PDB-8se8: HTRA-1 PD/SA bound to CKP 1G10

ID or keywords:

Entry

Database: PDB / ID: 8se8

Title

HTRA-1 PD/SA bound to CKP 1G10

Components

Cysteine knot peptide
Serine protease HTRA1

Keywords

PEPTIDE BINDING PROTEIN / Protease / Cysteine knot peptide / complex

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 / negative regulation of transforming growth factor beta receptor signaling pathway / placenta development ...
Similarity search - Function

Biological species

Homo sapiens (human)

Ecballium elaterium (jumping cucumber)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.18 Å

Authors

Ultsch, M.H.

Funding support

1items

Citation

Journal: To Be Published
Title: HTRA-1 PD/SA bound to CKP 1G10
Authors: Ultsch, M.H.

History

Deposition	Apr 8, 2023	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 3, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8se8.cif.gz	975.5 KB	Display	PDBx/mmCIF format
PDB format	pdb8se8.ent.gz	811.3 KB	Display	PDB format
PDBx/mmJSON format	8se8.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8se8_validation.pdf.gz	672.2 KB	Display	wwPDB validaton report
Full document	8se8_full_validation.pdf.gz	718.5 KB	Display
Data in XML	8se8_validation.xml.gz	92.4 KB	Display
Data in CIF	8se8_validation.cif.gz	124.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/se/8se8 ftp://data.pdbj.org/pub/pdb/validation_reports/se/8se8	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	#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

hetero molecules

370 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

hetero molecules

defined by author&software
Evidence: gel filtration
92.7 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

hetero molecules

defined by author&software
92.5 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

hetero molecules

defined by author&software
92.5 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
92.4 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	120.824, 155.362, 173.397
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: 4737.334 Da / Num. of mol.: 12 / Source method: obtained synthetically / Source: (synth.) Ecballium elaterium (jumping cucumber)
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO₄
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C₃H₈O₃
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.2 Å³/Da / Density % sol: 44.14 % / Description: Block
Crystal grow	Temperature: 291 K / Method: vapor diffusion / pH: 7 Details: 15% (w/v) PEG 3350, 4% Tacsimate pH6.0 and 0.1M Mg sulfate PH range: 4.0-8.0

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Data collection

Diffraction	Mean temperature: 93 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1 Å
Detector	Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Feb 16, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 3.18→95.38 Å / Num. obs: 46183 / % possible obs: 93.1 % / Redundancy: 4.7 % / B_iso Wilson estimate: 140.81 Å² / CC_1/2: 1 / R_merge(I) obs: 0.046 / R_rim(I) all: 0.059 / Net I/σ(I): 16.2
Reflection shell	Resolution: 3.18→3.297 Å / Redundancy: 4.8 % / R_merge(I) obs: 0.943 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2310 / CC_1/2: 0.569 / R_pim(I) all: 0.712 / R_rim(I) all: 1.188 / % possible all: 51.7

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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: 3.18→19.99 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.91 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2823	2227	4.85 %
R_work	0.2591	-	-
obs	0.2602	45930	83.33 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 3.18→19.99 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	18729	0	26	5	18760

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.001	19095
X-RAY DIFFRACTION	f_angle_d	0.438	26211
X-RAY DIFFRACTION	f_dihedral_angle_d	10.701	6042
X-RAY DIFFRACTION	f_chiral_restr	0.043	3206
X-RAY DIFFRACTION	f_plane_restr	0.003	3443

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 (%)
3.18-3.25	0.2462	14	0.4211	187	X-RAY DIFFRACTION	6
3.25-3.33	0.3343	31	0.3532	528	X-RAY DIFFRACTION	16
3.33-3.41	0.3755	72	0.3607	1511	X-RAY DIFFRACTION	46
3.41-3.5	0.3458	142	0.351	2948	X-RAY DIFFRACTION	91
3.5-3.6	0.3823	163	0.3499	3194	X-RAY DIFFRACTION	99
3.6-3.72	0.3543	182	0.3504	3213	X-RAY DIFFRACTION	99
3.72-3.85	0.3571	171	0.3394	3217	X-RAY DIFFRACTION	99
3.85-4.01	0.321	177	0.3143	3198	X-RAY DIFFRACTION	99
4.01-4.19	0.3229	186	0.3024	3208	X-RAY DIFFRACTION	99
4.19-4.4	0.2845	173	0.2649	3186	X-RAY DIFFRACTION	98
4.4-4.68	0.287	163	0.253	3171	X-RAY DIFFRACTION	97
4.68-5.03	0.2556	132	0.2526	3014	X-RAY DIFFRACTION	91
5.03-5.53	0.2873	155	0.2631	3271	X-RAY DIFFRACTION	99
5.53-6.31	0.3421	153	0.2974	3287	X-RAY DIFFRACTION	99
6.31-7.86	0.2588	158	0.2587	3299	X-RAY DIFFRACTION	98
7.87-19.99	0.2234	155	0.1888	3271	X-RAY DIFFRACTION	94

