9DPL: Human LysRS

Human LysRS bound to cellular modified tRNA-Lys3 and AIMP2. Determined by electron microscopy at 2.8 Å resolution. Released 12 Mar 2025.

Method: Electron microscopy
Resolution: 2.8 Å
Organism: Homo sapiens
Chains: 5
Atoms: 10,555
Mol. weight: 170.37 kDa
Ligands: AMP, MG, LYS
Released: 12 Mar 2025

Explore 9DPL in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9DPL contains 57 α-helices and 54 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: 28 helices, 27 β-strands

Element	Residues	Length	Sheet
α-helix	20-40	21
α-helix	76-89	14
α-helix	105-112	8
α-helix	115-116	2
β-strand	120	1	1
β-strand	126-137	12	1
β-strand	142-149	8	1
β-strand	152-159	8	1
α-helix	166-175	10
β-strand	181-190	10	1
β-strand	196-207	12	1
α-helix	212-215	4
α-helix	223-228	6
α-helix	230-236	7
α-helix	239-261	23
α-helix	263	1
β-strand	264-265	2	2
β-strand	271-272	2	3
α-helix	281-282	2
β-strand	284-287	4	3
β-strand	292-296	5	3
α-helix	301-310	10
β-strand	314-322	9	2
β-strand	328	1	4
β-strand	331	1	4
β-strand	334-343	10	2
α-helix	347-366	20
β-strand	370-373	4	5
β-strand	383-386	4	5
β-strand	392-395	4	2
α-helix	396-404	9
α-helix	408-410	3
α-helix	417-429	13
α-helix	435	1
α-helix	437	1
α-helix	440-447	8
α-helix	448-452	5
β-strand	460-463	4	2
β-strand	466	1	6
α-helix	467-469	3
β-strand	473	1	7
α-helix	474	1
β-strand	475	1	8
α-helix	476	1
β-strand	482	1	6
β-strand	483	1	8
β-strand	485-490	6	2
β-strand	493-500	8	2
β-strand	501	1	7
α-helix	505-520	16
α-helix	525-527	3
α-helix	531-539	9
β-strand	544-550	7	2
α-helix	551-559	9
α-helix	564-566	3

Chain B: 27 helices, 27 β-strands

Element	Residues	Length	Sheet
α-helix	73-89	17
α-helix	105-111	7
β-strand	120	1	9
β-strand	126-137	12	9
β-strand	142-148	7	9
β-strand	153-159	7	9
α-helix	166-173	8
β-strand	181-190	10	9
β-strand	196-207	12	9
α-helix	212-215	4
α-helix	223-228	6
α-helix	230-236	7
α-helix	239-261	23
β-strand	264-265	2	10
β-strand	271-272	2	11
α-helix	281-283	3
β-strand	284-286	3	11
β-strand	293-296	4	11
α-helix	297	1
α-helix	301-310	10
β-strand	315-322	8	10
β-strand	334-343	10	10
α-helix	347-366	20
β-strand	370-373	4	12
β-strand	375	1	13
β-strand	377	1	13
β-strand	383-386	4	12
β-strand	392-395	4	10
α-helix	396-404	9
α-helix	408-410	3
α-helix	411-413	3
α-helix	418-429	12
α-helix	435	1
α-helix	437	1
α-helix	440-451	12
α-helix	453-455	3
β-strand	460-463	4	10
β-strand	466	1	14
α-helix	467-469	3
β-strand	473	1	15
α-helix	474	1
β-strand	475	1	16
α-helix	476	1
β-strand	482	1	14
β-strand	483	1	16
β-strand	485-490	6	10
β-strand	493-500	8	10
β-strand	501	1	15
α-helix	505-520	16
α-helix	527-529	3
α-helix	531-537	7
β-strand	544-550	7	10
α-helix	553-559	7
α-helix	564-567	4

