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- PDB-8s0n: Crystal structure of the TMPRSS2 zymogen in complex with the nano... -

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Basic information

Entry
Database: PDB / ID: 8s0n
TitleCrystal structure of the TMPRSS2 zymogen in complex with the nanobody A07
Components
  • Transmembrane protease serine 2
  • nanobody A07
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: 2.3 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 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
D: nanobody A07
C: Transmembrane protease serine 2


Theoretical massNumber of molelcules
Total (without water)119,9084
Polymers119,9084
Non-polymers00
Water3,765209
1
A: Transmembrane protease serine 2
B: nanobody A07


Theoretical massNumber of molelcules
Total (without water)59,9542
Polymers59,9542
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: nanobody A07
C: Transmembrane protease serine 2


Theoretical massNumber of molelcules
Total (without water)59,9542
Polymers59,9542
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)161.869, 54.458, 165.822
Angle α, β, γ (deg.)90.000, 108.393, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Components on special symmetry positions
IDModelComponents
11A-647-

HOH

21C-629-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 148 through 211 or resid 224...
d_2ens_1(chain "C" and (resid 148 through 211 or resid 223...
d_1ens_2(chain "B" and resid 2 through 130)
d_2ens_2chain "D"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1CYSCYSLYSLYSAA148 - 21144 - 107
d_12ens_1LYSLYSLEULEUAA224 - 373120 - 269
d_13ens_1PROPROASPASPAA375 - 491271 - 387
d_21ens_1CYSCYSLYSLYSCD148 - 21144 - 107
d_22ens_1LYSLYSLYSLYSCD223119
d_23ens_1LEULEULEULEUCD225 - 373121 - 269
d_24ens_1PROPROASPASPCD375 - 491271 - 387
d_11ens_2GLYGLYSERSERBB2 - 13015 - 143
d_21ens_2GLYGLYSERSERDC2 - 13015 - 143

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(0.801083851095, 0.0318298066048, 0.597705217416), (0.0370083431584, -0.999308416178, 0.00361550728095), (0.597406935054, 0.0192237552974, -0.801707802869)-26.5943169996, 31.4957693174, 78.3698554471
2given(0.789475898176, -0.00640227750856, 0.613748170704), (-0.00120756844041, -0.999959863273, -0.00887770363004), (0.613780374383, 0.00626759012576, -0.789451942385)-26.095137716, 31.5174700836, 78.2372922933

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Components

#1: Protein Transmembrane protease serine 2 / Serine protease 10


Mass: 43922.445 Da / Num. of mol.: 2 / Mutation: S441A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TMPRSS2, PRSS10 / Production host: Drosophila melanogaster (fruit fly)
References: UniProt: O15393, transmembrane protease serine 2
#2: Antibody nanobody A07


Mass: 16031.511 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 209 / Source method: isolated from a natural source / Formula: H2O
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: 2.89 Å3/Da / Density % sol: 57.47 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 10 %w/v PEG 3000, 0.1 M imidazole (pH 8.0), 0.2 M lithium sulfate

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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
RadiationMonochromator: Si(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978565 Å / Relative weight: 1
ReflectionResolution: 2.3→25 Å / Num. obs: 50880 / % possible obs: 95 % / Redundancy: 7 % / Biso Wilson estimate: 40.89 Å2 / CC1/2: 0.99 / CC star: 0.998 / Rmerge(I) obs: 0.24 / Rpim(I) all: 0.097 / Rrim(I) all: 0.259 / Net I/av σ(I): 6.598 / Net I/σ(I): 6.6
Reflection shellResolution: 2.3→2.39 Å / Redundancy: 6.9 % / Rmerge(I) obs: 2.236 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 2545 / CC1/2: 0.316 / Rpim(I) all: 0.912 / Rrim(I) all: 2.417 / % possible all: 39.4

