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- PDB-7klg: SARS-CoV-2 RBD in complex with Fab 15033 -

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Basic information

Entry
Database: PDB / ID: 7klg
TitleSARS-CoV-2 RBD in complex with Fab 15033
Components
  • Fab 15033 heavy chain
  • Fab 15033 light chain
  • Spike glycoprotein
KeywordsVIRAL PROTEIN/Immune System / SARS-CoV-2 / spike glycoprotein / Fab / 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 / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / host cell endoplasmic reticulum-Golgi intermediate compartment membrane ...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 / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / entry receptor-mediated virion attachment to host cell / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / membrane fusion / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / host cell surface receptor binding / 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 / membrane / identical protein binding / 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 / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / 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 ...Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / 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 2 (HR2) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.2 Å
AuthorsLi, Z. / Rini, J.M.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
Citation
Journal: J Mol Biol / Year: 2021
Title: Tetravalent SARS-CoV-2 Neutralizing Antibodies Show Enhanced Potency and Resistance to Escape Mutations.
Authors: Shane Miersch / Zhijie Li / Reza Saberianfar / Mart Ustav / James Brett Case / Levi Blazer / Chao Chen / Wei Ye / Alevtina Pavlenco / Maryna Gorelik / Julia Garcia Perez / Suryasree ...Authors: Shane Miersch / Zhijie Li / Reza Saberianfar / Mart Ustav / James Brett Case / Levi Blazer / Chao Chen / Wei Ye / Alevtina Pavlenco / Maryna Gorelik / Julia Garcia Perez / Suryasree Subramania / Serena Singh / Lynda Ploder / Safder Ganaie / Rita E Chen / Daisy W Leung / Pier Paolo Pandolfi / Giuseppe Novelli / Giulia Matusali / Francesca Colavita / Maria R Capobianchi / Suresh Jain / J B Gupta / Gaya K Amarasinghe / Michael S Diamond / James Rini / Sachdev S Sidhu /
Abstract: Neutralizing antibodies (nAbs) hold promise as therapeutics against COVID-19. Here, we describe protein engineering and modular design principles that have led to the development of synthetic ...Neutralizing antibodies (nAbs) hold promise as therapeutics against COVID-19. Here, we describe protein engineering and modular design principles that have led to the development of synthetic bivalent and tetravalent nAbs against SARS-CoV-2. The best nAb targets the host receptor binding site of the viral S-protein and tetravalent versions block entry with a potency exceeding bivalent nAbs by an order of magnitude. Structural studies show that both the bivalent and tetravalent nAbs can make multivalent interactions with a single S-protein trimer, consistent with the avidity and potency of these molecules. Significantly, we show that the tetravalent nAbs show increased tolerance to potential virus escape mutants and an emerging variant of concern. Bivalent and tetravalent nAbs can be produced at large-scale and are as stable and specific as approved antibody drugs. Our results provide a general framework for enhancing antiviral therapies against COVID-19 and related viral threats, and our strategy can be applied to virtually any antibody drug.
#1: Journal: bioRxiv / Year: 2020
Title: Tetravalent SARS-CoV-2 Neutralizing Antibodies Show Enhanced Potency and Resistance to Escape Mutations.
Authors: Shane Miersch / Zhijie Li / Reza Saberianfar / Mart Ustav / James Brett Case / Levi Blazer / Chao Chen / Wei Ye / Alevtina Pavlenco / Maryna Gorelik / Julia Garcia Perez / Suryasree ...Authors: Shane Miersch / Zhijie Li / Reza Saberianfar / Mart Ustav / James Brett Case / Levi Blazer / Chao Chen / Wei Ye / Alevtina Pavlenco / Maryna Gorelik / Julia Garcia Perez / Suryasree Subramania / Serena Singh / Lynda Ploder / Safder Ganaie / Rita E Chen / Daisy W Leung / Pier Paolo Pandolfi / Giuseppe Novelli / Giulia Matusali / Francesca Colavita / Maria R Capobianchi / Suresh Jain / J B Gupta / Gaya K Amarasinghe / Michael S Diamond / James Rini / Sachdev S Sidhu
Abstract: Neutralizing antibodies (nAbs) hold promise as effective therapeutics against COVID-19. Here, we describe protein engineering and modular design principles that have led to the development of ...Neutralizing antibodies (nAbs) hold promise as effective therapeutics against COVID-19. Here, we describe protein engineering and modular design principles that have led to the development of synthetic bivalent and tetravalent nAbs against SARS-CoV-2. The best nAb targets the host receptor binding site of the viral S-protein and its tetravalent versions can block entry with a potency that exceeds the bivalent nAbs by an order of magnitude. Structural studies show that both the bivalent and tetravalent nAbs can make multivalent interactions with a single S-protein trimer, observations consistent with the avidity and potency of these molecules. Significantly, we show that the tetravalent nAbs show much increased tolerance to potential virus escape mutants. Bivalent and tetravalent nAbs can be produced at large-scale and are as stable and specific as approved antibody drugs. Our results provide a general framework for developing potent antiviral therapies against COVID-19 and related viral threats, and our strategy can be readily applied to any antibody drug currently in development.
History
DepositionOct 30, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 10, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 18, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Aug 25, 2021Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _citation.journal_id_ISSN / _struct_ncs_dom_lim.beg_auth_comp_id ..._citation.journal_id_ISSN / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Fab 15033 heavy chain
L: Fab 15033 light chain
I: Fab 15033 heavy chain
M: Fab 15033 light chain
B: Spike glycoprotein
A: Spike glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,6288
Polymers139,1856
Non-polymers4422
Water00
1
H: Fab 15033 heavy chain
L: Fab 15033 light chain
A: Spike glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,8144
Polymers69,5933
Non-polymers2211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6120 Å2
ΔGint-28 kcal/mol
Surface area28730 Å2
MethodPISA
2
I: Fab 15033 heavy chain
M: Fab 15033 light chain
B: Spike glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,8144
Polymers69,5933
Non-polymers2211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6100 Å2
ΔGint-32 kcal/mol
Surface area28350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)197.100, 197.100, 211.510
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 333 through 527 or resid 2001))
21chain B
12chain H
22chain I
13chain L
23chain M

