PDB-8cn6: CD59 in complex with CP-06 peptide

ID or keywords:

Entry

Database: PDB / ID: 8cn6

Title

CD59 in complex with CP-06 peptide

Components

CD59 glycoprotein
Cyclic peptide CP-06

Keywords

LIPID BINDING PROTEIN / Peptide bound Complex / Terminal Complement inhibitor

Function / homology

Function and homology information

negative regulation of activation of membrane attack complex / complement binding / regulation of complement-dependent cytotoxicity / regulation of complement activation / Cargo concentration in the ER / COPII-mediated vesicle transport / tertiary granule membrane / specific granule membrane / COPI-mediated anterograde transport / transport vesicle ...
Similarity search - Function

Biological species

Homo sapiens (human)
synthetic construct (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.43 Å

Authors

Bickel, J. / Ahmed, A. / Morgan, M. / Horrell, S. / El Omari, K. / Couves, E.C. / Bubeck, D. / Tate, E.

Funding support

European Union,

United Kingdom, 3items

Organization	Grant number	Country
European Research Council (ERC)	864751	European Union
Cancer Research UK	C24523/A26234	United Kingdom
Engineering and Physical Sciences Research Council	EP/L015498/1	United Kingdom

Citation

Journal: Angew.Chem.Int.Ed.Engl. / Year: 2025
Title: Macrocyclic Peptide Probes for Immunomodulatory Protein CD59: Potent Modulators of Bacterial Toxin Activity and Antibody-Dependent Cytotoxicity.
Authors: Bickel, J.K. / Ahmed, A.I.S. / Pidd, A.B. / Morgan, R.M. / McAllister, T.E. / Horrell, S. / Couves, E.C. / Nagaraj, H. / Bartlett, E.J. / El Omari, K. / Kawamura, A. / Bubeck, D. / Tate, E.W.

History

Deposition	Feb 22, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Nov 13, 2024	Provider: repository / Type: Initial release
Revision 1.1	May 28, 2025	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8cn6.cif.gz	469.1 KB	Display	PDBx/mmCIF format
PDB format	pdb8cn6.ent.gz	332 KB	Display	PDB format
PDBx/mmJSON format	8cn6.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8cn6_validation.pdf.gz	479.8 KB	Display	wwPDB validaton report
Full document	8cn6_full_validation.pdf.gz	494.4 KB	Display
Data in XML	8cn6_validation.xml.gz	22.6 KB	Display
Data in CIF	8cn6_validation.cif.gz	30.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/cn/8cn6 ftp://data.pdbj.org/pub/pdb/validation_reports/cn/8cn6	HTTPS FTP

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Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#54 - Jun 2004 Acetylcholinesterase similarity (1) #53 - May 2004 Serpins similarity (2) #194 - Feb 2016 Designer Insulins similarity (1) #205 - Jan 2017 Nuclear Pore Complex similarity (1) #14 - Feb 2001 Insulin similarity (1) #222 - Jun 2018 Proteins and Nanoparticles similarity (1)

Deposited unit

A: CD59 glycoprotein

B: CD59 glycoprotein

C: CD59 glycoprotein

D: CD59 glycoprotein

E: CD59 glycoprotein

F: CD59 glycoprotein

J: Cyclic peptide CP-06

G: Cyclic peptide CP-06

H: Cyclic peptide CP-06

hetero molecules

59.1 kDa, 9 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: CD59 glycoprotein

C: CD59 glycoprotein

G: Cyclic peptide CP-06

hetero molecules

defined by author
19.7 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: CD59 glycoprotein

E: CD59 glycoprotein

J: Cyclic peptide CP-06

defined by author
19.7 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

D: CD59 glycoprotein

F: CD59 glycoprotein

H: Cyclic peptide CP-06

hetero molecules

defined by author
19.7 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	30.94, 85.88, 96.57
Angle α, β, γ (deg.)	90, 90.03, 90
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Beg auth comp-ID: MET / Beg label comp-ID: MET / Auth asym-ID: A / Label asym-ID: A

