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- PDB-7kn5: Crystal structure of SARS-CoV-2 receptor binding domain complexed... -

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Basic information

Entry
Database: PDB / ID: 7kn5
TitleCrystal structure of SARS-CoV-2 receptor binding domain complexed with nanobodies VHH E and U
Components
  • Spike protein S1
  • VHH E
  • VHH U
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / SARS-CoV-2 / Nanobody / Spike / Coronavirus / COVID-19 / IMMUNE SYSTEM / Nanobody-antigen complex / single-domain antibody / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell ...Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell / membrane 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 / host cell surface receptor binding / symbiont-mediated suppression of host innate immune response / receptor ligand activity / endocytosis involved in viral entry into host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / identical protein binding / membrane / plasma membrane
Similarity search - Function
Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / 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 ...Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesSevere acute respiratory syndrome coronavirus 2
Vicugna pacos (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsLiu, H. / Yuan, M. / Zhu, X. / Wu, N.C. / Wilson, I.A.
Funding support United States, 2items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationOPP1170236 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI139445 United States
CitationJournal: Science / Year: 2021
Title: Structure-guided multivalent nanobodies block SARS-CoV-2 infection and suppress mutational escape.
Authors: Paul-Albert Koenig / Hrishikesh Das / Hejun Liu / Beate M Kümmerer / Florian N Gohr / Lea-Marie Jenster / Lisa D J Schiffelers / Yonas M Tesfamariam / Miki Uchima / Jennifer D Wuerth / Karl ...Authors: Paul-Albert Koenig / Hrishikesh Das / Hejun Liu / Beate M Kümmerer / Florian N Gohr / Lea-Marie Jenster / Lisa D J Schiffelers / Yonas M Tesfamariam / Miki Uchima / Jennifer D Wuerth / Karl Gatterdam / Natalia Ruetalo / Maria H Christensen / Caroline I Fandrey / Sabine Normann / Jan M P Tödtmann / Steffen Pritzl / Leo Hanke / Jannik Boos / Meng Yuan / Xueyong Zhu / Jonathan L Schmid-Burgk / Hiroki Kato / Michael Schindler / Ian A Wilson / Matthias Geyer / Kerstin U Ludwig / B Martin Hällberg / Nicholas C Wu / Florian I Schmidt /
Abstract: The pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to spread, with devastating consequences. For passive immunization efforts, nanobodies have size and cost ...The pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to spread, with devastating consequences. For passive immunization efforts, nanobodies have size and cost advantages over conventional antibodies. In this study, we generated four neutralizing nanobodies that target the receptor binding domain of the SARS-CoV-2 spike protein. We used x-ray crystallography and cryo-electron microscopy to define two distinct binding epitopes. On the basis of these structures, we engineered multivalent nanobodies with more than 100 times the neutralizing activity of monovalent nanobodies. Biparatopic nanobody fusions suppressed the emergence of escape mutants. Several nanobody constructs neutralized through receptor binding competition, whereas other monovalent and biparatopic nanobodies triggered aberrant activation of the spike fusion machinery. These premature conformational changes in the spike protein forestalled productive fusion and rendered the virions noninfectious.
History
DepositionNov 4, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2021Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Feb 24, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation_author.identifier_ORCID
Revision 1.3Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 20, 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: Spike protein S1
B: Spike protein S1
C: VHH E
D: VHH E
E: VHH U
F: VHH U
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,76613
Polymers107,8106
Non-polymers9567
Water7,476415
1
A: Spike protein S1
C: VHH E
E: VHH U
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,6409
Polymers53,9053
Non-polymers7356
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4140 Å2
ΔGint5 kcal/mol
Surface area20100 Å2
MethodPISA
2
B: Spike protein S1
D: VHH E
F: VHH U
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,1264
Polymers53,9053
Non-polymers2211
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3500 Å2
ΔGint-5 kcal/mol
Surface area20450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.525, 91.943, 84.998
Angle α, β, γ (deg.)90.000, 91.147, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22
13
23

