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

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Basic information

Entry
Database: PDB / ID: 8s0l
TitleCrystal structure of the TMPRSS2 zymogen in complex with the nanobody A07
Components
  • Nanobody A07
  • Transmembrane protease serine 2
KeywordsPROTEASE/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 / entry receptor-mediated virion attachment to host cell / Attachment and Entry / positive regulation of viral entry into host cell / serine-type endopeptidase activity ...transmembrane protease serine 2 / protein autoprocessing / Attachment and Entry / serine-type peptidase activity / viral translation / Induction of Cell-Cell Fusion / entry receptor-mediated virion attachment to host cell / Attachment and Entry / positive regulation of viral entry into host cell / serine-type endopeptidase activity / proteolysis / extracellular exosome / extracellular region / nucleoplasm / plasma membrane
Similarity search - Function
Scavenger receptor cysteine-rich domain / SRCR domain profile. / SRCR-like domain superfamily / Scavenger receptor Cys-rich / SRCR domain / Low-density lipoprotein (LDL) receptor class A, conserved site / LDL-receptor class A (LDLRA) domain signature. / LDL-receptor class A (LDLRA) domain profile. / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A repeat ...Scavenger receptor cysteine-rich domain / SRCR domain profile. / SRCR-like domain superfamily / Scavenger receptor Cys-rich / SRCR domain / Low-density lipoprotein (LDL) receptor class A, conserved site / LDL-receptor class A (LDLRA) domain signature. / LDL-receptor class A (LDLRA) domain profile. / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A repeat / LDL receptor-like superfamily / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Transmembrane protease serine 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Vicugna pacos (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsDuquerroy, S. / Fernandez, I. / Rey, F.
Funding support1items
OrganizationGrant numberCountry
Not funded
Citation
Journal: Cell / Year: 2024
Title: Structural basis of TMPRSS2 zymogen activation and recognition by the HKU1 seasonal coronavirus.
Authors: Fernandez, I. / Saunders, N. / Duquerroy, S. / Bolland, W.H. / Arbabian, A. / Baquero, E. / Blanc, C. / Lafaye, P. / Haouz, A. / Buchrieser, J. / Schwartz, O. / Rey, F.A.
#1: Journal: Nature / Year: 2023
Title: TMPRSS2 is a functional receptor for human coronavirus HKU1
Authors: Saunders, N. / Fernandez, I. / Planchais, C. / Michel, V. / Rajah, M.M. / Baquero Salazar, E. / Postal, J. / Porrot, F. / Guivel-Benhassine, F. / Blanc, C. / Chauveau-Le Friec, G. / Martin, ...Authors: Saunders, N. / Fernandez, I. / Planchais, C. / Michel, V. / Rajah, M.M. / Baquero Salazar, E. / Postal, J. / Porrot, F. / Guivel-Benhassine, F. / Blanc, C. / Chauveau-Le Friec, G. / Martin, A. / Grzelak, L. / Oktavia, R.M. / Meola, A. / Ahouzi, O. / Hoover-Watson, H. / Prot, M. / Delaune, D. / Cornelissen, M. / Deijs, M. / Meriaux, V. / Mouquet, H. / Simon-Loriere, E. / van der Hoek, L. / Lafaye, P. / Rey, F. / Buchrieser, J. / Schwartz, O.
History
DepositionFeb 14, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 26, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._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
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transmembrane protease serine 2
B: Nanobody A07
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,9714
Polymers59,7102
Non-polymers2612
Water7,224401
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2900 Å2
ΔGint-1 kcal/mol
Surface area21230 Å2
MethodPISA
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 number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-940-

HOH

21B-287-

HOH

31B-289-

HOH

41B-319-

HOH

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Components

#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
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 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 interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.65 Å3/Da / Density % sol: 53.54 %
Crystal growTemperature: 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

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.978565 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 18, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978565 Å / Relative weight: 1
ReflectionResolution: 1.8→25 Å / Num. obs: 58045 / % possible obs: 99.8 % / Redundancy: 6.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.106 / Net I/σ(I): 9.2
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 6.3 % / Rmerge(I) obs: 2.643 / Mean I/σ(I) obs: 0.6 / Num. unique obs: 4194 / CC1/2: 0.293 / % possible all: 98.3

