand | 59 | 1 | 2 |
| α-helix | 66-80 | 15 | |
| β-strand | 81 | 1 | 3 |
| α-helix | 84-86 | 3 | |
| β-strand | 89-90 | 2 | 4 |
| α-helix | 94-97 | 4 | |
| α-helix | 106-108 | 3 | |
| β-strand | 112 | 1 | 5 |
| β-strand | 114 | 1 | 3 |
| β-strand | 118-120 | 3 | 1 |
| α-helix | 124-126 | 3 | |
| β-strand | 129 | 1 | 6 |
| β-strand | 134 | 1 | 6 |
| α-helix | 136-143 | 8 | |
| β-strand | 147-148 | 2 | 1 |
| β-strand | 159-160 | 2 | 7 |
| α-helix | 162 | 1 | |
| β-strand | 163-167 | 5 | 4 |
| β-strand | 170-177 | 8 | 4 |
| α-helix | 182-190 | 9 | |
| β-strand | 195-196 | 2 | 7 |
| β-strand | 199 | 1 | 8 |
| β-strand | 207-212 | 6 | 4 |
| α-helix | 227-229 | 3 | |
| β-strand | 236-239 | 4 | 4 |
| β-strand | 246-251 | 6 | 4 |
| β-strand | 258-261 | 4 | 4 |
| α-helix | 272-275 | 4 | |
| α-helix | 277-278 | 2 | |
| β-strand | 279-286 | 8 | 1 |
| β-strand | 289-296 | 8 | 1 |
| α-helix | 301-302 | 2 | |
| β-strand | 303-309 | 7 | 9 |
| α-helix | 327-351 | 25 | |
| β-strand | 367-373 | 7 | 9 |
| α-helix | 387-392 | 6 | |
| β-strand | 405-408 | 4 | 9 |
| α-helix | 441-446 | 6 | |
| α-helix | 459-471 | 13 | |
| α-helix | 476-495 | 20 | |
| α-helix | 499-502 | 4 | |
| α-helix | 506-520 | 15 | |
| α-helix | 526-531 | 6 | |
| β-strand | 534 | 1 | 10 |
| α-helix | 535-538 | 4 | |
| α-helix | 553-555 | 3 | |
| β-strand | 556 | 1 | 10 |
Chain B: 23 helices, 26 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 10-15 | 6 | 11 |
| β-strand | 20 | 1 | 12 |
| α-helix | 32-46 | 15 | |
| β-strand | 51-54 | 4 | 11 |
| β-strand | 59 | 1 | 12 |
| α-helix | 66-80 | 15 | |
| β-strand | 89-90 | 2 | 13 |
| α-helix | 106-108 | 3 | |
| β-strand | 112 | 1 | 5 |
| β-strand | 118-120 | 3 | 11 |
| α-helix | 138-142 | 5 | |
| β-strand | 147-148 | 2 | 11 |
| β-strand | 159-160 | 2 | 14 |
| α-helix | 162 | 1 | |
| β-strand | 163-167 | 5 | 13 |
| β-strand | 170-177 | 8 | 13 |
| α-helix | 186-191 | 6 | |
| β-strand | 195-196 | 2 | 14 |
| β-strand | 197 | 1 | 15 |
| β-strand | 207-212 | 6 | 13 |
| β-strand | 236-239 | 4 | 13 |
| β-strand | 246-251 | 6 | 13 |
| β-strand | 258-261 | 4 | 13 |
| α-helix | 272-275 | 4 | |
| α-helix | 277-278 | 2 | |
| β-strand | 279-286 | 8 | 11 |
| β-strand | 289-296 | 8 | 11 |
| α-helix | 301-302 | 2 | |
| β-strand | 303-309 | 7 | 16 |
| α-helix | 326-351 | 26 | |
| α-helix | 354-357 | 4 | |
| α-helix | 364-366 | 3 | |
| β-strand | 367-373 | 7 | 16 |
| α-helix | 387-392 | 6 | |
| β-strand | 395 | 1 | 17 |
| β-strand | 398 | 1 | 17 |
| β-strand | 405-408 | 4 | 16 |
