8CPL: PDB entry 8CPL

YZw2 a scaffold for cryo-EM of small proteins of interest. Determined by X-ray diffraction at 1.6 Å resolution. Released 12 Jun 2024.

Method: X-ray diffraction
Resolution: 1.6 Å
Organisms: Escherichia coli, Staphylococcus aureus
Chains: 4
Atoms: 17,168
Mol. weight: 218.86 kDa
Ligands: PLP
Released: 12 Jun 2024

Explore 8CPL in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8CPL contains 99 α-helices and 80 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: 23 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	10-22	13
α-helix	28-41	14
α-helix	42-46	5
α-helix	48-53	6
α-helix	55-58	4
β-strand	66	1	1
β-strand	67-70	4	2
β-strand	75-78	4	2
β-strand	83-86	4	2
α-helix	89-91	3
α-helix	101-111	11
β-strand	122	1	3
α-helix	124-136	13
β-strand	141-147	7	4
α-helix	150-165	16
β-strand	172-176	5	4
α-helix	185-190	6
α-helix	194-197	4
α-helix	198-200	3
β-strand	207-210	4	4
α-helix	215-228	14
β-strand	232-237	6	4
β-strand	241	1	5
β-strand	247	1	5
α-helix	248-250	3
α-helix	253-264	12
β-strand	267-271	5	4
α-helix	285-287	3
β-strand	295-298	4	4
α-helix	300-303	4
β-strand	310-315	6	4
α-helix	316-319	4
α-helix	320-322	3
α-helix	337-352	16
α-helix	355-376	22
β-strand	381-387	7	6
β-strand	390-395	6	6
α-helix	398-410	13
β-strand	413-414	2	2
β-strand	418	1	7
β-strand	421	1	7
β-strand	424-427	4	6
α-helix	435-459	25

Chain B: 24 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	10-22	13
α-helix	28-41	14
α-helix	42-46	5
α-helix	49-53	5
α-helix	55-58	4
β-strand	66	1	3
β-strand	67-70	4	8
β-strand	75-78	4	8
β-strand	83-86	4	8
α-helix	89-91	3
α-helix	101-111	11
β-strand	122	1	1
α-helix	124-136	13
β-strand	141-147	7	9
α-helix	150-165	16
α-helix	166-168	3
β-strand	172-176	5	9
α-helix	185-190	6
α-helix	194-197	4
α-helix	198-200	3
β-strand	207-210	4	9
α-helix	215-228	14
β-strand	232-237	6	9
β-strand	241	1	10
β-strand	247	1	10
α-helix	248-250	3
α-helix	253-264	12
β-strand	267-271	5	9
α-helix	285-287	3
β-strand	295-298	4	9
α-helix	300-303	4
β-strand	310-315	6	9
α-helix	316-319	4
α-helix	320-322	3
α-helix	337-352	16
α-helix	355-376	22
β-strand	381-387	7	11
β-strand	390-395	6	11
α-helix	398-410	13
β-strand	413-414	2	8
β-strand	418	1	12
β-strand	421	1	12
β-strand	424-427	4	11
α-helix	435-463	29

Chain C: 28 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	10-22	13
α-helix	28-41	14
α-helix	42-46	5
α-helix	49-53	5
α-helix	55-58	4
β-strand	66	1	13
β-strand	67-70	4	14
β-strand	75-78	4	14
β-strand	83-86	4	14
α-helix	89-91	3
α-helix	101-111	11
β-strand	122	1	15
α-helix	124-136	13
β-strand	141-147	7	16
α-helix	150-165	16
α-helix	166-168	3
β-strand	172-176	5	16
α-helix	185-190	6
α-helix	194-197	4
α-helix	198-200	3
β-strand	207-210	4	16
α-helix	215-228	14
β-strand	232-237	6	16
β-strand	241	1	17
β-strand	247	1	17
α-helix	248-250	3
α-helix	253-264	12
α-helix	266	1
β-strand	267-271	5	16
α-helix	285-287	3
β-strand	295-298	4	16
α-helix	300-303	4
β-strand	310-315	6	16
α-helix	316-319	4
α-helix	320-322	3
α-helix	337-352	16
α-helix	355-376	22
β-strand	381-387	7	18
β-strand	390-395	6	18
α-helix	398-410	13
β-strand	413-414	2	14
β-strand	418	1	19
β-strand	421	1	19
β-strand	424-427	4	18
α-helix	435-465	31
α-helix	473-485	13
α-helix	487-489	3
α-helix	490-503	14

