4P3E: Human SRP S domain

Structure of the human SRP S domain. Determined by X-ray diffraction at 3.5 Å resolution. Released 16 Apr 2014.

Method: X-ray diffraction
Resolution: 3.5 Å
Organism: Homo sapiens
Chains: 3
Atoms: 5,140
Mol. weight: 81.04 kDa
Ligands: MG
Released: 16 Apr 2014

Explore 4P3E in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4P3E contains 13 α-helices and 7 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 B: 6 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	16	1	1
α-helix	20-23	4
β-strand	24	1	2
α-helix	29-31	3
β-strand	41	1	2
α-helix	46-54	9
β-strand	60-63	4	1
α-helix	76-78	3
β-strand	81-84	4	1
β-strand	87	1	3
β-strand	93	1	3
α-helix	101-111	11
α-helix	113-116	4

Chain C: 7 helices, 0 β-strands

Element	Residues	Length
α-helix	54-64	11
α-helix	72-90	19
α-helix	114-136	23
α-helix	141-164	24
α-helix	172-192	21
α-helix	196-215	20
α-helix	219-240	22

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
SRP RNA (124-mer)	A	RNA	125	Homo sapiens
Signal recognition particle 19 kDa protein	B	protein	128	Homo sapiens	P09132 (AlphaFold model)
Signal recognition particle subunit SRP68	C	protein	216	Homo sapiens	Q9UHB9 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>4P3E_1 SRP RNA (124-mer) (chains A)
GACUAAGUUCGGCAUCAAUAUGGUGACCUCCCGGGAGCGGGGGACCACCAGGUUGCCUAA
GGAGGGGUGAACCGGCCCAGGUCGGAAACGGAGCAGGUCAAAACUCCCGUGCUGAUCAGU
AGUUA

Sequence of entity 2 (B), FASTA

>4P3E_2 Signal recognition particle 19 kDa protein (chains B)
MACAAARSPADQDRFICIYPAYLNNKKTIAEGRRIPISKAVENPTATEIQDVCSAVGLNV
FLEKNKMYSREWNRDVQYRGRVRVQLKQEDGSLCLVQFPSRKSVMLYAAEMIPKLKTRTQ
LEHHHHHH

Sequence of entity 3 (C), FASTA

>4P3E_3 Signal recognition particle subunit SRP68 (chains C)
MGHHHHHHGSKANKEFGDSLSLEILQIIKESQQQHGLRHGDFQRYRGYCSRRQRRLRKTL
NFKMGNRHKFTGKKVTEDLLTDNRYLLLVLMDAERAWSYAMQLKQEANTEPRKRFHLLSR
LRKAVKHAEELERLCESNRVDAKTKLEAQAYTAYLSGMLRFEHQEWKAAIEAFNKCKTIY
EKLASAFTEEQAVLYNQRVEEISPNIRYCAYNIGDQ

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	4

Primary citation

SRP RNA remodeling by SRP68 explains its role in protein translocation. Grotwinkel, J.T., Wild, K., Segnitz, B. et al. Science (2014) 344:101-104. DOI 10.1126/science.1249094 · PubMed

Other PDB entries of the same protein (UniProt P09132 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1JID 1.8 Å, Human SRP19 in complex with helix 6 of Human SRP RNA
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
5M73 3.4 Å, Structure of the human SRP S domain with SRP72 RNA-binding domain
3KTV 3.8 Å, Crystal structure of the human SRP19/S-domain SRP RNA complex
2J37 8.7 Å, Model of mammalian srp bound to 80S rncs
1RY1 12.0 Å, Structure of the signal recognition particle interacting with the elongation-arrested…

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