4Z2M: FACT complex subunit SPT16

Crystal structure of human SPT16 Mid-AID/H3-H4 tetramer FACT Histone complex. Determined by X-ray diffraction at 2.98 Å resolution. Released 9 Mar 2016.

Method: X-ray diffraction
Resolution: 2.98 Å
Organism: Homo sapiens
Chains: 5
Atoms: 4,594
Mol. weight: 80 kDa
Released: 9 Mar 2016

Explore 4Z2M in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4Z2M contains 22 α-helices and 27 β-strands across 5 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 B: 10 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	661-668	8	1
β-strand	677-682	6	1
β-strand	686-691	6	1
β-strand	696-700	5	1
β-strand	704-710	7	1
β-strand	717-729	13	1
β-strand	734-743	10	1
β-strand	747-749	3	2
α-helix	764-790	27
β-strand	797-798	2	1
α-helix	799-800	2
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
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	902-910	9
α-helix	915-918	4
α-helix	921-925	5

Chain G: 3 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	64-73	10
β-strand	83-84	2	7
α-helix	86-113	28
β-strand	118-119	2	2
α-helix	121-131	11

Chain H: 3 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	31-41	11
β-strand	45-47	3	2
α-helix	50-75	26
β-strand	80-81	2	7
α-helix	83-92	10

Chain I: 3 helices, 2 β-strands

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

Chain J: 3 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	31-40	10
β-strand	45-46	2	9
α-helix	50-73	24
β-strand	80-81	2	8
α-helix	83-90	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
FACT complex subunit SPT16	B	protein	287	Homo sapiens	Q9Y5B9 (AlphaFold model)
Histone H3.1	G, I	protein	102	Homo sapiens	P68431 (AlphaFold model)
Histone H4	H, J	protein	103	Homo sapiens	P62805 (AlphaFold model)

Sequence of entity 1 (B), FASTA

>4Z2M_1 FACT complex subunit SPT16 (chains B)
GIVKQDSLVINLNRSNPKLKDLYIRPNIAQKRMQGSLEAHVNGFRFTSVRGDKVDILYNN
IKHALFQPCDGEMIIVLHFHLKNAIMFGKKRHTDVQFYTEVGEITTDLGKHQHMHDRDDL
YAEQMEREMRHKLKTAFKNFIEKVEALTKEELEFEVPFRDLGFNGAPYRSTCLLQPTSSA
LVNATEWPPFVVTLDEVELIHFERVQFHLKNFDMVIVYKDYSKKVTMINAIPVASLDPIK
EWLNSCDLKYTEGVQSLNWTKIMKTIVDDPEGFFEQGGWSFLEPEGE

Sequence of entity 2 (G, I), FASTA

>4Z2M_2 Histone H3.1 (chains G, I)
GVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQ
EACEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA

Sequence of entity 3 (H, J), FASTA

>4Z2M_3 Histone H4 (chains H, J)
MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLK
VFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Primary citation

Integrated molecular mechanism directing nucleosome reorganization by human FACT. Tsunaka, Y., Fujiwara, Y., Oyama, T. et al. Genes Dev (2016) 30:673-686. DOI 10.1101/gad.274183.115 · 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
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…
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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