5IIT: PDB entry 5IIT

Structure of SPX domain of the yeast inorganic polyphophate polymerase Vtc4 crystallized by carrier-driven crystallization in fusion with the macro domain of human histone macroH2A1.1. Determined by X-ray diffraction at 2.13 Å resolution. Released 27 Apr 2016.

Method: X-ray diffraction
Resolution: 2.13 Å
Organisms: Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Homo sapiens
Chains: 4
Atoms: 11,622
Mol. weight: 170.46 kDa
Ligands: MG
Released: 27 Apr 2016

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

Secondary structure: helices and β-sheets

5IIT contains 52 α-helices and 36 β-strands across 4 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: 14 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	15-18	4
α-helix	21-35	15
α-helix	42-89	48
β-strand	95	1	1
α-helix	96-138	43
α-helix	143-152	10
β-strand	157	1	2
α-helix	160-175	16
α-helix	184	1
β-strand	185-191	7	3
β-strand	197-202	6	3
α-helix	205-207	3
β-strand	212-216	5	3
α-helix	226-250	25
α-helix	253-254	2
β-strand	258-262	5	3
β-strand	270-274	5	3
α-helix	276-278	3
α-helix	284-301	18
β-strand	306-309	4	3
α-helix	321-338	18
β-strand	346-351	6	3
α-helix	354-366	13

Chain B: 14 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	15-18	4
α-helix	21-35	15
α-helix	42-89	48
β-strand	95	1	4
α-helix	96-138	43
α-helix	143-152	10
β-strand	157	1	5
α-helix	160-175	16
α-helix	184	1
β-strand	185-191	7	6
β-strand	197-202	6	6
α-helix	205-207	3
β-strand	212-216	5	6
α-helix	225-250	26
α-helix	253-254	2
β-strand	258-262	5	6
β-strand	270-274	5	6
α-helix	276-278	3
α-helix	284-301	18
β-strand	306-309	4	6
α-helix	321-338	18
β-strand	346-351	6	6
α-helix	354-366	13

Chain C: 12 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	15-18	4
α-helix	21-35	15
α-helix	42-89	48
β-strand	95	1	5
α-helix	96-138	43
α-helix	143-152	10
β-strand	157	1	4
α-helix	160-175	16
α-helix	184	1
β-strand	185-191	7	7
β-strand	197-202	6	7
β-strand	212-216	5	7
α-helix	226-250	25
β-strand	258-262	5	7
β-strand	270-274	5	7
α-helix	276-278	3
α-helix	284-301	18
β-strand	306-309	4	7
α-helix	321-338	18
β-strand	346-350	5	7
α-helix	354-366	13

Chain D: 12 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	15-18	4
α-helix	21-35	15
α-helix	42-89	48
β-strand	95	1	2
α-helix	96-138	43
α-helix	143-152	10
β-strand	157	1	1
α-helix	160-175	16
α-helix	184	1
β-strand	185-191	7	8
β-strand	197-202	6	8
β-strand	212-217	6	8
α-helix	225-250	26
β-strand	258-262	5	8
β-strand	270-275	6	8
α-helix	276-278	3
α-helix	284-301	18
β-strand	306-309	4	8
α-helix	321-338	18
β-strand	346-350	5	8
α-helix	354-366	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Vacuolar transporter chaperone 4,Core histone macro-H2A.1	A, B, C, D	protein	374	Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Homo sapiens	O75367 (AlphaFold model), P47075 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>5IIT_1 Vacuolar transporter chaperone 4,Core histone macro-H2A.1 (chains A, B, C, D)
MKFGEHLSKSLIRQYSYYYISYDDLKTELEDNLSKNNGQWTQELETDFLESLEIELDKVY
TFCKVKHSEVFRRVKEVQEQVQHTVRLLDSNNPPTQLDFEILEEELSDIIADVHDLAKFS
RLNYTGFQKIIKKHDKKTGFILKPVFQVRLDSKPFFKENYDELVVKISQLYDIARTSGAG
SDGFTVLSTKSLFLGQKLQVVQADIASIDSDAVVHPTNTDFYIGGEVGNTLEKKGGKEFV
EAVLELRKKNGPLEVAGAAVSAGHGLPAKFVIHCNSPVWGADKCEELLEKTVKNCLALAD
DKKLKSIAFPSIGSGRNGFPKQTAAQLILKAISSYFVSTMSSSIKTVYFVLFDSESIGIY
VQEMAKLEHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	2

Water and common crystallization additives (EDO, SO4, MES) 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 O75367 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3HSV 1.43 Å, Structures of SPOP-Substrate Complexes: Insights into Molecular Architectures of…
1ZR3 1.66 Å, Crystal structure of the macro-domain of human core histone variant macroH2A1.1 (form B)
3IVB 1.75 Å, Structures of SPOP-Substrate Complexes: Insights into Architectures of BTB-Cul3…
3IID 1.9 Å, Crystal structure of the macro domain of human histone macroH2A1.1 in complex with…
3IIF 2.1 Å, Crystal structure of the macro domain of human histone macroH2A1.1 in complex with…
3HQH 2.3 Å, Structures of SPOP-Substrate Complexes: Insights into Molecular Architectures of…
2FXK 2.54 Å, Crystal structure of the macro-domain of human core histone variant macroH2A1.1 (form A)
2F8N 2.9 Å, 2.9 Angstrom X-ray structure of hybrid macroH2A nucleosomes
9PM0 2.9 Å, nucleosome containing histone variant macroH2A
1ZR5 2.92 Å, Crystal structure of the macro-domain of human core histone variant macroH2A1.2
1U35 3.0 Å, Crystal structure of the nucleosome core particle containing the histone domain of…
7D3Y 3.11 Å, Crystal structure of the osPHR2-osSPX2 complex

Browse structure collections

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