PDB-8se7: HTRA-1 PDSA bound to CKP 1A8

ID or keywords:

Entry

Database: PDB / ID: 8se7

Title

HTRA-1 PDSA bound to CKP 1A8

Components

Cysteine knot peptide
Serine protease HTRA1

Keywords

PEPTIDE BINDING PROTEIN / Protease / Complex / Cysteine Knot peptide

Function / homology

Function and homology information

chorionic trophoblast cell differentiation / programmed cell death / growth factor binding / negative regulation of BMP signaling pathway / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / Degradation of the extracellular matrix / serine-type peptidase activity / molecular function activator activity / placenta development / negative regulation of transforming growth factor beta receptor signaling pathway ...
Similarity search - Function

Biological species

Homo sapiens (human)

Ecballium elaterium (jumping cucumber)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.96 Å

Authors

Ultsch, M.H. / Kirchhofer, D. / Wei, Y.

Funding support

1items

Citation

Journal: Nat Commun / Year: 2024
Title: Cystine-knot peptide inhibitors of HTRA1 bind to a cryptic pocket within the active site region.
Authors: Li, Y. / Wei, Y. / Ultsch, M. / Li, W. / Tang, W. / Tombling, B. / Gao, X. / Dimitrova, Y. / Gampe, C. / Fuhrmann, J. / Zhang, Y. / Hannoush, R.N. / Kirchhofer, D.

History

Deposition	Apr 8, 2023	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 3, 2024	Provider: repository / Type: Initial release
Revision 1.1	Oct 16, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Revision 1.2	Jan 15, 2025	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _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	8se7.cif.gz	977.5 KB	Display	PDBx/mmCIF format
PDB format	pdb8se7.ent.gz	811.8 KB	Display	PDB format
PDBx/mmJSON format	8se7.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8se7_validation.pdf.gz	647.8 KB	Display	wwPDB validaton report
Full document	8se7_full_validation.pdf.gz	682 KB	Display
Data in XML	8se7_validation.xml.gz	86.2 KB	Display
Data in CIF	8se7_validation.cif.gz	116.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/se/8se7 ftp://data.pdbj.org/pub/pdb/validation_reports/se/8se7	HTTPS FTP

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Related structure data

Related structure data	8sdmC 8sdpC 8se8C C: citing same article (ref.)
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	#46 - Oct 2003 Trypsin similarity (4) #126 - Jun 2010 Epidermal Growth Factor similarity (1) #182 - Feb 2015 Insulin receptor similarity (1) #237 - Sep 2019 Nanodiscs and HDL similarity (1) #56 - Aug 2004 Caspases similarity (1) #184 - Apr 2015 Glucagon similarity (1)

Deposited unit

A: Serine protease HTRA1

B: Serine protease HTRA1

C: Serine protease HTRA1

I: Cysteine knot peptide

X: Cysteine knot peptide

Y: Cysteine knot peptide

D: Serine protease HTRA1

E: Serine protease HTRA1

F: Serine protease HTRA1

G: Cysteine knot peptide

H: Cysteine knot peptide

J: Cysteine knot peptide

K: Serine protease HTRA1

L: Serine protease HTRA1

M: Serine protease HTRA1

N: Cysteine knot peptide

O: Cysteine knot peptide

P: Cysteine knot peptide

Q: Serine protease HTRA1

R: Serine protease HTRA1

S: Serine protease HTRA1

T: Cysteine knot peptide

U: Cysteine knot peptide

V: Cysteine knot peptide

368 kDa, 24 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Serine protease HTRA1

B: Serine protease HTRA1

C: Serine protease HTRA1

I: Cysteine knot peptide

X: Cysteine knot peptide

Y: Cysteine knot peptide

defined by author&software
Evidence: gel filtration
91.9 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

