4DPG: Human LysRS: P38/AIMP2 Complex I

Crystal Structure of Human LysRS: P38/AIMP2 Complex I. Determined by X-ray diffraction at 2.84 Å resolution. Released 13 Feb 2013.

Method: X-ray diffraction
Resolution: 2.84 Å
Organism: Homo sapiens
Chains: 12
Atoms: 33,740
Mol. weight: 503.81 kDa
Ligands: ALA, MG, APC, LYS
Released: 13 Feb 2013

Explore 4DPG in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4DPG contains 249 α-helices and 207 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: 31 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	73-90	18
α-helix	105-112	8
α-helix	115-116	2
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	212-214	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
α-helix	288-290	3
β-strand	292-296	5	3
α-helix	301-310	10
β-strand	314-322	9	2
β-strand	334-343	10	2
α-helix	347-366	20
β-strand	370-373	4	4
β-strand	383-386	4	4
α-helix	388	1
α-helix	391	1
β-strand	392-395	4	2
α-helix	396-403	8
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	2
β-strand	466	1	5
α-helix	467-469	3
β-strand	473	1	6
α-helix	474	1
β-strand	475	1	7
α-helix	476	1
β-strand	482	1	5
β-strand	483	1	7
β-strand	485-490	6	2
β-strand	493-500	8	2
β-strand	501	1	6
α-helix	502	1
α-helix	505-520	16
α-helix	531-540	10
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	105-112	8
α-helix	115-116	2
β-strand	120	1	8
β-strand	126-137	12	8
β-strand	142-149	8	8
β-strand	152-159	8	8
α-helix	160-162	3
α-helix	166-175	10
β-strand	181-190	10	8
β-strand	196-207	12	8
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	9
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	9
β-strand	328	1	10
β-strand	331	1	10
β-strand	334-343	10	9
α-helix	347-366	20
β-strand	370-373	4	11
β-strand	383-386	4	11
α-helix	388	1
α-helix	391	1
β-strand	392-395	4	9
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	9
β-strand	466	1	12
α-helix	467-469	3
β-strand	473	1	13
α-helix	474	1
β-strand	475	1	14
α-helix	476	1
β-strand	482	1	12
β-strand	483	1	14
β-strand	485-490	6	9
β-strand	493-500	8	9
β-strand	501	1	13
α-helix	502	1
α-helix	505-520	16
α-helix	531-538	8
α-helix	541-542	2
β-strand	544-550	7	9
α-helix	551-558	8
α-helix	564-566	3

Chain C: 31 helices, 25 β-strands

Element	Residues	Length	Sheet
α-helix	73-90	18
α-helix	105-112	8
α-helix	115-116	2
β-strand	120	1	15
β-strand	126-137	12	15
β-strand	142-149	8	15
β-strand	152-159	8	15
α-helix	166-175	10
β-strand	181-190	10	15
β-strand	196-207	12	15
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	16
β-strand	271-272	2	17
β-strand	284-287	4	17
α-helix	288-290	3
β-strand	292-296	5	17
α-helix	301-310	10
β-strand	314-322	9	16
β-strand	334-343	10	16
α-helix	347-366	20
β-strand	370-373	4	18
β-strand	383-386	4	18
α-helix	388	1
α-helix	391	1
β-strand	392-395	4	16
α-helix	396-403	8
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	16
β-strand	466	1	19
α-helix	467-469	3
β-strand	473	1	20
α-helix	474	1
β-strand	475	1	21
α-helix	476	1
β-strand	482	1	19
β-strand	483	1	21
β-strand	485-490	6	16
β-strand	493-500	8	16
β-strand	501	1	20
α-helix	502	1
α-helix	505-520	16
α-helix	531-540	10
α-helix	541-542	2
β-strand	544-550	7	16
α-helix	551-558	8
α-helix	564-567	4

