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- PDB-7neg: Crystal structure of the N501Y mutant receptor binding domain of ... -

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Basic information

Entry
Database: PDB / ID: 7neg
TitleCrystal structure of the N501Y mutant receptor binding domain of SARS-CoV-2 Spike glycoprotein in complex with COVOX-269 Fab
Components
  • (Antibody COVOX-269 Fab ...) x 2
  • Surface glycoprotein
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / SARS-CoV-2 B.1.1.7 variant / N501Y mutation / antibody / receptor-binding-domain / spike / neutralisation / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


: / endocytosis involved in viral entry into 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 ...: / endocytosis involved in viral entry into 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 / 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 / membrane => GO:0016020 / 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 (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
Spike glycoprotein / Spike glycoprotein
Similarity search - Component
Biological speciesHomo sapiens (human)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å
AuthorsZhou, D. / Ren, J. / Stuart, D.
Funding support United Kingdom, China, 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 China
CitationJournal: Cell / Year: 2021
Title: Reduced neutralization of SARS-CoV-2 B.1.1.7 variant by convalescent and vaccine sera.
Authors: Supasa, P. / Zhou, D. / Dejnirattisai, W. / Liu, C. / Mentzer, A.J. / Ginn, H.M. / Zhao, Y. / Duyvesteyn, H.M.E. / Nutalai, R. / Tuekprakhon, A. / Wang, B. / Paesen, G.C. / Slon-Campos, J. / ...Authors: Supasa, P. / Zhou, D. / Dejnirattisai, W. / Liu, C. / Mentzer, A.J. / Ginn, H.M. / Zhao, Y. / Duyvesteyn, H.M.E. / Nutalai, R. / Tuekprakhon, A. / Wang, B. / Paesen, G.C. / Slon-Campos, J. / Lopez-Camacho, C. / Hallis, B. / Coombes, N. / Bewley, K.R. / Charlton, S. / Walter, T.S. / Barnes, E. / Dunachie, S.J. / Skelly, D. / Lumley, S.F. / Baker, N. / Shaik, I. / Humphries, H.E. / Godwin, K. / Gent, N. / Sienkiewicz, A. / Dold, C. / Levin, R. / Dong, T. / Pollard, A.J. / Knight, J.C. / Klenerman, P. / Crook, D. / Lambe, T. / Clutterbuck, E. / Bibi, S. / Flaxman, A. / Bittaye, M. / Belij-Rammerstorfer, S. / Gilbert, S. / Hall, D.R. / Williams, M.A. / Paterson, N.G. / James, W. / Carroll, M.W. / Fry, E.E. / Mongkolsapaya, J. / Ren, J. / Stuart, D.I. / Screaton, G.R.
History
DepositionFeb 4, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 3, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 31, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Apr 28, 2021Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.3Jan 31, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Antibody COVOX-269 Fab heavy chain
L: Antibody COVOX-269 Fab light chain
E: Surface glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,83812
Polymers70,5193
Non-polymers1,3199
Water2,414134
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8460 Å2
ΔGint-46 kcal/mol
Surface area27270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)195.099, 84.950, 57.936
Angle α, β, γ (deg.)90.000, 100.634, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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Antibody , 2 types, 2 molecules HL

#1: Antibody Antibody COVOX-269 Fab heavy chain


Mass: 23557.420 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody Antibody COVOX-269 Fab light chain


Mass: 23299.961 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 / Sugars , 2 types, 2 molecules E

#3: Protein Surface glycoprotein


Mass: 23661.561 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Production host: Homo sapiens (human) / References: UniProt: A0A7D5QNT3, UniProt: P0DTC2*PLUS
#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-Glycam 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
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE

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Non-polymers , 3 types, 142 molecules

#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 134 / 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: 3.35 Å3/Da / Density % sol: 63.24 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.15 M ammonium sulfate, 0.1 M MES pH 6.0 and 15% PEG 4000.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jan 21, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.19→96 Å / Num. obs: 48007 / % possible obs: 99.9 % / Redundancy: 13 % / Biso Wilson estimate: 54.95 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.177 / Rpim(I) all: 0.05 / Net I/σ(I): 8.4
Reflection shellResolution: 2.19→2.23 Å / Redundancy: 9.1 % / Num. unique obs: 2371 / CC1/2: 0.47 / % possible all: 98.5

