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- PDB-7ps7: Crystal structure of the receptor binding domain of SARS-CoV-2 be... -

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Basic information

Entry
Database: PDB / ID: 7ps7
TitleCrystal structure of the receptor binding domain of SARS-CoV-2 beta variant spike glycoprotein in complex with Beta-40 Fab
Components
  • Beta-40 Fab light chain
  • Beta-40 heavy chain
  • Spike protein S1
KeywordsVIRAL PROTEIN / SARS-COV-2 B.1.1.7 (Alpha) VARIANT / B.1.351 (Beta) VARIANT / P.1 (Gamma) VARIANT / B.1.617.2 (Delta) VARIANT / ANTIBODY / RECEPTOR-BINDING-DOMAIN / SPIKE / NEUTRALISATION / VIRAL PROTEIN/IMMUNE SYSTEM / IMMUNE SYSTEM / 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 / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / 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 speciesSevere acute respiratory syndrome coronavirus 2
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.9 Å
AuthorsZhou, D. / Ren, J. / Stuart, D.I.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/ N00065X/1 United Kingdom
CAMS Innovation Fund for Medical Sciences (CIFMS)2018-I2M-2-002 United Kingdom
CitationJournal: Cell Host Microbe / Year: 2022
Title: The antibody response to SARS-CoV-2 Beta underscores the antigenic distance to other variants.
Authors: Chang Liu / Daming Zhou / Rungtiwa Nutalai / Helen M E Duyvesteyn / Aekkachai Tuekprakhon / Helen M Ginn / Wanwisa Dejnirattisai / Piyada Supasa / Alexander J Mentzer / Beibei Wang / James ...Authors: Chang Liu / Daming Zhou / Rungtiwa Nutalai / Helen M E Duyvesteyn / Aekkachai Tuekprakhon / Helen M Ginn / Wanwisa Dejnirattisai / Piyada Supasa / Alexander J Mentzer / Beibei Wang / James Brett Case / Yuguang Zhao / Donal T Skelly / Rita E Chen / Sile Ann Johnson / Thomas G Ritter / Chris Mason / Tariq Malik / Nigel Temperton / Neil G Paterson / Mark A Williams / David R Hall / Daniel K Clare / Andrew Howe / Philip J R Goulder / Elizabeth E Fry / Michael S Diamond / Juthathip Mongkolsapaya / Jingshan Ren / David I Stuart / Gavin R Screaton /
Abstract: Alpha-B.1.1.7, Beta-B.1.351, Gamma-P.1, and Delta-B.1.617.2 variants of SARS-CoV-2 express multiple mutations in the spike protein (S). These may alter the antigenic structure of S, causing escape ...Alpha-B.1.1.7, Beta-B.1.351, Gamma-P.1, and Delta-B.1.617.2 variants of SARS-CoV-2 express multiple mutations in the spike protein (S). These may alter the antigenic structure of S, causing escape from natural or vaccine-induced immunity. Beta is particularly difficult to neutralize using serum induced by early pandemic SARS-CoV-2 strains and is most antigenically separated from Delta. To understand this, we generated 674 mAbs from Beta-infected individuals and performed a detailed structure-function analysis of the 27 most potent mAbs: one binding the spike N-terminal domain (NTD), the rest the receptor-binding domain (RBD). Two of these RBD-binding mAbs recognize a neutralizing epitope conserved between SARS-CoV-1 and -2, while 18 target mutated residues in Beta: K417N, E484K, and N501Y. There is a major response to N501Y, including a public IgVH4-39 sequence, with E484K and K417N also targeted. Recognition of these key residues underscores why serum from Beta cases poorly neutralizes early pandemic and Delta viruses.
History
DepositionSep 22, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 15, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 22, 2021Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_src_gen ...entity / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity_src_gen.gene_src_common_name ..._entity.pdbx_description / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_gene / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_db_accession
Revision 1.2Dec 29, 2021Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3Jan 26, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.year
Revision 1.4Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: Spike protein S1
R: Spike protein S1
L: Beta-40 Fab light chain
B: Beta-40 Fab light chain
A: Beta-40 heavy chain
H: Beta-40 heavy chain


Theoretical massNumber of molelcules
Total (without water)140,5816
Polymers140,5816
Non-polymers00
Water0
1
E: Spike protein S1
B: Beta-40 Fab light chain
A: Beta-40 heavy chain


Theoretical massNumber of molelcules
Total (without water)70,2903
Polymers70,2903
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
R: Spike protein S1
L: Beta-40 Fab light chain
H: Beta-40 heavy chain


