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- PDB-7zf4: SARS-CoV-2 Omicron RBD in complex with Omi-9 Fab and nanobody F2 -

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Basic information

Entry
Database: PDB / ID: 7zf4
TitleSARS-CoV-2 Omicron RBD in complex with Omi-9 Fab and nanobody F2
Components
  • Nanobody F2
  • Omi-9 heavy chain
  • Omi-9 light chain
  • Spike protein S1
KeywordsVIRAL PROTEIN / SARS-CoV-2 / Omicron / RBD / antibody / Fab / Omi-3 / EY6A / 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 / 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 / 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 speciesLama glama (llama)
Homo sapiens (human)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.18 Å
AuthorsZhou, D. / Huo, J. / Ren, J. / Stuart, D.I.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
CAMS Innovation Fund for Medical Sciences (CIFMS)2018-I2M-2-002 United Kingdom
Medical Research Council (MRC, United Kingdom)MR/N00065X/1 United Kingdom
CitationJournal: Cell / Year: 2022
Title: Potent cross-reactive antibodies following Omicron breakthrough in vaccinees.
Authors: Rungtiwa Nutalai / Daming Zhou / Aekkachai Tuekprakhon / Helen M Ginn / Piyada Supasa / Chang Liu / Jiandong Huo / Alexander J Mentzer / Helen M E Duyvesteyn / Aiste Dijokaite-Guraliuc / ...Authors: Rungtiwa Nutalai / Daming Zhou / Aekkachai Tuekprakhon / Helen M Ginn / Piyada Supasa / Chang Liu / Jiandong Huo / Alexander J Mentzer / Helen M E Duyvesteyn / Aiste Dijokaite-Guraliuc / Donal Skelly / Thomas G Ritter / Ali Amini / Sagida Bibi / Sandra Adele / Sile Ann Johnson / Bede Constantinides / Hermione Webster / Nigel Temperton / Paul Klenerman / Eleanor Barnes / Susanna J Dunachie / Derrick Crook / Andrew J Pollard / Teresa Lambe / Philip Goulder / / Neil G Paterson / Mark A Williams / David R Hall / Juthathip Mongkolsapaya / Elizabeth E Fry / Wanwisa Dejnirattisai / Jingshan Ren / David I Stuart / Gavin R Screaton /
Abstract: Highly transmissible Omicron variants of SARS-CoV-2 currently dominate globally. Here, we compare neutralization of Omicron BA.1, BA.1.1, and BA.2. BA.2 RBD has slightly higher ACE2 affinity than BA. ...Highly transmissible Omicron variants of SARS-CoV-2 currently dominate globally. Here, we compare neutralization of Omicron BA.1, BA.1.1, and BA.2. BA.2 RBD has slightly higher ACE2 affinity than BA.1 and slightly reduced neutralization by vaccine serum, possibly associated with its increased transmissibility. Neutralization differences between sub-lineages for mAbs (including therapeutics) mostly arise from variation in residues bordering the ACE2 binding site; however, more distant mutations S371F (BA.2) and R346K (BA.1.1) markedly reduce neutralization by therapeutic antibody Vir-S309. In-depth structure-and-function analyses of 27 potent RBD-binding mAbs isolated from vaccinated volunteers following breakthrough Omicron-BA.1 infection reveals that they are focused in two main clusters within the RBD, with potent right-shoulder antibodies showing increased prevalence. Selection and somatic maturation have optimized antibody potency in less-mutated epitopes and recovered potency in highly mutated epitopes. All 27 mAbs potently neutralize early pandemic strains, and many show broad reactivity with variants of concern.
History
DepositionApr 1, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 8, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 15, 2022Group: 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
Revision 1.2Jun 22, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 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

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Assembly

Deposited unit
F: Nanobody F2
H: Omi-9 heavy chain
L: Omi-9 light chain
E: Spike protein S1


Theoretical massNumber of molelcules
Total (without water)85,4474
Polymers85,4474
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5440 Å2
ΔGint-29 kcal/mol
Surface area35290 Å2
Unit cell
Length a, b, c (Å)86.574, 205.147, 123.052
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Antibody Nanobody F2


Mass: 14962.622 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli K-12 (bacteria)
#2: Antibody Omi-9 heavy chain


Mass: 24127.980 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 Omi-9 light chain