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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: 7BEM

7bem


Resolution: 2.19→56.94 Å / SU ML: 0.3675 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.9719
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2228 2137 4.92 %
Rwork0.1945 41325 -
obs0.1959 43462 90.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 68.27 Å2
Refinement stepCycle: LAST / Resolution: 2.19→56.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4715 0 83 134 4932
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00444919
X-RAY DIFFRACTIONf_angle_d0.7016682
X-RAY DIFFRACTIONf_chiral_restr0.0456740
X-RAY DIFFRACTIONf_plane_restr0.0049853
X-RAY DIFFRACTIONf_dihedral_angle_d11.98841766
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.19-2.240.3839280.4156536X-RAY DIFFRACTION17.58
2.24-2.30.4132790.43061656X-RAY DIFFRACTION55.27
2.3-2.360.38561130.39872661X-RAY DIFFRACTION87.04
2.36-2.430.37191690.36342982X-RAY DIFFRACTION98.99
2.43-2.510.33181520.32733045X-RAY DIFFRACTION99.97
2.51-2.60.31451550.30142992X-RAY DIFFRACTION100
2.6-2.70.35911800.27263001X-RAY DIFFRACTION99.97
2.7-2.820.27111430.2373046X-RAY DIFFRACTION99.94
2.82-2.970.26561640.2153041X-RAY DIFFRACTION99.97
2.97-3.160.24241760.21543020X-RAY DIFFRACTION100
3.16-3.40.2651390.21563081X-RAY DIFFRACTION99.97
3.4-3.740.24961400.17713026X-RAY DIFFRACTION99.97
3.74-4.290.18221550.15363069X-RAY DIFFRACTION100
4.29-5.40.15031690.13173058X-RAY DIFFRACTION100
5.4-56.940.17971750.16473111X-RAY DIFFRACTION99.76
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)
12.99007584272-0.734474718132-1.210615881470.8357503004381.66465505264.1281978379-0.194256520326-0.384262087977-0.1926849126240.2330454256540.107189344316-0.0303648789210.078689345994-0.1605152028380.09983465885670.4710954392260.14212891946-0.01042139073640.4781603074220.1022591546170.370945499101-56.72361702959.8812329226736.2274433048
23.829962293052.35845151225-2.436591040148.6401924794.436822179396.77522756673-0.363871683467-0.8415702923830.0178037593802-0.840870647730.08876092632921.01424353739-1.01934192905-1.523915865490.144709156130.5888997028140.08122564592530.07227969371220.8115882326360.1075795784660.669833404981-97.612678072226.846712069142.6078796399
36.053163721.538251011721.785625443.259119435420.388300653754.1381625910.00317101800437-0.440251632966-0.3898501699120.378466920290.1446864318280.2739686580760.390142365778-0.0100726346801-0.1822016236430.4521399233910.08596116162960.06056222811960.5342760044190.1269434074730.439164017646-90.234589462718.064995053443.8494031379
47.77141699038-2.754523011282.215199134694.06349048524-0.09821570690373.43988539284-0.03124950482190.5554469596180.741058020947-0.168219936268-0.421937023029-0.257897324224-0.445185424509-0.4473042324350.4312996948560.5388036458960.124078750514-0.08322966742080.7151112120150.04475694156660.588056046954-71.161482928420.544876767214.6066154072
57.04185550247-3.304638734620.893948976154.0320568073-0.3852999163984.449242061070.10888888240.8179456100560.285631113631-0.0858047907762-0.183753039064-0.0672047389045-0.0233663068219-0.03306418953290.1484934684660.4487361286640.116935141150.008758706502550.619196988092-0.005933979715030.427020274097-63.582730775613.560310237615.8587409785
67.68506930743-6.50056442423-2.374808006235.628718974751.971857676680.754263675110.108186801040.9333949521310.176380485081-0.159966364406-0.366807104279-0.0327350585489-0.131093949378-0.1569584356830.2594111637580.504814017460.0536648084436-0.06618465412990.7165661034810.02868089447010.410632378566-85.986694508320.993566680218.3112825424
