8YJM: FACT complex subunit SPT16

Structure of human SPT16 MD-CTD and MCM2 HBD chaperoning a histone H3-H4 tetramer and a single chain H2B-H2A chimera. Determined by X-ray diffraction at 4.15 Å resolution. Released 20 Mar 2024.

Method: X-ray diffraction
Resolution: 4.15 Å
Organism: Homo sapiens
Chains: 7
Atoms: 6,879
Mol. weight: 116.12 kDa
Released: 20 Mar 2024

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

Secondary structure: helices and β-sheets

8YJM contains 37 α-helices and 37 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 A: 13 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	649-651	3
β-strand	661-668	8	1
β-strand	677-682	6	1
β-strand	686-691	6	1
β-strand	696-700	5	1
α-helix	701-703	3
β-strand	704-710	7	1
β-strand	717-728	12	1
β-strand	735-743	9	1
β-strand	748-750	3	2
α-helix	762-790	29
β-strand	797-798	2	1
α-helix	802-804	3
β-strand	806-808	3	3
β-strand	809	1	4
β-strand	815-817	3	3
β-strand	818-819	2	5
β-strand	823-826	4	5
α-helix	832	1
β-strand	833-836	4	5
α-helix	837-839	3
β-strand	840-846	7	6
β-strand	854-861	8	6
α-helix	867-868	2
β-strand	869-875	7	6
α-helix	876-878	3
α-helix	879-888	10
β-strand	893-896	4	6
α-helix	902-911	10
α-helix	913-918	6
α-helix	922-925	4
α-helix	941-944	4
β-strand	947	1	7

Chain B: 3 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	71	1	8
α-helix	77-80	4
β-strand	95	1	9
α-helix	104-106	3
α-helix	107-122	16

Chain C: 3 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	64-78	15
β-strand	83-84	2	10
α-helix	86-113	28
β-strand	118-119	2	2
α-helix	121-131	11

Chain D: 3 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	31-40	10
β-strand	45-47	3	2
α-helix	50-75	26
β-strand	80-81	2	10
α-helix	83-92	10

Chain E: 3 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	64-75	12
β-strand	83-84	2	9
α-helix	86-113	28
β-strand	118-119	2	8
α-helix	121-131	11

Chain F: 3 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	31-40	10
β-strand	45-46	2	8
α-helix	50-75	26
β-strand	80-81	2	9
α-helix	83-91	9
β-strand	96	1	11

Chain G: 9 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	38-48	11
β-strand	53-54	2	12
β-strand	55	1	7
α-helix	56-83	28
β-strand	88-89	2	13
α-helix	91-101	11
α-helix	104-123	20
α-helix	1017-1020	4
α-helix	1027-1036	10
β-strand	1042-1043	2	13
α-helix	1046-1072	27
β-strand	1077-1078	2	12
α-helix	1080-1088	9
α-helix	1091-1097	7
β-strand	1101	1	11

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 1/2/3/4/6,Histone H2A type 1-D	G	protein	213	Homo sapiens	P20671, P33778

Sequence of entity 1 (A), FASTA

>8YJM_1 FACT complex subunit SPT16 (chains A)
GPLGSGIVKQDSLVINLNRSNPKLKDLYIRPNIAQKRMQGSLEAHVNGFRFTSVRGDKVD
ILYNNIKHALFQPCDGEMIIVLHFHLKNAIMFGKKRHTDVQFYTEVGEITTDLGKHQHMH
DRDDLYAEQMEREMRHKLKTAFKNFIEKVEALTKEELEFEVPFRDLGFNGAPYRSTCLLQ
PTSSALVNATEWPPFVVTLDEVELIHFERVQFHLKNFDMVIVYKDYSKKVTMINAIPVAS
LDPIKEWLNSCDLKYTEGVQSLNWTKIMKTIVDDPEGFFEQGGWSFLEPEGEGSDAEEGD
SESEIEDETFNPSEDDYEEEEEDSDEDYSSEAEESDYSKESLGSEEESGK

Sequence of entity 2 (B), FASTA

>8YJM_2 DNA replication licensing factor MCM2 (chains B)
SLEEEEDGEELIGDGMERDYRAIPELDAYEAEGLALDDEDVEELTASQREAAERAMRQRD
REAGRGLGRMRRGLLYDSDEEDEERPARKRRQV

Sequence of entity 3 (C, E), FASTA

>8YJM_3 Histone H3.1 (chains C, E)
MKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEACEAYLVGLFEDTNLCAIHA
KRVTIMPKDIQLARRIRGERA

Sequence of entity 4 (D, F), FASTA

>8YJM_4 Histone H4 (chains D, F)
MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLK
VFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Sequence of entity 5 (G), FASTA

>8YJM_5 Histone H2B 1/2/3/4/6,Histone H2A type 1-D (chains G)
MGSSHHHHHHSSGLVPRGSHMRKESYSIYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFE
RIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSSKKAKTRS
SRAGLQFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRI
IPRHLQLAIRNDEELNKLLGKVTIAQGGVLPNI

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
8YJF 4.4 Å, Structure of human SPT16 MD-CTD and MCM2 HBD chaperoning a histone H3-H4 tetramer and an…
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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