6TTU: F-box/WD repeat-containing protein 1A
Ubiquitin Ligation to substrate by a cullin-RING E3 ligase at 3.7A resolution: NEDD8-CUL1-RBX1 N98R-SKP1-monomeric b-TRCP1dD-IkBa-UB~UBE2D2. Determined by electron microscopy at 3.7 Å resolution. Released 12 Feb 2020.
- Method
- Electron microscopy
- Resolution
- 3.7 Å
- Organism
- Homo sapiens
- Chains
- 8
- Atoms
- 12,746
- Mol. weight
- 227.74 kDa
- Ligands
- ZN
- Released
- 12 Feb 2020
Explore 6TTU in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
6TTU contains 67 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 C: 33 helices, 12 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 18-32 | 15 | |
| α-helix | 39-52 | 14 | |
| α-helix | 86-106 | 21 | |
| α-helix | 114-136 | 23 | |
| α-helix | 138-145 | 8 | |
| α-helix | 159-167 | 9 | |
| α-helix | 176-189 | 14 | |
| α-helix | 190-192 | 3 | |
| α-helix | 200-210 | 11 | |
| α-helix | 226-228 | 3 | |
| α-helix | 229-233 | 5 | |
| α-helix | 234-251 | 18 | |
| α-helix | 257-277 | 21 | |
| α-helix | 283-296 | 14 | |
| α-helix | 297-299 | 3 | |
| α-helix | 300-312 | 13 | |
| α-helix | 316-328 | 13 | |
| α-helix | 334-353 | 20 | |
| α-helix | 356-358 | 3 | |
| α-helix | 363-383 | 21 | |
| α-helix | 391-404 | 14 | |
| α-helix | 407-410 | 4 | |
| α-helix | 417-430 | 14 | |
| β-strand | 431 | 1 | 10 |
| α-helix | 439-454 | 16 | |
| α-helix | 459-475 | 17 | |
| β-strand | 479 | 1 | 10 |
| α-helix | 482-524 | 43 | |
| β-strand | 534-541 | 8 | 11 |
| α-helix | 557-570 | 14 | |
| β-strand | 580-582 | 3 | 11 |
| β-strand | 589-592 | 4 | 12 |
| β-strand | 599-602 | 4 | 12 |
| α-helix | 605-613 | 9 | |
| β-strand | 620-621 | 2 | 13 |
| α-helix | 622-626 | 5 | |
| α-helix | 633-644 | 12 | |
| β-strand | 668-669 | 2 | 13 |
| α-helix | 706-722 | 17 | |
| β-strand | 724 | 1 | 14 |
| α-helix | 727-738 | 12 | |
| α-helix | 746-758 | 13 | |
| β-strand | 762 | 1 | 15 |
| β-strand | 773 | 1 | 14 |
| β-strand | 774 | 1 | 15 |
Chain D: 9 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 4-15 | 12 | |
| β-strand | 21-25 | 5 | 20 |
| β-strand | 32-38 | 7 | 20 |
| α-helix | 39-40 | 2 | |
| β-strand | 49-55 | 7 | 20 |
| α-helix | 60-62 | 3 | |
| α-helix | 64-65 | 2 | |
| β-strand | 66-69 | 4 | 20 |
| β-strand | 75 | 1 | 21 |
| β-strand | 78 | 1 | 21 |
| β-strand | 83 | 1 | 20 |
| β-strand | 84 | 1 | 21 |
| α-helix | 87-90 | 4 | |
| α-helix | 99-111 | 13 | |
| α-helix | 121-129 | 9 | |
| α-helix | 133-141 | 9 | |
| α-helix | 142-146 | 5 | |
