9DPB: Human LysRS

Human LysRS bound to unmodified tRNA-Lys3 (Undocked State, AMPCPP bound). Determined by electron microscopy at 2.9 Å resolution. Released 12 Mar 2025.

Method: Electron microscopy
Resolution: 2.9 Å
Organism: Homo sapiens
Chains: 3
Atoms: 9,836
Mol. weight: 162.16 kDa
Ligands: LYS, APC, MG
Released: 12 Mar 2025

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

Secondary structure: helices and β-sheets

9DPB contains 43 α-helices and 51 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: 23 helices, 26 β-strands

Element	Residues	Length	Sheet
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	160-162	3
α-helix	166-173	8
β-strand	181-190	10	1
β-strand	196-207	12	1
α-helix	225-228	4
α-helix	230-236	7
α-helix	239-260	22
β-strand	264-265	2	2
β-strand	271-272	2	3
α-helix	281-283	3
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	392-394	3	2
α-helix	396-404	9
α-helix	407-410	4
α-helix	411-414	4
α-helix	417-429	13
α-helix	440-451	12
α-helix	453-455	3
β-strand	460-462	3	2
β-strand	465-466	2	6
β-strand	473	1	7
α-helix	474	1
β-strand	475	1	6
α-helix	476	1
β-strand	482-483	2	6
β-strand	485-490	6	2
β-strand	493-500	8	2
β-strand	501	1	7
α-helix	505-520	16
α-helix	531-537	7
β-strand	544-550	7	2
α-helix	551-558	8
α-helix	564-566	3

Chain B: 20 helices, 25 β-strands

Element	Residues	Length	Sheet
α-helix	73-89	17
α-helix	105-111	7
α-helix	115-116	2
β-strand	120	1	8
β-strand	126-137	12	8
β-strand	142-148	7	8
β-strand	153	1	8
β-strand	156-159	4	8
α-helix	166-173	8
β-strand	181-190	10	8
β-strand	196-207	12	8
α-helix	212-213	2
α-helix	223-228	6
α-helix	230-236	7
α-helix	239-260	22
β-strand	264-265	2	9
β-strand	271-272	2	10
β-strand	284	1	10
α-helix	292-294	3
β-strand	295-296	2	10
α-helix	301-310	10
β-strand	314-322	9	9
β-strand	334-343	10	9
α-helix	349-366	18
β-strand	370-373	4	11
β-strand	383-386	4	11
β-strand	392-394	3	9
α-helix	398-404	7
α-helix	417-429	13
α-helix	440-451	12
β-strand	460-462	3	9
β-strand	464-466	3	12
α-helix	467-469	3
β-strand	473	1	13
α-helix	474	1
β-strand	475	1	12
α-helix	476	1
β-strand	482-484	3	12
β-strand	485-490	6	9
β-strand	493-500	8	9
β-strand	501	1	13
α-helix	505-521	17
α-helix	531-538	8
β-strand	544-550	7	9
α-helix	551-558	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Lysine--tRNA ligase	A, B	protein	597	Homo sapiens	Q15046 (AlphaFold model)
tRNA-Lys3 (unmodified)	C	RNA	76	Homo sapiens

Sequence of entity 1 (A, B), FASTA

>9DPB_1 Lysine--tRNA ligase (chains A, B)
MAAVQAAEVKVDGSEPKLSKNELKRRLKAEKKVAEKEAKQKELSEKQLSQATAAATNHTT
DNGVGPEEESVDPNQYYKIRSQAIHQLKVNGEDPYPHKFHVDISLTDFIQKYSHLQPGDH
LTDITLKVAGRIHAKRASGGKLIFYDLRGEGVKLQVMANSRNYKSEEEFIHINNKLRRGD
IIGVQGNPGKTKKGELSIIPYEITLLSPCLHMLPHLHFGLKDKETRYRQRYLDLILNDFV
RQKFIIRSKIITYIRSFLDELGFLEIETPMMNIIPGGAVAKPFITYHNELDMNLYMRIAP
ELYHKMLVVGGIDRVYEIGRQFRNEGIDLTHNPEFTTCEFYMAYADYHDLMEITEKMVSG
MVKHITGSYKVTYHPDGPEGQAYDVDFTPPFRRINMVEELEKALGMKLPETNLFETEETR
KILDDICVAKAVECPPPRTTARLLDKLVGEFLEVTCINPTFICDHPQIMSPLAKWHRSKE
GLTERFELFVMKKEICNAYTELNDPMRQRQLFEEQAKAKAAGDDEAMFIDENFCTALEYG
LPPTAGWGMGIDRVAMFLTDSNNIKEVLLFPAMKPEDKKENVATTDTLESTTVGTSV

Sequence of entity 2 (C), FASTA

>9DPB_2 tRNA-Lys3 (unmodified) (chains C)
GCCCGGAUAGCUCAGUCGGUAGAGCAUCAGACUUUUAAUCUGAGGGUCCAGGGUUCAAGU
CCCUGUUCGGGCGCCA

Ligands and cofactors

ID	Name	Formula	Copies
LYS	Lysine	C6 H15 N2 O2	2
APC	Diphosphomethylphosphonic acid adenosyl ester	C11 H18 N5 O12 P3	2
MG	Magnesium ion	Mg	4

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
9DPL 2.8 Å, Human LysRS bound to cellular modified tRNA-Lys3 and AIMP2
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…
9DPA 3.0 Å, Human LysRS bound to unmodified tRNA-Lys3 (3'-CCA Docked State, AMP bound)

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