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- PDB-7oaq: Nanobody H3 AND C1 bound to RBD with Kent mutation -

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Basic information

Entry
Database: PDB / ID: 7oaq
TitleNanobody H3 AND C1 bound to RBD with Kent mutation
Components
  • (H3) x 2
  • Spike protein S1
KeywordsANTIVIRAL PROTEIN / RBD / nanobody / high affinity
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 / suppression by virus 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 / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / membrane fusion / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / host cell surface receptor binding / symbiont-mediated suppression of host innate immune response / 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 / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Betacoronavirus spike glycoprotein S1, receptor binding / 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
Similarity search - Domain/homology
CITRIC ACID / Spike glycoprotein
Similarity search - Component
Biological speciesLama glama (llama)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsNaismith, J.H. / Mikolajek, H.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Wellcome Trust100209/Z/12/Z) United Kingdom
Engineering and Physical Sciences Research CouncilEP/S025243/1 United Kingdom
Citation
Journal: Nat Commun / Year: 2021
Title: A potent SARS-CoV-2 neutralising nanobody shows therapeutic efficacy in the Syrian golden hamster model of COVID-19.
Authors: Jiandong Huo / Halina Mikolajek / Audrey Le Bas / Jordan J Clark / Parul Sharma / Anja Kipar / Joshua Dormon / Chelsea Norman / Miriam Weckener / Daniel K Clare / Peter J Harrison / Julia A ...Authors: Jiandong Huo / Halina Mikolajek / Audrey Le Bas / Jordan J Clark / Parul Sharma / Anja Kipar / Joshua Dormon / Chelsea Norman / Miriam Weckener / Daniel K Clare / Peter J Harrison / Julia A Tree / Karen R Buttigieg / Francisco J Salguero / Robert Watson / Daniel Knott / Oliver Carnell / Didier Ngabo / Michael J Elmore / Susan Fotheringham / Adam Harding / Lucile Moynié / Philip N Ward / Maud Dumoux / Tessa Prince / Yper Hall / Julian A Hiscox / Andrew Owen / William James / Miles W Carroll / James P Stewart / James H Naismith / Raymond J Owens /
Abstract: SARS-CoV-2 remains a global threat to human health particularly as escape mutants emerge. There is an unmet need for effective treatments against COVID-19 for which neutralizing single domain ...SARS-CoV-2 remains a global threat to human health particularly as escape mutants emerge. There is an unmet need for effective treatments against COVID-19 for which neutralizing single domain antibodies (nanobodies) have significant potential. Their small size and stability mean that nanobodies are compatible with respiratory administration. We report four nanobodies (C5, H3, C1, F2) engineered as homotrimers with pmolar affinity for the receptor binding domain (RBD) of the SARS-CoV-2 spike protein. Crystal structures show C5 and H3 overlap the ACE2 epitope, whilst C1 and F2 bind to a different epitope. Cryo Electron Microscopy shows C5 binding results in an all down arrangement of the Spike protein. C1, H3 and C5 all neutralize the Victoria strain, and the highly transmissible Alpha (B.1.1.7 first identified in Kent, UK) strain and C1 also neutralizes the Beta (B.1.35, first identified in South Africa). Administration of C5-trimer via the respiratory route showed potent therapeutic efficacy in the Syrian hamster model of COVID-19 and separately, effective prophylaxis. The molecule was similarly potent by intraperitoneal injection.
#1: Journal: Res Sq / Year: 2021
Title: A potent SARS-CoV-2 neutralising nanobody shows therapeutic efficacy in the Syrian golden hamster model of COVID-19
Authors: Huo, J. / Mikolajek, H. / Le Bas, A. / Clark, J. / Sharma, P. / Kipar, A. / Dormon, J. / Norman, C. / Weckener, M. / Clare, D. / Harrison, P. / Tree, J. / Buttigieg, K. / Salguero, F. / ...Authors: Huo, J. / Mikolajek, H. / Le Bas, A. / Clark, J. / Sharma, P. / Kipar, A. / Dormon, J. / Norman, C. / Weckener, M. / Clare, D. / Harrison, P. / Tree, J. / Buttigieg, K. / Salguero, F. / Watson, R. / Knott, D. / Carnell, O. / Ngabo, D. / Elmore, M. / Fotheringham, S. / Harding, A. / Ward, P. / Moynie, L. / Dumoux, M. / Hall, Y. / Hiscox, J. / Owen, A. / James, W. / Carroll, M. / Stewart, J. / Naismith, J. / Owens, R.
History
DepositionApr 20, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 11, 2021Provider: repository / Type: Initial release
Revision 2.0Oct 6, 2021Group: Atomic model / Data collection / Database references
Category: atom_site / citation ...atom_site / citation / citation_author / diffrn_source / pdbx_database_proc
Item: _atom_site.pdbx_tls_group_id / _diffrn_source.pdbx_synchrotron_site
Revision 2.1Jan 31, 2024Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / diffrn_source / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: H3
EEE: Spike protein S1
FFF: H3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,0086
Polymers53,5603
Non-polymers4493
Water6,756375
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3450 Å2
ΔGint-16 kcal/mol
Surface area21020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.857, 105.857, 112.709
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11EEE-801-

