8YJF: FACT complex subunit SPT16

Structure of human SPT16 MD-CTD and MCM2 HBD chaperoning a histone H3-H4 tetramer and an H2A-H2B dimer. Determined by X-ray diffraction at 4.4 Å resolution. Released 20 Mar 2024.

Method: X-ray diffraction
Resolution: 4.4 Å
Organism: Homo sapiens
Chains: 8
Atoms: 6,797
Mol. weight: 121.37 kDa
Released: 20 Mar 2024

Explore 8YJF in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8YJF contains 37 α-helices and 31 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: 14 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	658-660	3
β-strand	661-668	8	1
β-strand	677-682	6	1
β-strand	686-691	6	1
β-strand	697-700	4	1
β-strand	704-710	7	1
β-strand	717-730	14	1
β-strand	733-743	11	1
α-helix	757-761	5
α-helix	766-790	25
β-strand	797-798	2	1
β-strand	806-808	3	2
β-strand	809	1	3
β-strand	815-817	3	2
β-strand	818-819	2	4
β-strand	823-826	4	4
α-helix	832	1
β-strand	833-836	4	4
α-helix	837-839	3
β-strand	840-846	7	5
β-strand	854-861	8	5
α-helix	867-868	2
β-strand	869-875	7	5
α-helix	876-878	3
α-helix	879-886	8
β-strand	892-895	4	5
α-helix	899-900	2
α-helix	902-911	10
α-helix	913-918	6
α-helix	941-944	4
α-helix	946	1
β-strand	947	1	6
α-helix	948	1

Chain B: 2 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	78-81	4
β-strand	95	1	7
α-helix	107-123	17

Chain C: 3 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	64-78	15
β-strand	83-84	2	8
α-helix	86-113	28
β-strand	119	1	9
α-helix	121-131	11

Chain D: 3 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	31-40	10
β-strand	46	1	9
α-helix	50-74	25
β-strand	80-81	2	8
α-helix	83-93	11

Chain E: 3 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	64-76	13
β-strand	83-84	2	7
α-helix	86-113	28
β-strand	118-119	2	10
α-helix	121-131	11

Chain F: 3 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	31-40	10
β-strand	45-46	2	10
α-helix	50-75	26
β-strand	80-81	2	7
α-helix	83-91	9

Chain G: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	38-48	11
β-strand	53-54	2	11
β-strand	55	1	6
α-helix	56-83	28
α-helix	91-101	11
α-helix	104-121	18

Chain H: 5 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	17-21	5
α-helix	27-36	10
α-helix	47-72	26
β-strand	77-78	2	11
α-helix	80-88	9
α-helix	91-97	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
FACT complex subunit SPT16	A	protein	350	Homo sapiens	Q9Y5B9 (AlphaFold model)
DNA replication licensing factor MCM2	B	protein	93	Homo sapiens	P49736 (AlphaFold model)
Histone H3.1	C, E	protein	81	Homo sapiens	P68431 (AlphaFold model)
Histone H4	D, F	protein	103	Homo sapiens	P62805 (AlphaFold model)
Histone H2B type 2-E	G	protein	126	Homo sapiens	Q16778
Histone H2A type 1-D	H	protein	136	Homo sapiens	P20671

Sequence of entity 1 (A), FASTA

>8YJF_1 FACT complex subunit SPT16 (chains A)
GPLGSGIVKQDSLVINLNRSNPKLKDLYIRPNIAQKRMQGSLEAHVNGFRFTSVRGDKVD
ILYNNIKHALFQPCDGEMIIVLHFHLKNAIMFGKKRHTDVQFYTEVGEITTDLGKHQHMH
DRDDLYAEQMEREMRHKLKTAFKNFIEKVEALTKEELEFEVPFRDLGFNGAPYRSTCLLQ
PTSSALVNATEWPPFVVTLDEVELIHFERVQFHLKNFDMVIVYKDYSKKVTMINAIPVAS
LDPIKEWLNSCDLKYTEGVQSLNWTKIMKTIVDDPEGFFEQGGWSFLEPEGEGSDAEEGD
SESEIEDETFNPSEDDYEEEEEDSDEDYSSEAEESDYSKESLGSEEESGK

Sequence of entity 2 (B), FASTA

>8YJF_2 DNA replication licensing factor MCM2 (chains B)
SLEEEEDGEELIGDGMERDYRAIPELDAYEAEGLALDDEDVEELTASQREAAERAMRQRD
REAGRGLGRMRRGLLYDSDEEDEERPARKRRQV

Sequence of entity 3 (C, E), FASTA

>8YJF_3 Histone H3.1 (chains C, E)
MKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEACEAYLVGLFEDTNLCAIHA
KRVTIMPKDIQLARRIRGERA

Sequence of entity 4 (D, F), FASTA

>8YJF_4 Histone H4 (chains D, F)
MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLK
VFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Sequence of entity 5 (G), FASTA

>8YJF_5 Histone H2B type 2-E (chains G)
MPEPAKSAPAPKKGSKKAVTKAQKKDGKKRKRSRKESYSIYVYKVLKQVHPDTGISSKAM
GIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVT
KYTSSK

Sequence of entity 6 (H), FASTA

>8YJF_6 Histone H2A type 1-D (chains H)
MVMKDLLSGRGKQGGKARAKAKTRSSRAGLQFPVGRVHRLLRKGNYSERVGAGAPVYLAA
VLEYLTAEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGKVTIAQGGVLPNIQA
VLLPKKTESHHKAKGK

Primary citation

Structure of a histone hexamer bound by the chaperone domains of SPT16 and MCM2. Gan, S., Yang, W.S., Wei, L. et al. Sci China Life Sci (2024) 67:1305-1307. DOI 10.1007/s11427-024-2560-8 · PubMed

Other PDB entries of the same protein (UniProt Q9Y5B9 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5E5B 1.84 Å, Crystal structure of Human Spt16 N-terminal domain
5UMU 1.9 Å, Crystal structure of the middle double PH domain of human FACT complex subunit SPT16
4Z2N 1.92 Å, Crystal structure of human FACT SPT16 middle domain
8I17 1.98 Å, Structural basis for H2A-H2B recognitions by human Spt16
5UMT 2.09 Å, Crystal structure of N-terminal domain of human FACT complex subunit SPT16
5XM2 2.19 Å, Human N-terminal domain of FACT complex subunit SPT16
4Z2M 2.98 Å, Crystal structure of human SPT16 Mid-AID/H3-H4 tetramer FACT Histone complex
9EH2 3.1 Å, RNA polymerase II-DSIF-SPT6-PAF1c-TFIIS-IWS1-SETD2-FACT nucleosome upstream
9RZC 3.66 Å, State 3 MAP 1 SETD2 bound to distal H3 of upstream nucleosome
8YJM 4.15 Å, Structure of human SPT16 MD-CTD and MCM2 HBD chaperoning a histone H3-H4 tetramer and a…
9GW2 4.84 Å, State 2 MAP 1 SETD2 bound to proximal H3 of upstream nucleosome
6UPK 4.9 Å, Structure of FACT_subnucleosome complex 1

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