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- PDB-9izn: Crystal structure of HKU1A RBD bound to TMPRSS2 -

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Basic information

Entry
Database: PDB / ID: 9izn
TitleCrystal structure of HKU1A RBD bound to TMPRSS2
Components
  • Spike protein S1
  • Transmembrane protease serine 2
KeywordsVIRAL PROTEIN / Complex of a human coronavirus spike protein bound to receptor
Function / homology
Function and homology information


transmembrane protease serine 2 / symbiont-mediated induction of syncytium formation / protein autoprocessing / Attachment and Entry / serine-type peptidase activity / viral translation / Induction of Cell-Cell Fusion / Attachment and Entry / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of viral entry into host cell ...transmembrane protease serine 2 / symbiont-mediated induction of syncytium formation / protein autoprocessing / Attachment and Entry / serine-type peptidase activity / viral translation / Induction of Cell-Cell Fusion / 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 / membrane / plasma membrane
Similarity search - Function
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 ...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, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / 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 / Spike S1 subunit, receptor binding domain superfamily, 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, 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 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Transmembrane protease serine 2 / Spike glycoprotein
Similarity search - Component
Biological speciesHomo sapiens (human)
Human coronavirus HKU1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsWang, W. / Xu, Y. / Zhang, S.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32170158 China
National Natural Science Foundation of China (NSFC)32000659 China
CitationJournal: Hlife / Year: 2024
Title: High-resolution crystal structure of human coronavirus HKU1 receptor binding domain bound to TMPRSS2 receptor
Authors: Wang, W. / Guan, J. / Ren, M. / Li, Z. / Ji, W. / Chen, R. / Xu, Y. / Zhang, S.
History
DepositionAug 1, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Oct 23, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Transmembrane protease serine 2
A: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,4474
Polymers86,0042
Non-polymers4422
Water5,062281
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.324, 78.358, 257.364
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 43473.945 Da / Num. of mol.: 1 / Mutation: R255Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TMPRSS2, PRSS10 / Production host: Baculovirus expression vector pFastBac1-HM
References: UniProt: O15393, transmembrane protease serine 2
#2: Protein Spike protein S1


Mass: 42530.223 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human coronavirus HKU1 (isolate N1) / Gene: S, 3 / Production host: Baculovirus expression vector pFastBac1-HM / References: UniProt: Q5MQD0
#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.: 2 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 281 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 3.71 Å3/Da / Density % sol: 66.87 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 2% v/v Tacsimate pH 7.0, 5% v/v 2-Propanol, 0.1 M Imidazole (pH 7.0) and 8% w/v Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97946 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: May 11, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. obs: 51020 / % possible obs: 99.7 % / Redundancy: 9.93 % / CC1/2: 0.998 / Net I/σ(I): 12.74
Reflection shellResolution: 2.4→2.54 Å / Num. unique obs: 8031 / CC1/2: 0.295

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→19.91 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2605 2478 4.86 %
Rwork0.2145 --
obs0.2167 50958 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→19.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5462 0 28 281 5771
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002
X-RAY DIFFRACTIONf_angle_d0.514
X-RAY DIFFRACTIONf_dihedral_angle_d14.2572005
X-RAY DIFFRACTIONf_chiral_restr0.047826
X-RAY DIFFRACTIONf_plane_restr0.004991
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.450.43981340.37842653X-RAY DIFFRACTION99
2.45-2.50.39411460.37522601X-RAY DIFFRACTION100
2.5-2.550.37681320.36052664X-RAY DIFFRACTION100
2.55-2.610.38081400.33122654X-RAY DIFFRACTION100
2.61-2.670.33731320.30922645X-RAY DIFFRACTION100
2.67-2.750.32681350.30352678X-RAY DIFFRACTION100
2.75-2.830.33521310.28922647X-RAY DIFFRACTION100
2.83-2.920.36261420.28012686X-RAY DIFFRACTION100
2.92-3.020.29261360.26332686X-RAY DIFFRACTION100
3.02-3.140.33131380.25582679X-RAY DIFFRACTION100
3.14-3.290.27891280.24312665X-RAY DIFFRACTION100
3.29-3.460.28061410.23272700X-RAY DIFFRACTION100
3.46-3.670.28511390.21652691X-RAY DIFFRACTION100
3.67-3.950.23361490.19482713X-RAY DIFFRACTION100
3.95-4.350.22531420.1662704X-RAY DIFFRACTION100
4.35-4.970.18621220.15422750X-RAY DIFFRACTION100
4.97-6.230.20791510.182768X-RAY DIFFRACTION100
6.23-19.910.24791400.19822896X-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)
10.139-0.05760.2050.20390.08310.2451-0.1341.1347-0.2106-1.24360.2826-0.39190.17950.1157-01.79440.32160.04561.5128-0.25231.286722.5285-38.628435.9654
20.2145-0.0817-0.0360.0517-0.08050.29790.52060.3588-0.1625-1.25860.0872-0.5707-0.03080.11050.00041.51420.44210.15221.1498-0.12581.050826.5441-34.405336.1164
31.1558-1.06460.93322.0104-0.98381.37940.48620.2620.0648-1.0334-0.42460.23060.29890.35860.00240.83560.1982-0.1730.5239-0.05370.56822.7324-19.751150.8641
40.39690.23370.18591.0255-0.71780.64560.18250.2012-0.1412-0.3421-0.2650.03640.33240.276900.68590.1295-0.06340.59110.06990.617814.4486-22.90863.8367
50.9032-0.48420.46340.3744-0.54160.5470.2130.21570.0805-0.2874-0.23810.0588-0.0174-0.058600.66360.0908-0.04110.4922-0.0050.600612.7653-27.606266.5148
60.44690.3336-0.37180.2254-0.24190.34080.18070.3811-0.4869-0.7559-0.3441-0.09590.29110.386-0.04431.19780.3183-0.17610.641-0.15280.58079.4652-33.733848.4467
71.9590.54541.27680.64090.32761.4987-0.0526-0.1492-0.0536-0.04540.0474-0.02490.04740.1058-00.4594-0.01330.02640.5133-0.03820.5136.0629-32.3779101.0351
80.28210.3380.69260.80920.71370.5645-0.10710.15690.0993-0.14640.10860.222-0.35080.156600.6502-0.0699-0.10040.8382-0.0280.549464.346-8.6493131.5072
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 141 through 188 )
2X-RAY DIFFRACTION2chain 'B' and (resid 189 through 245 )
3X-RAY DIFFRACTION3chain 'B' and (resid 246 through 366 )
4X-RAY DIFFRACTION4chain 'B' and (resid 367 through 410 )
5X-RAY DIFFRACTION5chain 'B' and (resid 411 through 471 )
6X-RAY DIFFRACTION6chain 'B' and (resid 472 through 491 )
7X-RAY DIFFRACTION7chain 'A' and (resid 311 through 606 )
8X-RAY DIFFRACTION8chain 'A' and (resid 607 through 674 )

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