HOH

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Components

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Antibody , 2 types, 2 molecules AAAFFF

#1: Antibody H3


Mass: 14659.114 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)
#3: Antibody H3


Mass: 15134.849 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)

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Protein / Sugars , 2 types, 2 molecules EEE

#2: Protein Spike protein S1


Mass: 23765.652 Da / Num. of mol.: 1 / Mutation: N501Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: S, 2 / Production host: Homo sapiens (human) / References: UniProt: P0DTC2
#4: 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

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Non-polymers , 3 types, 377 molecules

#5: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 375 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.95 Å3/Da / Density % sol: 58.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 1.0 M Lithium chloride, 0.1 M Citrate pH 4, 20 % Peg 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 24, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.55→53 Å / Num. obs: 93033 / % possible obs: 100 % / Redundancy: 26.8 % / CC1/2: 1 / Rpim(I) all: 0.02 / Net I/σ(I): 16.9
Reflection shellResolution: 1.55→1.59 Å / Redundancy: 27.6 % / Mean I/σ(I) obs: 0.6 / Num. unique obs: 6677 / CC1/2: 0.6 / Rpim(I) all: 0.59 / % possible all: 93

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7oap

7oap


Resolution: 1.55→52.984 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.966 / SU B: 3.859 / SU ML: 0.056 / Cross valid method: FREE R-VALUE / ESU R: 0.068 / ESU R Free: 0.06
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1783 4722 5.113 %
Rwork0.155 87632 -
all0.156 --
obs-92354 99.27 %
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 36.162 Å2
Baniso -1Baniso -2Baniso -3
1--1.211 Å2-0 Å2-0 Å2
2---1.211 Å2-0 Å2
3---2.422 Å2
Refinement stepCycle: LAST / Resolution: 1.55→52.984 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3513 0 28 375 3916
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0133734
X-RAY DIFFRACTIONr_bond_other_d0.0030.0183333
X-RAY DIFFRACTIONr_angle_refined_deg1.3981.6555110
X-RAY DIFFRACTIONr_angle_other_deg1.341.5817683
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7285481
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.11421.667198
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.22515567
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1571524
X-RAY DIFFRACTIONr_chiral_restr0.0690.2478
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024366
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02964
X-RAY DIFFRACTIONr_nbd_refined0.210.2557
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1830.22999
X-RAY DIFFRACTIONr_nbtor_refined0.1730.21765
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0760.21755
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.2255
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2220.29
X-RAY DIFFRACTIONr_nbd_other0.1420.248
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1470.222
X-RAY DIFFRACTIONr_mcbond_it2.3171.1261825
X-RAY DIFFRACTIONr_mcbond_other2.2761.1251824
X-RAY DIFFRACTIONr_mcangle_it2.7741.7012285
X-RAY DIFFRACTIONr_mcangle_other2.7761.7032286
X-RAY DIFFRACTIONr_scbond_it3.1021.3951909
X-RAY DIFFRACTIONr_scbond_other3.0221.3891906
X-RAY DIFFRACTIONr_scangle_it3.6422.0072807