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	2.7298	0.0247	3.3646	5.8988	4.3528	8.1678	-0.0904	-0.7269	0.1936	0.4306	0.3153	-1.0233	-0.3872	0.3788	-0.0022	1.2041	0.088	-0.1864	1.237	-0.0549	1.35	32.4112	-65.9175	-9.0573
2	9.1325	0.5597	-3.4658	4.336	1.0118	4.9969	0.0942	1.1947	-0.5254	-0.544	0.0238	-0.2034	-0.1269	-0.2539	0	1.1162	0.0688	-0.0988	1.0943	-0.2025	1.1045	29.5894	-78.8013	-41.1939
3	6.4322	0.4956	2.165	3.7612	-2.0264	3.7215	-0.0939	-0.3685	0.121	0.1094	0.228	0.2102	-0.6225	-0.635	0.0001	1.1536	0.1761	0.1189	1.2888	-0.0874	1.0184	1.6828	-64.7215	-26.2467
4	-0.0233	-0.0435	0.0831	0.1414	-0.0692	-0.0194	1.1058	-0.9225	0.0771	0.8088	0.1546	1.3346	-3.0664	-0.6239	0.0003	2.6119	0.213	-0.1359	1.5237	-0.2305	1.8235	26.6538	-47.7704	-14.6666
5	1.2357	-0.0352	-0.4089	0.3666	-0.6629	0.8568	0.1576	-0.1938	1.8961	1.6156	-0.1773	-0.264	-0.9381	0.0417	0.0001	2.2551	-0.2513	0.48	1.5936	-0.0056	2.0131	40.6452	-61.2052	-38.7601
6	-0.0429	0.089	0.1437	0.4505	0.6878	0.9588	-1.3983	1.9069	-0.1324	-0.7092	0.2666	-1.7744	-1.7539	0.6486	0.0004	1.9917	0.0024	-0.0618	1.7766	0.1094	1.4505	10.3331	-54.2617	-41.2575
7	5.7453	1.8624	1.347	4.4193	1.8326	5.6982	0.0925	0.044	-0.7832	-0.3366	-0.0049	-0.4961	0.6857	-0.1163	-0.0011	1.4229	0.0826	0.0848	1.2304	0.1683	1.5094	63.6786	-50.7005	-53.9811
8	5.0957	-0.2116	0.7473	4.255	-1.0224	5.2225	-0.2411	-0.3889	0.1355	1.2332	0.295	-0.3767	-0.5706	-0.2715	0	1.6892	-0.1285	0.0282	1.3066	0.3119	1.4628	68.9939	-32.6444	-25.9777
9	4.6754	-2.2232	-0.6737	8.3961	-0.5291	4.2661	0.0733	0.1796	0.0668	-0.245	-0.2562	1.1979	-0.11	-0.4713	0.0001	1.1139	-0.1153	0.0359	1.2808	0.1424	1.6193	62.1618	-15.7334	-53.8787
10	0.2998	-0.187	0.3082	0.2083	0.2213	0.7657	0.5232	-0.0169	0.4692	0.8296	0.5706	0.3478	-1.0652	-1.7526	0.001	1.7505	0.1834	0.0533	2.024	0.2164	2.2552	45.442	-43.4573	-57.0145
11	0.1242	-0.2333	0.2359	0.1837	-0.3658	0.3844	-0.8909	-0.3463	-0.1652	0.6608	-0.0127	2.5168	0.6005	-0.6214	-0.0004	2.263	-0.1345	0.3954	2.4446	0.5981	2.5257	51.5746	-45.1471	-26.1451
12	0.4137	-0.3613	-0.1901	0.286	0.1881	0.0959	0.2659	-0.551	1.5167	1.7144	-1.2488	0.811	-0.5135	-1.1916	0.0006	1.5946	-0.2839	0.5505	2.1486	0.2716	2.9619	46.7657	-16.023	-41.5442
13	4.8131	-1.7856	-0.1002	6.2682	-0.9349	1.9227	-0.42	0.7221	-0.2256	-0.4561	0.3307	-0.3335	0.4679	0.0607	0	1.7102	-0.0696	0.0619	1.3585	-0.1185	1.1554	21.8358	-51.0347	-82.9113
14	4.417	0.6607	-0.281	6.1397	0.2085	2.1406	0.1353	-0.3463	0.4136	-0.1752	0.137	-0.2748	-0.6284	0.023	0.0001	1.6128	-0.0744	-0.0842	1.4109	0.1664	1.3183	18.2253	-17.9862	-78.6633
15	4.8967	1.4354	-2.1404	4.5203	-1.2225	7.0052	-0.1316	0.0873	-0.1037	0.0423	0.5574	0.5344	0.3206	-0.7577	-0	1.2667	-0.0158	-0.3066	1.3171	0.1801	1.3373	-6.5845	-39.4479	-68.3123
16	0.2141	-0.06	-0.1444	-0.0179	0.1356	0.0487	-0.564	-1.3024	-0.4263	2.3625	0.033	-0.0854	-1.2359	-0.2409	-0.0003	2.8656	0.1838	-0.0533	1.7126	-0.0993	1.887	19.3247	-55.5647	-62.5685
17	0.1153	0.37	0.2913	1.3106	-0.259	0.4697	1.4607	-1.3203	-0.4031	-2.4254	-0.9893	-1.2831	0.155	2.2813	0.0092	2.2941	-0.0868	-0.6465	2.6707	0.4307	2.3217	34.1979	-26.4482	-68.2491
18	0.122	0.2647	0.1442	0.3966	0.4074	0.3603	0.2865	0.1767	1.1839	1.7275	0.7349	0.2036	-0.6018	0.0034	-0.0002	1.8688	-0.3143	-0.3442	1.884	-0.0815	2.0238	3.1035	-30.1399	-53.2733
19	5.124	2.412	-0.1886	9.5778	0.1837	3.6197	-0.2371	-0.2622	-0.2565	-0.3046	0.0061	0.3477	-0.0003	-0.5067	0	1.1934	0.2574	0.0804	1.6041	0.0594	1.1991	-3.4854	-18.1707	-22.7276
20	3.2805	0.4084	0.0341	3.7759	-1.2371	7.6241	-0.2981	0.3816	0.1621	0.5206	0.1845	-0.3996	-0.4242	0.7764	-0.0005	1.3063	-0.1012	-0.1449	1.6915	-0.0417	1.3294	21.7632	3.5571	-33.2613
21	5.8311	-0.3062	1.1128	2.2422	-0.6514	5.4206	0.0125	0.1192	-0.8344	0.2616	0.2408	-0.3145	-0.1652	-0.1738	-0.0002	1.5349	-0.0842	-0.1838	1.6488	-0.0747	1.3846	26.6353	-15.587	-3.7066
22	0.2735	-0.3049	-0.0101	0.2001	-0.0614	-0.0368	0.5814	-0.9724	-0.7332	1.3521	1.0292	-2.0934	-0.1283	-1.0621	0.0007	2.0052	0.4088	0.2735	2.029	0.1062	2.7686	7.9929	-34.9175	-23.171
23	1.0042	-0.7991	0.1347	0.4755	-0.1002	-0.0004	0.7805	1.9342	-0.8313	0.0761	-0.7742	1.6099	1.0437	1.4724	-0	1.9467	0.0163	-0.0438	2.3713	-0.3251	1.7958	19.5095	-12.9426	-44.5046
24	0.1966	-0.2012	-0.267	0.2482	0.0349	0.2691	0.2308	0.6137	-1.8135	-1.8785	-0.2882	-1.1157	-1.1701	0.3175	-0.0024	2.4048	0.4202	-0.224	2.6771	-0.6525	2.1296	37.7348	-22.2988	-19.9848

