PDB-4jb8: Caspase-7 in Complex with DARPin C7_16

ID or keywords:

Entry

Database: PDB / ID: 4jb8

Title

Caspase-7 in Complex with DARPin C7_16

Components

Caspase-7 subunit p11Caspase 7
Caspase-7 subunit p20Caspase 7
DARPin C7_16

Keywords

Hydrolase/DE NOVO PROTEIN / Complex structure / selected DARPin C7_16 / Hydrolase-DE NOVO PROTEIN complex

Function / homology

Function and homology information

caspase-7 / lymphocyte apoptotic process / positive regulation of plasma membrane repair / cellular response to staurosporine / cysteine-type endopeptidase activity involved in execution phase of apoptosis / SMAC, XIAP-regulated apoptotic response / Activation of caspases through apoptosome-mediated cleavage / SMAC (DIABLO) binds to IAPs / SMAC(DIABLO)-mediated dissociation of IAP:caspase complexes / cysteine-type endopeptidase activity involved in apoptotic process ...
Similarity search - Function

Biological species

Homo sapiens (human)
synthetic construct (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.7 Å

Authors

Fluetsch, A. / Seeger, M.A. / Gruetter, M.G.

Citation

Journal: Protein Sci. / Year: 2013
Title: Design, construction, and characterization of a second-generation DARPin library with reduced hydrophobicity.
Authors: Seeger, M.A. / Zbinden, R. / Flutsch, A. / Gutte, P.G. / Engeler, S. / Roschitzki-Voser, H. / Grutter, M.G.

History

Deposition	Feb 19, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 21, 2013	Provider: repository / Type: Initial release
Revision 1.1	Oct 9, 2013	Group: Database references
Revision 1.2	Nov 15, 2017	Group: Refinement description / Category: software
Revision 1.3	Sep 20, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4jb8.cif.gz	176.9 KB	Display	PDBx/mmCIF format
PDB format	pdb4jb8.ent.gz	140.9 KB	Display	PDB format
PDBx/mmJSON format	4jb8.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/jb/4jb8 ftp://data.pdbj.org/pub/pdb/validation_reports/jb/4jb8	HTTPS FTP

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Related structure data

Related structure data	4j7wC 4j8yC 3ibcS 4j92 PDB Unreleased entry S: Starting model for refinement C: citing same article (ref.)
Similar structure data	2oan-1 5hld-d 3jyh-2 3n0t-1 4lsz-d 3ukv-d 5y2g-d 6p74-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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	#56 - Aug 2004 Caspases similarity (20) #224 - Aug 2018 Legumain similarity (11) #177 - Sep 2014 Apoptosomes similarity (3) #19 - Jul 2001 Actin similarity (1)

Deposited unit

A: Caspase-7 subunit p20

B: Caspase-7 subunit p11

P: DARPin C7_16

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

1

A: Caspase-7 subunit p20

B: Caspase-7 subunit p11

P: DARPin C7_16

A: Caspase-7 subunit p20

B: Caspase-7 subunit p11

P: DARPin C7_16

defined by author
101 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	143.880, 52.510, 60.090
Angle α, β, γ (deg.)	90.00, 96.92, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	B-444- HOH
2	1	B-446- HOH

#1: Protein	Caspase-7 subunit p20 / Caspase 7 Mass: 19750.766 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CASP7, MCH3 / Production host: Escherichia coli (E. coli) / References: UniProt: P55210, caspase-7
#2: Protein	Caspase-7 subunit p11 / Caspase 7 Mass: 12424.015 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CASP7, MCH3 / Production host: Escherichia coli (E. coli) / References: UniProt: P55210, caspase-7
#3: Protein	DARPin C7_16 Mass: 18203.930 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 257 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.24 Å³/Da / Density % sol: 45 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.3 Details: 0.2M MgCl2, 100mM Tris, 9% PEG 1000, 9% PEG 8000, pH 8.3, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
Detector	Type: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 13, 2011
Radiation	Monochromator: X06SA / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.7→50 Å / Num. all: 49199 / Num. obs: 49154 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shell	Resolution: 1.7→1.74 Å / % possible all: 99.9