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111THRTHRPROPRO(chain A and (resid 333 through 527 or resid 2001))AF333 - 5276 - 200
121NAGNAGNAGNAG(chain A and (resid 333 through 527 or resid 2001))AH2001
211THRTHRNAGNAGchain BBE - G333 - 20016
112GLUGLUCYSCYSchain HHA1 - 2311 - 223
212GLUGLUCYSCYSchain IIC1 - 2311 - 223
113ASPASPCYSCYSchain LLB1 - 2341 - 214
213ASPASPCYSCYSchain MMD1 - 2341 - 214

NCS ensembles :
ID
1
2
3

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Components

#1: Antibody Fab 15033 heavy chain


Mass: 23513.260 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IgH / Plasmid: PBcmvW / Production host: Homo sapiens (human) / Strain (production host): HEK293F
#2: Antibody Fab 15033 light chain


Mass: 23448.020 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGK / Plasmid: PBcmvW / Production host: Homo sapiens (human) / Strain (production host): HEK293F
#3: Protein Spike glycoprotein / S glycoprotein / E2 / Peplomer protein


Mass: 22631.422 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 / Plasmid: PBtreW / Production host: Homo sapiens (human) / Strain (production host): HEK293F GnT1-minus / 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.: 2 / 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
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: 4.25 Å3/Da / Density % sol: 71.03 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 1.4 M (NH4)2SO4, 10% 1,2-propanediol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 1.5215 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 13, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5215 Å / Relative weight: 1
ReflectionResolution: 3.05→47.99 Å / Num. obs: 46622 / % possible obs: 99.9 % / Redundancy: 12.917 % / Biso Wilson estimate: 81.487 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.291 / Rrim(I) all: 0.303 / Χ2: 0.708 / Net I/σ(I): 7.1 / Num. measured all: 602214 / Scaling rejects: 175
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
3.05-3.1612.6724.5240.658521462046180.2944.707100
3.16-3.2813.3183.0220.9657906435043480.5223.138100
3.28-3.4113.131.911.5253362406640640.7351.984100
3.41-3.5512.5631.2162.2946961374037380.8581.26699.9
3.55-3.7113.2430.8893.2148031362836270.9390.923100
3.71-3.8712.7020.6464.138423302530250.9670.673100
3.87-4.0513.5140.4635.6639027288828880.9810.48100
4.05-4.2613.3750.3067.6937478280228020.9910.318100
4.26-4.4812.6560.2289.4430171238723840.9940.23799.9
4.48-4.7213.2630.17212.0228291213521330.9960.17999.9
4.72-512.8290.16812.1625620199919970.9960.17599.9
5-47.9912.5860.09815.9213842311027109980.9980.10299.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.16rc1_3535refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6w41

6w41


Resolution: 3.2→47.99 Å / SU ML: 0.47 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 34.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2902 2018 5.01 %
Rwork0.2709 38277 -
obs0.2719 40295 99.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 176.11 Å2 / Biso mean: 96.7806 Å2 / Biso min: 64.13 Å2
Refinement stepCycle: final / Resolution: 3.2→47.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9689 0 28 0 9717
Biso mean--108.19 --
Num. residues----1269
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A0X-RAY DIFFRACTION4.711TORSIONAL
12B0X-RAY DIFFRACTION4.711TORSIONAL
21H1342X-RAY DIFFRACTION4.711TORSIONAL
22I1342X-RAY DIFFRACTION4.711TORSIONAL
31L1296X-RAY DIFFRACTION4.711TORSIONAL
32M1296X-RAY DIFFRACTION4.711TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.2001-3.28010.43751420.41562700100
3.2801-3.36870.36581410.39782683100
3.3687-3.46780.39011420.35542696100
3.4678-3.57970.31511430.34642705100
3.5797-3.70760.31591420.31822709100
3.7076-3.8560.33311420.31642699100
3.856-4.03140.29441430.29332702100
4.0314-4.24390.30441430.27512721100
4.2439-4.50960.24841440.24862729100
4.5096-4.85740.24571440.23172729100
4.8574-5.34570.25021440.23682751100
5.3457-6.11790.30411460.2472774100
6.1179-7.70270.33271490.25782820100
7.7027-47.990.23741530.2199285995
Refinement TLS params.Method: refined / Origin x: 49.2613 Å / Origin y: 28.533 Å / Origin z: 26.8796 Å
111213212223313233
T0.5935 Å2-0.0806 Å2-0.0344 Å2-0.8209 Å20.0448 Å2--0.6932 Å2
L0.6496 °20.8566 °2-0.0046 °2-1.1434 °20.0909 °2--0.2066 °2
S-0.3181 Å °0.2881 Å °-0.002 Å °-0.1712 Å °0.3922 Å °-0.0601 Å °-0.0091 Å °0.0293 Å °-0.0732 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allH1 - 231
2X-RAY DIFFRACTION1allL1 - 234
3X-RAY DIFFRACTION1allI1 - 231
4X-RAY DIFFRACTION1allM1 - 234
5X-RAY DIFFRACTION1allB333 - 2001
6X-RAY DIFFRACTION1allA329 - 528
7X-RAY DIFFRACTION1allA2001

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