6UPK: FACT_subnucleosome complex 1
Structure of FACT_subnucleosome complex 1. Determined by electron microscopy at 4.9 Å resolution. Released 11 Dec 2019.
- Method
- Electron microscopy
- Resolution
- 4.9 Å
- Organisms
- Homo sapiens, Escherichia coli
- Chains
- 10
- Atoms
- 13,861
- Mol. weight
- 313.4 kDa
- Released
- 11 Dec 2019
Explore 6UPK in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
6UPK contains 42 α-helices and 73 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: 3 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 64-78 | 15 | |
| β-strand | 83-84 | 2 | 1 |
| α-helix | 86-113 | 28 | |
| α-helix | 121-130 | 10 | |
Chain B: 4 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 26-28 | 3 | |
| α-helix | 31-40 | 10 | |
| α-helix | 49-76 | 28 | |
| β-strand | 80-81 | 2 | 1 |
| α-helix | 83-93 | 11 | |
Chain C: 5 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 27-37 | 11 | |
| α-helix | 46-73 | 28 | |
| β-strand | 77-78 | 2 | 2 |
| α-helix | 81-86 | 6 | |
| α-helix | 92-96 | 5 | |
| α-helix | 113-115 | 3 | |
Chain D: 4 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 41-44 | 4 | |
| β-strand | 53-54 | 2 | 2 |
| α-helix | 56-83 | 28 | |
| α-helix | 91-101 | 11 | |
| α-helix | 104-123 | 20 | |
Chain E: 5 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 39-42 | 4 | |
| α-helix | 45-56 | 12 | |
| α-helix | 65-78 | 14 | |
| β-strand | 83-84 | 2 | 3 |
| α-helix | 86-114 | 29 | |
| β-strand | 118 | 1 | 4 |
| α-helix | 122-131 | 10 | |
Chain F: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 25-28 | 4 | |
| α-helix | 31-40 | 10 | |
| β-strand | 45 | 1 | 4 |
| α-helix | 50-75 | 26 | |
| β-strand | 80-81 | 2 | 3 |
| α-helix | 84-93 | 10 | |
Chain G: 11 helices, 27 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 530-532 | 3 | 5 |
| β-strand | 537-541 | 5 | 5 |
| β-strand | 546-550 | 5 | 5 |
| α-helix | 551-553 | 3 | |
| β-strand | 554-562 | 9 | 6 |
| β-strand | 565-572 | 8 | 6 |
| β-strand | 593 | 1 | 7 |
| β-strand | 597-601 | 5 | 6 |
| α-helix | 617-635 | 19 | |
| α-helix | 649-651 | 3 | |
| β-strand | 661-668 | 8 | 8 |
| β-strand | 677-683 | 7 | 8 |
| β-strand | 686-691 | 6 | 8 |
| β-strand | 698-700 | 3 | 8 |
| β-strand | 704-710 | 7 | 8 |
| β-strand | 717 | 1 | 9 |
| β-strand | 719-730 | 12 | 8 |
| β-strand | 733-741 | 9 | 8 |
| β-strand | 743 | 1 | 9 |
| α-helix | 764-787 | 24 | |
| β-strand | 798 | 1 | 8 |
| α-helix | 799-800 | 2 | |
| β-strand | 806-808 | 3 | 10 |
| β-strand | 809 | 1 | 11 |
| β-strand | 815-817 | 3 | 10 |
| β-strand | 818-819 | 2 | 12 |
| β-strand | 824-826 | 3 | 12 |
| α-helix | 832 | 1 | |
| β-strand | 833-834 | 2 | 12 |
| β-strand | 840-846 | 7 | 13 |
| β-strand | 855-861 | 7 | 13 |
| α-helix | 867-869 | 3 | |
| β-strand | 870-874 | 5 | 13 |
| α-helix | 879-889 | 11 | |
| β-strand | 894-895 | 2 | 13 |
| α-helix | 902-909 | 8 | |
| α-helix | 917-919 | 3 | |
| α-helix | 921-923 | 3 | |
Chain H: 6 helices, 38 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 6-7 | 2 | 14 |
| β-strand | 11-12 | 2 | 15 |
| β-strand | 20 | 1 | 15 |
| β-strand | 22-25 | 4 | 14 |