| α-helix | 441-448 | 8 | |
| α-helix | 459-471 | 13 | |
| α-helix | 478-494 | 17 | |
| α-helix | 498-503 | 6 | |
| α-helix | 508-520 | 13 | |
| α-helix | 526-531 | 6 | |
| β-strand | 534 | 1 | 18 |
| α-helix | 535-538 | 4 | |
| α-helix | 543-546 | 4 | |
| α-helix | 549-551 | 3 | |
| α-helix | 553-555 | 3 | |
| β-strand | 556 | 1 | 18 |
Chain C: 20 helices, 17 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3-10 | 8 | 19 |
| β-strand | 21-24 | 4 | 19 |
| β-strand | 29-34 | 6 | 20 |
| α-helix | 42-52 | 11 | |
| α-helix | 55 | 1 | |
| α-helix | 61-63 | 3 | |
| α-helix | 69-72 | 4 | |
| β-strand | 76-86 | 11 | 19 |
| β-strand | 92-103 | 12 | 19 |
| β-strand | 109-113 | 5 | 19 |
| β-strand | 117-122 | 6 | 19 |
| β-strand | 125-130 | 6 | 19 |
| α-helix | 133-144 | 12 | |
| α-helix | 148-150 | 3 | |
| α-helix | 151-155 | 5 | |
| β-strand | 156 | 1 | 20 |
| α-helix | 164-166 | 3 | |
| α-helix | 169-179 | 11 | |
| α-helix | 182-292 | 111 | |
| α-helix | 300-376 | 77 | |
| α-helix | 388-412 | 25 | |
| α-helix | 944-972 | 29 | |
| α-helix | 976-1050 | 75 | |
| α-helix | 1052-1105 | 54 | |
| α-helix | 1109-1159 | 51 | |
| β-strand | 1167-1173 | 7 | 21 |
| α-helix | 1177-1179 | 3 | |
| β-strand | 1189-1195 | 7 | 21 |
| β-strand | 1196 | 1 | 22 |
| β-strand | 1199 | 1 | 22 |
| α-helix | 1209-1227 | 19 | |
| β-strand | 1233-1237 | 5 | 20 |
| α-helix | 1245-1265 | 21 | |
| β-strand | 1269-1273 | 5 | 20 |
| α-helix | 1277-1286 | 10 | |
| β-strand | 1292-1297 | 6 | 20 |
| β-strand | 1303-1308 | 6 | 20 |
Chain D: 19 helices, 19 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3-10 | 8 | 23 |
| β-strand | 12 | 1 | 24 |
| β-strand | 21-24 | 4 | 23 |
| β-strand | 29-34 | 6 | 25 |
| α-helix | 40-52 | 13 | |
| α-helix | 54-56 | 3 | |
| β-strand | 66 | 1 | 24 |
| α-helix | 69-72 | 4 | |
| β-strand | 76-86 | 11 | 23 |
| β-strand | 92-102 | 11 | 23 |
| β-strand | 110-113 | 4 | 23 |
| β-strand | 117-122 | 6 | 23 |
| β-strand | 125-130 | 6 | 23 |
| α-helix | 133-144 | 12 | |
| α-helix | 148-150 | 3 | |
| α-helix | 151-155 | 5 | |
| α-helix | 160-166 | 7 | |
| α-helix | 169-179 | 11 | |
| α-helix | 182-207 | 26 | |
| α-helix | 209-292 | 84 | |
| α-helix | 300-377 | 78 | |
| α-helix | 388-411 | 24 | |
| α-helix | 943-972 | 30 | |
| α-helix | 976-1050 | 75 | |
| α-helix | 1052-1105 | 54 | |
| α-helix | 1107-1158 | 52 | |
| β-strand | 1167-1170 | 4 | 26 |
| β-strand | 1173 | 1 | 27 |
| β-strand | 1189 | 1 | 27 |
| β-strand | 1192-1196 | 5 | 26 |
| β-strand | 1199-1201 | 3 | 26 |
| α-helix | 1209-1227 | 19 | |
