5L3Q: GTPase heterodimer of human SRP54 and SRalpha

Structure of the GTPase heterodimer of human SRP54 and SRalpha. Determined by X-ray diffraction at 3.2 Å resolution. Released 8 Jun 2016.

Method: X-ray diffraction
Resolution: 3.2 Å
Organism: Homo sapiens
Chains: 4
Atoms: 9,156
Mol. weight: 242.19 kDa
Ligands: GNP, MG, AMP
Released: 8 Jun 2016

Explore 5L3Q in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5L3Q contains 54 α-helices and 36 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: 13 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	25-41	17
α-helix	46-58	13
α-helix	71-74	4
α-helix	76-87	12
α-helix	92-94	3
α-helix	96-97	2
β-strand	102-107	6	1
α-helix	114-127	14
β-strand	132-137	6	1
α-helix	144-154	11
β-strand	159-160	2	1
α-helix	168-180	13
β-strand	186-191	6	1
α-helix	199-212	14
β-strand	216-222	7	1
β-strand	225	1	2
α-helix	229-239	11
β-strand	242-248	7	1
α-helix	258-266	9
β-strand	270-274	5	1
β-strand	282-284	3	1
α-helix	287-295	9

Chain B: 15 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	335-351	17
α-helix	356-370	15
α-helix	373-376	4
α-helix	381-397	17
α-helix	405-414	10
α-helix	418	1
β-strand	419-424	6	3
α-helix	431-444	14
β-strand	449-454	6	3
α-helix	461-475	15
α-helix	478-480	3
β-strand	487-490	4	3
α-helix	498-512	15
β-strand	516-521	6	3
α-helix	529-542	14
β-strand	546-552	7	3
β-strand	555	1	2
α-helix	558-572	15
β-strand	584-588	5	3
α-helix	590-592	3
α-helix	599-606	8
β-strand	611-615	5	3
β-strand	623-624	2	3
α-helix	628-637	10

Chain C: 12 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	25-40	16
α-helix	46-58	13
α-helix	74-87	14
α-helix	92-94	3
α-helix	96-97	2
β-strand	102-107	6	4
α-helix	114-127	14
β-strand	132-137	6	4
α-helix	144-154	11
β-strand	159-160	2	4
α-helix	168-180	13
β-strand	186-191	6	4
α-helix	199-212	14
β-strand	216-222	7	4
β-strand	225	1	5
α-helix	229-239	11
β-strand	244-248	5	4
α-helix	258-266	9
β-strand	270-274	5	4
β-strand	282-284	3	4
α-helix	287-295	9

Chain D: 14 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	335-351	17
α-helix	356-370	15
α-helix	381-397	17
α-helix	405-414	10
α-helix	418	1
β-strand	419-424	6	6
α-helix	431-444	14
β-strand	449-454	6	6
α-helix	461-475	15
α-helix	478-480	3
β-strand	487-490	4	6
α-helix	498-512	15
β-strand	516-521	6	6
α-helix	529-542	14
β-strand	546-552	7	6
β-strand	555	1	5
α-helix	558-572	15
β-strand	584-588	5	6
α-helix	590-592	3
α-helix	599-606	8
β-strand	611-615	5	6
β-strand	623-624	2	6
α-helix	628-636	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Signal recognition particle 54 kDa protein	A, C	protein	442	Homo sapiens	P61011 (AlphaFold model)
Signal recognition particle receptor subunit alpha	B, D	protein	638	Homo sapiens	P08240 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>5L3Q_1 Signal recognition particle 54 kDa protein (chains A, C)
HHHHHHMVLADLGRKITSALRSLSNATIINEEVLNAMLKEVCTALLEADVNIKLVKQLRE
NVKSAIDLEEMASGLNKRKMIQHAVFKELVKLVDPGVKAWTPTKGKQNVIMFVGLQGSGK
TTTCSKLAYYYQRKGWKTCLICADTFRAGAFDQLKQNATKARIPFYGSYTEMDPVIIASE
GVEKFKNENFEIIIVDTSGRHKQEDSLFEEMLQVANAIQPDNIVYVMDASIGQACEAQAK
AFKDKVDVASVIVTKLDGHAKGGGALSAVAATKSPIIFIGTGEHIDDFEPFKTQPFISKL
LGMGDIEGLIDKVNELKLDDNEALIEKLKHGQFTLRDMYEQFQNIMKMGPFSQILGMIPG
FGTDFMSKGNEQESMARLKKLMTIMDSMNDQELDSTDGAKVFSKQPGRIQRVARGSGVST
RDVQELLTQYTKFAQMVKKMGG

Sequence of entity 2 (B, D), FASTA

>5L3Q_2 Signal recognition particle receptor subunit alpha (chains B, D)
MLDFFTIFSKGGLVLWCFQGVSDSCTGPVNALIRSVLLQERGGNNSFTHEALTLKYKLDN
QFELVFVVGFQKILTLTYVDKLIDDVHRLFRDKYRTEIQQQSALSLLNGTFDFQNDFLRL
LREAEESSKIRAPTTMKKFEDSEKAKKPVRSMIETRGEKPKEKAKNSKKKGAKKEGSDGP
LATSKPVPAEKSGLPVGPENGVELSKEELIRRKREEFIQKHGRGMEKSNKSTKSDAPKEK
GKKAPRVWELGGCANKEVLDYSTPTTNGTPEAALSEDINLIRGTGSGGQLQDLDCSSSDD
EGAAQNSTKPSATKGTLGGMFGMLKGLVGSKSLSREDMESVLDKMRDHLIAKNVAADIAV
QLCESVANKLEGKVMGTFSTVTSTVKQALQESLVQILQPQRRVDMLRDIMDAQRRQRPYV
VTFCGVNGVGKSTNLAKISFWLLENGFSVLIAACDTFRAGAVEQLRTHTRRLSALHPPEK
HGGRTMVQLFEKGYGKDAAGIAMEAIAFARNQGFDVVLVDTAGRMQDNAPLMTALAKLIT
VNTPDLVLFVGEALVGNEAVDQLVKFNRALADHSMAQTPRLIDGIVLTKFDTIDDKVGAA
ISMTYITSKPIVFVGTGQTYCDLRSLNAKAVVAALMKA

Ligands and cofactors

ID	Name	Formula	Copies
GNP	Phosphoaminophosphonic acid-guanylate ester	C10 H17 N6 O13 P3	4
MG	Magnesium ion	Mg	4
AMP	Adenosine monophosphate	C10 H14 N5 O7 P	2

Water and common crystallization additives (SO4, GOL) 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 P61011 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1QB2 2.1 Å, Crystal structure of the conserved subdomain of human protein SRP54M at 2.1A resolution:…
6Y2Z 2.15 Å, NG domain of human SRP54
6Y32 2.6 Å, Structure of the GTPase heterodimer of human SRP54 and SRalpha
6Y30 2.65 Å, NG domain of human SRP54 T115A mutant
7QWQ 2.83 Å, Ternary complex of ribosome nascent chain with SRP and NAC
1MFQ 3.1 Å, Crystal Structure Analysis of a Ternary S-Domain Complex of Human Signal Recognition…
7NFX 3.2 Å, Mammalian ribosome nascent chain complex with SRP and SRP receptor in early state A
6Y31 4.0 Å, NG domain of human SRP54 T117 deletion mutant

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