7EK9: Apo streptavidin at cryogenic temperature

Crystal structure of apo streptavidin at cryogenic temperature. Determined by X-ray diffraction at 1.1 Å resolution. Released 29 Sept 2021.

Method: X-ray diffraction
Resolution: 1.1 Å
Organism: Streptomyces avidinii
Chains: 4
Atoms: 4,462
Mol. weight: 52.4 kDa
Ligands: MRD
Released: 29 Sept 2021

Explore 7EK9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7EK9 contains 7 α-helices and 32 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: 1 helix, 8 β-strands

Element	Residues	Length	Sheet
β-strand	19-23	5	1
β-strand	28-33	6	1
β-strand	38-44	7	1
β-strand	54-60	7	1
β-strand	71-80	10	1
β-strand	85-97	13	1
β-strand	103-112	10	1
α-helix	116-121	6
β-strand	123-131	9	1

Chain B: 2 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	19-22	4	2
β-strand	28-33	6	2
β-strand	38-44	7	2
α-helix	50-52	3
β-strand	54-60	7	2
β-strand	71-80	10	2
β-strand	85-97	13	2
β-strand	103-112	10	2
α-helix	116-121	6
β-strand	123-131	9	2

Chain C: 2 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	19-22	4	2
β-strand	28-33	6	2
β-strand	38-44	7	2
β-strand	53-60	8	2
α-helix	69-70	2
β-strand	71-80	10	2
β-strand	85-97	13	2
β-strand	103-112	10	2
α-helix	116-121	6
β-strand	123-131	9	2

Chain D: 2 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	19-22	4	1
β-strand	28-34	7	1
β-strand	38-43	6	1
α-helix	50-52	3
β-strand	54-60	7	1
β-strand	71-80	10	1
β-strand	85-97	13	1
β-strand	103-112	10	1
α-helix	116-121	6
β-strand	123-131	9	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Streptavidin	A, B, C, D	protein	123	Streptomyces avidinii	P22629 (AlphaFold model)

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

>7EK9_1 Streptavidin (chains A, B, C, D)
EAGITGTWYNQLGSTFIVTAGADGALTGTYESAVGNAESRYVLTGRYDSAPATDGSGTAL
GWTVAWKNNYRNAHSATTWSGQYVGGAEARINTQWLLTSGTTEANAWKSTLVGHDTFTKV
KPS

Ligands and cofactors

ID	Name	Formula	Copies
MRD	(4R)-2-methylpentane-2,4-diol	C6 H14 O2	3

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

Primary citation

Crystal structure of apo streptavidin at cryogenic temperature. DeMirci, H. To be published.

Other PDB entries of the same protein (UniProt P22629 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2F01 0.85 Å, Epi-biotin complex with core streptavidin
9PUA 0.94 Å, L-Biotin-streptavidin binding
3RY2 0.95 Å, Wild-type core streptavidin-biotin complex at atomic resolution
9PUB 0.95 Å, Biotin-streptavidin binding
1LUQ 0.96 Å, Full Matrix Error Analysis of Streptavidin
2GH7 1.0 Å, Epi-biotin complex with core streptavidin
3WYQ 1.0 Å, Crystal structure of the low-immunogenic core streptavidin mutant LISA-314…
4GDA 1.0 Å, Circular Permuted Streptavidin A50/N49
6T2L 1.0 Å, Streptavidin variants harbouring an artificial organocatalyst based cofactor
3RY1 1.03 Å, Wild-type core streptavidin at atomic resolution
5N8B 1.03 Å, Crystal structure of streptavidin with peptide afpdylaeyhgg
5N8J 1.05 Å, CRYSTAL STRUCTURE OF STREPTAVIDIN WITH PEPTIDE D-amino acid containing peptide…

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