Theoretical massNumber of molelcules
Total (without water)70,2903
Polymers70,2903
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.239, 139.872, 116.411
Angle α, β, γ (deg.)90.000, 100.045, 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-IDDetails
d_1ens_1chain "A"
d_2ens_1chain "H"
d_1ens_2chain "B"
d_2ens_2chain "L"
d_1ens_3(chain "E" and (resid 334 through 478 or resid 481 through 488 or resid 490 through 527))
d_2ens_3(chain "R" and (resid 334 through 478 or resid 481 through 488 or resid 490 through 527))

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1VALCYSE1 - 221
d_21ens_1VALCYSF1 - 221
d_11ens_2GLNTHRD1 - 210
d_21ens_2GLNTHRC1 - 210
d_11ens_3ASNTHRA1 - 145
d_12ens_3ASNCYSA148 - 155
d_13ens_3PHELYSA157 - 194
d_21ens_3ASNTHRB1 - 145
d_22ens_3ASNCYSB148 - 155
d_23ens_3PHELYSB157 - 194

NCS ensembles :
ID
ens_1
ens_2
ens_3

NCS oper:
IDCodeMatrixVector
1given(0.999002707525, 0.0236220878389, -0.0378891451966), (0.017444315118, -0.987634788912, -0.155798650828), (-0.0411009273333, 0.154982323818, -0.987061899314)21.2053632085, -32.3074677937, 87.1025457375
2given(0.999388995024, 0.025048616626, -0.0243762882691), (0.0211675137534, -0.988735146506, -0.148171341445), (-0.0278131800798, 0.147564822601, -0.988661241348)21.4884145236, -32.1248328001, 87.3494354095
3given(0.999927463388, -0.000441531741799, 0.0120363205764), (-1.64114134927E-5, -0.999376865505, -0.0352970313794), (0.0120444050896, 0.0352942735192, -0.999304381339)20.1767808055, -35.5924800405, 88.1481592805

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Components

#1: Protein Spike protein S1


Mass: 23646.551 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: Homo sapiens (human) / References: UniProt: P0DTC2
#2: Antibody Beta-40 Fab light chain


Mass: 22603.990 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody Beta-40 heavy chain


Mass: 24039.812 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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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: 2.35 Å3/Da / Density % sol: 47.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 12.5% (w/v) PEG 1000, 12.5% (w/v) PEG 3350, 12.5% (v/v) MPD, 0.02 M of each carboxylic acid and 0.1 M MES/imidazole pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97624 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Aug 10, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97624 Å / Relative weight: 1
ReflectionResolution: 3.9→60 Å / Num. obs: 11890 / % possible obs: 99.4 % / Redundancy: 6.3 % / Biso Wilson estimate: 137.98 Å2 / CC1/2: 0.988 / Rmerge(I) obs: 0.389 / Rpim(I) all: 0.166 / Net I/σ(I): 4.9
Reflection shellResolution: 3.9→3.96 Å / Mean I/σ(I) obs: 0.5 / Num. unique obs: 583 / CC1/2: 0.246

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Processing

Software
NameVersionClassification
GDA1.19_4092data collection
PHENIX1.19_4092refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7PRY