Chains D and F: 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	22
β-strand	126-137	12	22
β-strand	142-149	8	22
β-strand	152-159	8	22
α-helix	160-162	3
α-helix	166-175	10
β-strand	181-190	10	22
β-strand	196-207	12	22
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	23
β-strand	271-272	2	17
α-helix	281-283	3
β-strand	284-287	4	17
β-strand	292-296	5	17
α-helix	301-309	9
β-strand	314-322	9	23
β-strand	328	1	24
β-strand	331	1	24
β-strand	334-343	10	23
α-helix	347-366	20
β-strand	370-373	4	25
β-strand	383-386	4	25
α-helix	388	1
α-helix	391	1
β-strand	392-395	4	23
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	23
β-strand	466	1	26
α-helix	467-469	3
β-strand	473	1	27
α-helix	474	1
β-strand	475	1	28
α-helix	476	1
β-strand	482	1	26
β-strand	483	1	28
β-strand	485-490	6	23
β-strand	493-500	8	23
β-strand	501	1	27
α-helix	502	1
α-helix	505-520	16
α-helix	531-538	8
α-helix	541-542	2
β-strand	544-550	7	23
α-helix	551-559	9
α-helix	564-566	3

Chain E: 32 helices, 25 β-strands

Element	Residues	Length	Sheet
α-helix	73-90	18
α-helix	105-112	8
α-helix	115-116	2
β-strand	120	1	29
β-strand	126-137	12	29
β-strand	142-149	8	29
β-strand	152-159	8	29
α-helix	166-175	10
β-strand	181-190	10	29
β-strand	196-207	12	29
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	30
β-strand	271-272	2	31
α-helix	281-283	3
β-strand	284-287	4	31
α-helix	288-290	3
β-strand	292-296	5	31
α-helix	301-310	10
β-strand	314-322	9	30
β-strand	334-343	10	30
α-helix	347-366	20
β-strand	370-373	4	32
β-strand	383-386	4	32
α-helix	388	1
α-helix	391	1
β-strand	392-395	4	30
α-helix	396-403	8
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	30
β-strand	466	1	33
α-helix	467-469	3
β-strand	473	1	34
α-helix	474	1
β-strand	475	1	35
α-helix	476	1
β-strand	482	1	33
β-strand	483	1	35
β-strand	485-490	6	30
β-strand	493-500	8	30
β-strand	501	1	34
α-helix	502	1
α-helix	505-520	16
α-helix	531-540	10
α-helix	541-542	2
β-strand	544-550	7	30
α-helix	551-558	8
α-helix	564-567	4

Chain G: 31 helices, 25 β-strands

Element	Residues	Length	Sheet
α-helix	73-90	18
α-helix	105-112	8
α-helix	115-116	2
β-strand	120	1	43
β-strand	126-137	12	43
β-strand	142-149	8	43
β-strand	152-159	8	43
α-helix	166-175	10
β-strand	181-190	10	43
β-strand	196-207	12	43
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	44
β-strand	271-272	2	45
α-helix	281-283	3
β-strand	284-287	4	45
α-helix	288-290	3
β-strand	292-296	5	45
α-helix	301-310	10
β-strand	314-322	9	44
β-strand	334-343	10	44
α-helix	347-366	20
β-strand	370-373	4	46
β-strand	383-386	4	46
α-helix	388	1
α-helix	391	1
β-strand	392-395	4	44
α-helix	396-403	8
α-helix	407-410	4
α-helix	411-413	3
α-helix	417-429	13
α-helix	435	1
α-helix	440-447	8
α-helix	448-452	5
α-helix	453-455	3
β-strand	460-463	4	44
β-strand	466	1	47
α-helix	467-469	3
β-strand	473	1	48
α-helix	474	1
β-strand	475	1	49
α-helix	476	1
β-strand	482	1	47
β-strand	483	1	49
β-strand	485-490	6	44
β-strand	493-500	8	44
β-strand	501	1	48
α-helix	502	1
α-helix	505-520	16
α-helix	531-540	10
β-strand	544-550	7	44
α-helix	551-558	8
α-helix	564-567	4