Chain N: 1 helix, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 1-6 | 6 | 16 |
| β-strand | 12-17 | 6 | 16 |
| β-strand | 22 | 1 | 17 |
| α-helix | 23-31 | 9 | |
| β-strand | 41-45 | 5 | 16 |
| β-strand | 48-49 | 2 | 16 |
| β-strand | 55 | 1 | 17 |
| β-strand | 66-71 | 6 | 16 |
Chain R: 3 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 22-24 | 3 | 12 |
| β-strand | 26-33 | 8 | 11 |
| α-helix | 52-53 | 2 | |
| α-helix | 54-57 | 4 | |
| β-strand | 70-72 | 3 | 18 |
| β-strand | 78-80 | 3 | 18 |
| α-helix | 81-90 | 10 | |
| β-strand | 93 | 1 | 19 |
| β-strand | 100 | 1 | 19 |
Chain S: 8 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3-7 | 5 | 9 |
| β-strand | 13-17 | 5 | 9 |
| α-helix | 18-21 | 4 | |
| α-helix | 25-30 | 6 | |
| β-strand | 39-40 | 2 | 9 |
| α-helix | 46-58 | 13 | |
| α-helix | 69-75 | 7 | |
| α-helix | 79-92 | 14 | |
| α-helix | 95-107 | 13 | |
| α-helix | 114-121 | 8 | |
| α-helix | 131-137 | 7 | |
Chain T: 10 helices, 30 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 180-186 | 7 | |
| α-helix | 190-198 | 9 | |
| α-helix | 202-209 | 8 | |
| α-helix | 213-221 | 9 | |
| α-helix | 224-235 | 12 | |
| α-helix | 237-246 | 10 | |
| α-helix | 248-251 | 4 | |
| α-helix | 266-288 | 23 | |
| β-strand | 294 | 1 | 1 |
| β-strand | 297 | 1 | 2 |
| β-strand | 308-311 | 4 | 3 |
| β-strand | 315-319 | 5 | 3 |
| β-strand | 324-329 | 6 | 3 |
| β-strand | 334 | 1 | 2 |
| β-strand | 335-340 | 6 | 3 |
| β-strand | 346-351 | 6 | 4 |
| β-strand | 355-360 | 6 | 4 |
| β-strand | 365-369 | 5 | 4 |
| β-strand | 375-379 | 5 | 4 |
| β-strand | 386-392 | 7 | 5 |
| β-strand | 395-400 | 6 | 5 |
| β-strand | 404-412 | 9 | 5 |
| β-strand | 415-422 | 8 | 5 |
| β-strand | 429-434 | 6 | 6 |
| β-strand | 438-443 | 6 | 6 |
| β-strand | 447-452 | 6 | 6 |
| β-strand | 457-463 | 7 | 6 |
| β-strand | 469-475 | 7 | 7 |
| β-strand | 478-483 | 6 | 7 |
| β-strand | 488-492 | 5 | 7 |
| β-strand | 498-502 | 5 | 7 |
| β-strand | 509-514 | 6 | 8 |
| β-strand | 518-523 | 6 | 8 |
| β-strand | 528-532 | 5 | 8 |
| α-helix | 533-537 | 5 | |
| α-helix | 543-545 | 3 | |
| β-strand | 547-551 | 5 | 8 |
| β-strand | 560-563 | 4 | 1 |
| β-strand | 567-571 | 5 | 1 |
| β-strand | 578-581 | 4 | 1 |
Chain U: 3 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-6 | 5 | 22 |
| β-strand | 12-16 | 5 | 22 |
| β-strand | 22 | 1 | 23 |
| α-helix | 23-34 | 12 | |
| α-helix | 38-40 | 3 | |
| β-strand | 42-44 | 3 | 22 |
| β-strand | 49 | 1 | 22 |
| β-strand | 55 | 1 | 23 |