74.658297774-0.4155316904021.462631328064.990106935331.48896838815.48822320004-0.0910013662367-0.7070608449650.07427970753830.8401721244670.191941651071-0.05624745814130.15232406457-0.408759661594-0.09638050223250.5551713807080.1058225210320.02827560143990.6021149974230.04948221283810.524583734362-92.521536533230.702702473346.0596457947
82.97904413904-0.323247986611.07006163274.173085838432.469012118564.471633716030.007364029103130.2984849600360.33562028926-0.2744877289910.309210327509-0.301562338497-0.2387494668660.373949900424-0.1782898388730.3187365199420.00904504907713-0.00203293784870.5343311665420.05120979894840.447629102888-86.86602309533.302891435232.7138656263
92.693567543580.3296976463231.726167700426.601065860554.769648289796.730622171370.08122852222690.484345619534-0.1800917569220.2830158213560.186544265994-0.2191873703590.5238551447190.477732826394-0.3563789677680.415330671697-0.0289189541447-0.01761636315170.5703056401240.04615045448320.515572189607-84.358534379422.523979855929.7272582131
102.78120982843-0.05735821092181.109221658934.920781579383.173984745697.28794283967-0.0528811867621-0.2407111157190.3798744585950.06345871329650.0338706863190.209308844524-0.563475988103-0.4440559099410.08856990913380.38440818680.03470631999420.0126786290290.5463936418640.04514905682650.541334612044-90.734094392337.854309150138.1873081748
113.297778986051.188395584491.240102326624.512784243650.4034063467073.81064543832-0.05143972889860.3945754732870.396493695758-0.884074790342-0.2442336221-1.28136385366-0.6594850776040.6161830996330.2342469732480.585804384045-0.060990938250.1252597562190.7168096620040.08214695039880.894144632422-21.297952462119.101609459212.7854803369
121.174640178351.82165877647-0.1527158418573.537857977911.920243946766.549229160430.463157166882-1.13235633388-1.07617902575-0.04984834873270.284309016606-1.75823115701-0.8167802690660.939138194966-0.6803409230171.09351192075-0.293859009505-0.3176223713871.26857523602-0.02729883205951.3579622561-12.691704510623.493379185823.178123178
134.394602466320.275782071439-0.2129507762463.550584627280.04430383902943.65202791637-0.0310852378485-0.3601914009650.09489583103080.0566336385765-0.101321240173-0.125178206671-0.208320556350.1733865427920.1219490779080.3487307613420.0684938849667-0.0138885228160.423293119777-0.004558392664130.442346713239-33.634894277812.689146949918.0072256764
144.180674874893.62729431133-1.116323032335.70349994465-1.336063529732.3245819877-0.067663405069-0.155855123867-0.111148425544-0.0291268443471-0.1075742693720.154726987221-0.118573235402-0.1612521954250.1808505497740.515264902290.1206189984490.00653023513790.472437853748-0.1080617430.468183859516-41.47455884887.0275390099115.2372959065
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 123 )HA1 - 1231 - 123
22chain 'H' and (resid 124 through 138 )HA124 - 138124 - 136
33chain 'H' and (resid 139 through 219 )HA139 - 219137 - 217
44chain 'L' and (resid 2 through 18 )LE2 - 181 - 17
55chain 'L' and (resid 19 through 103 )LE19 - 10318 - 102
66chain 'L' and (resid 104 through 114 )LE104 - 114103 - 113
77chain 'L' and (resid 115 through 129 )LE115 - 129114 - 128
88chain 'L' and (resid 130 through 156 )LE130 - 156129 - 155
99chain 'L' and (resid 157 through 175 )LE157 - 175156 - 174
1010chain 'L' and (resid 176 through 215 )LE176 - 215175 - 214
1111chain 'E' and (resid 334 through 380 )EH334 - 3801 - 47
1212chain 'E' and (resid 381 through 394 )EH381 - 39448 - 61
1313chain 'E' and (resid 395 through 469 )EH395 - 46962 - 136
1414chain 'E' and (resid 470 through 516 )EH470 - 516137 - 183

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