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- PDB-8s0m: Crystal structure of the HKU1 receptor binding domain in complex ... -

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Basic information

Entry
Database: PDB / ID: 8s0m
TitleCrystal structure of the HKU1 receptor binding domain in complex with TMPRSS2 and the nanobody A01
Components
  • Nanobody A01
  • Spike protein S1
  • Transmembrane protease serine 2
KeywordsVIRAL PROTEIN/RECEPTOR / coronavirus receptor / VIRAL PROTEIN / PROTEASE / NANOBODY / VIRAL PROTEIN-RECEPTOR 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 / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of viral entry into host cell ...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 / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / endocytosis involved in viral entry into host cell / fusion of virus membrane with host plasma membrane / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / viral envelope / host cell plasma membrane / virion membrane / proteolysis / extracellular exosome / extracellular region / nucleoplasm / identical protein binding / membrane / plasma membrane
Similarity search - Function
Spike (S) protein S1 subunit, receptor-binding domain, HKU1-like / Scavenger receptor cysteine-rich domain / SRCR domain profile. / SRCR-like domain superfamily / Scavenger receptor Cys-rich / SRCR domain / Spike (S) protein S1 subunit, N-terminal domain, murine hepatitis virus-like / Low-density lipoprotein (LDL) receptor class A, conserved site / LDL-receptor class A (LDLRA) domain signature. / LDL-receptor class A (LDLRA) domain profile. ...Spike (S) protein S1 subunit, receptor-binding domain, HKU1-like / Scavenger receptor cysteine-rich domain / SRCR domain profile. / SRCR-like domain superfamily / Scavenger receptor Cys-rich / SRCR domain / Spike (S) protein S1 subunit, N-terminal domain, murine hepatitis virus-like / Low-density lipoprotein (LDL) receptor class A, conserved site / LDL-receptor class A (LDLRA) domain signature. / LDL-receptor class A (LDLRA) domain profile. / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / 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 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, N-terminal domain superfamily / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein, betacoronavirus / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
PHOSPHATE ION / Transmembrane protease serine 2 / Spike glycoprotein
Similarity search - Component
Biological speciesHomo sapiens (human)
Vicugna pacos (alpaca)
Human coronavirus HKU1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.55 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 / 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
B: Transmembrane protease serine 2
E: Transmembrane protease serine 2
U: Nanobody A01
A: Spike protein S1
D: Spike protein S1
V: Nanobody A01
hetero molecules


Theoretical massNumber of molelcules
Total (without water)200,45013
Polymers198,9516
Non-polymers1,4997
Water181
1
B: Transmembrane protease serine 2
U: Nanobody A01
A: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,6588
Polymers99,4753
Non-polymers1,1835
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Transmembrane protease serine 2
D: Spike protein S1
V: Nanobody A01
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,7925
Polymers99,4753
Non-polymers3162
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)201.870, 201.870, 210.300
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

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Protein , 2 types, 4 molecules BEAD

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


Mass: 43678.176 Da / Num. of mol.: 2
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
#3: Protein Spike protein S1


Mass: 40835.695 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human coronavirus HKU1 (isolate N5) / Gene: S, 3 / Cell (production host): S2 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: Q0ZME7

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Antibody , 1 types, 2 molecules UV

#2: Antibody Nanobody A01


Mass: 14961.493 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)

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Sugars , 2 types, 5 molecules

#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#5: 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.: 4 / 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

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Non-polymers , 2 types, 3 molecules

#6: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 6.22 Å3/Da / Density % sol: 80.22 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.35 M NaH2PO4, 0.65 M K2HPO4

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Data collection

DiffractionMean temperature: 283 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9786 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 23, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 3.55→25 Å / Num. obs: 58457 / % possible obs: 99.6 % / Redundancy: 43.3 % / CC1/2: 1 / Rmerge(I) obs: 0.265 / Net I/σ(I): 14.6
Reflection shellResolution: 3.55→3.64 Å / Redundancy: 41.4 % / Mean I/σ(I) obs: 0.4 / Num. unique obs: 4358 / CC1/2: 0.223 / % possible all: 100