| β-strand | 30-33 | 4 | 14 |
| β-strand | 40-42 | 3 | 14 |
| β-strand | 48-53 | 6 | 16 |
| β-strand | 62-66 | 5 | 16 |
| β-strand | 71-73 | 3 | 16 |
| β-strand | 74-75 | 2 | 15 |
| α-helix | 81-89 | 9 | |
| β-strand | 110 | 1 | 7 |
| β-strand | 111-114 | 4 | 17 |
| β-strand | 119-122 | 4 | 17 |
| β-strand | 127-130 | 4 | 17 |
| β-strand | 138-141 | 4 | 6 |
| β-strand | 146-149 | 4 | 6 |
| β-strand | 159-164 | 6 | 6 |
| α-helix | 177-179 | 3 | |
| β-strand | 200-201 | 2 | 18 |
| β-strand | 205-207 | 3 | 19 |
| β-strand | 212-214 | 3 | 19 |
| β-strand | 215-218 | 4 | 18 |
| β-strand | 222-226 | 5 | 18 |
| β-strand | 232-235 | 4 | 18 |
| β-strand | 239-246 | 8 | 19 |
| β-strand | 252-264 | 13 | 19 |
| β-strand | 269-278 | 10 | 19 |
| β-strand | 282 | 1 | 20 |
| α-helix | 293-298 | 6 | |
| β-strand | 309 | 1 | 20 |
| α-helix | 310-322 | 13 | |
| β-strand | 327 | 1 | 19 |
| α-helix | 335-337 | 3 | |
| β-strand | 342-344 | 3 | 21 |
| β-strand | 349-351 | 3 | 21 |
| β-strand | 352-354 | 3 | 22 |
| β-strand | 358-361 | 4 | 22 |
| β-strand | 367-370 | 4 | 22 |
| β-strand | 374-378 | 5 | 23 |
| β-strand | 388-395 | 8 | 23 |
| β-strand | 400-406 | 7 | 23 |
| α-helix | 408-420 | 13 | |
| β-strand | 425-426 | 2 | 23 |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Histone H3.1 | A, E | protein | 136 | Homo sapiens | P68431 (AlphaFold model) |
| Histone H4 | B, F | protein | 103 | Homo sapiens | P62805 (AlphaFold model) |
| Histone H2A | C | protein | 130 | Homo sapiens | Q93077 (AlphaFold model) |
| Histone H2B | D | protein | 126 | Homo sapiens | P62807 (AlphaFold model) |
| FACT complex subunit SPT16 | G | protein | 966 | Homo sapiens | Q9Y5B9 |
| FACT complex subunit SSRP1 | H | protein | 640 | Homo sapiens | Q08945 |
| DNA (79-mer) | I | DNA | 79 | Escherichia coli | |
| DNA (79-mer) | J | DNA | 79 | Escherichia coli | |
Sequence of entity 1 (A, E), FASTA
>6UPK_1 Histone H3.1 (chains A, E)
MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTE
LLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEACEAYLVGLFEDTNLCAIHAKRVTI
MPKDIQLARRIRGERA
Sequence of entity 2 (B, F), FASTA
>6UPK_2 Histone H4 (chains B, F)
MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLK
VFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG
Sequence of entity 3 (C), FASTA
>6UPK_3 Histone H2A (chains C)
MSGRGKQGGKARAKAKSRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLT
AEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGRVTIAQGGVLPNIQAVLLPKK
TESHHKAKGK
Sequence of entity 4 (D), FASTA
>6UPK_4 Histone H2B (chains D)
MPEPAKSAPAPKKGSKKAVTKAQKKDGKKRKRSRKESYSVYVYKVLKQVHPDTGISSKAM
GIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVT
KYTSSK
Sequence of entity 5 (G), FASTA
>6UPK_5 FACT complex subunit SPT16 (chains G)
MHHHHHHAVTLDKDAYYRRVKRLYSNWRKGEDEYANVDAIVVSVGVDEEIVYAKSTALQT
WLFGYELTDTIMVFCDDKIIFMASKKKVEFLKQIANTKGNENANGAPAITLLIREKNESN
KSSFDKMIEAIKESKNGKKIGVFSKDKFPGEFMKSWNDCLNKEGFDKIDISAVVAYTIAV
KEDGELNLMKKAASITSEVFNKFFKERVMEIVDADEKVRHSKLAESVEKAIEEKKYLAGA
DPSTVEMCYPPIIQSGGNYNLKFSVVSDKNHMHFGAITCAMGIRFKSYCSNLVRTLMVDP