| β-strand | 1235-1237 | 3 | 25 |
| α-helix | 1245-1262 | 18 | |
| β-strand | 1270-1273 | 4 | 25 |
| α-helix | 1277-1285 | 9 | |
| β-strand | 1292-1297 | 6 | 25 |
| β-strand | 1303-1308 | 6 | 25 |
Chain E: 5 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 616-622 | 7 | |
| β-strand | 625 | 1 | 7 |
| β-strand | 628 | 1 | 8 |
| α-helix | 629-633 | 5 | |
| α-helix | 642-648 | 7 | |
| α-helix | 653-655 | 3 | |
| α-helix | 680-683 | 4 | |
| β-strand | 685 | 1 | 15 |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Double-strand break repair protein | A, B | protein | 730 | Thermochaetoides thermophila | G0RYR3 (AlphaFold model) |
| DH domain-containing protein | C, D | protein | 1315 | Thermochaetoides thermophila | G0SHW7 (AlphaFold model) |
| FHA domain-containing protein | E | protein | 954 | Thermochaetoides thermophila | G0SAV1 (AlphaFold model) |
Sequence of entity 1 (A, B), FASTA
>7ZR1_1 Double-strand break repair protein (chains A, B)
MPQTAGPDTIRILVSTDNHVGYEERDPIRKDDSWRTFDEIMQLARTKDVDMVLLGGDLFH
DNKPSRKAMYQVMRSLRKNCLGMKPCELEFLSDPAEVFEGAFPHVNYYDPDINVSIPVFS
IHGNHDDPSGDGHLCSLDLLQVAGLVNYFGRVPEADNIHVKPILLQKGKTKLALYGMSNV
RDERIHRTFRDNKVRFYRPSQQTGDWFNLLTLHQNHYAHTPTGYLSENMLPDFLDLVIWG
HEHECLIDPKKNPETGFHVMQPGSSIATSLVPGEAVPKHIAILSITGKSFEVEKIPLRTV
RPFVIREITLATDKRFKGLEKKQDNRQEVTKRLMQIVEEMIAEANEMWRSLHEDSQDDED
EEQPLPLIRLKVEYSSPEGTKFEVENPQRFSNRFAGKVANQNDVVHFYRKKTGTTRKPKE
GKRELPEGIAEALEDSDSISVDALVQEFFAQQSLKILPQAPFGDAVNQFVSKDDKHAVEM
FVMDSLSSQVRGLLQLDDDKINEGLDSHIEDFRKVMEKNFLSGQQKQAQRRRRFKEKPEG
WDSDLNGHWTLQPEAIEELSSSPEPAKEGGRVRPASRITVGDEDNLFEEEEFVQKTTAKR
APTTRATRKTAAATRATTATKASAPAKKSIAAPRGRKRANPFQDSAEEEEDVIMDDDDDY
KPAPPVKAPPPKPARETQTRGAPKTRQTTLNFSQAERPTRTTQKAIEISDDEISEDDAFE
SMPARKSKRY
Sequence of entity 2 (C, D), FASTA
>7ZR1_2 DH domain-containing protein (chains C, D)
MSKIEKLSILGVRSFGPHHPETIAFNTPLTLIVGYNGSGKTTVIECLKYATTGELPPNST
RNGAFIHDPDLVGEKEVRAQVKLSFRSTIGESYVVTRNIQLLVQRNNKRTQKTLEGSLLL
RNNGERTVISTRVAELDKLVSEKLGVPPAILDAVIFCHQDDSLWPMSEPAALKKRFDEIF
EAQKYTKVIENIRLLKKKKGDELKILKEREVQDKANKERAEKVDRLMAQLTREILEAREK
CNELSKQMEEESAKIKDKYEQANSFLKIMNDLQTKTEKLEYKKDAIVELRSRIEELPDPD
EVLRNTLDEYEQTINRIVADRDHKAAQFHDLQAELKSARDQHTAKAAEQGKHQSDKEKYE
RQLVARERMIREAAERHEIRGYNGDLDDRRIAIFNERIQKILNDKRRELERLQRENQEEL
DRKTAVIAERESRKQSVIRDRKAAKDRIISLGKDMASIQGELSSIDIDEGTEEMLRAEMK
ELQARIEAAKADEQNANLDAQIKEVNEEIWKLESLSAKLARELVECTRLASERAQLDLRR
KQLAERKRELEIMTNTWNEQFSTLLGEGWRPETLERDFSDVLKQQQLLVGEHRKKKDATQ
QELKQAEYQLSNARNLHNKLTNEMEACMRAVQTAMKEARDLDSAPPVDEYITMLETDEKE
LAEVETALKLYDELKKHYSTIKDRALRFNKCYICDRDFTNQEAAKTRLLEKVAKRLGDEE
