3H7H: Transcription elongation factor SPT4

Name: PDB 3H7H: Crystal structure of the human transcription elongation factor DSIF, hSpt4/hSpt5 (176-273)
Published: 2009-12-08
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transcription

Crystal structure of the human transcription elongation factor DSIF, hSpt4/hSpt5 (176-273). Determined by X-ray diffraction at 1.55 Å resolution. Released 8 Dec 2009.

Method: X-ray diffraction
Resolution: 1.55 Å
Organism: Homo sapiens
Chains: 2
Atoms: 1,951
Mol. weight: 25.49 kDa
Ligands: ZN
Released: 8 Dec 2009

Explore 3H7H in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3H7H contains 13 α-helices and 12 β-strands across 2 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: 7 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3
β-strand	13-16	4	1
β-strand	21	1	2
β-strand	22-24	3	1
α-helix	25-31	7
α-helix	37-40	4
α-helix	46-52	7
β-strand	53-54	2	1
β-strand	57-63	7	2
α-helix	66-68	3
α-helix	70-74	5
β-strand	83-89	7	2
α-helix	95-103	9
β-strand	115-116	2	3

Chain B: 6 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	178-183	6	2
α-helix	189-203	15
β-strand	214-217	4	2
β-strand	224-229	6	2
α-helix	232-239	8
α-helix	243-248	6
β-strand	253-254	2	2
α-helix	255-256	2
α-helix	257-259	3
α-helix	262-264	3
β-strand	267-268	2	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Transcription elongation factor SPT4	A	protein	120	Homo sapiens	P63272 (AlphaFold model)
Transcription elongation factor SPT5	B	protein	106	Homo sapiens	O00267 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>3H7H_1 Transcription elongation factor SPT4 (chains A)
GAMGALETVPKDLRHLRACLLCSLVKTIDQFEYDGCDNCDAYLQMKGNREMVYDCTSSSF
DGIIAMMSPEDSWVSKWQRVSNFKPGVYAVSVTGRLPQGIVRELKSRGVAYKSRDTAIKT

Sequence of entity 2 (B), FASTA

>3H7H_2 Transcription elongation factor SPT5 (chains B)
GSHMDPNLWTVKCKIGEERATAISLMRKFIAYQFTDTPLQIKSVVAPEHVKGYIYVEAYK
QTHVKQAIEGVGNLRLGYWNQQMVPIKEMTDVLKVVKEVANLGSGC

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1

Water and common crystallization additives (BME) are not listed.

Primary citation

Crystal structure of the human transcription elongation factor DSIF hSpt4 subunit in complex with the hSpt5 dimerization interface. Wenzel, S., Martins, B.M., Rosch, P. et al. Biochem J (2010) 425:373-380. DOI 10.1042/BJ20091422 · PubMed

Other PDB entries of the same protein (UniProt P63272 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9HVQ 2.0 Å, Structure of the transcribing Pol II-DSIF-PAF-SPT6-RECQL5 complex
9MLC 2.4 Å, Pol II-DSIF-SPT6-PAF1c-TFIIS-IWS1-ELOF1-LEDGF-nucleosome activated elongation complex…
8UHD 2.8 Å, Structure of paused transcription complex Pol II-DSIF-NELF - post-translocated
9EGX 2.9 Å, RNA polymerase II-DSIF-SPT6-PAF1c-TFIIS-IWS1-hexasome, bp +27
9EGY 2.9 Å, RNA polymerase II-DSIF-SPT6-PAF1c-TFIIS-IWS1-nucleosome, bp +27
9EGZ 2.9 Å, RNA polymerase II-DSIF-SPT6-PAF1c-TFIIS-IWS1-SETD2-nucleosome, bp +27
7UND 3.0 Å, Pol II-DSIF-SPT6-PAF1c-TFIIS-nucleosome complex (stalled at +38)
6GMH 3.1 Å, Structure of activated transcription complex Pol II-DSIF-PAF-SPT6
6TED 3.1 Å, Structure of complete, activated transcription complex Pol II-DSIF-PAF-SPT6 uncovers…
9EH1 3.1 Å, RNA polymerase II-DSIF-SPT6-PAF1c-TFIIS-IWS1-SETD2-nucleosome, 20 bp upstream
9EH2 3.1 Å, RNA polymerase II-DSIF-SPT6-PAF1c-TFIIS-IWS1-SETD2-FACT nucleosome upstream
9G0A 3.1 Å, Influenza A/H7N9 polymerase post-cleavage cap-snatching complex

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