5VKO: SPT6 tSH2-RPB1 1468-1500 pT1471, pS1493

Name: PDB 5VKO: SPT6 tSH2-RPB1 1468-1500 pT1471, pS1493
Published: 2017-09-20
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transcription

SPT6 tSH2-RPB1 1468-1500 pT1471, pS1493. Determined by X-ray diffraction at 1.8 Å resolution. Released 20 Sept 2017.

Method: X-ray diffraction
Resolution: 1.8 Å
Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Chains: 2
Atoms: 2,125
Mol. weight: 28.8 kDa
Ligands: IPA
Released: 20 Sept 2017

Explore 5VKO in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5VKO contains 11 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: 8 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	1259	1	1
α-helix	1264-1271	8
β-strand	1279-1283	5	1
β-strand	1290-1298	9	1
β-strand	1301-1310	10	1
α-helix	1318-1319	2
β-strand	1321-1324	4	1
β-strand	1327-1329	3	1
α-helix	1332-1334	3
α-helix	1335-1340	6
α-helix	1341-1351	11
β-strand	1356	1	2
α-helix	1361-1374	14
β-strand	1380-1385	6	2
β-strand	1392-1398	7	2
α-helix	1404-1405	2
β-strand	1406-1412	7	2
β-strand	1417-1419	3	2
β-strand	1422-1424	3	2
α-helix	1427-1445	19

Chain B: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	1474-1476	3
α-helix	1480-1483	4
α-helix	1492-1495	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Transcription elongation factor SPT6	A	protein	211	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P23615 (AlphaFold model)
DNA-directed RNA polymerase II subunit RPB1	B	protein	34	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P04050 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5VKO_1 Transcription elongation factor SPT6 (chains A)
GIDPFTAKRTHRVINHPYYFPFNGRQAEDYLRSKERGEFVIRQSSRGDDHLVITWKLDKD
LFQHIDIQELEKENPLALGKVLIVDNQKYNDLDQIIVEYLQNKVRLLNEMTSSEKFKSGT
KKDVVKFIEDYSRVNPNKSVYYFSLNHDNPGWFYLMFKINANSKLYTWNVKLTNTGYFLV
NYNYPSVIQLCNGFKTLLKSNSSKNRMNNYR

Sequence of entity 2 (B), FASTA

>5VKO_2 DNA-directed RNA polymerase II subunit RPB1 (chains B)
CGGVTPYSNESGLVNADLDVKDELMFSPLVDSGS

Ligands and cofactors

ID	Name	Formula	Copies
IPA	Isopropyl alcohol	C3 H8 O	1

Primary citation

A novel SH2 recognition mechanism recruits Spt6 to the doubly phosphorylated RNA polymerase II linker at sites of transcription. Sdano, M.A., Fulcher, J.M., Palani, S. et al. Elife (2017) 6. DOI 10.7554/eLife.28723 · PubMed

Other PDB entries of the same protein (UniProt P23615 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3PSK 2.1 Å, Crystal Structure of the Spt6 Tandem SH2 Domain from Saccharomyces cerevisiae, Form…
3OAK 2.15 Å, Crystal structure of a Spn1 (Iws1)-Spt6 complex
5VKL 2.2 Å, SPT6 tSH2-RPB1 1476-1500 pS1493
3PSF 2.59 Å, Crystal Structure of the Spt6 core domain from Saccharomyces cerevisiae, Form…
3PSJ 2.7 Å, Crystal Structure of the Spt6 Tandem SH2 Domain from Saccharomyces cerevisiae, Form…
3PSI 3.3 Å, Crystal Structure of the Spt6 core domain from Saccharomyces cerevisiae, Form…
7O3D 3.71 Å, Cooperation between the intrinsically disordered and ordered regions of Spt6 regulates…
7O6B 3.88 Å, Cooperation between the intrinsically disordered and ordered regions of Spt6 regulates…
2L3T Solution structure of tandem SH2 domain from Spt6

Browse structure collections

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