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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: 3.55→24.97 Å / SU ML: 0.5 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2213 2755 4.75 %
Rwork0.1929 --
obs0.1943 58058 99.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.55→24.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12567 0 94 1 12662
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00412973
X-RAY DIFFRACTIONf_angle_d0.78817641
X-RAY DIFFRACTIONf_dihedral_angle_d12.3624597
X-RAY DIFFRACTIONf_chiral_restr0.0551919
X-RAY DIFFRACTIONf_plane_restr0.0052278
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.55-3.610.37861070.35782573X-RAY DIFFRACTION92
3.61-3.680.31691290.33462737X-RAY DIFFRACTION98
3.68-3.750.33811530.32492745X-RAY DIFFRACTION100
3.75-3.820.33361370.31672781X-RAY DIFFRACTION100
3.82-3.910.31591370.28122752X-RAY DIFFRACTION100
3.91-40.29131570.24822771X-RAY DIFFRACTION100
4-4.10.27951390.23822780X-RAY DIFFRACTION100
4.1-4.210.24711510.21232784X-RAY DIFFRACTION100
4.21-4.330.21771380.19482745X-RAY DIFFRACTION100
4.33-4.470.21851410.17332782X-RAY DIFFRACTION100
4.47-4.630.18981350.17562796X-RAY DIFFRACTION100
4.63-4.810.23361340.15462781X-RAY DIFFRACTION100
4.81-5.030.18521330.15842789X-RAY DIFFRACTION100
5.03-5.290.20861310.16182796X-RAY DIFFRACTION100
5.29-5.620.22371220.18252795X-RAY DIFFRACTION100
5.62-6.050.20781660.18032749X-RAY DIFFRACTION100
6.05-6.650.23721340.21282792X-RAY DIFFRACTION100
6.65-7.580.23081550.20092786X-RAY DIFFRACTION100
7.59-9.460.18321350.17242809X-RAY DIFFRACTION100
9.47-24.970.21210.17982760X-RAY DIFFRACTION97
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)
11.70530.5548-1.65630.9015-0.38491.58470.2616-1.21320.24120.8803-0.0058-0.29880.36830.39710.00142.5062-0.2249-0.09212.79750.1791.84415.02268.693658.9383
23.78010.2652-1.27533.21360.18983.03370.2409-0.48590.21810.38290.00180.15720.2468-0.56390.00221.6692-0.16590.07462.141-0.10431.60414.178181.1936.3398
30.30.32430.1160.2622-0.0320.38230.4310.9393-0.3904-0.9005-0.15840.06230.96980.746-0.00173.45370.367-0.11612.3368-0.15482.294228.3558148.6246-19.756
44.00070.90350.7393.5623-0.8742.3090.36810.1334-0.5696-1.1095-0.26740.4806-0.06270.35060.00232.68940.292-0.44291.67480.16762.036418.0787158.82133.6082
53.47590.26080.50911.5028-0.41490.5485-0.0605-0.4896-0.05420.32980.2712-0.19340.49110.23780.00011.99210.1623-0.3662.2868-0.32421.932337.91881.464444.8794
60.98-0.76990.24580.5764-0.12180.52310.5708-0.1371-0.6741-1.0765-0.31910.52980.8998-0.5179-03.32970.4628-0.69442.12-0.03773.277218.1885125.245-4.6499
72.8441-0.8389-1.36632.58771.33343.19360.36630.23090.4003-0.30130.1527-0.69050.02840.2061-0.00171.72470.16380.0741.8942-0.00161.793239.735575.1659-0.8486
80.3967-0.39070.08250.67820.1860.23911.5343-0.7903-0.80580.3767-0.4972-0.86871.52290.2654-0.00963.412-0.25690.33212.4984-0.07342.264741.154539.4737-31.667
93.6727-1.61051.73873.1781-0.63162.1981-0.1025-0.1926-0.32570.29460.47240.8014-0.0274-0.110801.97320.2042-0.13491.80560.42282.095631.9971125.118540.4722
100.34290.13480.28750.03980.11010.2335-0.02120.75370.67090.36490.4746-0.5016-0.18962.2422-0.00092.5129-0.16660.03573.02250.30792.477270.6648121.657674.0765
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 128 through 251 )
2X-RAY DIFFRACTION2chain 'B' and (resid 260 through 492 )
3X-RAY DIFFRACTION3chain 'E' and (resid 148 through 251 )
4X-RAY DIFFRACTION4chain 'E' and (resid 258 through 492 )
5X-RAY DIFFRACTION5chain 'U'
6X-RAY DIFFRACTION6chain 'V'
7X-RAY DIFFRACTION7chain 'A' and (resid 10 through 303)
8X-RAY DIFFRACTION8chain 'A' and (resid 304 through 366)
9X-RAY DIFFRACTION9chain 'D' and (resid 10 through 301 )
10X-RAY DIFFRACTION10chain 'D' and (resid 305 through 366 )

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