KKELLEDQAAFMKSLDILRAVRVKYDTYQRLSSELPQLSREIDSETNRREDLVRRLEDQD
LAFREADNKLQEMETLNKHVMKITQLLKDISDAEKQVERSQQLSNIETRSADEINEEQTT
CAEQTRAAQAKLTKLTAEKQRLKDLVRQLEVERLQLENKISSAVQQLERKKRLQESIARH
KEDQNQARNAVQEADEELERLEPEIAGARAALDEARQACRAKEQKVAAERDAIAQTVSEL
NMINSEIQEYLDRGGPSSLAANQRAIANLETQMANLEGEMRELTVQINKLNKEIDNSDAK
KRNIADNLTYRKNLREKDALEREIAELEARNAQEDYDRLIKEAHYLEAHRSKLNADRERL
MGMMSTKDEEFRRLNEEYELDLKDAKAKYKETHIKVETTKAAIEDLGRGMAAVDHAIMQY
HSKMMEQINRTIAELWQSTYQGTDIDTIQIRSDVESTTSSDSGTRRNYNYRVSMVKGDTE
MDMRGRCSAGQKVLASIIIRLALAESFCANCGLIALDEPTTNLDSDNIRSLAESLHGIIK
ARQAQGNLQLIVITHDEEFLKYMQCSDFCDDFYRVKRDEKQNSVIVRESITRITE
Sequence of entity 3 (E), FASTA
>7ZR1_3 FHA domain-containing protein (chains E)
MWILESELFDGKRLWLRPGKTYLFGRTVAEAGQLTISDKTVSRKHLTIHIDNVPEGGGRN
LRSRSNVIVEDLESKKGTLVNGVQIRGQKTTLTEDVNEIKLGLCPKTLKIRWHPIVLSFS
FTSKELRADPWTNLRDSLEQLDIKYSAEYEPTTTHVVSKKRNTSKGLQALINGRYIVTDS
FINAIVQATEIPEGEEGASSALEQDFEANWPNPLDHLPPRGEEPGNHTTETYAPDARRQE
VFDGYTFIFYEKKQYDNLFPAISAGKGKALLKEVVPNRTRVDEFVRYVKSVAGEKGLGSF
EDGSEGKGVVVVRYTPKGEDSAWYAEFFTKFAQQLDHRPIDQKEFLEAILACDASMLRRP
LEAMSQPVSVSASVEPQSSEKVRPAVEDRKEVEQSAPKQLQPSAEVPATEESAPAPHRRE
RRTGRSRFKGFDFDDDDIIIETPQAQSSTQVPALPQVPSASQDSLFVSQREPSLAPSEPM
LEEEAPCNTRTTRQTHRKRVLSPLPEHDNSALLDEIAPITAAVKRRRIEAGQDPVPPLPE
PEPEREDEDVEMVEESPPRKGKKGAATTAKGKGKKIKQEDEENVLELARRRREEAEAAAA
AERQRLAQLGDDDIDYAAIRRLHIIEEIEVRQPEPHGPNRTREQDIADGRWDPRWNGRKN
FKRFRRQGETGVRMPVQSVIVPLEEVRTKEYGIGDDYWLEDEEGRVPRRPKETQTQERST
IGSVRDGSGFAAAAASGKGKEKDKENEKEVGRPGSSAAAAKQRSKPAPRRTVLTLDSSDE
DEDEPSPHAPGIDTISDSEPEVVSSFPSVIPASEPSRSRAAKAAERANALRSSAHSSQSQ
TQQHRESQLSTGSSKIQLTLAPGSSSLSFSRSGTAAGRNENGKRPFGSFVSGESTASGRG
MSVESGSVRGESASKRQKQGSSGGGSFLATRRKDDGSEEESEDDELKFRFGRRR
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| MN | Manganese (II) ion | Mn | 4 |
| MG | Magnesium ion | Mg | 2 |
| AGS | Phosphothiophosphoric acid-adenylate ester | C10 H16 N5 O12 P3 S | 2 |
Primary citation
Cryo-EM structure of the Mre11-Rad50-Nbs1 complex reveals the molecular mechanism of scaffolding functions. Rotheneder, M., Stakyte, K., van de Logt, E. et al. Mol Cell (2023) 83:167-185.e9. DOI 10.1016/j.molcel.2022.12.003 · PubMed
Other PDB entries of the same protein (UniProt G0RYR3 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 4YKE 2.78 Å, Crystal structure of eukaryotic Mre11 catalytic domain from Chaetomium thermophilum
- 5DA9 3.0 Å, ATP-gamma-S bound Rad50 from Chaetomium thermophilum in complex with the Rad50-binding…
Browse structure collections
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