PDB-8s0l: Crystal structure of the TMPRSS2 zymogen in complex with the nano...

ID or keywords:

Entry

Database: PDB / ID: 8s0l

Title

Crystal structure of the TMPRSS2 zymogen in complex with the nanobody A07

Components

Nanobody A07
Transmembrane protease serine 2

Keywords

PROTEASE/NANOBODY INHIBITOR / PROTEASE / NANOBODY / INHIBITOR / ZYMOGEN / PROTEIN BINDING / PROTEASE-NANOBODY INHIBITOR complex

Function / homology

Function and homology information

transmembrane protease serine 2 / protein autoprocessing / Attachment and Entry / serine-type peptidase activity / viral translation / Induction of Cell-Cell Fusion / Attachment and Entry / positive regulation of viral entry into host cell / serine-type endopeptidase activity / proteolysis ...
Similarity search - Function

Biological species

Homo sapiens (human)

Vicugna pacos (alpaca)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.8 Å

Authors

Duquerroy, S. / Fernandez, I. / Rey, F.

Funding support

1items

Citation

Journal: To Be Published
Title: Structural insights into TMPRSS2 maturation and HKU1 binding
Authors: Fernandez, I. / Saunders, N. / Duquerroy, S. / Boland, W.H. / Arbabian, A. / Baquero, E. / Lafaye, P. / Haouz, A. / Buchrieser, J. / Schwartz, O. / Rey, F.

History

Deposition	Feb 14, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jun 26, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8s0l.cif.gz	227.1 KB	Display	PDBx/mmCIF format
PDB format	pdb8s0l.ent.gz	178.5 KB	Display	PDB format
PDBx/mmJSON format	8s0l.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	8s0l_validation.pdf.gz	464.8 KB	Display	wwPDB validaton report
Full document	8s0l_full_validation.pdf.gz	470.5 KB	Display
Data in XML	8s0l_validation.xml.gz	24.3 KB	Display
Data in CIF	8s0l_validation.cif.gz	36.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/s0/8s0l ftp://data.pdbj.org/pub/pdb/validation_reports/s0/8s0l	HTTPS FTP

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Related structure data

Related structure data	8s0mC 8s0nC 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	#136 - Apr 2011 Nanobodies similarity (1) #21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1) #159 - Mar 2013 Erythrocruorin similarity (6) #246 - Jun 2020 SARS-CoV-2 Spike similarity (1) #264 - Dec 2021 SARS-CoV-2 Spike Variants similarity (1)

Deposited unit

A: Transmembrane protease serine 2

B: Nanobody A07

hetero molecules

60 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	182.665, 53.808, 65.477
Angle α, β, γ (deg.)	90.00, 100.74, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	A-940- HOH
2	1	B-287- HOH
3	1	B-289- HOH
4	1	B-319- HOH

#1: Protein

Transmembrane protease serine 2 / Serine protease 10

Mass: 43678.176 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Homo sapiens (human) / Gene: TMPRSS2, PRSS10 / Cell line (production host): S2 / Production host:

Drosophila melanogaster (fruit fly)
References: UniProt: O15393, transmembrane protease serine 2

#2: Antibody

Nanobody A07

Mass: 16031.511 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Vicugna pacos (alpaca) / Production host:

Escherichia coli (E. coli)

#3: Sugar

ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE

Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₈H₁₅NO₆

Identifier	Type	Program
DGlcpNAcb	CONDENSED IUPAC CARBOHYDRATE SYMBOL	GMML 1.0
N-acetyl-b-D-glucopyranosamine	COMMON NAME	GMML 1.0
b-D-GlcpNAc	IUPAC CARBOHYDRATE SYMBOL	PDB-CARE 1.0
GlcNAc	SNFG CARBOHYDRATE SYMBOL	GMML 1.0

#4: Chemical

ChemComp-CA / CALCIUM ION

Mass: 40.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Ca

#5: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 401 / 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: 2.65 Å³/Da / Density % sol: 53.54 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 20 %w/v PEG 3350, 0.05 M HEPES (pH 7.0), 1 %w/v Tryptone, 0.001 %w/v NaN3

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.978565 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 18, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.978565 Å / Relative weight: 1
Reflection	Resolution: 1.8→25 Å / Num. obs: 58045 / % possible obs: 99.8 % / Redundancy: 6.4 % / CC_1/2: 0.998 / R_merge(I) obs: 0.106 / Net I/σ(I): 9.2
Reflection shell	Resolution: 1.8→1.85 Å / Redundancy: 6.3 % / R_merge(I) obs: 2.643 / Mean I/σ(I) obs: 0.6 / Num. unique obs: 4194 / CC_1/2: 0.293 / % possible all: 98.3

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.8→24.82 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.28 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2154	2568	4.43 %
R_work	0.1769	-	-
obs	0.1786	57982	99.77 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.8→24.82 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3850	0	15	401	4266

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	4125
X-RAY DIFFRACTION	f_angle_d	1.013	5620
X-RAY DIFFRACTION	f_dihedral_angle_d	13.479	1486
X-RAY DIFFRACTION	f_chiral_restr	0.068	594
X-RAY DIFFRACTION	f_plane_restr	0.009	739

