8AQI: NanoLuc luciferase

NanoLuc luciferase with bound coelenteramide in surface allosteric site. Determined by X-ray diffraction at 1.99 Å resolution. Released 23 Aug 2023.

Method: X-ray diffraction
Resolution: 1.99 Å
Organism: Oplophorus gracilirostris
Chains: 8
Atoms: 11,291
Mol. weight: 165.05 kDa
Ligands: CEI
Released: 23 Aug 2023

Explore 8AQI in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8AQI contains 40 α-helices and 94 β-strands across 8 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: 4 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3
β-strand	8-16	9	1
α-helix	18-24	7
α-helix	30-34	5
β-strand	36-37	2	2
β-strand	41-47	7	1
β-strand	51-61	11	1
α-helix	69-77	9
β-strand	81-84	4	1
β-strand	87-99	13	1
β-strand	105-109	5	1
β-strand	113-120	8	1
β-strand	124-130	7	1
β-strand	136-143	8	1
β-strand	149-155	7	1
β-strand	158-166	9	1

Chain B: 7 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3
β-strand	8-16	9	3
α-helix	18-23	6
α-helix	30-33	4
β-strand	36-37	2	4
β-strand	40-47	8	3
β-strand	51-61	11	3
α-helix	69-71	3
α-helix	74-77	4
β-strand	81-84	4	3
β-strand	87-98	12	3
α-helix	104	1
β-strand	105-109	5	3
β-strand	112-120	9	3
β-strand	125-130	6	3
β-strand	136-143	8	3
β-strand	149-154	6	3
β-strand	159-166	8	3
α-helix	167-168	2

Chain C: 5 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	3-6	4
β-strand	8-16	9	2
α-helix	18-23	6
α-helix	30-32	3
β-strand	36-37	2	1
β-strand	41-47	7	2
β-strand	51-61	11	2
α-helix	71-77	7
β-strand	81-84	4	2
β-strand	87-99	13	2
β-strand	105-109	5	2
β-strand	112-120	9	2
β-strand	125-130	6	2
β-strand	136-143	8	2
β-strand	149-155	7	2
β-strand	158-166	9	2
α-helix	167-168	2

Chain D: 4 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	4-6	3
β-strand	8-16	9	4
α-helix	18-24	7
α-helix	30-33	4
β-strand	36-37	2	3
β-strand	41-47	7	4
β-strand	51-61	11	4
α-helix	73-76	4
β-strand	81-84	4	4
β-strand	87-99	13	4
β-strand	105-109	5	4
β-strand	112-120	9	4
β-strand	124-130	7	4
β-strand	136-143	8	4
β-strand	149-155	7	4
β-strand	158-166	9	4

Chain E: 4 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	8-16	9	5
α-helix	18-25	8
α-helix	30-34	5
β-strand	41-46	6	5
β-strand	51-61	11	5
α-helix	67-77	11
β-strand	81-84	4	5
β-strand	87-98	12	5
α-helix	103-104	2
β-strand	105-106	2	5
β-strand	108-109	2	5
β-strand	112	1	5
β-strand	115-120	6	5
β-strand	124-130	7	5
β-strand	136-143	8	5
β-strand	149-155	7	5
β-strand	159-166	8	5

Chain F: 6 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3
β-strand	8-16	9	6
α-helix	18-24	7
α-helix	31-34	4
β-strand	41-47	7	6
β-strand	51-61	11	6
α-helix	74-77	4
β-strand	81-84	4	6
β-strand	87-99	13	6
β-strand	105-109	5	6
β-strand	112-120	9	6
β-strand	124-130	7	6
α-helix	135	1
β-strand	136-143	8	6
β-strand	149-155	7	6
β-strand	158-166	9	6
α-helix	167-168	2

Chain G: 6 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3
β-strand	8-16	9	7
α-helix	18-24	7
α-helix	30-34	5
β-strand	40-47	8	7
β-strand	51-61	11	7
α-helix	69-76	8
β-strand	81-84	4	7
β-strand	87-98	12	7
α-helix	104	1
β-strand	105-109	5	7
β-strand	112-120	9	7
β-strand	124-130	7	7
β-strand	136-143	8	7
β-strand	149-155	7	7
β-strand	158-166	9	7
α-helix	167-168	2

Chain H: 4 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3
β-strand	8-16	9	8
α-helix	18-24	7
β-strand	41-47	7	8
β-strand	51-61	11	8
α-helix	80-81	2
β-strand	82-84	3	8
β-strand	87-98	12	8
β-strand	105-109	5	8
β-strand	112-120	9	8
β-strand	125-130	6	8
α-helix	135	1
β-strand	136-143	8	8
β-strand	149-155	7	8
β-strand	158-166	9	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
NanoLuc luciferase	A, B, C, D, E, F, G, H	protein	181	Oplophorus gracilirostris	Q9GV45 (AlphaFold model)

Sequence of entity 1 (A, B, C, D, E, F, G, H), FASTA

>8AQI_1 NanoLuc luciferase (chains A, B, C, D, E, F, G, H)
MHHHHHHSDNMVFTLEDFVGDWRQTAGYNLDQVLEQGGVSSLFQNLGVSVTPIQRIVLSG
ENGLKIDIHVIIPYEGLSGDQMGQIEKIFKVVYPVDDHHFKVILHYGTLVIDGVTPNMID
YFGRPYEGIAVFDGKKITVTGTLWNGNKIIDERLINPDGSLLFRVTINGVTGWRLCERIL
A

Ligands and cofactors

ID	Name	Formula	Copies
CEI	N-[3-benzyl-5-(4-hydroxyphenyl)pyrazin-2-yl]-2-(4-hydroxyphenyl)acetamide	C25 H21 N3 O3	2

Water and common crystallization additives (CL, PG4) are not listed.

Primary citation

Illuminating the mechanism and allosteric behavior of NanoLuc luciferase. Nemergut, M., Pluskal, D., Horackova, J. et al. Nat Commun (2023) 14:7864-7864. DOI 10.1038/s41467-023-43403-y · PubMed

Other PDB entries of the same protein (UniProt Q9GV45 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7SNS 1.55 Å, 1.55A Resolution Structure of NanoLuc Luciferase
8AQ6 1.69 Å, NanoLuc luciferase with bound furimamide in surface allosteric site
7VSX 1.7 Å, Crystal structure of QL-nanoKAZ (Reverse mutant of nanoKAZ with L18Q and V27L)
7SNX 1.7 Å, 1.70A Resolution Structure of NanoBiT Complementation Reporter Complex of LgBit and…
5B0U 1.71 Å, Crystal structure of the mutated 19 kDa protein of Oplophorus luciferase (nanoKAZ)
7SNW 1.8 Å, 1.80A Resolution Structure of NanoLuc Luciferase with Bound Inhibitor PC 16026576
5IBO 1.95 Å, 1.95A resolution structure of NanoLuc luciferase
7SNR 2.0 Å, 2.00A Resolution Structure of NanoLuc Luciferase
7SNY 2.1 Å, 2.10A Resolution Structure of NanoBiT Complementation Reporter Large Subunit LgBiT
7SNT 2.2 Å, 2.20A Resolution Structure of NanoLuc Luciferase with Bound Substrate Analog…
9UPV 2.7 Å, Cryo-EM structure of CXCR4 complexed with agonist SDVX1
8AQH 2.8 Å, NanoLuc-Y94A luciferase mutant

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