5L3S: Signal recognition particle 54 kDa protein

Structure of the GTPase heterodimer of crenarchaeal SRP54 and FtsY. Determined by X-ray diffraction at 1.9 Å resolution. Released 8 Jun 2016.

Method: X-ray diffraction
Resolution: 1.9 Å
Organisms: Sulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2), Sulfolobus acidocaldarius
Chains: 8
Atoms: 19,033
Mol. weight: 274.56 kDa
Ligands: GNP, MG, 5GP
Released: 8 Jun 2016

Explore 5L3S in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5L3S contains 105 α-helices and 76 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: 13 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	18-36	19
α-helix	41-57	17
α-helix	67-80	14
α-helix	87-89	3
β-strand	97-102	6	1
α-helix	109-122	14
β-strand	127-131	5	1
α-helix	139-150	12
β-strand	153-156	4	1
α-helix	163-176	14
β-strand	181-185	5	1
α-helix	193-195	3
α-helix	196-209	14
β-strand	213-219	7	1
β-strand	222	1	2
α-helix	226-236	11
β-strand	241-245	5	1
α-helix	254-263	10
α-helix	265	1
β-strand	266-271	6	1
β-strand	279-281	3	1
α-helix	284-291	8

Chain B: 13 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	87-89	3	3
α-helix	90	1
α-helix	92-108	17
α-helix	113-127	15
β-strand	131-133	3	3
α-helix	138-157	20
α-helix	162-168	7
β-strand	174-179	6	4
α-helix	186-199	14
β-strand	204-209	6	4
α-helix	216-227	12
β-strand	230-232	3	4
α-helix	240-253	14
β-strand	258-263	6	4
α-helix	271-284	14
β-strand	288-294	7	4
β-strand	297	1	2
α-helix	300-311	12
β-strand	316-320	5	4
α-helix	330-333	4
α-helix	334-338	5
β-strand	342-346	5	4
β-strand	354-356	3	4
α-helix	359-367	9

Chain C: 13 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	18-36	19
α-helix	41-57	17
α-helix	68-81	14
α-helix	87-89	3
β-strand	97-102	6	5
α-helix	109-122	14
β-strand	127-132	6	5
α-helix	139-150	12
β-strand	153-155	3	5
α-helix	163-176	14
β-strand	181-186	6	5
α-helix	193-195	3
α-helix	196-209	14
β-strand	213-219	7	5
β-strand	222	1	6
α-helix	226-236	11
β-strand	241-245	5	5
α-helix	254-263	10
α-helix	265	1
β-strand	266-271	6	5
β-strand	279-281	3	5
α-helix	284-291	8

Chain D: 12 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	96-107	12
α-helix	113-127	15
α-helix	138-156	19
α-helix	162-167	6
β-strand	174-179	6	7
α-helix	186-199	14
β-strand	204-209	6	7
α-helix	216-227	12
β-strand	230-232	3	7
α-helix	240-254	15
β-strand	258-263	6	7
α-helix	271-284	14
β-strand	288-294	7	7
β-strand	297	1	6
α-helix	300-311	12
β-strand	316-320	5	7
α-helix	330-333	4
α-helix	334-338	5
β-strand	342-346	5	7
β-strand	354-356	3	7
α-helix	359-366	8

Chain E: 13 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	18-36	19
α-helix	41-57	17
α-helix	67-82	16
α-helix	87-88	2
β-strand	97-102	6	8
α-helix	109-122	14
β-strand	127-131	5	8
α-helix	139-150	12
β-strand	153-156	4	8
α-helix	163-176	14
β-strand	181-185	5	8
α-helix	193-195	3
α-helix	196-209	14
β-strand	213-219	7	8
β-strand	222	1	9
α-helix	226-236	11
β-strand	241-245	5	8
α-helix	254-263	10
α-helix	265	1
β-strand	266-271	6	8
β-strand	279-281	3	8
α-helix	284-291	8

Chain F: 13 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	88-89	2	10
α-helix	92-108	17
α-helix	113-127	15
β-strand	131-132	2	10
α-helix	138-157	20
α-helix	162-168	7
β-strand	174-179	6	11
α-helix	186-199	14
β-strand	204-209	6	11
α-helix	216-227	12
β-strand	230-232	3	11
α-helix	233-235	3
α-helix	240-254	15
β-strand	258-263	6	11
α-helix	271-284	14
β-strand	288-294	7	11
β-strand	297	1	9
α-helix	300-311	12
β-strand	316-320	5	11
α-helix	330-333	4
α-helix	334-338	5
β-strand	342-346	5	11
β-strand	354-356	3	11
α-helix	359-366	8