D: Serine protease HTRA1

E: Serine protease HTRA1

F: Serine protease HTRA1

G: Cysteine knot peptide

H: Cysteine knot peptide

J: Cysteine knot peptide

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

3

K: Serine protease HTRA1

L: Serine protease HTRA1

M: Serine protease HTRA1

N: Cysteine knot peptide

O: Cysteine knot peptide

P: Cysteine knot peptide

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

4

Q: Serine protease HTRA1

R: Serine protease HTRA1

S: Serine protease HTRA1

T: Cysteine knot peptide

U: Cysteine knot peptide

V: Cysteine knot peptide

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

Unit cell

Length a, b, c (Å)	116.030, 152.721, 165.850
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Serine protease HTRA1 / High-temperature requirement A serine peptidase 1 / L56 / Serine protease 11 Mass: 26060.838 Da / Num. of mol.: 12 / Mutation: S328A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HTRA1, HTRA, PRSS11 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q92743, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Protein/peptide	Cysteine knot peptide Mass: 4587.140 Da / Num. of mol.: 12 / Source method: obtained synthetically / Source: (synth.) Ecballium elaterium (jumping cucumber)
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H₂O
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: 2.11 Å³/Da / Density % sol: 41.73 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion / pH: 7.5 Details: 6%(w/v) PEG20000, 0.04M HEPES pH 7.5, 15%(w/v) PEG 3350, 0.06M Citric acid pH 3.5 PH range: 4.0-8.0

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Data collection

Diffraction	Mean temperature: 91 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 26, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.96→54.23 Å / Num. obs: 48024 / % possible obs: 94.8 % / Redundancy: 6.2 % / CC_1/2: 0.948 / R_merge(I) obs: 0.129 / R_pim(I) all: 0.083 / R_rim(I) all: 0.154 / Net I/σ(I): 12.9
Reflection shell	Resolution: 2.96→3.07 Å / R_merge(I) obs: 1.27 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 2402 / CC_1/2: 1 / R_pim(I) all: 0.821 / R_rim(I) all: 1.519

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Processing

Software

Name	Version	Classification
PHENIX	(1.20.1_4487: ???)	refinement
XDS		data reduction
STARANISO		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.96→54.23 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 33.9 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2957	1990	4.15 %
R_work	0.2696	-	-
obs	0.2707	47915	77.59 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.96→54.23 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	18999	0	0	7	19006

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	19358
X-RAY DIFFRACTION	f_angle_d	0.507	26507
X-RAY DIFFRACTION	f_dihedral_angle_d	10.554	6325
X-RAY DIFFRACTION	f_chiral_restr	0.045	3246
X-RAY DIFFRACTION	f_plane_restr	0.003	3437

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 (%)
2.96-3.04	0.6322	5	0.4141	97	X-RAY DIFFRACTION	2
3.04-3.12	0.2472	14	0.3817	405	X-RAY DIFFRACTION	10
3.12-3.21	0.3901	59	0.3766	1157	X-RAY DIFFRACTION	28
3.21-3.32	0.4438	87	0.3456	2300	X-RAY DIFFRACTION	54
3.32-3.44	0.345	179	0.3389	3943	X-RAY DIFFRACTION	95
3.44-3.57	0.3185	169	0.3292	4189	X-RAY DIFFRACTION	100
3.57-3.74	0.3292	187	0.3264	4194	X-RAY DIFFRACTION	100
3.74-3.93	0.3232	188	0.3145	4164	X-RAY DIFFRACTION	100
3.93-4.18	0.2811	162	0.283	4250	X-RAY DIFFRACTION	100
4.18-4.5	0.2632	197	0.2433	4196	X-RAY DIFFRACTION	100
4.5-4.95	0.2733	183	0.223	4111	X-RAY DIFFRACTION	97
4.95-5.67	0.2859	184	0.2592	4273	X-RAY DIFFRACTION	100
5.67-7.14	0.3103	187	0.2689	4295	X-RAY DIFFRACTION	100
7.14-54.23	0.2754	189	0.2348	4351	X-RAY DIFFRACTION	97

