5E4W: CpSRP43 chromodomains 2 and 3

Crystal structure of cpSRP43 chromodomains 2 and 3 in complex with the Alb3 tail. Determined by X-ray diffraction at 2.8 Å resolution. Released 2 Dec 2015.

Method: X-ray diffraction
Resolution: 2.8 Å
Organisms: Escherichia coli O157:H7, Arabidopsis thaliana
Chains: 6
Atoms: 3,545
Mol. weight: 50.12 kDa
Ligands: CA
Released: 2 Dec 2015

Explore 5E4W in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5E4W contains 21 α-helices and 36 β-strands across 6 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: 6 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	14-17	4	1
α-helix	22	1
α-helix	23-27	5
β-strand	32-38	7	1
α-helix	43-47	5
α-helix	49-58	10
β-strand	60	1	2
β-strand	63	1	2
β-strand	64-69	6	1
α-helix	77-80	4
β-strand	84-85	2	3
β-strand	87-92	6	1
β-strand	95-101	7	1
α-helix	106-119	14

Chain B: 6 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	15-16	2	1
α-helix	22	1
α-helix	23-27	5
β-strand	32-38	7	1
α-helix	43-47	5
α-helix	49-58	10
β-strand	60	1	4
β-strand	63	1	4
β-strand	64-69	6	1
α-helix	77-80	4
β-strand	84-85	2	5
β-strand	87-92	6	1
β-strand	95-101	7	1
α-helix	106-118	13

Chain C: 4 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	268-269	2	5
β-strand	272-281	10	6
β-strand	284-291	8	6
β-strand	297-301	5	6
α-helix	302-304	3
α-helix	307-314	8
β-strand	317-320	4	7
β-strand	322-330	9	8
β-strand	337-343	7	8
β-strand	350-353	4	8
α-helix	354-356	3
α-helix	359-368	10

Chain D: 5 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	268-269	2	3
β-strand	272-278	7	9
β-strand	281	1	10
β-strand	284	1	10
β-strand	286-291	6	9
β-strand	297-301	5	9
α-helix	302-304	3
α-helix	307-314	8
β-strand	317-321	5	11
β-strand	322-330	9	12
β-strand	337-343	7	12
β-strand	350-353	4	12
α-helix	354-356	3
α-helix	359-363	5
α-helix	366-368	3

Chain E: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	456-459	4	7

Chain F: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	455-459	5	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Thioredoxin-1	A, B	protein	109	Escherichia coli O157:H7	P0AA27 (AlphaFold model)
Signal recognition particle 43 kDa protein, chloroplastic	C, D	protein	105	Arabidopsis thaliana	O22265 (AlphaFold model)
Inner membrane protein ALBINO3, chloroplastic	E, F	protein	9	Arabidopsis thaliana	Q8LBP4 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5E4W_1 Thioredoxin-1 (chains A, B)
DKIIHLTDDSFDTDVLKADGAILVDFWAEWCGPCKMIAPILDEIADEYQGKLTVAKLNID
QNPGTAPKYGIRGIPTLLLFKNGEVAATKVGALSKGQLKEFLDANLAGS

Sequence of entity 2 (C, D), FASTA

>5E4W_2 Signal recognition particle 43 kDa protein, chloroplastic (chains C, D)
QVFEYAEVDEIVEKRGKGKDVEYLVRWKDGGDCEWVKGVHVAEDVAKDYEDGLEYAVAES
VIGKRVGDDGKTIEYLVKWTDMSDATWEPQDNVDSTLVLLYQQQQ

Sequence of entity 3 (E, F), FASTA

>5E4W_3 Inner membrane protein ALBINO3, chloroplastic (chains E, F)
SKRSKRKRT

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	2

Water and common crystallization additives (GOL) are not listed.

Primary citation

Structural basis for cpSRP43 chromodomain selectivity and dynamics in Alb3 insertase interaction. Horn, A., Hennig, J., Ahmed, Y.L. et al. Nat Commun (2015) 6:8875-8875. DOI 10.1038/ncomms9875 · PubMed

Other PDB entries of the same protein (UniProt P0AA27 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3DXB 2.2 Å, Structure of the UHM domain of Puf60 fused to thioredoxin
5IKN 4.8 Å, Crystal Structure of the T7 Replisome in the Absence of DNA

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