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod 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
RfactorNum. reflection% reflection
Rfree0.2154 2568 4.43 %
Rwork0.1769 --
obs0.1786 57982 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→24.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3850 0 15 401 4266
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014125
X-RAY DIFFRACTIONf_angle_d1.0135620
X-RAY DIFFRACTIONf_dihedral_angle_d13.4791486
X-RAY DIFFRACTIONf_chiral_restr0.068594
X-RAY DIFFRACTIONf_plane_restr0.009739
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.840.43581540.40322946X-RAY DIFFRACTION97
1.84-1.870.40431470.38553080X-RAY DIFFRACTION100
1.87-1.910.38051470.353039X-RAY DIFFRACTION100
1.91-1.960.28961390.29693037X-RAY DIFFRACTION100
1.96-2.010.30721310.263079X-RAY DIFFRACTION100
2.01-2.060.27221420.24183099X-RAY DIFFRACTION100
2.06-2.120.29841450.22763057X-RAY DIFFRACTION100
2.12-2.190.25861350.22763064X-RAY DIFFRACTION100
2.19-2.270.24191270.21223074X-RAY DIFFRACTION100
2.27-2.360.22541470.18033086X-RAY DIFFRACTION100
2.36-2.470.20621310.17463071X-RAY DIFFRACTION100
2.47-2.60.22261690.17573051X-RAY DIFFRACTION100
2.6-2.760.20591610.17223068X-RAY DIFFRACTION100
2.76-2.970.2711260.18113125X-RAY DIFFRACTION100
2.97-3.270.2051620.16943070X-RAY DIFFRACTION100
3.27-3.740.19581540.15993085X-RAY DIFFRACTION100
3.74-4.710.16551340.12893154X-RAY DIFFRACTION100
4.71-24.820.16171170.14723229X-RAY DIFFRACTION100
Refinement TLS params.

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

IDL11 (°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)
10.5684-0.0629-0.07890.56830.11740.71190.3879-0.303-0.0615-0.03750.24590.5309-0.2393-0.35070.00671.22490.0492-0.0781.243-0.20441.200728.82715.465822.4111
22.4906-0.12941.42250.6175-0.091.6309-0.0972-0.6132-0.03950.23230.1219-0.089-0.0617-0.12010.00470.40910.07140.03840.49170.00620.33633.7229-6.038616.0417
32.04590.60720.07661.7935-0.03831.0268-0.0968-0.02630.0763-0.050.05020.0829-0.03650.02500.25830.01090.01050.25220.01710.255318.9653-1.65-2.9728
41.53040.372601.9113-0.33530.6668-0.15750.04130.096-0.19670.1093-0.06890.01820.04910.00020.2762-0.01760.00430.29370.00370.294528.69753.281-7.4283
50.0870.0182-0.06820.0719-0.0070.10480.0229-0.0542-0.06410.46140.1211-0.7782-0.12690.3104-0.00010.4296-0.0353-0.1430.4129-0.00350.696621.637327.3338-16.5398
60.03650.02520.00290.0312-0.01640.0284-0.11740.2710.3214-0.5546-0.12280.2161-0.1535-0.3448-0.00070.50320.0225-0.06480.39920.02740.42231.172132.8402-28.7529
70.2283-0.01020.22960.5964-0.13210.24770.00470.14780.0030.1365-0.0835-0.2113-0.0840.05480.00020.3421-0.0147-0.03630.29880.01220.354816.03422.6973-18.6484
80.08290.00310.0020.1109-0.06460.0381-0.0143-0.18220.07840.6378-0.01520.2022-0.0311-0.0606-0.00020.4851-0.01360.03360.3433-0.01560.41874.111326.7008-12.0185
90.25120.1470.32260.7164-0.02310.47920.1180.1067-0.5323-0.01820.00090.36970.3667-0.16980.00340.406-0.0124-0.05630.3581-0.00190.46256.399115.7233-20.5832
100.23710.23940.18910.6263-0.09710.47970.15020.02640.0767-0.2727-0.15940.11680.00770.01470.00010.39230.0238-0.01840.3946-0.03360.37286.587724.5086-24.2752
110.0011-0.02690.00780.2798-0.12960.05880.0075-0.1796-0.06160.2934-0.0449-0.0394-0.0931-0.0536-0.00010.3757-0.0508-0.03310.31610.04810.395613.323819.2751-11.4575
120.21530.06860.00410.07720.02870.12340.10850.42920.472-0.4857-0.1670.6911-0.5459-0.3849-0.0020.41750.058-0.09310.34360.04650.4642.539535.5835-23.1936
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 117 through 142 )
2X-RAY DIFFRACTION2chain 'A' and (resid 143 through 277 )
3X-RAY DIFFRACTION3chain 'A' and (resid 278 through 410 )
4X-RAY DIFFRACTION4chain 'A' and (resid 411 through 491 )
5X-RAY DIFFRACTION5chain 'B' and (resid 2 through 9 )
6X-RAY DIFFRACTION6chain 'B' and (resid 10 through 19 )
7X-RAY DIFFRACTION7chain 'B' and (resid 20 through 41 )
8X-RAY DIFFRACTION8chain 'B' and (resid 42 through 53 )
9X-RAY DIFFRACTION9chain 'B' and (resid 54 through 75 )
10X-RAY DIFFRACTION10chain 'B' and (resid 76 through 93 )
11X-RAY DIFFRACTION11chain 'B' and (resid 94 through 123 )
12X-RAY DIFFRACTION12chain 'B' and (resid 124 through 130 )

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