Chain D: 24 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	10-22	13
α-helix	28-41	14
α-helix	42-46	5
α-helix	49-53	5
α-helix	55-58	4
β-strand	66	1	15
β-strand	67-70	4	20
β-strand	75-78	4	20
β-strand	83-86	4	20
α-helix	89-91	3
α-helix	101-111	11
β-strand	122	1	13
α-helix	124-136	13
β-strand	141-147	7	21
α-helix	150-165	16
α-helix	166-168	3
β-strand	172-176	5	21
α-helix	185-190	6
α-helix	194-197	4
α-helix	198-200	3
β-strand	207-210	4	21
α-helix	215-228	14
β-strand	232-237	6	21
β-strand	241	1	22
β-strand	247	1	22
α-helix	248-250	3
α-helix	253-264	12
β-strand	267-271	5	21
α-helix	285-288	4
β-strand	295-298	4	21
α-helix	300-303	4
β-strand	310-315	6	21
α-helix	316-319	4
α-helix	320-322	3
α-helix	337-352	16
α-helix	355-376	22
β-strand	381-387	7	23
β-strand	390-395	6	23
α-helix	398-410	13
β-strand	413-414	2	20
β-strand	418	1	24
β-strand	421	1	24
β-strand	424-427	4	23
α-helix	435-463	29

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Putrescine aminotransferase,Immunoglobulin G-binding protein A	A, B, C, D	protein	501	Escherichia coli, Staphylococcus aureus	P38507 (AlphaFold model), P42588 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>8CPL_1 Putrescine aminotransferase,Immunoglobulin G-binding protein A (chains A, B, C, D)
SASALACSAHALNLIEKRTLDHEEMKALNREVIEYFKEHVNPGFLEYRKSVTAGGDYGAV
EWQAGSLNTLVDTQGQEFIDCLGGFGIFNVGHRNPVVVSAVQNQLAKQPLHSQELLDPLR
AMLAKTLAALTPGKLKYSFFCNSGTESVEAALKLAKAYQSPRGKFTFIATSGAFHGKSLG
ALSATAKSTFRKPFMPLLPGFRHVPFGNIEAMRTALNECKKTGDDVAAVILEPIQGEGGV
ILPPPGYLTAVRKLCDEFGALMILDEVQTGMGRTGKMFACEHENVQPDILCLAKALGGGV
MPIGATIATEEVFSVLFDNPFLHTTTFGGNPLACAAALATINVLLEQNLPAQAEQKGDML
LDGFRQLAREYPDLVQEARGKGMLMAIEFVDNEIGYNFASEMFRQRVLVAGTLNNAKTIR
IEPPLTLTIEQCELVIKAARKALAAMRVSVEQQNAFYEILHLPNLNEEQRNAFIQSLKDD
PSQSANLLAEAKKLNDAQAPK

Ligands and cofactors

ID	Name	Formula	Copies
PLP	Pyridoxal-5'-phosphate	C8 H10 N O6 P	4

Primary citation

Engineered imaging scaffolds for cryo-EM of small proteins of interest. Moche, M., Nygren, P.A., Nilvebrant, J. To be published.

Other PDB entries of the same protein (UniProt P38507 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4NPD 0.9 Å, High-resolution structure of C domain of staphylococcal protein A at cryogenic temperature
4NPE 1.42 Å, High-resolution structure of C domain of staphylococcal protein A at room temperature
4NPF 1.49 Å, High-resolution structure of two tandem B domains of staphylococcal protein A connected…
4ZMD 1.87 Å, C domain of staphylococcal protein A mutant - Q9W
4ZNC 2.28 Å, Fc fragment of human IgG in complex with the C domain of staphylococcal protein A mutant…
1LP1 2.3 Å, Protein Z in complex with an in vitro selected affibody
5CBN 2.3 Å, Fusion protein of mbp3-16 and B4 domain of protein A from staphylococcal aureus with…
4WWI 2.31 Å, Crystal structure of the C domain of staphylococcal protein A in complex with the Fc…
5H7D 2.57 Å, Crystal structure of the YgjG-protein A-Zpa963-calmodulin complex
5EWX 2.6 Å, Fusion protein of T4 lysozyme and B4 domain of protein A from staphylococcal aureus with…
5H76 2.6 Å, Crystal structure of the DARPin-Protein A fusion protein
5H79 2.7 Å, Crystal structure of a repeat protein with three Protein A repeat module

Browse structure collections

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