5IIQ: Vacuolar transporter chaperone 4

Structure of the SPX-TTM domain fragment of the yeast inorganic polyphophate polymerase Vtc4 (form B). Determined by X-ray diffraction at 3.03 Å resolution. Released 27 Apr 2016.

Method: X-ray diffraction
Resolution: 3.03 Å
Organism: Saccharomyces cerevisiae
Chains: 1
Atoms: 3,807
Mol. weight: 57.42 kDa
Ligands: POP
Released: 27 Apr 2016

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

Secondary structure: helices and β-sheets

5IIQ contains 17 α-helices and 11 β-strands across 1 chain. 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: 17 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	2-8	7
α-helix	22-35	14
α-helix	42-86	45
α-helix	96-137	42
α-helix	143-152	10
α-helix	161-175	15
β-strand	194-203	10	1
α-helix	208-218	11
β-strand	221	1	1
α-helix	232-235	4
β-strand	236-243	8	1
α-helix	248-254	7
β-strand	261-268	8	1
β-strand	275-282	8	1
α-helix	286-288	3
α-helix	290-292	3
β-strand	293-300	8	1
α-helix	301-309	9
α-helix	314-324	11
α-helix	329-348	20
β-strand	352-364	13	1
β-strand	372-384	13	1
α-helix	414-416	3
β-strand	417-419	3	1
β-strand	423-432	10	1
α-helix	439-445	7
β-strand	450-452	3	1
α-helix	458-466	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Vacuolar transporter chaperone 4	A	protein	485	Saccharomyces cerevisiae	P47075 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5IIQ_1 Vacuolar transporter chaperone 4 (chains A)
GAMGKFGEHLSKSLIRQYSYYYISYDDLKTELEDNLSKNNGQWTQELETDFLESLEIELD
KVYTFCKVKHSEVFRRVKEVQEQVQHTVRLLDSNNPPTQLDFEILEEELSDIIADVHDLA
KFSRLNYTGFQKIIKKHDKKTGFILKPVFQVRLDSKPFFKENYDELVVKISQLYDIARTS
GRPIKGDSSAGGKQQNFVRQTTKYWVHPDNITELKLIILKHLPVLVFNTNKEFEREDSAI
TSIYFDNENLDLYYGRLRKDEGAEAHRLRWYGGMSTDTIFVERKTHREDWTGEKSVKARF
ALKERHVNDFLKGKYTVDQVFAKMRKEGKKPMNEIENLEALASEIQYVMLKKKLRPVVRS
FYNRTAFQLPGDARVRISLDTELTMVREDNFDGVDRTHKNWRRTDIGVDWPFKQLDDKDI
CRFPYAVLEVKLQTQLGQEPPEWVRELVGSHLVEPVPKFSKFIHGVATLLNDKVDSIPFW
LPQGS

Ligands and cofactors

ID	Name	Formula	Copies
POP	Pyrophosphate 2-	H2 O7 P2	1

Water and common crystallization additives (SO4) are not listed.

Primary citation

Control of eukaryotic phosphate homeostasis by inositol polyphosphate sensor domains. Wild, R., Gerasimaite, R., Jung, J.Y. et al. Science (2016) 352:986-990. DOI 10.1126/science.aad9858 · PubMed

Other PDB entries of the same protein (UniProt P47075 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3G3T 1.85 Å, Crystal structure of a eukaryotic polyphosphate polymerase in complex with orthophosphate
3G3R 2.0 Å, Crystal structure of a eukaryotic polyphosphate polymerase in complex with AppNHp-Mn2+
3G3U 2.07 Å, Crystal structure of a eukaryotic polyphosphate polymerase in complex with pyrophosphate
5IIT 2.13 Å, Structure of SPX domain of the yeast inorganic polyphophate polymerase Vtc4 crystallized…
3G3Q 2.64 Å, Crystal structure of a eukaryotic polyphosphate polymerase in complex with a phosphate…
5IIG 2.99 Å, Structure of the SPX-TTM domain fragment of the yeast inorganic polyphophate polymerase…
7YTJ 3.0 Å, Cryo-EM structure of VTC complex
9UMG 3.04 Å, Cryo-EM structure of VTC complex(Vtc5/Vtc4/Vtc3/Vtc1)
8I6V 3.06 Å, Cryo-EM structure of the polyphosphate polymerase VTC complex(Vtc4/Vtc3/Vtc1)
5LNC 3.29 Å, Structure of SPX domain of the yeast inorganic polyphophate polymerase Vtc4 crystallized…

Browse structure collections

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