7SAK: LaM4 Nanobody

Crystal Structure of LaM4 Nanobody bound to mCherry. Determined by X-ray diffraction at 1.15 Å resolution. Released 14 Sept 2022.

Method: X-ray diffraction
Resolution: 1.15 Å
Organisms: Discosoma sp., Lama glama
Chains: 2
Atoms: 3,526
Mol. weight: 42.65 kDa
Released: 14 Sept 2022

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

Secondary structure: helices and β-sheets

7SAK contains 11 α-helices and 25 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, 13 β-strands

Element	Residues	Length	Sheet
β-strand	12-22	11	1
β-strand	25-36	12	1
β-strand	41-50	10	1
α-helix	52	1
α-helix	54	1
α-helix	58-60	3
α-helix	62-64	3
β-strand	74	1	1
α-helix	82-85	4
β-strand	91-99	9	1
β-strand	104-114	11	1
β-strand	117-127	11	1
β-strand	140-143	4	1
α-helix	144-145	2
β-strand	146-153	8	1
β-strand	156-167	12	1
β-strand	172-183	12	1
α-helix	188-190	3
β-strand	193-204	12	1
β-strand	210-221	12	1
α-helix	226-229	4

Chain B: 3 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	5-9	5	2
β-strand	13-14	2	3
β-strand	20-27	8	2
α-helix	31-33	3
β-strand	35-41	7	4
β-strand	48-53	6	4
β-strand	60-62	3	4
β-strand	70-75	6	2
β-strand	80-85	6	2
α-helix	90-92	3
β-strand	94-101	8	4
α-helix	110-112	3
β-strand	115-116	2	4
β-strand	120-122	3	4
β-strand	123-124	2	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
mCherry	A	protein	237	Discosoma sp.	D1MPT3 (AlphaFold model)
LaM4	B	protein	144	Lama glama

Sequence of entity 1 (A), FASTA

>7SAK_1 mCherry (chains A)
SNGMVSKGEEDNMAIIKEFMRFKVHMEGSVNGHEFEIEGEGEGRPYEGTQTAKLKVTKGG
PLPFAWDILSPQFXSKAYVKHPADIPDYLKLSFPEGFKWERVMNFEDGGVVTVTQDSSLQ
DGEFIYKVKLRGTNFPSDGPVMQKKTMGWEASSERMYPEDGALKGEIKQRLKLKDGGHYD
AEVKTTYKAKKPVQLPGAYNVNIKLDITSHNEDYTIVEQYERAEGRHSTGGMDELYK

Sequence of entity 2 (B), FASTA

>7SAK_2 LaM4 (chains B)
MGSSHHHHHHSSGLVPRGSMAQVQLVESGGSLVQPGGSLRLSCAASGRFAESSSMGWFRQ
APGKEREFVAAISWSGGATNYADSAKGRFTLSRDNTKNTVYLQMNSLKPDDTAVYYCAAN
LGNYISSNQRLYGYWGQGTQVTVS

Primary citation

High-efficiency recombinant protein purification using mCherry and YFP nanobody affinity matrices. Cong, A.T.Q., Witter, T.L., Schellenberg, M.J. Protein Sci (2022) 31:e4383-e4383. DOI 10.1002/pro.4383 · PubMed

Other PDB entries of the same protein (UniProt D1MPT3 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3NED 0.95 Å, mRouge
6MZ3 1.09 Å, mCherry pH sensitive mutant - M66T (mCherryTYG)
3LF3 1.15 Å, Crystal Structure of Fast Fluorescent Timer Fast-FT
31AL 1.5 Å, Synchrotron structure of non-photoactivated PAmCherry1
3KCS 1.5 Å, Crystal structure of PAmCherry1 in the dark state
9FEL 1.5 Å, LSSmCherry1 - Directionality of Optical Properties of Fluorescent Proteins
6YLM 1.6 Å, mCherry
31JT 1.63 Å, SFX structure of non-photoactivated PAmCherry1
3KCT 1.65 Å, CRYSTAL STRUCTURE OF PAmCherry1 in the photoactivated state
3NEZ 1.7 Å, mRojoA
5H89 1.76 Å, Crystal structure of mRojoA mutant - T16V - P63Y - W143G - L163V
3LF4 1.81 Å, Crystal Structure of Fluorescent Timer Precursor Blue102

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