6Y2Z: NG domain of human SRP54

NG domain of human SRP54. Determined by X-ray diffraction at 2.15 Å resolution. Released 23 Sept 2020.

Method: X-ray diffraction
Resolution: 2.15 Å
Organism: Homo sapiens
Chains: 2
Atoms: 4,891
Mol. weight: 66.99 kDa
Ligands: MG, PO4
Released: 23 Sept 2020

Explore 6Y2Z in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6Y2Z contains 29 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	4-19	16
α-helix	25-40	16
α-helix	46-59	14
α-helix	71-86	16
α-helix	92-94	3
α-helix	96-97	2
β-strand	102-108	7	1
α-helix	114-127	14
β-strand	132-136	5	1
α-helix	143-155	13
β-strand	159-160	2	1
α-helix	168-181	14
β-strand	186-190	5	1
α-helix	198-212	15
β-strand	216-222	7	1
α-helix	223-228	6
α-helix	229-237	9
β-strand	243-248	6	1
α-helix	256-265	10
α-helix	268-269	2
β-strand	270-274	5	1
β-strand	282-284	3	1
α-helix	287-295	9

Chain B: 14 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	-2-0	3
α-helix	4-19	16
α-helix	25-41	17
α-helix	46-59	14
α-helix	71-87	17
α-helix	92-94	3
β-strand	102-108	7	2
α-helix	114-127	14
β-strand	132-136	5	2
α-helix	143-155	13
β-strand	159-160	2	2
α-helix	168-181	14
β-strand	186-190	5	2
α-helix	198-212	15
β-strand	216-222	7	2
α-helix	223-228	6
α-helix	229-238	10
β-strand	243-248	6	2
α-helix	256-265	10
β-strand	270-274	5	2
β-strand	282-284	3	2
α-helix	287-295	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Signal recognition particle 54 kDa protein	A, B	protein	303	Homo sapiens	P61011 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>6Y2Z_1 Signal recognition particle 54 kDa protein (chains A, B)
MGHHHHHMVLADLGRKITSALRSLSNATIINEEVLNAMLKEVCTALLEADVNIKLVKQLR
ENVKSAIDLEEMASGLNKRKMIQHAVFKELVKLVDPGVKAWTPTKGKQNVIMFVGLQGSG
KTTTCSKLAYYYQRKGWKTCLICADTFRAGAFDQLKQNATKARIPFYGSYTEMDPVIIAS
EGVEKFKNENFEIIIVDTSGRHKQEDSLFEEMLQVANAIQPDNIVYVMDASIGQACEAQA
KAFKDKVDVASVIVTKLDGHAKGGGALSAVAATKSPIIFIGTGEHIDDFEPFKTQPFISK
LLG

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	2
PO4	Phosphate ion	O4 P	2

Primary citation

Structural and Functional Impact of SRP54 Mutations Causing Severe Congenital Neutropenia. Juaire, K.D., Lapouge, K., Becker, M.M.M. et al. Structure (2021) 29:15. DOI 10.1016/j.str.2020.09.008 · 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:…
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…
5L3Q 3.2 Å, Structure of the GTPase heterodimer of human SRP54 and SRalpha
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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