7pry


Resolution: 3.9→57.31 Å / SU ML: 0.8123 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 36.903
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.284 568 4.8 %
Rwork0.2333 11261 -
obs0.2358 11829 98.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 171.85 Å2
Refinement stepCycle: LAST / Resolution: 3.9→57.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9460 0 0 0 9460
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00849710
X-RAY DIFFRACTIONf_angle_d0.840713262
X-RAY DIFFRACTIONf_chiral_restr0.04641482
X-RAY DIFFRACTIONf_plane_restr0.00661712
X-RAY DIFFRACTIONf_dihedral_angle_d11.72093422
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2EX-RAY DIFFRACTIONcartesian NCS0.0182889848797
ens_2d_2RX-RAY DIFFRACTIONcartesian NCS0.0164976604203
ens_3d_2LX-RAY DIFFRACTIONcartesian NCS0.151513804179
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.9-4.290.3891220.33482777X-RAY DIFFRACTION97.74
4.29-4.910.32421450.26682807X-RAY DIFFRACTION99.26
4.91-6.180.33561550.25742823X-RAY DIFFRACTION99.33
6.18-57.310.21561460.18172854X-RAY DIFFRACTION99.24
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)
17.033326876140.9835071143751.666775372576.89291449854-0.8794853803214.947335135270.0472462374616-0.5097090644330.5455161627870.544310227544-0.0737881022895-0.685511637106-0.3811142775290.0289679905175-0.1308493785851.061831882430.1251245024080.03848956691561.150423618430.1753678113191.270848779643.24977776408-9.4502855156942.6229927742
25.062149483352.49040377963-0.6638062831138.24248351935-0.6475280349236.554283778580.134422709906-0.465107775158-0.0174182944119-0.098689281154-0.0713926206195-0.2144693303580.340495032525-0.1789910787910.02634442109740.9706991941760.0523944816264-0.06230031403951.315329560850.1145373038891.2690644612323.950390595-27.673868522845.2451512286
38.016379830540.04251274767880.3080251392816.571297483990.05083338036554.33792482876-0.371862278710.39453211522-0.4412158521730.530030837550.1423298718340.2195060497820.7786312113850.02222815973570.1119112392881.318840711760.02789636542790.2408865874290.9156648377020.1242176446450.99192159880110.8580965311-46.082920045577.0593917453
46.08805503806-1.103001579071.607493982236.1505345631-2.69669952651.836158688510.675051935618-0.273683667538-0.5789264818041.49748995629-0.1226747504810.5319985859610.782096077602-1.04946764432-0.474980483732.193736960110.1050191949650.3081199348011.357076272040.2710361527331.552751469014.97894184929-39.4376414411115.849987567
51.11331504819-3.67087584674-2.281055837695.752983021114.128635510024.96322445421-0.09827991369650.5016185754190.526878843689-0.104765294655-0.07316775282810.433781705576-0.890410151545-0.4604233494690.0954924654321.222165374390.0369276344681-0.07520167764261.256884031720.3546314367171.49966467317-0.554787190949-27.609470859277.9073342162
65.05855453495-3.723526221073.515478524076.5284601824-2.542503217381.20335160557-0.3328903665160.13673050729-1.058208379370.499036731680.3666305476160.577063838454-0.7118255791980.173111844553-0.2424726547581.211249572720.1112450325650.1412524233321.469977000680.06459257032531.246980826789.46560321151-27.5742488704105.694016232
72.707527737313.818270463110.1953610799043.418041263810.6542473431173.9221345323-0.3246647038360.3853775473960.718352782372-0.705355577683-0.9170330284680.337708334417-0.8749609230540.9589709814040.8524908104591.353223206860.1375855649-0.3371424956471.590831924820.2350781258491.66732677915-10.164310915711.804426488512.4511330382
84.936830782750.6406369259364.294639656140.6604077929924.730372566065.28389692464-1.212071606781.31808422080.91365107648-1.44181575012-0.2865022065-0.588138857194-1.5358903856-0.01876666464341.782767932542.43931595117-0.308535827439-0.005887287845811.372509194140.4903899413442.55332734327-17.516368930111.1139158728-26.6494083723
94.859224937044.326633367130.35866222626.855749823582.475857539998.189119013450.146865900602-0.242464870102-0.1427821568640.335895524041-0.1433962954990.6349368749660.295665627112-0.203631233667-0.1916813238851.309111412850.116595618371-0.02343792828981.355150566130.05309499900811.14596859404-21.6712204711-6.409864685979.20360376911
105.575928645180.170995114618-1.884812420637.88633281685-2.197206010221.55267999485-0.687640466210.3609635450861.20609286067-0.7943942301330.693610923366-1.429438849910.9208110978980.447318649870.0798732239551.831541856240.04379712864920.2340949378181.41759543206-0.2354075000511.55580135479-12.4296905086-2.09346556848-18.5179856908
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'E' and (resid 334 through 527)EA334 - 5271 - 194
22chain 'R' and (resid 334 through 527)RB334 - 5271 - 194
33chain 'H' and (resid 2 through 123)HF2 - 1232 - 123
44chain 'H' and (resid 124 through 226)HF124 - 226124 - 226
55chain 'L' and (resid 1 through 108)LC1 - 1081 - 108
66chain 'L' and (resid 109 through 210)LC109 - 210109 - 210
77chain 'A' and (resid 2 through 123)AE2 - 1232 - 123
88chain 'A' and (resid 124 through 226)AE124 - 226124 - 226
99chain 'B' and (resid 1 through 108)BD1 - 1081 - 108
1010chain 'B' and (resid 109 through 210)BD109 - 210109 - 210

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