Dom-ID	Component-ID	Ens-ID	End auth comp-ID	End label comp-ID	Auth seq-ID	Label seq-ID
1	1	1	GLN	GLN	0 - 74	1 - 75
2	1	1	GLN	GLN	0 - 74	1 - 75
3	2	2	GLN	GLN	0 - 74	1 - 75
4	2	2	GLN	GLN	0 - 74	1 - 75
5	3	3	GLU	GLU	0 - 76	1 - 77
6	3	3	GLU	GLU	0 - 76	1 - 77
7	4	4	GLN	GLN	0 - 74	1 - 75
8	4	4	GLN	GLN	0 - 74	1 - 75
9	5	5	GLU	GLU	0 - 76	1 - 77
10	5	5	GLU	GLU	0 - 76	1 - 77
11	6	6	LEU	LEU	0 - 75	1 - 76
12	6	6	LEU	LEU	0 - 75	1 - 76
13	7	7	GLN	GLN	0 - 74	1 - 75
14	7	7	GLN	GLN	0 - 74	1 - 75
15	8	8	LEU	LEU	0 - 75	1 - 76
16	8	8	LEU	LEU	0 - 75	1 - 76
17	9	9	GLN	GLN	0 - 74	1 - 75
18	9	9	GLN	GLN	0 - 74	1 - 75
19	10	10	GLN	GLN	0 - 74	1 - 75
20	10	10	GLN	GLN	0 - 74	1 - 75
21	11	11	LEU	LEU	0 - 75	1 - 76
22	11	11	LEU	LEU	0 - 75	1 - 76
23	12	12	GLN	GLN	0 - 74	1 - 75
24	12	12	GLN	GLN	0 - 74	1 - 75
25	13	13	GLN	GLN	0 - 74	1 - 75
26	13	13	GLN	GLN	0 - 74	1 - 75
27	14	14	GLU	GLU	0 - 76	1 - 77
28	14	14	GLU	GLU	0 - 76	1 - 77
29	15	15	GLN	GLN	0 - 74	1 - 75
30	15	15	GLN	GLN	0 - 74	1 - 75

NCS ensembles :

ID	Details
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4
3	Local NCS retraints between domains: 5 6
4	Local NCS retraints between domains: 7 8
5	Local NCS retraints between domains: 9 10
6	Local NCS retraints between domains: 11 12
7	Local NCS retraints between domains: 13 14
8	Local NCS retraints between domains: 15 16
9	Local NCS retraints between domains: 17 18
10	Local NCS retraints between domains: 19 20
11	Local NCS retraints between domains: 21 22
12	Local NCS retraints between domains: 23 24
13	Local NCS retraints between domains: 25 26
14	Local NCS retraints between domains: 27 28
15	Local NCS retraints between domains: 29 30

#1: Protein	CD59 glycoprotein / 1F5 antigen / 20 kDa homologous restriction factor / HRF-20 / HRF20 / MAC-inhibitory protein / MAC- ...1F5 antigen / 20 kDa homologous restriction factor / HRF-20 / HRF20 / MAC-inhibitory protein / MAC-IP / MEM43 antigen / Membrane attack complex inhibition factor / MACIF / Membrane inhibitor of reactive lysis / MIRL / Protectin Mass: 8987.199 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CD59, MIC11, MIN1, MIN2, MIN3, MSK21 / Production host: Escherichia coli (E. coli) / References: UniProt: P13987
#2: Protein/peptide	Cyclic peptide CP-06 Mass: 1684.859 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.13 Å³/Da / Density % sol: 42.38 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.01 M ZnCl2, 0.1 M HEPES pH 7.0, 20% w/v PEG 6000

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
Detector	Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 10, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 2.43→48.332 Å / Num. obs: 18920 / % possible obs: 99.1 % / Redundancy: 3.4 % / B_iso Wilson estimate: 78.67 Å² / CC_1/2: 0.99 / R_merge(I) obs: 0.102 / R_pim(I) all: 0.066 / R_rim(I) all: 0.122 / Net I/σ(I): 7
Reflection shell	Resolution: 2.43→2.47 Å / R_merge(I) obs: 0.23 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 1967 / CC_1/2: 0.29 / R_pim(I) all: 0.143 / R_rim(I) all: 0.272 / % possible all: 99.5

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0425	refinement
xia2		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.43→48.332 Å / Cor.coef. F_o:F_c: 0.944 / Cor.coef. F_o:F_c free: 0.917 / SU B: 45.581 / SU ML: 0.436 / Cross valid method: FREE R-VALUE / ESU R: 0.908 / ESU R Free: 0.352
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2983	969	5.127 %
R_work	0.2353	17932	-
all	0.239	-	-
obs	-	18901	98.948 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 78.563 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.882 Å²	0 Å²	0.344 Å²
2-	-	1.587 Å²	0 Å²
3-	-	-	0.294 Å²

Refinement step

Cycle: LAST / Resolution: 2.43→48.332 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3691	0	362	10	4063

