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

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