5L3V: Crenarchaeal SRP54 GTPase

Structure of the crenarchaeal SRP54 GTPase bound to GDP. Determined by X-ray diffraction at 2.3 Å resolution. Released 8 Jun 2016.

Method: X-ray diffraction
Resolution: 2.3 Å
Organism: Sulfolobus solfataricus
Chains: 2
Atoms: 4,777
Mol. weight: 67.52 kDa
Ligands: GDP
Released: 8 Jun 2016

Explore 5L3V in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5L3V contains 31 α-helices and 16 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: 15 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	5-13	9
α-helix	19-36	18
α-helix	41-55	15
α-helix	59-61	3
α-helix	66-81	16
α-helix	87-89	3
β-strand	97-102	6	1
α-helix	109-122	14
β-strand	127-132	6	1
α-helix	139-150	12
β-strand	153-156	4	1
α-helix	163-176	14
β-strand	181-186	6	1
α-helix	194-209	16
β-strand	213-219	7	1
α-helix	220-225	6
α-helix	226-236	11
β-strand	241-245	5	1
α-helix	253-262	10
α-helix	265	1
β-strand	266-271	6	1
β-strand	279-281	3	1
α-helix	284-292	9

Chain B: 16 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	3-14	12
α-helix	19-36	18
α-helix	41-55	15
α-helix	59-61	3
α-helix	66-81	16
α-helix	86-89	4
β-strand	97-102	6	2
α-helix	109-122	14
β-strand	127-132	6	2
α-helix	139-150	12
β-strand	153-156	4	2
α-helix	163-176	14
β-strand	181-186	6	2
α-helix	192-194	3
α-helix	195-209	15
β-strand	213-219	7	2
α-helix	220-225	6
α-helix	226-236	11
β-strand	241-245	5	2
α-helix	253-263	11
α-helix	265	1
β-strand	266-271	6	2
β-strand	279-281	3	2
α-helix	284-292	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Signal recognition particle 54 kDa protein	A, B	protein	299	Sulfolobus solfataricus	Q97ZE7 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5L3V_1 Signal recognition particle 54 kDa protein (chains A, B)
HHHHHHMLENIRDAVRKFLTGSTPYEKAVDEFIKDLQKSLISSDVNVKLVFSLTAKIKER
LNKEKPPSVLERKEWFISIVYDELSKLFGGDKEPNVNPTKLPFIIMLVGVQGSGKTTTAG
KLAYFYKKRGYKVGLVAADVYRPAAYDQLLQLGNQIGVQVYGEPNNQNPIEIAKKGVDIF
VKNKMDIIIVDTAGRHGYGEETKLLEEMKEMYDVLKPDDVILVIDASIGQKAYDLASRFH
QASPIGSVIITKMDGTAKGGGALSAVVATGATIKFIGTGEKIDELETFNAKRFVSRILG

Ligands and cofactors

ID	Name	Formula	Copies
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	2

Water and common crystallization additives (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:

5L3S 1.9 Å, Structure of the GTPase heterodimer of crenarchaeal SRP54 and FtsY
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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