5L3R: PDB entry 5L3R

Structure of the GTPase heterodimer of chloroplast SRP54 and FtsY from Arabidopsis thaliana. Determined by X-ray diffraction at 2.5 Å resolution. Released 8 Jun 2016.

Method: X-ray diffraction
Resolution: 2.5 Å
Organism: Arabidopsis thaliana
Chains: 4
Atoms: 8,672
Mol. weight: 130.68 kDa
Ligands: GCP, MG
Released: 8 Jun 2016

Explore 5L3R in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5L3R contains 50 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: 12 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	104-116	13
α-helix	121-138	18
α-helix	146-161	16
α-helix	168-170	3
β-strand	177-182	6	1
α-helix	189-201	13
β-strand	207-212	6	1
α-helix	219-230	12
β-strand	234-235	2	1
α-helix	243-256	14
β-strand	261-266	6	1
α-helix	274-287	14
β-strand	291-297	7	1
β-strand	300	1	2
α-helix	304-314	11
β-strand	319-323	5	1
α-helix	333-341	9
α-helix	343-344	2
β-strand	345-349	5	1
β-strand	357-359	3	1
α-helix	362-369	8

Chain B: 13 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	80-85	6
α-helix	90-92	3
α-helix	93-106	14
α-helix	111-126	16
α-helix	133-148	16
β-strand	165-171	7	3
α-helix	177-190	14
β-strand	195-198	4	3
α-helix	207-218	12
β-strand	221-223	3	3
α-helix	232-245	14
β-strand	250-253	4	3
α-helix	263-277	15
β-strand	286-292	7	3
β-strand	295	1	2
α-helix	299-310	12
β-strand	314-318	5	3
α-helix	329-336	8
α-helix	338-339	2
β-strand	340-344	5	3
β-strand	352-354	3	3
α-helix	357-364	8

Chain C: 12 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	100-116	17
α-helix	121-138	18
α-helix	146-161	16
α-helix	166-170	5
β-strand	177-182	6	4
α-helix	189-201	13
β-strand	207-212	6	4
α-helix	219-230	12
β-strand	234-235	2	4
α-helix	243-256	14
β-strand	261-266	6	4
α-helix	274-287	14
β-strand	291-297	7	4
β-strand	300	1	5
α-helix	304-314	11
β-strand	319-323	5	4
α-helix	333-341	9
α-helix	343-344	2
β-strand	345-349	5	4
β-strand	357-359	3	4
α-helix	362-369	8

Chain D: 13 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	80-85	6
α-helix	90-92	3
α-helix	93-106	14
α-helix	111-126	16
α-helix	133-148	16
β-strand	165-170	6	6
α-helix	177-190	14
β-strand	195-200	6	6
α-helix	207-218	12
β-strand	221-223	3	6
α-helix	232-245	14
β-strand	250-255	6	6
α-helix	263-277	15
β-strand	286-292	7	6
β-strand	295	1	5
α-helix	299-310	12
β-strand	314-318	5	6
α-helix	329-336	8
α-helix	338-339	2
β-strand	340-344	5	6
β-strand	352-354	3	6
α-helix	357-364	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Signal recognition particle 54 kDa protein, chloroplastic	A, C	protein	301	Arabidopsis thaliana	P37107 (AlphaFold model)
Cell division protein FtsY homolog, chloroplastic	B, D	protein	293	Arabidopsis thaliana	O80842 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>5L3R_1 Signal recognition particle 54 kDa protein, chloroplastic (chains A, C)
HHHHHHMFGQLTGGLEAAWSKLKGEEVLTKDNIAEPMRDIRRALLEADVSLPVVRRFVQS
VSDQAVGMGVIRGVKPDQQLVKIVHDELVKLMGGEVSELQFAKSGPTVILLAGLQGVGKT
TVCAKLACYLKKQGKSCMLIAGDVYRPAAIDQLVILGEQVGVPVYTAGTDVKPADIAKQG
LKEAKKNNVDVVIMDTAGRLQIDKGMMDELKDVKKFLNPTEVLLVVDAMTGQEAAALVTT
FNVEIGITGAILTKLDGDSRGGAALSVKEVSGKPIKLVGRGERMEDLEPFYPDRMAGRIL
G

Sequence of entity 2 (B, D), FASTA

>5L3R_2 Cell division protein FtsY homolog, chloroplastic (chains B, D)
HHHHHHVIDELLLFWNLAETDRVLDELEEALLVSDFGPKITVRIVERLREDIMSGKLKSG
SEIKDALKESVLEMLAKKNSKTELQLGFRKPAVIMIVGVNGGGKTTSLGKLAHRLKNEGT
KVLMAAGDTFRAAASDQLEIWAERTGCEIVVAEGDKAKAATVLSKAVKRGKEEGYDVVLC
DTSGRLHTNYSLMEELIACKKAVGKIVSGAPNEILLVLDGNTGLNMLPQAREFNEVVGIT
GLILTKLDGSARGGCVVSVVEELGIPVKFIGVGEAVEDLQPFDPEAFVNAIFS

Ligands and cofactors

ID	Name	Formula	Copies
GCP	Phosphomethylphosphonic acid guanylate ester	C11 H18 N5 O13 P3	4
MG	Magnesium ion	Mg	4

Water and common crystallization additives (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 P37107 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3UI2 3.18 Å, Crystal structure of the cpSRP54 tail bound to cpSRP43
2HUG 3D Solution Structure of the Chromo-2 Domain of cpSRP43 complexed with cpSRP54 peptide

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