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

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Basic information

Entry
Database: PDB / ID: 7prz
TitleCrystal structure of the receptor binding domain of SARS-CoV-2 beta variant spike glycoprotein in complex with beta-22 Fabs
Components
  • Beta-22 Fab heavy chain
  • Beta-22 Fab light chain
  • Spike protein S1
KeywordsVIRAL PROTEIN / SARS-CoV-2 alpha variant / beta variant / gamma variant / delta variant / B.1.1.7 / B.1.351 / P.1 / B.1.617.2 / antibody / receptor-binding-domain / spike / neutralisation / VIRAL PROTEIN/IMMUNE SYSTEM
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 / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated endocytosis of virus by host cell / membrane fusion / 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 / 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
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 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: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: entity / entity_src_gen ...entity / entity_src_gen / reflns / 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 / _reflns.d_resolution_low / _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
Revision 1.5Nov 6, 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
H: Beta-22 Fab heavy chain
E: Spike protein S1
L: Beta-22 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,68920
Polymers72,3103
Non-polymers2,37917
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9140 Å2
ΔGint-173 kcal/mol
Surface area30070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)199.378, 199.378, 202.444
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Space group name HallR32"
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x-y,-y,-z
#5: -x,-x+y,-z
#6: y,x,-z
#7: x+1/3,y+2/3,z+2/3
#8: -y+1/3,x-y+2/3,z+2/3
#9: -x+y+1/3,-x+2/3,z+2/3
#10: x-y+1/3,-y+2/3,-z+2/3
#11: -x+1/3,-x+y+2/3,-z+2/3
#12: y+1/3,x+2/3,-z+2/3
#13: x+2/3,y+1/3,z+1/3
#14: -y+2/3,x-y+1/3,z+1/3
#15: -x+y+2/3,-x+1/3,z+1/3
#16: x-y+2/3,-y+1/3,-z+1/3
#17: -x+2/3,-x+y+1/3,-z+1/3
#18: y+2/3,x+1/3,-z+1/3

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Components

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Antibody , 2 types, 2 molecules HL

#1: Antibody Beta-22 Fab heavy chain


Mass: 24457.369 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody Beta-22 Fab light chain


Mass: 24205.961 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Protein / Non-polymers , 2 types, 16 molecules E

#2: Protein Spike protein S1


Mass: 23646.551 Da / Num. of mol.: 1
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
#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: SO4

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Sugars , 2 types, 2 molecules

#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#5: Polysaccharide alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-6DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE

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Details

Has ligand of interestN
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: 5.35 Å3/Da / Density % sol: 77.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: containing 0.2 M Lithium sulfate, 0.1 M MES pH 6.0 and 20% (w/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97626 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jun 26, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97626 Å / Relative weight: 1
ReflectionResolution: 3.2→87.32 Å / Num. obs: 25724 / % possible obs: 99.8 % / Redundancy: 57.5 % / Biso Wilson estimate: 121.27 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.473 / Rpim(I) all: 0.063 / Net I/σ(I): 9.4
Reflection shellResolution: 3.2→3.25 Å / Mean I/σ(I) obs: 0.5 / Num. unique obs: 1210 / CC1/2: 0.549

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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: 7NXA

