4C7O: Signal recognition particle protein

The structural basis of FtsY recruitment and GTPase activation by SRP RNA. Determined by X-ray diffraction at 2.6 Å resolution. Released 20 Nov 2013.

Method: X-ray diffraction
Resolution: 2.6 Å
Organism: ESCHERICHIA COLI
Chains: 5
Atoms: 10,374
Mol. weight: 143.56 kDa
Ligands: GDP, MG, ALF
Released: 20 Nov 2013

Explore 4C7O in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4C7O contains 50 α-helices and 38 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: 12 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	5-15	11
α-helix	24-40	17
α-helix	45-60	16
α-helix	70-86	17
β-strand	101-106	6	1
α-helix	113-126	14
β-strand	132-136	5	1
α-helix	144-155	12
β-strand	158-160	3	1
α-helix	168-181	14
β-strand	186-190	5	1
α-helix	199-212	14
β-strand	216-222	7	1
β-strand	225	1	2
α-helix	229-239	11
β-strand	244-248	5	1
α-helix	258-266	9
α-helix	268-269	2
β-strand	270-274	5	1
β-strand	282-284	3	1
α-helix	287-295	9

Chain B: 12 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	31-43	13
α-helix	48-64	17
α-helix	70-86	17
α-helix	90-92	3
β-strand	100-105	6	3
α-helix	112-125	14
β-strand	130-133	4	3
α-helix	142-152	11
β-strand	157-158	2	3
α-helix	166-179	14
β-strand	184-187	4	3
α-helix	188	1
α-helix	197-210	14
β-strand	220-226	7	3
β-strand	229	1	2
α-helix	232-244	13
β-strand	248-252	5	3
α-helix	262-270	9
β-strand	274-278	5	3
β-strand	286-288	3	3
α-helix	291-299	9

Chain C: 12 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	3-15	13
α-helix	24-40	17
α-helix	45-59	15
α-helix	62-64	3
α-helix	70-86	17
β-strand	101-107	7	4
α-helix	113-126	14
β-strand	132-136	5	4
α-helix	144-155	12
β-strand	158-160	3	4
α-helix	168-181	14
β-strand	186-190	5	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, 11 β-strands

Element	Residues	Length	Sheet
α-helix	27	1
β-strand	28	1	6
α-helix	29	1
α-helix	31-43	13
α-helix	48-64	17
β-strand	69	1	6
α-helix	70-85	16
α-helix	86-88	3
α-helix	90-92	3
β-strand	100-105	6	7
α-helix	112-125	14
β-strand	130-135	6	7
α-helix	142-153	12
β-strand	157-158	2	7
α-helix	166-179	14
β-strand	184-189	6	7
α-helix	197-211	15
β-strand	220-226	7	7
β-strand	229	1	5
α-helix	232-244	13
β-strand	248-252	5	7
α-helix	262-270	9
β-strand	274-278	5	7
β-strand	286-288	3	7
α-helix	291-300	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Signal recognition particle protein	A, C	protein	298	ESCHERICHIA COLI	P0AGD7 (AlphaFold model)
Signal recognition particle receptor ftsy	B, D	protein	278	ESCHERICHIA COLI	P10121 (AlphaFold model)
Srp RNA	E	RNA	48	ESCHERICHIA COLI

Sequence of entity 1 (A, C), FASTA

>4C7O_1 SIGNAL RECOGNITION PARTICLE PROTEIN (chains A, C)
MFDNLTDRLSRTLRNISGRGRLTEDNVKDTLREVRMALLEADVALPVVREFINRVKEKAV
GHEVNKSLTPGQEFVKIVRNELVAAMGEENQTLNLAAQPPAVVLMAGLQGAGKTTSVGKL
GKFLREKHKKKVLVVSADVYRPAAIKQLETLAEQVGVDFFPSDVGQKPVDIVNAALKEAK
LKFYDVLLVDTAGRLHVDEAMMDEIKQVHASINPVETLFVVDAMTGQDAANTAKAFNEAL
PLTGVVLTKVDGDARGGAALSIRHITGKPIKFLGVGEKTEALEPFHPDRIASRILGMG

Sequence of entity 2 (B, D), FASTA

>4C7O_2 SIGNAL RECOGNITION PARTICLE RECEPTOR FTSY (chains B, D)
GKKIDDDLFEELEEQLLIADVGVETTRKIITNLTEGASRKQLRDAEALYGLLKEEMGEIL
AKVDEPLNVEGKAPFVILMVGVNGVGKTTTIGKLARQFEQQGKSVMLAAGDTFRAAAVEQ
LQVWGQRNNIPVIAQHTGADSASVIFDAIQAAKARNIDVLIADTAGRLQNKSHLMEELKK
IVRVMKKLDVEAPHEVMLTIDASTGQNAVSQAKLFHEAVGLTGITLTKLDGTAKGGVIFS
VADQFGIPIRYIGVGERIEDLRPFKADDFIEALFARED

Sequence of entity 3 (E), FASTA

>4C7O_3 SRP RNA (chains E)
UGUUGGUUCUCCCGCAACGCGGAAGCGUGUGCCGGGAUGUAGCUGGCA

Ligands and cofactors

ID	Name	Formula	Copies
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	5
MG	Magnesium ion	Mg	4
ALF	Tetrafluoroaluminate ion	Al F4	4

Primary citation

The Structural Basis of Ftsy Recruitment and Gtpase Activation by Srp RNA. Voigts-Hoffmann, F., Schmitz, N., Shen, K. et al. Mol Cell (2013) 52:643. DOI 10.1016/J.MOLCEL.2013.10.005 · PubMed

Other PDB entries of the same protein (UniProt P0AGD7 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1HQ1 1.52 Å, Structural and energetic analysis of RNA recognition by a universally conserved protein…
1DUL 1.8 Å, Structure of the ribonucleoprotein core of the E. Coli signal recognition particle
3LQX 1.93 Å, SRP ribonucleoprotein core complexed with cobalt hexammine
2PXD 2.0 Å, Variant 1 of Ribonucleoprotein Core of the E. Coli Signal Recognition Particle
2PXE 2.0 Å, Variant 4 of Ribonucleoprotein Core of the E. Coli Signal Recognition Particle
2PXF 2.0 Å, Variant 5 of Ribonucleoprotein Core of the E. Coli Signal Recognition Particle
2PXV 2.0 Å, Variant 6 of Ribonucleoprotein Core of the E. Coli Signal Recognition Particle
7O9I 2.49 Å, Escherichia coli Ffh in complex with pppGpp
2PXB 2.5 Å, Variant 2 of Ribonucleoprotein Core of the E. Coli Signal Recognition Particle
2PXK 2.5 Å, Variant 8 of Ribonucleoprotein Core of the E. Coli Signal Recognition Particle
2PXL 2.5 Å, Variant 9 of Ribonucleoprotein Core of the E. Coli Signal Recognition Particle
2PXP 2.5 Å, Variant 13 of Ribonucleoprotein Core of the E. Coli Signal Recognition Particle

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