Chain G: 14 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	18-36	19
α-helix	41-57	17
α-helix	59-61	3
α-helix	66-81	16
α-helix	87-89	3
β-strand	97-102	6	12
α-helix	109-122	14
β-strand	127-131	5	12
α-helix	139-150	12
β-strand	153-155	3	12
α-helix	163-176	14
β-strand	181-185	5	12
α-helix	193-195	3
α-helix	196-209	14
β-strand	213-219	7	12
β-strand	222	1	13
α-helix	226-236	11
β-strand	241-245	5	12
α-helix	254-263	10
α-helix	265	1
β-strand	266-271	6	12
β-strand	279-281	3	12
α-helix	284-291	8

Chain H: 14 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	92-94	3
α-helix	96-108	13
α-helix	113-127	15
α-helix	138-157	20
α-helix	162-168	7
β-strand	174-179	6	14
α-helix	186-199	14
β-strand	204-209	6	14
α-helix	216-227	12
β-strand	230-232	3	14
α-helix	240-253	14
β-strand	258-263	6	14
α-helix	271-284	14
β-strand	288-294	7	14
β-strand	297	1	13
α-helix	300-311	12
β-strand	316-320	5	14
α-helix	322-324	3
α-helix	330-333	4
α-helix	334-338	5
β-strand	342-346	5	14
β-strand	354-356	3	14
α-helix	359-366	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Signal recognition particle 54 kDa protein	A, C, E, G	protein	298	Sulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)	Q97ZE7 (AlphaFold model)
Signal recognition particle receptor FtsY	B, D, F, H	protein	296	Sulfolobus acidocaldarius	P27414 (AlphaFold model)

Sequence of entity 1 (A, C, E, G), FASTA

>5L3S_1 Signal recognition particle 54 kDa protein (chains A, C, E, G)
HHHHHHMLENIRDAVRKFLTGSTPYEKAVDEFIKDLQKSLISSDVNVKLVFSLTAKIKER
LNKEKPPSVLERKEWFISIVYDELSKLFGGDKEPNVNPTKLPFIIMLVGVQGSGKTTTAG
KLAYFYKKRGYKVGLVAADVYRPAAYDQLLQLGNQIGVQVYGEPNNQNPIEIAKKGVDIF
VKNKMDIIIVDTAGRHGYGEETKLLEEMKEMYDVLKPDDVILVIDASIGQKAYDLASRFH
QASPIGSVIITKMDGTAKGGGALSAVVATGATIKFIGTGEKIDELETFNAKRFVSRIL

Sequence of entity 2 (B, D, F, H), FASTA

>5L3S_2 Signal recognition particle receptor FtsY (chains B, D, F, H)
HHHHHHRSFFDFLKYKTIKEDDLNDVIEELRFQLLDSDVSYEVTEKILEDLKNNLIGKKV
SRREEVEEIVINTLKKSITEILTKNQKTDLIEKIRSSGKKPFVIIFFGVNGVGKTTTIAK
VVNMLKKNNLSTIIAASDTFRAAAQEQLAYHASKLEVQLIRGKYGADPASVAFDAISFAK
SRNIDVVLIDTAGRMHIDSDLVEELKKVLRIAKPDFRILILDSLAGSDALEQARHFENNV
GYDAVILTKVDADAKGGIALSLAYELKKPVVYMGVGQNYDDLIPFSPDWFVERIFS

Ligands and cofactors

ID	Name	Formula	Copies
GNP	Phosphoaminophosphonic acid-guanylate ester	C10 H17 N6 O13 P3	8
MG	Magnesium ion	Mg	8
5GP	Guanosine-5'-monophosphate	C10 H14 N5 O8 P	4

Water and common crystallization additives (GOL, SO4) are not listed.

Primary citation

Structural Basis for Conserved Regulation and Adaptation of the Signal Recognition Particle Targeting Complex. Wild, K., Bange, G., Motiejunas, D. et al. J Mol Biol (2016) 428:2880-2897. DOI 10.1016/j.jmb.2016.05.015 · PubMed

Other PDB entries of the same protein (UniProt Q97ZE7 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5L3V 2.3 Å, Structure of the crenarchaeal SRP54 GTPase bound to GDP
3KL4 3.5 Å, Recognition of a signal peptide by the signal recognition particle
1QZX 4.0 Å, Crystal structure of the complete core of archaeal SRP and implications for inter-domain…
1QZW 4.1 Å, Crystal structure of the complete core of archaeal SRP and implications for inter-domain…
3ZN8 12.0 Å, Structural Basis of Signal Sequence Surveillance and Selection by the SRP-SR Complex
2IY3 16.0 Å, Structure of the E. Coli Signal Regognition Particle

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