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.012	4168
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	3641
X-RAY DIFFRACTION	r_angle_refined_deg	2.777	1.855	5662
X-RAY DIFFRACTION	r_angle_other_deg	1.061	1.795	8396
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	8.647	5	453
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	20.707	5	60
X-RAY DIFFRACTION	r_dihedral_angle_other_2_deg	9.328	5	84
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.896	10	646
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	13.729	10	201
X-RAY DIFFRACTION	r_chiral_restr	0.136	0.2	597
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.02	4983
X-RAY DIFFRACTION	r_gen_planes_other	0.003	0.02	1041
X-RAY DIFFRACTION	r_nbd_refined	0.254	0.2	845
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.224	0.2	3424
X-RAY DIFFRACTION	r_nbtor_refined	0.206	0.2	1896
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.095	0.2	2454
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.236	0.2	85
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.049	0.2	1
X-RAY DIFFRACTION	r_metal_ion_refined	0.279	0.2	2
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.223	0.2	22
X-RAY DIFFRACTION	r_nbd_other	0.241	0.2	112
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.296	0.2	5
X-RAY DIFFRACTION	r_mcbond_it	7.441	5.186	1830
X-RAY DIFFRACTION	r_mcbond_other	7.44	5.187	1830
X-RAY DIFFRACTION	r_mcangle_it	10.109	9.297	2277
X-RAY DIFFRACTION	r_mcangle_other	10.108	9.299	2278
X-RAY DIFFRACTION	r_scbond_it	8.661	5.72	2338
X-RAY DIFFRACTION	r_scbond_other	8.661	5.721	2338
X-RAY DIFFRACTION	r_scangle_it	12.077	10.328	3385
X-RAY DIFFRACTION	r_scangle_other	12.075	10.327	3386
X-RAY DIFFRACTION	r_lrange_it	14.724	54.961	4401
X-RAY DIFFRACTION	r_lrange_other	14.724	54.962	4400
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.107	0.05	2250
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.131	0.05	2206
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.111	0.05	2323
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.124	0.05	2236
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.137	0.05	2254
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.115	0.05	2277
X-RAY DIFFRACTION	r_ncsr_local_group_7	0.104	0.05	2266
X-RAY DIFFRACTION	r_ncsr_local_group_8	0.11	0.05	2306
X-RAY DIFFRACTION	r_ncsr_local_group_9	0.124	0.05	2205
X-RAY DIFFRACTION	r_ncsr_local_group_10	0.118	0.05	2248
X-RAY DIFFRACTION	r_ncsr_local_group_11	0.123	0.05	2262
X-RAY DIFFRACTION	r_ncsr_local_group_12	0.1	0.05	2272
X-RAY DIFFRACTION	r_ncsr_local_group_13	0.135	0.05	2224
X-RAY DIFFRACTION	r_ncsr_local_group_14	0.128	0.05	2281
X-RAY DIFFRACTION	r_ncsr_local_group_15	0.11	0.05	2218

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.10703	0.05009
1	2	A	X-RAY DIFFRACTION	Local ncs	0.10703	0.05009
2	3	A	X-RAY DIFFRACTION	Local ncs	0.13084	0.0501
2	4	A	X-RAY DIFFRACTION	Local ncs	0.13084	0.0501
3	5	A	X-RAY DIFFRACTION	Local ncs	0.11079	0.0501
3	6	A	X-RAY DIFFRACTION	Local ncs	0.11079	0.0501
4	7	A	X-RAY DIFFRACTION	Local ncs	0.12377	0.0501
4	8	A	X-RAY DIFFRACTION	Local ncs	0.12377	0.0501
5	9	A	X-RAY DIFFRACTION	Local ncs	0.13661	0.05009
5	10	A	X-RAY DIFFRACTION	Local ncs	0.13661	0.05009
6	11	A	X-RAY DIFFRACTION	Local ncs	0.11537	0.0501
6	12	A	X-RAY DIFFRACTION	Local ncs	0.11537	0.0501
7	13	A	X-RAY DIFFRACTION	Local ncs	0.10357	0.0501
7	14	A	X-RAY DIFFRACTION	Local ncs	0.10357	0.0501
8	15	A	X-RAY DIFFRACTION	Local ncs	0.1098	0.0501
8	16	A	X-RAY DIFFRACTION	Local ncs	0.1098	0.0501
9	17	A	X-RAY DIFFRACTION	Local ncs	0.12388	0.0501
9	18	A	X-RAY DIFFRACTION	Local ncs	0.12388	0.0501
10	19	A	X-RAY DIFFRACTION	Local ncs	0.11821	0.0501
10	20	A	X-RAY DIFFRACTION	Local ncs	0.11821	0.0501
11	21	A	X-RAY DIFFRACTION	Local ncs	0.12294	0.0501
11	22	A	X-RAY DIFFRACTION	Local ncs	0.12294	0.0501
12	23	A	X-RAY DIFFRACTION	Local ncs	0.0996	0.0501
12	24	A	X-RAY DIFFRACTION	Local ncs	0.0996	0.0501
13	25	A	X-RAY DIFFRACTION	Local ncs	0.13483	0.0501
13	26	A	X-RAY DIFFRACTION	Local ncs	0.13483	0.0501
14	27	A	X-RAY DIFFRACTION	Local ncs	0.12808	0.0501
14	28	A	X-RAY DIFFRACTION	Local ncs	0.12808	0.0501
15	29	A	X-RAY DIFFRACTION	Local ncs	0.10984	0.0501
15	30	A	X-RAY DIFFRACTION	Local ncs	0.10984	0.0501

