7SAJ: LaM2 Nanobody

Crystal Structure of LaM2 Nanobody bound to mCherry. Determined by X-ray diffraction at 2.37 Å resolution. Released 14 Sept 2022.

Method: X-ray diffraction
Resolution: 2.37 Å
Organisms: Discosoma sp., Lama glama
Chains: 10
Atoms: 13,653
Mol. weight: 204.23 kDa
Released: 14 Sept 2022

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

Secondary structure: helices and β-sheets

7SAJ contains 50 α-helices and 126 β-strands across 10 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: 6 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	58-64	7
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	188-191	4
β-strand	193-204	12	1
β-strand	210-220	11	1

Chain B: 3 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	17-21	5	2
β-strand	24-26	3	3
β-strand	32-39	8	2
α-helix	43-45	3
β-strand	48-53	6	3
β-strand	60-65	6	3
β-strand	72-74	3	3
β-strand	79	1	2
β-strand	82-87	6	2
β-strand	92-97	6	2
α-helix	102-104	3
β-strand	106-113	8	3
α-helix	124-126	3
β-strand	127-128	2	3
β-strand	134-138	5	3

Chains C and G: 7 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	12-22	11	4
β-strand	25-36	12	4
β-strand	41-50	10	4
α-helix	52	1
α-helix	54	1
α-helix	58-60	3
α-helix	62-64	3
β-strand	74	1	4
α-helix	82-85	4
β-strand	91-99	9	4
β-strand	104-114	11	4
β-strand	117-127	11	4
β-strand	140-143	4	4
α-helix	144-145	2
β-strand	146-153	8	4
β-strand	156-167	12	4
β-strand	172-183	12	4
α-helix	188-191	4
β-strand	193-204	12	4
β-strand	210-220	11	4

Chains D, F and H: 3 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	17-21	5	5
β-strand	24-26	3	6
β-strand	32-39	8	5
α-helix	43-45	3
β-strand	48-53	6	6
β-strand	60-65	6	6
β-strand	72-74	3	6
β-strand	79	1	5
β-strand	82-87	6	5
β-strand	92-97	6	5
α-helix	102-104	3
β-strand	106-113	8	6
α-helix	124-126	3
β-strand	127-130	4	6
β-strand	134-138	5	6

Chain E: 7 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	12-22	11	7
β-strand	25-36	12	7
β-strand	41-50	10	7
α-helix	52	1
α-helix	54	1
α-helix	58-64	7
β-strand	74	1	7
α-helix	82-85	4
β-strand	91-99	9	7
β-strand	104-114	11	7
β-strand	117-127	11	7
β-strand	140-143	4	7
α-helix	144-145	2
β-strand	146-153	8	7
β-strand	156-167	12	7
β-strand	172-183	12	7
α-helix	188	1
β-strand	189-190	2	8
α-helix	191	1
β-strand	193-204	12	7
β-strand	210-220	11	7

Chain I: 7 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	12-22	11	12
β-strand	25-36	12	12
α-helix	37-39	3
β-strand	41-50	10	12
α-helix	52	1
α-helix	54	1
α-helix	58-64	7
β-strand	74	1	12
α-helix	82-85	4
β-strand	91-99	9	12
β-strand	104-114	11	12
β-strand	117-127	11	12
β-strand	140-143	4	12
α-helix	144-145	2
β-strand	146-153	8	12
β-strand	156-167	12	12
β-strand	172-183	12	12
α-helix	188-191	4
β-strand	193-204	12	12
β-strand	210-220	11	12

Chain J: 4 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	17-21	5	13
β-strand	24-26	3	8
β-strand	32-39	8	13
α-helix	43-45	3
β-strand	48-53	6	8
β-strand	60-65	6	8
β-strand	72-74	3	8
β-strand	79	1	13
β-strand	82-87	6	13
β-strand	92-97	6	13
α-helix	102-104	3
β-strand	106-113	8	8
α-helix	114	1
α-helix	124-126	3
β-strand	127-130	4	8
β-strand	134-138	5	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
mCherry	A, C, E, G, I	protein	237	Discosoma sp.	D1MPT3 (AlphaFold model)
nanobody LaM2	B, D, F, H, J	protein	127	Lama glama

Sequence of entity 1 (A, C, E, G, I), FASTA

>7SAJ_1 mCherry (chains A, C, E, G, I)
SNGMVSKGEEDNMAIIKEFMRFKVHMEGSVNGHEFEIEGEGEGRPYEGTQTAKLKVTKGG
PLPFAWDILSPQFXSKAYVKHPADIPDYLKLSFPEGFKWERVMNFEDGGVVTVTQDSSLQ
DGEFIYKVKLRGTNFPSDGPVMQKKTMGWEASSERMYPEDGALKGEIKQRLKLKDGGHYD
AEVKTTYKAKKPVQLPGAYNVNIKLDITSHNEDYTIVEQYERAEGRHSTGGMDELYK

Sequence of entity 2 (B, D, F, H, J), FASTA

>7SAJ_2 nanobody LaM2 (chains B, D, F, H, J)
MAQVQLVESGGGLVQAGGSLRLSCATSGFTFSDYAMGWFRQAPGKEREFVAAISWSGHVT
DYADSVKGRFTISRDNVKNTVYLQMNSLKPEDTAVYSCAAAKSGTWWYQRSENDFGSWGQ
GTQVTVS

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
7SAK 1.15 Å, Crystal Structure of LaM4 Nanobody bound to mCherry
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

Browse structure collections

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