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain 'A' and (resid 334 through 345 or (resid 346...A334 - 527
121(chain 'A' and (resid 334 through 345 or (resid 346...A1001
211(chain 'B' and (resid 334 or (resid 335 and (name...B334 - 527
221(chain 'B' and (resid 334 or (resid 335 and (name...B1001
112(chain 'C' and (resid 1 through 18 or resid 20...C1 - 17
122(chain 'C' and (resid 1 through 18 or resid 20...C20 - 112
212(chain 'D' and ((resid 1 and (name N or name...D1 - 17
222(chain 'D' and ((resid 1 and (name N or name...D20 - 112
113(chain 'E' and (resid 2 through 3 or (resid 4...E2 - 8
123(chain 'E' and (resid 2 through 3 or (resid 4...E11 - 63
133(chain 'E' and (resid 2 through 3 or (resid 4...E66 - 110
213(chain 'F' and (resid 2 through 9 or (resid 11...F2 - 8
223(chain 'F' and (resid 2 through 9 or (resid 11...F11 - 63
233(chain 'F' and (resid 2 through 9 or (resid 11...F66 - 110

NCS ensembles :
ID
1
2
3

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Spike protein S1


Mass: 26095.348 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: S, 2 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P0DTC2

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Antibody , 2 types, 4 molecules CDEF

#2: Antibody VHH E


Mass: 14109.523 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) / Strain (production host): WK6
#3: Antibody VHH U


Mass: 13699.978 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) / Strain (production host): WK6

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Sugars , 2 types, 2 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: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam 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
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#6: 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 / 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

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Non-polymers , 2 types, 420 molecules

#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 415 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.92 Å3/Da / Density % sol: 57.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20% PEG-3000, 0.1 M citrate pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.97946 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 10, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.87→50 Å / Num. obs: 96843 / % possible obs: 95.1 % / Redundancy: 6.2 % / Biso Wilson estimate: 33.27 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.035 / Net I/σ(I): 29
Reflection shellResolution: 1.87→1.9 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 3542 / CC1/2: 0.651 / Rpim(I) all: 0.452 / % possible all: 70.5

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
HKL-2000data reduction
HKL-2000data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6XC7, 6WAQ