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
XDS0.6.6.0data reduction
Aimlessdata scaling
STARANISOv3.350data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→24.42 Å / SU ML: 0.332 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.9624
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2458 2556 5.03 %
Rwork0.2109 48268 -
obs0.2126 50824 82.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 63.89 Å2
Refinement stepCycle: LAST / Resolution: 2.3→24.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7036 0 0 209 7245
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00377223
X-RAY DIFFRACTIONf_angle_d0.84069821
X-RAY DIFFRACTIONf_chiral_restr0.05691041
X-RAY DIFFRACTIONf_plane_restr0.00771270
X-RAY DIFFRACTIONf_dihedral_angle_d12.73912567
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.617237415411
ens_2d_2BBX-RAY DIFFRACTIONTorsion NCS0.354945634533
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.340.3759650.32391170X-RAY DIFFRACTION36.56
2.34-2.390.3358660.30831390X-RAY DIFFRACTION43.08
2.39-2.440.3345940.30211661X-RAY DIFFRACTION51.83
2.44-2.50.3778950.31551796X-RAY DIFFRACTION55.73
2.5-2.560.30371180.2892063X-RAY DIFFRACTION64.53
2.56-2.630.30951400.29582248X-RAY DIFFRACTION70.61
2.63-2.710.3261250.29592610X-RAY DIFFRACTION80.11
2.71-2.80.34281480.28562851X-RAY DIFFRACTION88.6
2.8-2.90.31811720.29233138X-RAY DIFFRACTION97.44
2.9-3.010.38331600.27263246X-RAY DIFFRACTION99.71
3.01-3.150.31091790.24353215X-RAY DIFFRACTION99.41
3.15-3.320.24881870.22333183X-RAY DIFFRACTION99.38
3.32-3.520.23391610.2153236X-RAY DIFFRACTION99.44
3.52-3.790.21661620.18543233X-RAY DIFFRACTION99.62
3.79-4.170.1921670.17273282X-RAY DIFFRACTION99.65
4.17-4.770.17411620.14593284X-RAY DIFFRACTION99.74
4.77-60.20311600.17463322X-RAY DIFFRACTION99.89
6-24.420.22391950.19023340X-RAY DIFFRACTION99.19
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)
11.84926183934-0.199090430823-0.8669388905031.667767421990.3547811703652.82445485242-0.08577079450540.244259875344-0.08804058655370.1048517100920.04461771159750.342899441939-0.255065664296-0.6705136869790.001924858575410.2181139118140.09114762346910.01232586579810.3716759218980.04391310414920.333725497546-19.267729940918.632601292218.2186356152
22.00069520131.06878144156-0.2827913380953.23671362544-0.4394160884381.41001334202-0.0371068859587-0.102374746766-0.1348632090830.325342232434-0.0357360400306-0.3954321220030.1816810585250.2588921150820.03977793908530.2782479802650.123200690711-0.04120420870690.258455829177-0.003423770405250.3918686352426.8786477252644.111501850319.3547983095
31.37140506908-0.4293051815210.3798671665532.6817107743-0.2712028664931.94696167580.163173815957-0.0603594985850.03663486331550.404791313458-0.0901050381156-0.452803323965-0.1397096205120.4104902348370.006006899249270.923336107554-0.0305488527328-0.02289417012910.3739585745350.01677599983330.479091235918-9.11592811092-12.694204884867.4072295863
41.65803351569-0.0298237646463-0.6192240635161.681505989030.3397377899843.65617193084-0.2324445630550.215344728815-0.1073090824560.164882126420.1432847284080.319666562631-0.0738981145776-0.8020230477460.05172559179770.6600626204850.02358043153960.1374025646770.4032991395960.04149892929820.372954869582-30.62488067612.218021310652.5304257724
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain 'A' and resid 148 through 492)AA148 - 4921 - 324
22(chain 'B' and resid 2 through 131)BB2 - 1311 - 130
33(chain 'D' and resid 2 through 130)DC2 - 1301 - 129
44(chain 'C' and resid 148 through 491)CD148 - 4911 - 324

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