5VKL: SPT6 tSH2-RPB1 1476-1500 pS1493

Name: PDB 5VKL: SPT6 tSH2-RPB1 1476-1500 pS1493
Published: 2017-10-25
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transcription

SPT6 tSH2-RPB1 1476-1500 pS1493. Determined by X-ray diffraction at 2.2 Å resolution. Released 25 Oct 2017.

Method: X-ray diffraction
Resolution: 2.2 Å
Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Chains: 2
Atoms: 1,942
Mol. weight: 27.64 kDa
Released: 25 Oct 2017

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

Secondary structure: helices and β-sheets

5VKL 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	1361-1373	13
β-strand	1380-1385	6	2
β-strand	1392-1398	7	2
α-helix	1404-1405	2
β-strand	1406-1413	8	2
β-strand	1416-1419	4	2
β-strand	1422-1424	3	2
α-helix	1427-1445	19

Chain B: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	1482-1484	3
α-helix	1488-1490	3
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	23	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P04050 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5VKL_1 Transcription elongation factor SPT6 (chains A)
GIDPFTAKRTHRVINHPYYFPFNGRQAEDYLRSKERGEFVIRQSSRGDDHLVITWKLDKD
LFQHIDIQELEKENPLALGKVLIVDNQKYNDLDQIIVEYLQNKVRLLNEMTSSEKFKSGT
KKDVVKFIEDYSRVNPNKSVYYFSLNHDNPGWFYLMFKINANSKLYTWNVKLTNTGYFLV
NYNYPSVIQLCNGFKTLLKSNSSKNRMNNYR

Sequence of entity 2 (B), FASTA

>5VKL_2 DNA-directed RNA polymerase II subunit RPB1 (chains B)
ESGLVNADLDVKDELMFSPLVDS

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:

5VKO 1.8 Å, SPT6 tSH2-RPB1 1468-1500 pT1471, pS1493
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
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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