X-RAY DIFFRACTIONr_scangle_other3.6422.0092808
X-RAY DIFFRACTIONr_lrange_it3.95415.1924110
X-RAY DIFFRACTIONr_lrange_other3.9615.2074111
X-RAY DIFFRACTIONr_rigid_bond_restr8.60837067
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.590.3963130.3896366X-RAY DIFFRACTION98.3942
1.59-1.6340.3543330.3396173X-RAY DIFFRACTION98.4564
1.634-1.6810.3062930.3066092X-RAY DIFFRACTION98.6557
1.681-1.7330.272940.265844X-RAY DIFFRACTION98.777
1.733-1.790.2543310.2175681X-RAY DIFFRACTION98.8978
1.79-1.8520.1752900.175525X-RAY DIFFRACTION99.1306
1.852-1.9220.1772820.1435371X-RAY DIFFRACTION99.2277
1.922-2.0010.1582650.1255156X-RAY DIFFRACTION99.3585
2.001-2.090.1522530.1194988X-RAY DIFFRACTION99.2802
2.09-2.1920.1562640.1164733X-RAY DIFFRACTION99.6014
2.192-2.310.1552670.114523X-RAY DIFFRACTION99.5842
2.31-2.450.1622160.1144336X-RAY DIFFRACTION99.6934
2.45-2.6190.1522220.1174041X-RAY DIFFRACTION99.8829
2.619-2.8290.1671850.1273824X-RAY DIFFRACTION99.8506
2.829-3.0980.1672310.1453462X-RAY DIFFRACTION100
3.098-3.4630.172020.1543166X-RAY DIFFRACTION99.9703
3.463-3.9980.1541560.1522840X-RAY DIFFRACTION100
3.998-4.8930.1481240.1292439X-RAY DIFFRACTION100
4.893-6.9050.2011220.1861909X-RAY DIFFRACTION100
6.905-52.9840.23790.2271131X-RAY DIFFRACTION99.7527
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)
14.19910.9967-1.23664.6212-0.52865.69840.1564-0.9005-0.06350.8081-0.1031-0.0449-0.09840.3673-0.05330.6369-0.1282-0.02580.5405-0.09280.112516.919-15.26710.636
23.40480.7335-0.41043.87980.05175.52780.1652-0.95630.36170.9783-0.0710.0457-0.40620.2191-0.09420.6387-0.1129-0.00880.5447-0.1060.119114.916-14.93811.43
37.52225.6725-0.83111.2447-0.37821.5734-0.03380.3370.4751-0.3110.17930.3915-0.2514-0.0217-0.14550.28760.03450.02320.25040.01640.2227.562-9.384-19.979
41.39740.6187-0.54552.80870.22281.45080.132-0.15280.17720.233-0.0535-0.0101-0.17170.1325-0.07850.1973-0.03390.00620.1823-0.02520.025914.655-19.395-14.108
50.69251.67820.39266.7499-0.10911.4181-0.00150.1036-0.1801-0.06670.126-0.51590.02940.368-0.12460.15350.00220.01860.2082-0.01780.108320.366-33.27-23.405
60.61110.4650.02832.59670.52280.81150.027-0.0764-0.01370.1636-0.00460.04810.02940.1284-0.02240.1558-0.003-0.00660.16890.00960.005310.286-34.861-16.149
79.1567-5.937-9.86074.7745.885511.01530.4839-0.23341.05070.22350.5469-0.6736-0.6990.0259-1.03080.55150.06640.13650.4368-0.16760.344425-1.538-21.117
84.11131.13740.652111.052-2.45832.8007-0.0056-0.01570.04720.1384-0.05760.2260.0705-0.23340.06320.1676-0.0257-0.01740.2424-0.00340.0325-10.293-49.662-35.765
92.8876-0.12220.87392.07720.26782.85320.03420.2656-0.0814-0.0732-0.02670.12850.13860.0098-0.00750.1731-0.0004-0.01320.1809-0.01640.0106-2.862-49.464-35.616
1011.65132.1912-3.17130.4816-0.14846.23770.191-0.6731-0.03590.1337-0.13490.05660.3264-0.5174-0.0560.35090.00220.08720.27170.05940.232-9.317-55.311-21.818
111.73530.11490.73170.78920.09422.05280.04070.0002-0.1809-0.007-0.00970.04970.2115-0.0529-0.0310.1687-0.0017-0.01350.13340.0020.0261-0.978-51.462-28.815
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLAAA1 - 64
2X-RAY DIFFRACTION2ALLAAA65 - 124
3X-RAY DIFFRACTION3ALLEEE334 - 346
4X-RAY DIFFRACTION4ALLEEE347 - 457
5X-RAY DIFFRACTION5ALLEEE458 - 473
6X-RAY DIFFRACTION6ALLEEE474 - 515
7X-RAY DIFFRACTION7ALLEEE516 - 530
8X-RAY DIFFRACTION8ALLFFF1 - 12
9X-RAY DIFFRACTION9ALLFFF13 - 36
10X-RAY DIFFRACTION10ALLFFF37 - 47
11X-RAY DIFFRACTION11ALLFFF48 - 127

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