6xc7

6waq


Resolution: 1.87→38.57 Å / SU ML: 0.2117 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 20.5799
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2133 4699 4.85 %
Rwork0.1768 92100 -
obs0.1785 96799 94.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.32 Å2
Refinement stepCycle: LAST / Resolution: 1.87→38.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6794 0 62 415 7271
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01297042
X-RAY DIFFRACTIONf_angle_d1.18799575
X-RAY DIFFRACTIONf_chiral_restr0.08651010
X-RAY DIFFRACTIONf_plane_restr0.0091248
X-RAY DIFFRACTIONf_dihedral_angle_d11.17954198
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.87-1.890.39391060.32091984X-RAY DIFFRACTION62.28
1.89-1.910.3011480.29672371X-RAY DIFFRACTION73.87
1.91-1.940.29521380.26832574X-RAY DIFFRACTION80.93
1.94-1.960.27951260.24162870X-RAY DIFFRACTION88.33
1.96-1.990.24541720.21773049X-RAY DIFFRACTION94.76
1.99-2.020.23871870.2013118X-RAY DIFFRACTION97.38
2.02-2.040.22551690.19613136X-RAY DIFFRACTION97.84
2.04-2.070.23551640.19413193X-RAY DIFFRACTION98.91
2.07-2.110.22971720.19573190X-RAY DIFFRACTION99.09
2.11-2.140.23121520.20013185X-RAY DIFFRACTION99.08
2.14-2.180.20971700.19743225X-RAY DIFFRACTION98.98
2.18-2.220.25441130.19323203X-RAY DIFFRACTION99.07
2.22-2.260.22681820.18923192X-RAY DIFFRACTION98.74
2.26-2.310.19691530.18563221X-RAY DIFFRACTION98.37
2.31-2.360.22961540.18993181X-RAY DIFFRACTION98.46
2.36-2.410.25641570.19333188X-RAY DIFFRACTION98.76
2.41-2.470.22911350.18333084X-RAY DIFFRACTION95.15
2.47-2.540.21821630.1852965X-RAY DIFFRACTION91.89
2.54-2.610.19761860.18343162X-RAY DIFFRACTION99.11
2.61-2.70.24621810.18623192X-RAY DIFFRACTION98.94
2.7-2.790.23731440.19053227X-RAY DIFFRACTION99.32
2.79-2.910.21741650.18823203X-RAY DIFFRACTION98.48
2.91-3.040.24041480.18873221X-RAY DIFFRACTION98.94
3.04-3.20.22831690.19183180X-RAY DIFFRACTION98.41
3.2-3.40.20761950.18213159X-RAY DIFFRACTION97.64
3.4-3.660.19661690.17272947X-RAY DIFFRACTION91.49
3.66-4.030.20991740.15723179X-RAY DIFFRACTION97.53
4.03-4.610.19091280.13883273X-RAY DIFFRACTION99.5
4.61-5.810.16421530.14913263X-RAY DIFFRACTION99.16
5.81-38.570.19031260.16823165X-RAY DIFFRACTION93.81
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)
10.698188241533-0.141966136434-0.1474541654890.424383839142-0.08125300637520.6088609130480.02562510206640.115273358128-0.0277399792288-0.0251205555611-0.01222704302490.206452760581-0.0327313427226-0.1132646282026.42836517795E-50.1877245310530.02916861724630.0014935734090.2317962896910.01656685023570.31690248849814.8102705817-8.4101615588739.5962140379
20.8096876437550.3060818162160.1235135881540.6484033269020.6498227164070.798452610616-0.04189270924120.205768603503-0.153403911011-0.195770387484-0.01096713301680.0767968927498-0.221361606674-0.0442139364632-0.02306421038980.386265265080.00251114170164-0.03892217414970.24004062891-0.05379475979740.181062941091-40.55653434587.4450111316910.6695837177
30.4865712695-0.01871415654-0.216192688780.254142468696-0.05380755129510.2481054904820.00174963853563-0.317572275850.03505425714730.1304330078460.0140236877842-0.161030529218-0.01301910991220.253865762772-0.000382684729340.2899150696960.0035620805812-0.03990626073240.4377915053420.002156231519910.2167370384943.0014748378-3.2177191558459.7006155559
40.238891824996-0.165624864459-0.1086886841070.257766682563-0.1333969938290.602639083639-0.0698953386547-0.06007953979810.241369850144-0.002116930076540.0248258057152-0.187369245330.0518653073330.1399145173582.20732298141E-50.1623149974760.0128416997978-0.02322079511320.2833454845920.01549247233360.358272755869-22.85488630361.7895322834439.6428052949
50.238262503344-0.05670116025120.1580690314880.2414887393350.16958556170.355182948638-0.311221833976-0.738268499099-0.6527572595010.4355439657230.4145069505380.909163967280.397548374204-0.808334172414-0.02449023561950.4539173997440.0469904450430.3213759601260.6867234191160.3887186866410.7362572814611.81176753877-25.116428581860.9709614811
60.135847851182-0.1061067676620.05682775641050.12331911782-0.04149771726160.149968749609-0.2965150561650.5491011192970.334409543238-0.8489015243020.140609354756-0.312067573704-0.7194678151220.521925876229-0.07617319566811.46358350332-0.9275258707940.1876902916610.6144083902420.3748134016390.269331100196-20.977398168229.43035796574.41054276253
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resseq 334:528)
2X-RAY DIFFRACTION2(chain B and resseq 334:528)
3X-RAY DIFFRACTION3(chain C and resseq 1:113)
4X-RAY DIFFRACTION4(chain D and resseq 1:113)
5X-RAY DIFFRACTION5(chain E and resseq 2:111)
6X-RAY DIFFRACTION6(chain F and resseq 2:111)

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