Mass: 23199.555 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#4: Protein Spike protein S1 / SARS-CoV-2 Omicron Spike protein


Mass: 23157.164 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

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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: 3.2 Å3/Da / Density % sol: 61.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Sodium acetate trihydrate pH 4.5 and 30% (w/v) PEG 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jan 31, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 4.18→67 Å / Num. obs: 8472 / % possible obs: 100 % / Redundancy: 13.4 % / Biso Wilson estimate: 150.89 Å2 / CC1/2: 0.877 / Rmerge(I) obs: 0.728 / Rpim(I) all: 0.207 / Net I/σ(I): 2.5
Reflection shellResolution: 4.18→4.25 Å / Mean I/σ(I) obs: 0.4 / Num. unique obs: 410 / CC1/2: 0.34

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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: 7qnw

7qnw


Resolution: 4.18→61.53 Å / SU ML: 0.7789 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 47.7485
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3853 415 5.07 %
Rwork0.3695 7769 -
obs0.3702 8184 96.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 195.6 Å2
Refinement stepCycle: LAST / Resolution: 4.18→61.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5694 0 0 0 5694
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085875
X-RAY DIFFRACTIONf_angle_d1.13038013
X-RAY DIFFRACTIONf_chiral_restr0.0806886
X-RAY DIFFRACTIONf_plane_restr0.00821033
X-RAY DIFFRACTIONf_dihedral_angle_d12.71222086
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.18-4.780.41021210.41722375X-RAY DIFFRACTION90.24
4.78-6.020.41351490.40292632X-RAY DIFFRACTION99.82
6.02-61.530.36441450.33882762X-RAY DIFFRACTION99.79
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)
14.028964387181.22588436233-1.137109276711.909089549870.2176925312831.21521339062-1.262642936340.723472837847-1.42823783458-0.476472352698-0.445323425108-0.0429568689465-0.79486301808-1.41772036071-0.5209858405460.2461562184021.64058341129-1.708393320971.27564903253-0.309045047161.5466837851921.5116163523-1.34275887966-44.0665879648
21.3357613502-1.160016817010.3933065252623.216688444710.5532567775151.83422564806-0.08893711764020.175170467306-1.879440170141.96822520074-0.8549378936830.04143239182521.396178797860.4021218347520.5098370873962.01637353432-0.1306660139530.48141065882.110972355450.2091027579061.8480168873642.1781146278-36.8910573912-47.6261734184
30.736283127579-0.122905563136-0.7280594232885.269892792970.1967272893150.793332577807-0.0266018507722-0.87737131743-0.3510887553560.216171871155-0.657563000089-3.88251465543-0.1799850908020.1208295553330.2785876273471.75858585298-0.42720129068-0.7596587228491.826928180221.295630542561.9876043833744.32431388274.10425310426-46.267434012
41.709250891480.251626128451-0.139200303612.443950500221.374844956861.973569263780.518668697372.09777450266-0.209425771767-1.335613531970.9138870149970.375980732382-0.2058610908730.7660524961380.2316056508911.252930805080.4597395623780.6064871059731.866005001520.4119185409691.0730314039547.6939840148-26.2106370876-58.1841949021
50.309783380716-0.2493359749780.0888489257091.091281267360.3282074290720.9523071369780.573501598358-0.2927281912230.6490812810890.5026806715680.5275165193570.239502141888-0.106982758085-0.1960739214890.674178428704-1.058301230420.8349809083460.8287036251541.82326207255-0.7500231960941.4011940810138.097761626857.9991278657-17.8170178366
61.81083891463-1.335231763720.1515856011242.08718615407-0.2432625647720.5819421228270.185202257228-0.3578812081230.0186545402083-0.245653738888-0.869617518231-0.138612034251-1.11046684197-0.629304907583-0.09665691328981.66477163432-0.5686434944960.1744011681891.561084152340.3432527252041.5788447380419.634409413634.253935421-25.2547991005
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'H' and (resid 2 through 122 )HB2 - 1222 - 122
22chain 'H' and (resid 123 through 224 )HB123 - 224123 - 224
33chain 'L' and (resid 2 through 110 )LC2 - 1102 - 110
44chain 'L' and (resid 112 through 214 )LC112 - 214112 - 214
55chain 'F'FA1 - 1241 - 124
66chain 'E'ED333 - 527333 - 527

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