Chain D: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	2-5	4

Chain E: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Lysine--tRNA ligase	A, B	protein	597	Homo sapiens	Q15046 (AlphaFold model)
tRNA-Lys3 (Cellular modified)	C	RNA	76	Homo sapiens
Aminoacyl tRNA synthase complex-interacting multifunctional protein 2	D, E	protein	36	Homo sapiens	Q13155 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>9DPL_1 Lysine--tRNA ligase (chains A, B)
MAAVQAAEVKVDGSEPKLSKNELKRRLKAEKKVAEKEAKQKELSEKQLSQATAAATNHTT
DNGVGPEEESVDPNQYYKIRSQAIHQLKVNGEDPYPHKFHVDISLTDFIQKYSHLQPGDH
LTDITLKVAGRIHAKRASGGKLIFYDLRGEGVKLQVMANSRNYKSEEEFIHINNKLRRGD
IIGVQGNPGKTKKGELSIIPYEITLLSPCLHMLPHLHFGLKDKETRYRQRYLDLILNDFV
RQKFIIRSKIITYIRSFLDELGFLEIETPMMNIIPGGAVAKPFITYHNELDMNLYMRIAP
ELYHKMLVVGGIDRVYEIGRQFRNEGIDLTHNPEFTTCEFYMAYADYHDLMEITEKMVSG
MVKHITGSYKVTYHPDGPEGQAYDVDFTPPFRRINMVEELEKALGMKLPETNLFETEETR
KILDDICVAKAVECPPPRTTARLLDKLVGEFLEVTCINPTFICDHPQIMSPLAKWHRSKE
GLTERFELFVMKKEICNAYTELNDPMRQRQLFEEQAKAKAAGDDEAMFIDENFCTALEYG
LPPTAGWGMGIDRVAMFLTDSNNIKEVLLFPAMKPEDKKENVATTDTLESTTVGTSV

Sequence of entity 2 (C), FASTA

>9DPL_2 tRNA-Lys3 (Cellular modified) (chains C)
GCCCGGAUAGCUCAGUCGGUAGAGCAUCAGACUUUUAAUCUGAGGGUCCAGGGUUCAAGU
CCCUGUUCGGGCGCCA

Sequence of entity 3 (D, E), FASTA

>9DPL_3 Aminoacyl tRNA synthase complex-interacting multifunctional protein 2 (chains D, E)
MPMYQVKPYHGGGAPLRVELPTCMYRLPNVHGRSYG

Ligands and cofactors

ID	Name	Formula	Copies
AMP	Adenosine monophosphate	C10 H14 N5 O7 P	2
MG	Magnesium ion	Mg	2
LYS	Lysine	C6 H15 N2 O2	2

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

Primary citation

Structural basis for aminoacylation of cellular modified tRNALys3 by human lysyl-tRNA synthetase. Devarkar, S.C., Budding, C.R., Pathirage, C. et al. Nucleic Acids Res (2025) 53. DOI 10.1093/nar/gkaf114 · PubMed

Other PDB entries of the same protein (UniProt Q15046 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6ILD 1.88 Å, Crystal Structure of Human LysRS: P38/AIMP2 Complex II
4YCU 2.1 Å, Crystal structure of cladosporin in complex with human lysyl-tRNA synthetase
8XP4 2.26 Å, Crystal Structure of human lysyl-tRNA synthetase with acetyllysine
3BJU 2.31 Å, Crystal Structure of tetrameric form of human lysyl-tRNA synthetase
6CHD 2.5 Å, Crystal Structure of Human Lysyl-tRNA Synthetase complexed with L-Lysylsulfamoyl Adenosine
7EA9 2.5 Å, Crystal Structure of human lysyl-tRNA synthetase Y145H mutant
6ILH 2.5 Å, Crystal Structure of human lysyl-tRNA synthetase L350H mutant
8HYR 2.55 Å, Crystal structure of human KARS apo
4DPG 2.84 Å, Crystal Structure of Human LysRS: P38/AIMP2 Complex I
4YCW 2.9 Å, Crystal structure of cladosporin in complex with plasmodium like human lysyl-tRNA…
9DPB 2.9 Å, Human LysRS bound to unmodified tRNA-Lys3 (Undocked State, AMPCPP bound)
9DPA 3.0 Å, Human LysRS bound to unmodified tRNA-Lys3 (3'-CCA Docked State, AMP bound)

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