7EA9: Human lysyl-tRNA synthetase Y145H mutant

Crystal Structure of human lysyl-tRNA synthetase Y145H mutant. Determined by X-ray diffraction at 2.5 Å resolution. Released 31 Mar 2021.

Method: X-ray diffraction
Resolution: 2.5 Å
Organism: Homo sapiens
Chains: 4
Atoms: 16,581
Mol. weight: 243.41 kDa
Ligands: KAA
Released: 31 Mar 2021

Explore 7EA9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7EA9 contains 122 α-helices and 108 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: 31 helices, 27 β-strands

Element	Residues	Length	Sheet
α-helix	73-89	17
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	166-175	10
β-strand	181-190	10	1
β-strand	196-207	12	1
α-helix	212-214	3
α-helix	223-228	6
α-helix	230-236	7
α-helix	238-260	23
α-helix	263	1
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	301-309	9
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
α-helix	388	1
α-helix	391	1
β-strand	392-395	4	2
α-helix	396-404	9
α-helix	407-410	4
α-helix	411-413	3
α-helix	417-429	13
α-helix	435	1
α-helix	440-451	12
α-helix	453-455	3
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	527-529	3
α-helix	531-538	8
α-helix	541-542	2
β-strand	544-550	7	2
α-helix	551-558	8
α-helix	564-567	4

Chain B: 31 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	142-149	8	9
β-strand	152-159	8	9
α-helix	160-162	3
α-helix	166-175	10
β-strand	181-190	10	9
β-strand	196-207	12	9
α-helix	212-214	3
α-helix	223-228	6
α-helix	230-236	7
α-helix	238-260	23
α-helix	263	1
β-strand	264-265	2	10
β-strand	271-272	2	11
α-helix	281-283	3
β-strand	284-287	4	11
β-strand	292-296	5	11
α-helix	301-309	9
β-strand	314-322	9	10
β-strand	328	1	12
β-strand	331	1	12
β-strand	334-343	10	10
α-helix	347-366	20
β-strand	370-373	4	13
β-strand	383-386	4	13
α-helix	388	1
α-helix	391	1
β-strand	392-395	4	10
α-helix	396-404	9
α-helix	407-410	4
α-helix	411-413	3
α-helix	417-429	13
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	531-538	8
α-helix	541-542	2
β-strand	544-550	7	10
α-helix	551-558	8
α-helix	564-567	4

Chain C: 30 helices, 27 β-strands

Element	Residues	Length	Sheet
α-helix	73-89	17
α-helix	105-112	8
α-helix	115-116	2
β-strand	120	1	17
β-strand	126-137	12	17
β-strand	142-149	8	17
β-strand	152-159	8	17
α-helix	160-162	3
α-helix	166-175	10
β-strand	181-190	10	17
β-strand	196-207	12	17
α-helix	212-214	3
α-helix	223-228	6
α-helix	230-236	7
α-helix	238-260	23
α-helix	263	1
β-strand	264-265	2	18
β-strand	271-272	2	19
α-helix	281-283	3
β-strand	284-287	4	19
β-strand	292-296	5	19
α-helix	301-309	9
β-strand	314-322	9	18
β-strand	328	1	20
β-strand	331	1	20
β-strand	334-343	10	18
α-helix	347-366	20
β-strand	370-373	4	21
β-strand	383-386	4	21
α-helix	388	1
α-helix	391	1
β-strand	392-395	4	18
α-helix	396-404	9
α-helix	407-410	4
α-helix	411-413	3
α-helix	417-429	13
α-helix	435	1
α-helix	440-451	12
α-helix	453-455	3
β-strand	460-463	4	18
β-strand	466	1	22
α-helix	467-469	3
β-strand	473	1	23
α-helix	474	1
β-strand	475	1	24
α-helix	476	1
β-strand	482	1	22
β-strand	483	1	24
β-strand	485-490	6	18
β-strand	493-500	8	18
β-strand	501	1	23
α-helix	505-520	16
α-helix	527-529	3
α-helix	531-538	8
β-strand	544-550	7	18
α-helix	551-558	8
α-helix	564-567	4

Chain D: 30 helices, 27 β-strands

Element	Residues	Length	Sheet
α-helix	73-89	17
α-helix	105-111	7
β-strand	120	1	25
β-strand	126-137	12	25
β-strand	142-149	8	25
β-strand	152-159	8	25
α-helix	160-162	3
α-helix	166-175	10
β-strand	181-190	10	25
β-strand	196-207	12	25
α-helix	223-228	6
α-helix	230-236	7
α-helix	238-260	23
α-helix	263	1
β-strand	264-265	2	26
β-strand	271-272	2	27
α-helix	281-283	3
β-strand	284-287	4	27
β-strand	292-296	5	27
α-helix	301-309	9
β-strand	314-322	9	26
β-strand	328	1	28
β-strand	331	1	28
β-strand	334-343	10	26
α-helix	347-366	20
β-strand	370-373	4	29
β-strand	383-386	4	29
α-helix	388	1
α-helix	391	1
β-strand	392-395	4	26
α-helix	396-404	9
α-helix	407-410	4
α-helix	411-413	3
α-helix	417-429	13
α-helix	435	1
α-helix	437	1
α-helix	440-451	12
α-helix	453-455	3
β-strand	460-463	4	26
β-strand	466	1	30
α-helix	467-469	3
β-strand	473	1	31
α-helix	474	1
β-strand	475	1	32
α-helix	476	1
β-strand	482	1	30
β-strand	483	1	32
β-strand	485-490	6	26
β-strand	493-500	8	26
β-strand	501	1	31
α-helix	505-520	16
α-helix	527-529	3
α-helix	531-538	8
α-helix	541-542	2
β-strand	544-550	7	26
α-helix	551-558	8
α-helix	564-567	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Lysine--tRNA ligase	A, B, C, D	protein	521	Homo sapiens	Q15046 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>7EA9_1 Lysine--tRNA ligase (chains A, B, C, D)
MSVDPNQYYKIRSQAIHQLKVNGEDPYPHKFHVDISLTDFIQKYSHLQPGDHLTDITLKV
AGRIHAKRASGGKLIFHDLRGEGVKLQVMANSRNYKSEEEFIHINNKLRRGDIIGVQGNP
GKTKKGELSIIPYEITLLSPCLHMLPHLHFGLKDKETRYRQRYLDLILNDFVRQKFIIRS
KIITYIRSFLDELGFLEIETPMMNIIPGGAVAKPFITYHNELDMNLYMRIAPELYHKMLV
VGGIDRVYEIGRQFRNEGIDLTHNPEFTTCEFYMAYADYHDLMEITEKMVSGMVKHITGS
YKVTYHPDGPEGQAYDVDFTPPFRRINMVEELEKALGMKLPETNLFETEETRKILDDICV
AKAVECPPPRTTARLLDKLVGEFLEVTCINPTFICDHPQIMSPLAKWHRSKEGLTERFEL
FVMKKEICNAYTELNDPMRQRQLFEEQAKAKAAGDDEAMFIDENFCTALEYGLPPTAGWG
MGIDRVAMFLTDSNNIKEVLLFPAMKPEDKKENLEHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
KAA	5'-O-[(L-lysylamino)sulfonyl]adenosine	C16 H26 N8 O7 S	4

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

Primary citation

Structural analyses of a human lysyl-tRNA synthetase mutant associated with autosomal recessive nonsyndromic hearing impairment. Wu, S., Hei, Z., Zheng, L. et al. Biochem Biophys Res Commun (2021) 554:83-88. DOI 10.1016/j.bbrc.2021.03.093 · 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
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…
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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