SQEVQENYNFLLQLQEELLKELRHGVKICDVYNAVMDVVKKQKPELLNKITKNLGFGMGI
EFREGSLVINSKNQYKLKKGMVFSINLGFSDLTNKEGKKPEEKTYALFIGDTVLVDEDGP
ATVLTSVKKKVKNVGIFLKNEDEEEEEEEKDEAEDLLGRGSRAALLTERTRNEMTAEEKR
RAHQKELAAQLNEEAKRRLTEQKGEQQIQKARKSNVSYKNPSLMPKEPHIREMKIYIDKK
YETVIMPVFGIATPFHIATIKNISMSVEGDYTYLRINFYCPGSALGRNEGNIFPNPEATF
VKEITYRASNIKAPGEQTVPALNLQNAFRIIKEVQKRYKXXXXXXXXXXXXVKQDSLVIN
LNRSNPKLKDLYIRPNIAQKRMQGSLEAHVNGFRFTSVRGDKVDILYNNIKHALFQPCDG
EMIIVLHFHLKNAIMFGKKRHTDVQFYTEVGEITTDLGKHQHMHDRDDLYAEQMEREMRH
KLKTAFKNFIEKVEALTKEELEFEVPFRDLGFNGAPYRSTCLLQPTSSALVNATEWPPFV
VTLDEVELIHFERVQFHLKNFDMVIVYKDYSKKVTMINAIPVASLDPIKEWLNSCDLKYT
EGVQSLNWTKIMKTIVDDPEGFFEQGGWSFLXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXX
Sequence of entity 6 (H), FASTA
>6UPK_6 FACT complex subunit SSRP1 (chains H)
MAETLEFNDVYQEVKGSMNDGRLRLSRQGIIFKNSKTGKVDNIQAGELTEGIWRRVALGH
GLKLLTKNGHVYKYDGFRESEFEKLSDFFKTHYRLELMEKDLCVKGWNWGTVKFGGQLLS
FDIGDQPVFEIPLSNVSQCTTGKNEVTLEFHQNDDAEVSLMEVRFYVPPTQXXXXXXXXX
XXXXXXXXXXXXXXXXDAICIFRELQCLTPRGRYDIRIYPTFLHLHGKTFDYKIPYTTVL
RLFLLPHKDQRQMFFVISLDPPIKQGQTRYHFLILLFSKDEDISLTLNMNEEEVEKRFEG
RLTKNMSGSLYEMVSRVMKALVNRKITVPGNFQGHSGAQCITCSYKASSGLLYPLERGFI
YVHKPPVHIRFDEISFVNFARGTTTTRSFDFEIETKQGTQYTFSSIEREEYGKLFDFVNA
KKLNIKNRGLKEGMNPSYDEYADSDEDQHDAYLERMKEEGKIREENANDSSDDSGEETDE
SFNPGEEEEDVAEEFDSNASASSSSNEGDSDRDEKKRKQLKKAKMAKDRKSRKKPVEVKK
GKDPNAPKRPMSAYMLWLNASREKIKSDHPGISITDLSKKAGEIWKGMSKEKKEEWDRKA
EDARRDYEKAMKEYEGGRGESSKRDKSKKKKKVKVKMEKK
Sequence of entity 7 (I), FASTA
>6UPK_7 DNA (79-mer) (chains I)
TCGTAGACAGCTCTAGCACCGCTTAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCG
CCAAGGGGATTACTCCCTA
Sequence of entity 8 (J), FASTA
>6UPK_8 DNA (79-mer) (chains J)
TAGGGAGTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCG
GTGCTAGAGCTGTCTACGA
Primary citation
FACT caught in the act of manipulating the nucleosome. Liu, Y., Zhou, K., Zhang, N. et al. Nature (2020) 577:426-431. DOI 10.1038/s41586-019-1820-0 · PubMed
Other PDB entries of the same protein (UniProt P68431 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 5SVY 1.05 Å, MORC3 CW in complex with histone H3K4me1
- 2V89 1.1 Å, Crystal structure of RAG2-PHD finger in complex with H3K4me3 peptide at 1.1A resolution
- 5SZC 1.19 Å, Structure of human Dpf3 double-PHD domain bound to histone H3 tail peptide with…
- 5SZB 1.2 Å, Structure of human Dpf3 double-PHD domain bound to histone H3 tail peptide with…
- 6BHD 1.25 Å, Crystal structure of SETDB1 with a modified H3 peptide
- 4UP0 1.28 Å, Ternary crystal structure of the Pygo2 PHD finger in complex with the B9L HD1 domain and…
- 5WXH 1.3 Å, Crystal structure of TAF3 PHD finger bound to H3K4me3
- 5FFV 1.3 Å, Crystal structure of the bromodomain of human BRPF1 in complex with H3K14ac histone…
- 4L7X 1.35 Å, Crystal structure of the DIDO PHD finger in complex with H3K4me3
- 6BHE 1.35 Å, Crystal structure of SETDB1 with a modified H3 peptide
- 6BHI 1.4 Å, Crystal structure of SETDB1 with a modified H3 peptide
- 3ASL 1.41 Å, Structure of UHRF1 in complex with histone tail
Browse structure collections
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