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	3.8147	0.3584	1.8272	4.0282	2.3143	3.998	-0.0486	-1.227	0.5636	0.1591	0.1663	-0.4826	-0.4912	0.0383	-0.0528	0.6083	0.1326	-0.1253	0.891	-0.2656	0.5984	-26.6324	12.1157	-7.9494
2	6.0454	0.4704	-3.3319	4.079	0.2224	4.1274	0.1845	0.7974	0.1998	-0.3921	0.0217	-0.0783	-0.1772	-0.404	0.0023	0.3397	0.0506	-0.0916	0.4213	-0.0428	0.4133	-30.4259	-1.5401	-38.8491
3	6.1511	-2.0468	1.8761	3.2145	-1.8481	4.7243	-0.503	-0.525	0.1566	0.1041	0.1586	0.06	-0.4628	-0.6818	-0.0166	0.5136	0.125	-0.0076	0.8265	-0.0433	0.3623	-58.1172	11.3527	-22.8342
4	2.1397	0.9246	-2.1194	0.3943	-0.9138	2.0888	0.0795	0.2047	1.0486	-1.5669	0.0107	0.3144	-1.0316	-0.8909	0.5585	1.7742	0.3153	-0.5566	0.7619	-0.5244	1.5379	-33.0973	30.0997	-14.2607
5	0.4365	-0.1031	0.1748	0.4618	-0.4676	0.4823	-0.1854	-0.1046	1.1062	0.182	0.2743	-1.3513	-1.4054	0.3843	0.0001	1.106	-0.0847	0.087	0.6982	-0.0297	1.306	-20.2058	16.332	-36.9623
6	0.4462	-0.183	-0.3574	0.673	0.4181	0.3951	-0.7634	0.6666	0.4456	-1.238	-0.8087	-0.0997	-1.4259	0.9858	-0.0641	1.101	-0.0915	-0.2331	1.2378	0.4076	0.9803	-51.7653	21.9911	-37.999
7	3.5374	1.0079	1.5001	4.0523	-0.1188	3.6891	0.1193	-0.1885	-0.5847	-0.717	-0.0441	-0.2784	0.721	-0.2347	0.0167	0.9213	-0.0202	-0.1512	0.4949	0.2124	0.8866	3.8236	25.5264	-51.3891
8	2.1129	-0.054	-0.0501	2.8461	-1.3916	4.0246	0.12	-0.2922	0.0388	1.8075	0.0145	0.1315	-0.304	-0.194	0.0018	1.6837	-0.3421	-0.2942	0.6556	0.1962	0.8687	6.0349	45.0915	-23.5727
9	2.6172	-0.2109	-0.2215	7.1312	-1.4847	2.6088	0.3362	-0.0753	0.1128	-0.1653	-0.4413	0.3885	0.1384	-0.2978	0.0032	0.4733	-0.0796	-0.0127	0.5767	-0.0211	0.6292	1.9124	61.1433	-53.1801
10	0.0978	0.1111	0.0226	0.1078	0.0178	0.0097	0.1483	-0.8557	-0.9842	-1.0931	0.5815	1.7977	0.1932	-1.3856	0.0006	1.0882	-0.0636	-0.4075	1.247	0.2386	1.5593	-14.497	32.7232	-55.2122
11	0.1212	-0.0779	-0.0968	0.0411	0.0619	0.0747	0.4088	0.129	0.3413	1.0344	-0.6387	0.7547	0.9492	-0.695	-0.0011	1.4901	-0.2208	0.3293	0.7501	0.1194	1.5522	-10.2866	32.5946	-23.6108
12	0.9447	0.5127	-1.4041	1.4911	-1.0745	2.1606	0.6705	-1.0863	-0.5681	0.7358	-0.2348	0.8077	0.0888	-0.9482	0.4439	0.804	-0.6163	0.3457	1.4177	0.1383	1.5825	-15.3324	59.9851	-42.7399
13	4.7236	-3.4918	0.2156	4.994	-0.1462	2.2618	0.0079	-0.0419	-0.0611	0.3908	0.1024	-0.0248	0.2099	0.2687	-0.0005	0.7358	-0.0623	-0.0207	0.5006	-0.0902	0.435	-37.7939	22.8776	-78.2225
14	4.5501	1.5941	0.3939	4.7766	0.2734	2.5058	-0.106	-0.2265	0.6246	0.2982	0.1416	-0.3281	-0.5199	0.1366	-0.0013	0.7219	-0.0034	-0.0438	0.4878	-0.0126	0.8655	-40.7432	57.153	-77.1148
15	3.7625	0.7162	-1.84	2.5481	-1.51	3.843	-0.155	0.0362	0.3278	0.4311	0.572	0.2103	-0.0581	-0.6256	0.0001	0.7885	0.0418	0.0494	0.6923	0.0164	0.9248	-66.9818	36.0095	-65.0118
16	0.2398	0.0839	0.1654	0.0343	0.0442	0.1771	0.1551	-0.8517	-0.4117	0.3338	0.3464	0.3886	-0.4505	-0.8613	0.0009	1.5347	0.0086	-0.0785	0.9673	0.0126	0.7506	-38.7578	21.2048	-58.1601
17	0.0303	-0.0511	0.0766	0.0799	-0.1312	0.1922	0.0526	-0.956	-0.1639	0.3415	0.1174	-0.8902	0.1736	0.497	0	0.872	-0.0764	-0.3327	1.1111	-0.1573	1.5786	-25.9323	49.0112	-66.4011
18	1.7605	-0.4972	0.4962	0.4175	-0.5587	0.7658	0.0479	-0.0347	1.1198	1.7696	-0.1526	-0.1505	-0.3223	2.4877	0.0038	2.1965	-0.1166	-0.3328	1.8381	-0.5406	0.9427	-57.4873	43.8551	-48.685
19	3.9661	0.5334	2.1272	4.5993	1.3184	2.9769	0.6356	-1.1175	-0.9264	0.244	-0.105	0.5523	0.2771	-1.3246	0.047	0.6183	-0.1798	-0.1064	1.2259	0.269	0.9502	-59.8451	60.275	-21.6969
20	3.7669	-0.151	-0.0342	3.4451	-0.3053	5.5609	-0.0549	0.4114	-0.0305	0.3113	-0.1537	-0.5083	-0.5238	0.1181	-0.0005	0.5223	-0.0758	-0.1581	0.576	-0.0218	0.6612	-33.8104	79.0501	-33.3232
21	3.3408	-2.1948	0.5498	3.6367	-0.2015	3.4119	-0.2368	-0.3667	-0.0626	0.6683	0.217	0.045	-0.1733	0.0085	-0.0019	0.8267	-0.1902	-0.197	0.9886	-0.0653	0.4281	-31.6669	61.5555	-2.1389
22	0.2731	-0.3437	0.2009	0.4233	-0.2459	0.1287	0.5163	-0.1059	-0.5906	0.3973	0.166	-0.5446	1.1079	0.0741	0.9451	1.5886	0.1631	-0.954	0.3795	0.315	3.018	-49.8361	43.0437	-22.2999
23	0.0818	0.0083	0.0714	0.0348	-0.0328	0.098	0.2122	0.8313	-1.065	-0.5871	-0.9203	0.3534	0.8654	0.0165	0.0018	0.829	0.1262	0.1602	1.052	-0.3542	1.2062	-37.3452	62.6421	-43.6066
24	0.2502	-0.0543	-0.0584	0.2285	0.121	0.0683	0.1873	0.1186	0.641	-0.8435	-0.3589	0.18	0.5686	0.0771	0	1.0199	-0.0063	-0.1027	1.7061	-0.1023	0.6686	-21.2346	52.5308	-17.4297