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Processing

Software

Name	Version	Classification
PHASER		phasing
PHENIX	(phenix.refine: 1.8_1069)	refinement
XDS		data reduction
XSCALE		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 3IBC

3ibc

Resolution: 1.7→48.765 Å / SU ML: 0.16 / σ(F): 1.37 / Phase error: 24.86 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1937	1962	4 %	RANDOM by Phenix
R_work	0.1722	-	-	-
obs	0.1731	49087	99.79 %	-
all	-	49199	-	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.7→48.765 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3062	0	0	257	3319

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	3180
X-RAY DIFFRACTION	f_angle_d	1.008	4317
X-RAY DIFFRACTION	f_dihedral_angle_d	13.763	1145
X-RAY DIFFRACTION	f_chiral_restr	0.074	471
X-RAY DIFFRACTION	f_plane_restr	0.005	566

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.7-1.7426	0.2812	139	0.2542	3329	X-RAY DIFFRACTION	100
1.7426-1.7898	0.2883	136	0.2434	3305	X-RAY DIFFRACTION	100
1.7898-1.8424	0.2414	140	0.2361	3358	X-RAY DIFFRACTION	100
1.8424-1.9019	0.2934	140	0.2236	3362	X-RAY DIFFRACTION	100
1.9019-1.9699	0.229	139	0.2091	3341	X-RAY DIFFRACTION	100
1.9699-2.0487	0.2847	140	0.196	3365	X-RAY DIFFRACTION	100
2.0487-2.142	0.2071	140	0.1816	3353	X-RAY DIFFRACTION	100
2.142-2.2549	0.2433	139	0.1784	3340	X-RAY DIFFRACTION	100
2.2549-2.3962	0.2284	140	0.1783	3375	X-RAY DIFFRACTION	100
2.3962-2.5812	0.1981	140	0.1734	3356	X-RAY DIFFRACTION	100
2.5812-2.8409	0.1916	141	0.184	3380	X-RAY DIFFRACTION	100
2.8409-3.2519	0.1828	140	0.1775	3372	X-RAY DIFFRACTION	100
3.2519-4.0968	0.1746	142	0.1519	3410	X-RAY DIFFRACTION	100
4.0968-48.7846	0.1598	146	0.1541	3479	X-RAY DIFFRACTION	100