| α-helix | 56-59 | 4 | |
| β-strand | 66-70 | 5 | 22 |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| F-box/WD repeat-containing protein 1A | T | protein | 605 | Homo sapiens | Q9Y297 (AlphaFold model) |
| S-phase kinase-associated protein 1 | S | protein | 163 | Homo sapiens | P63208 (AlphaFold model) |
| Cullin-1 | C | protein | 776 | Homo sapiens | Q13616 (AlphaFold model) |
| NEDD8 | N | protein | 77 | Homo sapiens | Q15843 (AlphaFold model) |
| E3 ubiquitin-protein ligase RBX1 | R | protein | 108 | Homo sapiens | P62877 |
| Ubiquitin-conjugating enzyme E2 D2 | D | protein | 147 | Homo sapiens | P62837 |
| Polyubiquitin-C | U | protein | 76 | Homo sapiens | P0CG48 |
| Cys-lys-lys-ala-arg-his-asp-sep-gly | I | protein | 30 | Homo sapiens | P25963 |
Sequence of entity 1 (T), FASTA
>6TTU_1 F-box/WD repeat-containing protein 1A (chains T)
MDPAEAVLQEKALKFMCSMPRSLWLGCSSLADSMPSLRCLYNPGTGALTAFQNSSEREDC
NNGEPPRKIIPEKNSLRQTYNSCARLCLNQETVCLASTAMKTENCVAKTKLANGTSSMIV
PKQRKLSASYEKEKELCVKYFEQWSESDQVEFVEHLISQMCHYQHGHINSYLKPMLQRDF
ITALPARGLDHIAENILSYLDAKSLCAAELVCKEWYRVTSDGMLWKKLIERMVRTDSLWR
GLAERRGWGQYLFKNKPPDGNAPPNSFYRALYPKIIQDIETIESNWRCGRHSLQRIHCRS
ETSKGVYCLQYDDQKIVSGLRDNTIKIWDKNTLECKRILTGHTGSVLCLQYDERVIITGS
SDSTVRVWDVNTGEMLNTLIHHCEAVLHLRFNNGMMVTCSKDRSIAVWDMASPTDITLRR
VLVGHRAAVNVVDFDDKYIVSASGDRTIKVWNTSTCEFVRTLNGHKRGIACLQYRDRLVV
SGSSDNTIRLWDIECGACLRVLEGHEELVRCIRFDNKRIVSGAYDGKIKVWDLVAALDPR
APAGTLCLRTLVEHSGRVFRLQFDEFQIVSSSHDDTILIWDFLNDPAAQAEPPRSPSRTY
TYISR
Sequence of entity 2 (S), FASTA
>6TTU_2 S-phase kinase-associated protein 1 (chains S)
MPSIKLQSSDGEIFEVDVEIAKQSVTIKTMLEDLGMDDEGDDDPVPLPNVNAAILKKVIQ
WCTHHKDDPPPPEDDENKEKRTDDIPVWDQEFLKVDQGTLFELILAANYLDIKGLLDVTC
KTVANMIKGKTPEEIRKTFNIKNDFTEEEEAQVRKENQWCEEK
Sequence of entity 3 (C), FASTA
>6TTU_3 Cullin-1 (chains C)
MSSTRSQNPHGLKQIGLDQIWDDLRAGIQQVYTRQSMAKSRYMELYTHVYNYCTSVHQSN
QARGAGVPPSKSKKGQTPGGAQFVGLELYKRLKEFLKNYLTNLLKDGEDLMDESVLKFYT
QQWEDYRFSSKVLNGICAYLNRHWVRRECDEGRKGIYEIYSLALVTWRDCLFRPLNKQVT
NAVLKLIEKERNGETINTRLISGVVQSYVELGLNEDDAFAKGPTLTVYKESFESQFLADT
ERFYTRESTEFLQQNPVTEYMKKAEARLLEEQRRVQVYLHESTQDELARKCEQVLIEKHL
EIFHTEFQNLLDADKNEDLGRMYNLVSRIQDGLGELKKLLETHIHNQGLAAIEKCGEAAL
NDPKMYVQTVLDVHKKYNALVMSAFNNDAGFVAALDKACGRFINNNAVTKMAQSSSKSPE
LLARYCDSLLKKSSKNPEEAELEDTLNQVMVVFKYIEDKDVFQKFYAKMLAKRLVHQNSA
SDDAEASMISKLKQACGFEYTSKLQRMFQDIGVSKDLNEQFKKHLTNSEPLDLDFSIQVL
SSGSWPFQQSCTFALPSELERSYQRFTAFYASRHSGRKLTWLYQLSKGELVTNCFKNRYT
LQASTFQMAILLQYNTEDAYTVQQLTDSTQIKMDILAQVLQILLKSKLLVLEDENANVDE