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain 'A' and resid 162 through 372)
2	X-RAY DIFFRACTION	2	(chain 'B' and resid 162 through 368)
3	X-RAY DIFFRACTION	3	(chain 'C' and resid 161 through 368)
4	X-RAY DIFFRACTION	4	(chain 'I' and resid 4 through 35)
5	X-RAY DIFFRACTION	5	(chain 'X' and resid 1 through 37)
6	X-RAY DIFFRACTION	6	(chain 'Y' and resid 3 through 38)
7	X-RAY DIFFRACTION	7	(chain 'D' and resid 165 through 371)
8	X-RAY DIFFRACTION	8	(chain 'E' and resid 164 through 367)
9	X-RAY DIFFRACTION	9	(chain 'F' and resid 163 through 370)
10	X-RAY DIFFRACTION	10	(chain 'G' and resid 4 through 37)
11	X-RAY DIFFRACTION	11	(chain 'H' and resid 4 through 36)
12	X-RAY DIFFRACTION	12	(chain 'J' and resid 3 through 36)
13	X-RAY DIFFRACTION	13	(chain 'K' and resid 162 through 367)
14	X-RAY DIFFRACTION	14	(chain 'L' and resid 163 through 368)
15	X-RAY DIFFRACTION	15	(chain 'M' and resid 162 through 370)
16	X-RAY DIFFRACTION	16	(chain 'N' and resid 3 through 37)
17	X-RAY DIFFRACTION	17	(chain 'O' and resid 4 through 37)
18	X-RAY DIFFRACTION	18	(chain 'P' and resid 3 through 34)
19	X-RAY DIFFRACTION	19	(chain 'Q' and resid 161 through 370)
20	X-RAY DIFFRACTION	20	(chain 'R' and resid 162 through 370)
21	X-RAY DIFFRACTION	21	(chain 'S' and resid 162 through 372)
22	X-RAY DIFFRACTION	22	(chain 'T' and resid 4 through 34)
23	X-RAY DIFFRACTION	23	(chain 'U' and resid 4 through 36)
24	X-RAY DIFFRACTION	24	(chain 'V' and resid 3 through 36)

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