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	6.7811	-1.97	-2.5119	1.0258	1.7869	3.3927	0.4139	0.2444	1.8443	-0.6528	0.3299	-0.1089	-0.9334	-0.2919	-0.463	0.4324	0.0222	0.0526	0.4047	0.1293	0.6286	-5.0767	23.6874	-37.3278
2	2.6507	0.0998	-0.1366	2.6915	-0.8794	2.6722	-0.0825	-0.4864	-0.5273	0.4527	0.1926	0.2606	0.1184	-0.2324	-0.0977	0.2772	0.022	0.0398	0.31	0.0902	0.3079	-14.1868	3.9935	-16.4215
3	0.1689	0.5315	-0.8344	4.6092	1.1599	9.4609	-0.1664	-0.1334	0.1638	0.2924	0.2946	0.3519	-0.502	-0.0021	-0.4053	0.3491	0.03	0.0789	0.2173	0.0034	0.2852	-15.55	16.583	-16.9549
4	2.0944	0.1266	-0.0375	3.1752	-0.9151	1.8234	0.0042	-0.0061	-0.5717	0.0934	0.0637	0.3775	0.2602	-0.3346	-0.0719	0.2897	-0.039	0.0007	0.2566	0.0232	0.3902	-18.3626	3.7596	-21.7827
5	2.8027	0.0541	-0.1849	1.8025	0.0722	2.8164	0.0928	0.3112	-0.2831	-0.1831	-0.1296	0.259	0.373	-0.2749	0.0404	0.2629	-0.0434	-0.027	0.2565	-0.0114	0.315	-17.0153	6.1671	-29.2648
6	5.9936	2.0164	-1.2116	2.2366	-0.1041	3.6322	0.119	0.1521	-0.8812	0.2021	0.2581	0.3128	0.2191	-0.095	-0.441	0.6019	0.0507	0.059	0.2925	0.0276	0.7778	-7.1075	-8.0446	-20.5685
7	2.6255	-0.2826	-0.0431	1.5066	-1.0764	2.23	-0.0115	0.5456	-0.363	-0.262	0.0172	0.098	0.2984	-0.0903	0.0124	0.296	-0.0049	-0.0255	0.2785	-0.0689	0.2805	-10.8869	3.6702	-33.2406
8	6.4464	2.4396	0.7201	4.547	-0.6775	2.6496	0.0461	-0.8966	-0.7999	-0.0172	-0.1657	-0.7586	0.2871	0.4518	0.1681	0.6078	0.0549	-0.0023	0.6464	0.0673	0.517	9.2472	-0.4558	-14.2396
9	3.1335	-0.2537	0.0889	2.0527	1.8104	5.6064	0.0295	1.0916	-0.0473	-0.6623	-0.0638	0.5379	-0.0769	-0.3622	0.1256	0.4347	0.0294	-0.0754	0.4501	-0.0014	0.3738	-6.117	7.7763	-43.6866
10	3.1395	-1.1853	0.3184	3.5864	-0.3377	2.2985	-0.1522	-0.4373	-0.5476	0.5038	0.0439	-0.1423	0.7509	0.4904	-0.0128	0.4448	0.0446	-0.0063	0.3917	0.0002	0.3156	1.4514	1.843	-21.6574
11	4.151	-0.2039	-0.8823	2.6744	-2.1081	4.1835	-0.141	-1.0536	-0.0865	1.051	0.253	-0.0318	-0.0981	0.0215	-0.0491	0.5172	0.0336	-0.0216	0.5513	-0.0033	0.3422	-2.4059	5.0409	-8.9913
12	3.8391	-0.6892	1.0806	1.9716	-3.0293	5.2415	0.1664	-0.918	0.3191	1.562	0.2398	0.5183	-0.8842	0.1019	-0.3453	0.4151	-0.0176	0.0777	0.3475	-0.0657	0.3251	-4.5994	17.7145	-15.3091
13	2.6142	-0.7442	0.5376	2.7836	-0.8343	2.2266	0.1327	-0.4014	0.3808	0.1101	0.007	0.1581	-0.2436	0.1619	-0.1252	0.2956	-0.0135	0.02	0.2435	-0.0586	0.2833	0.3344	18.3407	-22.1285
14	2.1591	-1.3545	0.3488	6.2951	-2.4758	3.3004	-0.353	-0.5775	-0.2463	1.5326	0.3077	-0.2168	-0.349	0.1301	0.0062	0.65	-0.0011	-0.0017	0.6335	-0.0128	0.4033	6.837	4.7872	-5.9538
15	1.9681	0.1038	0.8566	1.833	-0.8479	2.9314	0.1951	-0.3895	-0.3371	0.3626	-0.0194	-0.1631	0.4501	0.4568	-0.0591	0.3656	0.024	-0.0438	0.3791	0.0335	0.2563	4.5845	5.316	-19.1273
16	3.3457	0.3822	-4.2906	2.9288	1.7339	9.4907	0.4446	0.5885	0.468	-0.0637	0.1183	0.1882	-0.4943	-0.7909	-0.5053	0.3091	0.0558	0.0396	0.2699	0.0642	0.3205	-5.5273	21.0006	-31.5925
17	6.6383	-1.2011	-1.5597	4.1546	1.7821	8.3606	0.4736	-0.6244	0.434	0.6756	0.0646	-0.6243	0.169	1.1947	-0.5473	0.452	-0.0024	-0.0095	0.4879	-0.0617	0.3782	-19.8248	27.1305	2.4112
18	1.9808	0.2672	0.7008	2.5408	1.5309	3.3156	-0.0881	-0.2163	0.42	-0.046	-0.0183	-0.2687	-0.5638	0.0739	0.0394	0.3034	-0.02	0.1058	0.2927	-0.0847	0.428	-23.5015	30.4836	-2.5234
19	4.0902	-1.5093	0.3326	6.4734	0.3771	5.2029	0.4335	-0.6809	0.1582	0.8559	-0.2811	-0.3061	0.7452	-0.5559	-0.1792	0.4584	-0.131	-0.0273	0.372	-0.0022	0.2999	-28.3374	20.9976	-1.5125
20	3.0345	0.636	0.2821	0.5972	0.6709	3.0441	0.316	-0.3058	0.2825	0.0965	0.0488	0.0341	0.1253	-0.1151	-0.3439	0.3258	0.0253	0.0155	0.247	0.026	0.3174	-29.3146	21.2745	-10.4454
21	4.6523	-1.4318	0.7389	4.6639	-1.0558	6.7684	0.2238	-1.1686	0.2074	0.4546	-0.3112	0.4877	0.6969	-1.415	0.0103	0.3618	-0.1243	0.0535	0.485	-0.0308	0.3709	-37.8011	19.2317	-6.6135
22	2.8395	1.146	-1.0027	1.3574	0.6629	1.8653	0.0696	0.4511	-0.1681	-0.0114	-0.0068	0.0888	0.0976	-0.4112	-0.0526	0.2423	0.0009	-0.0142	0.2571	0.0384	0.2729	-33.6753	12.2843	-19.2107
23	4.0332	-0.0853	0.3157	3.1813	0.0514	2.0139	0.0227	0.8304	-0.769	-0.2923	-0.2019	-0.2854	0.2671	0.0417	0.0914	0.3046	-0.0124	-0.0096	0.3807	-0.0697	0.4091	-31.1259	3.3469	-22.9858
24	8.6865	-1.4789	1.2019	6.7293	-0.7048	5.8156	0.2403	0.1529	-1.142	-0.7758	-0.3004	0.8782	0.9996	-0.7732	0.0309	0.3241	-0.1252	-0.0164	0.3872	-0.0338	0.4194	-40.6252	0.7445	-20.1407