Chain H: 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	50
β-strand	126-137	12	50
β-strand	142-149	8	50
β-strand	152-159	8	50
α-helix	160-162	3
α-helix	166-175	10
β-strand	181-190	10	50
β-strand	196-207	12	50
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	51
β-strand	271-272	2	45
α-helix	281-282	2
β-strand	283-287	5	45
β-strand	292-296	5	45
α-helix	301-309	9
β-strand	314-322	9	51
β-strand	328	1	52
β-strand	331	1	52
β-strand	334-343	10	51
α-helix	347-366	20
β-strand	370-373	4	53
β-strand	383-386	4	53
α-helix	388	1
α-helix	391	1
β-strand	392-395	4	51
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	51
β-strand	466	1	54
α-helix	467-469	3
β-strand	473	1	55
α-helix	474	1
β-strand	475	1	56
α-helix	476	1
β-strand	482	1	54
β-strand	483	1	56
β-strand	485-490	6	51
β-strand	493-500	8	51
β-strand	501	1	55
α-helix	502	1
α-helix	505-520	16
α-helix	531-538	8
α-helix	541-542	2
β-strand	544-550	7	51
α-helix	551-559	9
α-helix	564-566	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Lysine--tRNA ligase	A, B, C, D, E, F, G, H	protein	513	Homo sapiens	Q15046 (AlphaFold model)
Aminoacyl tRNA synthase complex-interacting multifunctional protein 2	I, J, K, L	protein	54	Homo sapiens	Q13155 (AlphaFold model)

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

>4DPG_1 Lysine--tRNA ligase (chains A, B, C, D, E, F, G, H)
MSVDPNQYYKIRSQAIHQLKVNGEDPYPHKFHVDISLTDFIQKYSHLQPGDHLTDITLKV
AGRIHAKRASGGKLIFYDLRGEGVKLQVMANSRNYKSEEEFIHINNKLRRGDIIGVQGNP
GKTKKGELSIIPYEITLLSPCLHMLPHLHFGLKDKETRYRQRYLDLILNDFVRQKFIIRS
KIITYIRSFLDELGFLEIETPMMNIIPGGAVAKPFITYHNELDMNLYMRIAPELYHKMLV
VGGIDRVYEIGRQFRNEGIDLTHNPEFTTCEFYMAYADYHDLMEITEKMVSGMVKHITGS
YKVTYHPDGPEGQAYDVDFTPPFRRINMVEELEKALGMKLPETNLFETEETRKILDDICV
AKAVECPPPRTTARLLDKLVGEFLEVTCINPTFICDHPQIMSPLAKWHRSKEGLTERFEL
FVMKKEICNAYTELNDPMRQRQLFEEQAKAKAAGDDEAMFIDENFCTALEYGLPPTAGWG
MGIDRVAMFLTDSNNIKEVLLFPAMKPEDKKEN

Sequence of entity 2 (I, J, K, L), FASTA

>4DPG_2 Aminoacyl tRNA synthase complex-interacting multifunctional protein 2 (chains I, J, K, L)
MPMYQVKPYHGGGAPLRVELPTCMYRLPNVHGRSYGPAPGAGHVQEESHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
ALA	Alanine	C3 H7 N O2	1
MG	Magnesium ion	Mg	12
APC	Diphosphomethylphosphonic acid adenosyl ester	C11 H18 N5 O12 P3	8
LYS	Lysine	C6 H15 N2 O2	8

Primary citation

Structural Switch of Lysyl-tRNA Synthetase between Translation and Transcription. Ofir-Birin, Y., Fang, P., Bennett, S.P. et al. Mol Cell (2013) 49:30-42. DOI 10.1016/j.molcel.2012.10.010 · 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
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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