VELKPDTLIKLYLGYKNKKLRVNINVPMKTEQKQEQETTHKNIEEDRKLLIQAAIVRIMK
MRKVLKHQQLLGEVLTQLSSRFKPRVPVIKKCIDILIEKEYLERVDGEKDTYSYLA
Sequence of entity 4 (N), FASTA
>6TTU_4 NEDD8 (chains N)
SMLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDEKTAADY
KILGGSVLHLVLALRGG
Sequence of entity 5 (R), FASTA
>6TTU_5 E3 ubiquitin-protein ligase RBX1 (chains R)
MAAAMDVDTPSGTNSGAGKKRFEVKKWNAVALWAWDIVVDNCAICRNHIMDLCIECQANQ
ASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDRREWEFQKYGH
Sequence of entity 6 (D), FASTA
>6TTU_6 Ubiquitin-conjugating enzyme E2 D2 (chains D)
MALKRIHKELNDLARDPPAQISAGPVGDDMFHWQATIMGPNDSPYQGGVFFLTIHFPTDY
PFKPPKVAFTTRIYHPNINSNGSICLDILRSQWSPALTISKVLLSIASLLDDPNPDDPLV
PEIARIYKTDREKYNRIAREWTQKYAM
Sequence of entity 7 (U), FASTA
>6TTU_7 Polyubiquitin-C (chains U)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGG
Sequence of entity 8 (I), FASTA
>6TTU_8 CYS-LYS-LYS-ALA-ARG-HIS-ASP-SEP-GLY (chains I)
CKKERLLDDRHDSGLDSMKDEEDYKDDDDK
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ZN | Zinc ion | Zn | 3 |
Primary citation
NEDD8 nucleates a multivalent cullin-RING-UBE2D ubiquitin ligation assembly. Baek, K., Krist, D.T., Prabu, J.R. et al. Nature (2020) 578:461-466. DOI 10.1038/s41586-020-2000-y · PubMed
Other PDB entries of the same protein (UniProt Q9Y297 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 9T9W 1.16 Å, Crystal structure of beta-TrCP bound by diphosphorylated I-kappa-B-alpha degron peptide
- 9TES 1.22 Å, Crystal structure of beta-TrCP bound by diphosphorylated PDCD4 degron peptide
- 9TDZ 1.35 Å, Crystal structure of beta-TrCP bound by diphosphorylated claspin degron peptide
- 9TG7 1.68 Å, Crystal structure of beta-TrCP bound by monophosphorylated WEE1 degron peptide
- 9T8Y 1.79 Å, Crystal structure of beta-TrCP bound by monophosphorylated NRF2 degron peptide.
- 9TFU 2.0 Å, Crystal structure of beta-TrCP bound by monophosphorylated ATF4 degron peptide
- 6M90 2.05 Å, Monophosphorylated pSer33 b-Catenin peptide, b-TrCP/Skp1, NRX-2776 ternary complex
- 9T95 2.15 Å, Crystal structure of beta-TrCP bound by diphosphorylated NRF2 degron peptide.
- 6M92 2.35 Å, Monophosphorylated pSer33 b-Catenin peptide, b-TrCP/Skp1, NRX-2663 ternary complex
- 6M91 2.4 Å, Monophosphorylated pSer33 b-Catenin peptide, b-TrCP/Skp1, NRX-103094 ternary complex
- 2P64 2.5 Å, D domain of b-TrCP
- 6M93 2.5 Å, Monophosphorylated pSer33 b-Catenin peptide, b-TrCP/Skp1, NRX-1933 ternary complex
Browse structure collections
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