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 54:62)
2	X-RAY DIFFRACTION	2	(chain A and resid 63:97)
3	X-RAY DIFFRACTION	3	(chain A and resid 98:102)
4	X-RAY DIFFRACTION	4	(chain A and resid 103:121)
5	X-RAY DIFFRACTION	5	(chain A and resid 122:144)
6	X-RAY DIFFRACTION	6	(chain A and resid 145:156)
7	X-RAY DIFFRACTION	7	(chain A and resid 157:185)
8	X-RAY DIFFRACTION	8	(chain A and resid 186:196)
9	X-RAY DIFFRACTION	9	(chain B and resid 211:219)
10	X-RAY DIFFRACTION	10	(chain B and resid 220:230)
11	X-RAY DIFFRACTION	11	(chain B and resid 231:241)
12	X-RAY DIFFRACTION	12	(chain B and resid 242:252)
13	X-RAY DIFFRACTION	13	(chain B and resid 253:268)
14	X-RAY DIFFRACTION	14	(chain B and resid 269:281)
15	X-RAY DIFFRACTION	15	(chain B and resid 282:296)
16	X-RAY DIFFRACTION	16	(chain B and resid 297:302)
17	X-RAY DIFFRACTION	17	(chain P and resid 13:29)
18	X-RAY DIFFRACTION	18	(chain P and resid 30:50)
19	X-RAY DIFFRACTION	19	(chain P and resid 51:67)
20	X-RAY DIFFRACTION	20	(chain P and resid 68:93)
21	X-RAY DIFFRACTION	21	(chain P and resid 94:105)
22	X-RAY DIFFRACTION	22	(chain P and resid 106:146)
23	X-RAY DIFFRACTION	23	(chain P and resid 147:158)
24	X-RAY DIFFRACTION	24	(chain P and resid 159:170)

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