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 (%)
1.8-1.84	0.4358	154	0.4032	2946	X-RAY DIFFRACTION	97
1.84-1.87	0.4043	147	0.3855	3080	X-RAY DIFFRACTION	100
1.87-1.91	0.3805	147	0.35	3039	X-RAY DIFFRACTION	100
1.91-1.96	0.2896	139	0.2969	3037	X-RAY DIFFRACTION	100
1.96-2.01	0.3072	131	0.26	3079	X-RAY DIFFRACTION	100
2.01-2.06	0.2722	142	0.2418	3099	X-RAY DIFFRACTION	100
2.06-2.12	0.2984	145	0.2276	3057	X-RAY DIFFRACTION	100
2.12-2.19	0.2586	135	0.2276	3064	X-RAY DIFFRACTION	100
2.19-2.27	0.2419	127	0.2122	3074	X-RAY DIFFRACTION	100
2.27-2.36	0.2254	147	0.1803	3086	X-RAY DIFFRACTION	100
2.36-2.47	0.2062	131	0.1746	3071	X-RAY DIFFRACTION	100
2.47-2.6	0.2226	169	0.1757	3051	X-RAY DIFFRACTION	100
2.6-2.76	0.2059	161	0.1722	3068	X-RAY DIFFRACTION	100
2.76-2.97	0.271	126	0.1811	3125	X-RAY DIFFRACTION	100
2.97-3.27	0.205	162	0.1694	3070	X-RAY DIFFRACTION	100
3.27-3.74	0.1958	154	0.1599	3085	X-RAY DIFFRACTION	100
3.74-4.71	0.1655	134	0.1289	3154	X-RAY DIFFRACTION	100
4.71-24.82	0.1617	117	0.1472	3229	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	0.5684	-0.0629	-0.0789	0.5683	0.1174	0.7119	0.3879	-0.303	-0.0615	-0.0375	0.2459	0.5309	-0.2393	-0.3507	0.0067	1.2249	0.0492	-0.078	1.243	-0.2044	1.2007	28.827	15.4658	22.4111
2	2.4906	-0.1294	1.4225	0.6175	-0.09	1.6309	-0.0972	-0.6132	-0.0395	0.2323	0.1219	-0.089	-0.0617	-0.1201	0.0047	0.4091	0.0714	0.0384	0.4917	0.0062	0.336	33.7229	-6.0386	16.0417
3	2.0459	0.6072	0.0766	1.7935	-0.0383	1.0268	-0.0968	-0.0263	0.0763	-0.05	0.0502	0.0829	-0.0365	0.025	0	0.2583	0.0109	0.0105	0.2522	0.0171	0.2553	18.9653	-1.65	-2.9728
4	1.5304	0.3726	0	1.9113	-0.3353	0.6668	-0.1575	0.0413	0.096	-0.1967	0.1093	-0.0689	0.0182	0.0491	0.0002	0.2762	-0.0176	0.0043	0.2937	0.0037	0.2945	28.6975	3.281	-7.4283
5	0.087	0.0182	-0.0682	0.0719	-0.007	0.1048	0.0229	-0.0542	-0.0641	0.4614	0.1211	-0.7782	-0.1269	0.3104	-0.0001	0.4296	-0.0353	-0.143	0.4129	-0.0035	0.6966	21.6373	27.3338	-16.5398
6	0.0365	0.0252	0.0029	0.0312	-0.0164	0.0284	-0.1174	0.271	0.3214	-0.5546	-0.1228	0.2161	-0.1535	-0.3448	-0.0007	0.5032	0.0225	-0.0648	0.3992	0.0274	0.4223	1.1721	32.8402	-28.7529
7	0.2283	-0.0102	0.2296	0.5964	-0.1321	0.2477	0.0047	0.1478	0.003	0.1365	-0.0835	-0.2113	-0.084	0.0548	0.0002	0.3421	-0.0147	-0.0363	0.2988	0.0122	0.3548	16.034	22.6973	-18.6484
8	0.0829	0.0031	0.002	0.1109	-0.0646	0.0381	-0.0143	-0.1822	0.0784	0.6378	-0.0152	0.2022	-0.0311	-0.0606	-0.0002	0.4851	-0.0136	0.0336	0.3433	-0.0156	0.4187	4.1113	26.7008	-12.0185
9	0.2512	0.147	0.3226	0.7164	-0.0231	0.4792	0.118	0.1067	-0.5323	-0.0182	0.0009	0.3697	0.3667	-0.1698	0.0034	0.406	-0.0124	-0.0563	0.3581	-0.0019	0.4625	6.3991	15.7233	-20.5832
10	0.2371	0.2394	0.1891	0.6263	-0.0971	0.4797	0.1502	0.0264	0.0767	-0.2727	-0.1594	0.1168	0.0077	0.0147	0.0001	0.3923	0.0238	-0.0184	0.3946	-0.0336	0.3728	6.5877	24.5086	-24.2752
11	0.0011	-0.0269	0.0078	0.2798	-0.1296	0.0588	0.0075	-0.1796	-0.0616	0.2934	-0.0449	-0.0394	-0.0931	-0.0536	-0.0001	0.3757	-0.0508	-0.0331	0.3161	0.0481	0.3956	13.3238	19.2751	-11.4575
12	0.2153	0.0686	0.0041	0.0772	0.0287	0.1234	0.1085	0.4292	0.472	-0.4857	-0.167	0.6911	-0.5459	-0.3849	-0.002	0.4175	0.058	-0.0931	0.3436	0.0465	0.464	2.5395	35.5835	-23.1936

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 117 through 142 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 143 through 277 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 278 through 410 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 411 through 491 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 2 through 9 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 10 through 19 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 20 through 41 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 42 through 53 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 54 through 75 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 76 through 93 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 94 through 123 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 124 through 130 )

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