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
2.43-2.493	0.407	72	0.376	1299	0.378	1376	0.896	0.885	99.6366	0.368
2.493-2.561	0.409	75	0.393	1301	0.394	1382	0.861	0.883	99.5658	0.39
2.561-2.635	0.438	61	0.366	1246	0.369	1315	0.834	0.907	99.3916	0.344
2.635-2.716	0.409	62	0.334	1217	0.337	1283	0.89	0.935	99.6882	0.303
2.716-2.805	0.394	67	0.291	1213	0.295	1288	0.87	0.947	99.3789	0.259
2.805-2.903	0.401	72	0.324	1103	0.329	1182	0.901	0.933	99.4078	0.299
2.903-3.012	0.337	60	0.285	1121	0.288	1188	0.92	0.948	99.4108	0.26
3.012-3.134	0.333	49	0.264	1068	0.267	1129	0.942	0.961	98.9371	0.232
3.134-3.273	0.303	55	0.226	997	0.23	1063	0.94	0.97	98.9652	0.205
3.273-3.432	0.247	52	0.205	1009	0.207	1075	0.958	0.975	98.6977	0.191
3.432-3.617	0.279	38	0.225	898	0.227	956	0.951	0.972	97.908	0.216
3.617-3.835	0.324	57	0.217	880	0.223	950	0.934	0.978	98.6316	0.213
3.835-4.098	0.272	36	0.219	807	0.221	866	0.956	0.971	97.3441	0.219
4.098-4.424	0.332	31	0.195	807	0.199	852	0.928	0.978	98.3568	0.207
4.424-4.842	0.276	49	0.173	666	0.181	724	0.958	0.984	98.7569	0.193
4.842-5.406	0.185	40	0.186	639	0.186	689	0.984	0.982	98.5486	0.206
5.406-6.23	0.306	35	0.225	577	0.23	620	0.954	0.976	98.7097	0.257
6.23-7.598	0.403	20	0.229	488	0.235	518	0.952	0.972	98.0695	0.269
7.598-10.615	0.227	25	0.206	374	0.208	405	0.971	0.977	98.5185	0.258
10.615-48.332	0.376	13	0.323	222	0.326	239	0.876	0.91	98.3264	0.421

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	0.5579	0.233	1.3533	8.0231	1.2128	6.4109	0.0017	-0.2399	-0.2036	0.1167	-0.3521	-0.0679	0.0943	-0.069	0.3503	0.1594	0.0382	-0.0159	0.2086	0.2261	0.3144	-12.3847	-12.1068	-7.8774
2	2.9753	0.4459	0.4961	5.6542	0.3651	7.4031	0.0027	-0.2007	0.1607	-0.2435	-0.103	-0.0097	-0.0529	-0.1241	0.1003	0.0418	-0.001	-0.0327	0.2131	0.0592	0.0686	-4.2783	2.5264	13.5324
3	2.8059	-1.7528	0.0981	7.4288	0.8186	7.4178	-0.0502	0.3394	-0.5466	-0.015	0.0444	0.2463	0.4581	0.2767	0.0057	0.1662	0.0157	-0.0727	0.0976	-0.0702	0.1627	-11.3756	-18.8313	-31.2555
4	1.8981	-0.6234	-0.7517	7.5037	0.2232	5.914	0.197	0.3126	0.3744	-0.3329	-0.2542	-0.1443	-0.0923	-0.0903	0.0572	0.1658	-0.0643	-0.0501	0.1375	0.1313	0.1397	-12.3777	11.2365	-40.3847
5	5.291	-0.8154	-1.9657	4.9766	1.7715	8.4232	-0.0163	-0.0157	-0.0017	0.4475	-0.0603	-0.1578	0.1015	0.05	0.0767	0.0633	-0.052	-0.0488	0.1871	0.1002	0.0664	-3.6947	-3.8092	36.8698
6	4.385	1.5684	-1.0355	7.4057	0.4284	8.8783	0.145	-0.3261	0.6774	0.2234	-0.0827	0.1427	-0.3669	0.261	-0.0623	0.1075	-0.0214	-0.0556	0.0286	-0.043	0.192	-11.5443	17.6693	-17.0518

Refinement TLS group

Selection: ALL

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