7nxa


Resolution: 3.2→87.32 Å / SU ML: 0.4803 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.5351
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2229 1326 5.17 %
Rwork0.1904 24332 -
obs0.1922 25658 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 131.38 Å2
Refinement stepCycle: LAST / Resolution: 3.2→87.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4950 0 137 0 5087
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00345205
X-RAY DIFFRACTIONf_angle_d0.60127096
X-RAY DIFFRACTIONf_chiral_restr0.0448786
X-RAY DIFFRACTIONf_plane_restr0.0053892
X-RAY DIFFRACTIONf_dihedral_angle_d11.75351839
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.320.3591390.33832627X-RAY DIFFRACTION97.7
3.32-3.480.26061410.27032682X-RAY DIFFRACTION99.93
3.48-3.660.26321510.2362669X-RAY DIFFRACTION99.89
3.66-3.890.27631390.21572705X-RAY DIFFRACTION99.96
3.89-4.190.22311490.19272697X-RAY DIFFRACTION99.96
4.19-4.610.17591280.15062728X-RAY DIFFRACTION100
4.61-5.280.19141470.15082708X-RAY DIFFRACTION100
5.28-6.650.24111460.19492747X-RAY DIFFRACTION100
6.65-87.320.21121860.18492769X-RAY DIFFRACTION99.66
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)
18.21992070493-1.057264027354.257389704143.021402229541.419441051226.311407633120.7652413326651.2954287314-0.178027073145-0.976528348593-0.878971785184-0.309101691381-0.310850571316-0.2290577308280.1778252592281.358368277970.6441093571580.2584316300411.30346647090.0633086891380.97748698976462.0296712332-31.059168687433.6522982132
23.1707025382-0.7511975888891.213921555531.905516277020.7042183055631.180196471710.3300159602870.414846430624-0.0583018486762-0.251927269907-0.3011148442160.0308619047061-0.285698353314-0.449602484776-0.1284905064971.214137374370.544168560020.1035261133381.370807238740.05080318443590.96096274838259.0978472885-31.469334984332.1471560893
32.368761077732.017329692.030986972512.367435313542.268654352032.159567078481.609924321760.314594701042-0.4506605360760.133816098603-1.234950342680.929346709842-1.348969825660.00974271508204-2.37310363241.204995116140.4040247908350.1725725908421.88626304931-0.1479243854631.2463232889223.6542549768-15.280719030549.7178712591
44.94677473317-2.64356298222-1.187060596795.06460953767-3.853921866244.062837107550.9377639463860.946946886950.359034522441-0.564863085449-0.9902465539010.316339919214-0.419075111548-0.0365438623260.09931024505011.033442723010.3138051285770.008234188994311.50659542209-0.3873085647051.1286359030733.6641216144-13.635686071246.5030395424
51.196075043611.74808676538-0.6999121251014.330819559340.459703488021.479653936520.3402844588290.0463994496277-0.4210329015470.4159151001310.024268193099-0.722345206431-0.9590799578150.448125294149-0.05990098589871.260208392340.1348844320730.2478081629060.9448092937710.09127700709671.2511360989998.6921932776-38.506964432860.826280463
65.96696877737-1.921814840271.37991949033.27274860972-1.118559097596.42723231274-0.0930228698087-0.2201401917060.5188072048150.6073719350030.576952513949-0.22754602984-0.891260652214-0.374122963922-0.6014616356980.9131125609730.2537552580540.1074952164650.899004133104-0.02302982451891.0040583644290.3889597999-42.509831016869.3977475935
73.14096970732-0.0007584973607343.241317002372.61686519381-3.867741637298.69315871456-0.651918795441-0.5035686023750.3969124470560.6420446523761.098768057670.232460465502-1.34642666532-1.02445913967-0.3331324692240.7966338972040.2601284744270.26253618910.8017164291360.07534001424971.0445093416785.769021841-42.858891978257.4416697057
80.84760831099-0.7398170247141.872717201861.80841653659-0.6954947984345.740635854730.2258238606820.06499092566360.191630521852-0.1125039951670.00510978154275-0.126150575788-0.335855096293-0.616985795199-0.3932333928210.8378005309620.2106842323060.2403380601550.8443793021660.1447558532791.0350572639183.7991517016-42.823583204250.4781699355
94.418904073941.561868848830.8953588729924.869713243281.406443921559.64869471741-0.2792752090630.306487706085-0.895647323704-0.1592793331890.6929727946510.2277129661320.521673596771-0.714621656758-0.616230304891.516647301130.3794076260380.2431075133211.267481807440.04781457251931.1190073680581.7044100313-48.402426785728.2760009396
101.94112602123-1.790126992632.943603592561.47436098964-1.470123030584.982150345640.0917970769015-0.2184333733940.2543906316780.1764568888220.3137523041450.0336185945822-0.889786664331-0.567232495915-0.2568308478850.9645502534840.1693146232780.261340375340.8985464599750.07177495813610.97519165437685.594608283-41.033382608156.9045201283
117.57372751743-1.40083659906-0.427464520896.56579835016-0.4882436062976.034465440350.0565144525994-0.084893529088-0.7156989288820.534408762455-0.2074189619640.2559660063370.530288987371-0.1057038390960.2491946540061.225649942180.187132013509-0.01409658815830.932419487654-0.1109448868220.92095286542955.7602403139-45.191216598750.1144016477
125.38918483109-4.72673393210.1790917935043.164038585850.982932470318-0.4516906971230.5337356165661.1801964263-0.775562732754-0.497723388654-0.9585980608891.053531742850.423289965123-0.5388661702280.4708567379621.003877858140.09578022316530.03164110705781.66202911175-0.410848420441.3693068916829.1878761405-30.209040007846.3153591189
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'H' and (resid 1 through 60 )HA1 - 601 - 60
22chain 'H' and (resid 61 through 130 )HA61 - 13061 - 130
33chain 'H' and (resid 131 through 145 )HA131 - 145131 - 143
44chain 'H' and (resid 146 through 227 )HA146 - 227144 - 225
55chain 'E' and (resid 329 through 353 )EB329 - 3531 - 25
66chain 'E' and (resid 354 through 391 )EB354 - 39126 - 63
77chain 'E' and (resid 392 through 409 )EB392 - 40964 - 81
88chain 'E' and (resid 410 through 469 )EB410 - 46982 - 141
99chain 'E' and (resid 470 through 489 )EB470 - 489142 - 161
1010chain 'E' and (resid 490 through 526 )EB490 - 526162 - 198
1111chain 'L' and (resid 1 through 96 )LC1 - 961 - 96
1212chain 'L' and (resid 97 through 217)LC97 - 40197

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Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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