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 370)
3	X-RAY DIFFRACTION	3	(chain 'C' and resid 162 through 370)
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 1 through 38)
7	X-RAY DIFFRACTION	7	(chain 'D' and resid 162 through 371)
8	X-RAY DIFFRACTION	8	(chain 'E' and resid 162 through 370)
9	X-RAY DIFFRACTION	9	(chain 'F' and resid 163 through 370)
10	X-RAY DIFFRACTION	10	(chain 'G' and resid 3 through 37)
11	X-RAY DIFFRACTION	11	(chain 'H' and resid 2 through 36)
12	X-RAY DIFFRACTION	12	(chain 'J' and resid 3 through 36)
13	X-RAY DIFFRACTION	13	(chain 'K' and resid 165 through 370)
14	X-RAY DIFFRACTION	14	(chain 'L' and resid 163 through 370)
15	X-RAY DIFFRACTION	15	(chain 'M' and resid 162 through 370)
16	X-RAY DIFFRACTION	16	(chain 'N' and resid 2 through 37)
17	X-RAY DIFFRACTION	17	(chain 'O' and resid 4 through 40)
18	X-RAY DIFFRACTION	18	(chain 'P' and resid 3 through 34)
19	X-RAY DIFFRACTION	19	(chain 'Q' and resid 164 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 371)
22	X-RAY DIFFRACTION	22	(chain 'T' and resid 4 through 37)
23	X-RAY DIFFRACTION	23	(chain 'U' and resid 1 through 36)
24	X-RAY DIFFRACTION	24	(chain 'V' and resid 3 through 34)

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