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Basic information

Entry
Database: PDB / ID: 7zff
TitleOmi-42 Fab
Components
  • Omi-42 Heavy chain
  • Omi-42 light chain
KeywordsIMMUNE SYSTEM / SARS-CoV-2 / Omicron / BA.1 / BA.2 / RBD / antibody / Fab / Omi-42
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 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 1, 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

Downloads & links

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Assembly

Deposited unit
L: Omi-42 light chain
H: Omi-42 Heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,74810
Polymers47,0112
Non-polymers7378
Water99155
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5280 Å2
ΔGint-27 kcal/mol
Surface area19340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.830, 49.380, 72.290
Angle α, β, γ (deg.)90.000, 115.593, 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

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Components

#1: Antibody Omi-42 light chain


Mass: 22629.980 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody Omi-42 Heavy chain


Mass: 24381.258 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: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 55 / Source method: isolated from a natural source / Formula: H2O
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: 2.19 Å3/Da / Density % sol: 43.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Tris pH 8.0, 30% w/v Polyethylene glycol monomethyl ether 2,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.963 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 27, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.963 Å / Relative weight: 1
ReflectionResolution: 2.32→66 Å / Num. obs: 16530 / % possible obs: 92.6 % / Redundancy: 6.2 % / Biso Wilson estimate: 43.89 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.182 / Rpim(I) all: 0.078 / Net I/σ(I): 8
Reflection shellResolution: 2.32→2.36 Å / Mean I/σ(I) obs: 0.5 / Num. unique obs: 500 / CC1/2: 0.348

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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: 7QNY

7qny


Resolution: 2.32→65.2 Å / SU ML: 0.373 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.9127
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2686 865 5.25 %
Rwork0.2312 15619 -
obs0.2334 16484 92.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.62 Å2
Refinement stepCycle: LAST / Resolution: 2.32→65.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3232 0 48 55 3335
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00223358
X-RAY DIFFRACTIONf_angle_d0.51954566
X-RAY DIFFRACTIONf_chiral_restr0.0427507
X-RAY DIFFRACTIONf_plane_restr0.0054579
X-RAY DIFFRACTIONf_dihedral_angle_d11.44171182
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.32-2.470.38421020.33571796X-RAY DIFFRACTION64.54
2.47-2.660.36831440.31832502X-RAY DIFFRACTION89.69
2.66-2.920.341610.27852802X-RAY DIFFRACTION99.76
2.92-3.350.2891510.25772787X-RAY DIFFRACTION99.93
3.35-4.220.24391610.21332834X-RAY DIFFRACTION100
4.22-65.20.22221460.1922898X-RAY DIFFRACTION100
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)
17.248341061340.4126544418430.8964797848070.464104453323-0.2831811832843.69411862039-0.3950854464450.5684081559470.0669684733832-0.3450947761430.5555846962-0.2095121602850.820201833948-1.10530919691-0.3625953713780.458988455143-0.1421596268190.01064626138370.493610618892-0.04335081455360.413215489284-20.3312014647-15.2702166921-13.8902574278
21.658617826020.602546767658-1.584757179891.08110133503-0.4826519548365.20736138928-0.0841248391583-0.000220865991347-0.0589046929939-0.2274290404850.0296426588107-0.07882138791250.357166506129-0.2000246720870.07381463716550.399826887373-0.0133086120543-0.02127358665640.239780983426-0.07137490809920.27292155063-12.2322901677-9.88427070216-17.7281143172
30.8203531576320.559958678998-1.03720879762.631065056442.250903791246.488233761050.02317506179560.108706888350.07961106101220.007083733760190.1472776575690.0009729965210680.01989359668640.0672834211555-0.06449924748710.2751544943880.00887855879311-0.02657481513220.3716772814160.01104262633740.337260243854-22.0250339007-4.8526138106316.0598122594
40.4634925803160.706907335844-0.2142484853586.77239565271-4.40343203383.289787839440.474209527288-0.0906736637307-1.071921325561.79780598123-0.4267486927820.418700001197-0.002662191072850.503428182008-0.2854138923810.4264548804920.1806354053230.02922871622290.3628102825-0.01649465405190.745550532937-34.4083379779-3.8047284870422.9981896716
54.40001790416-1.17222171138-1.378782974944.299030066733.763671858135.01122349985-0.0720575257830.256443805097-0.091118317719-0.179990964468-0.1449201819320.126570189909-0.2813496382380.2503318150440.2604448255520.376200557006-0.0283910862582-0.002065811692920.2367633925330.04587919572160.359502113256-25.3791198831-3.0239225415519.027951807
65.91300737252-3.64116016728-3.429099380564.87127173624.622681711744.41364191248-0.384003295002-0.218321739803-0.4733287288541.000100268010.8892120223440.1305632600211.142424947130.566738305804-0.5378155214850.6419893765750.04672166429150.01667807243520.4249872567740.1164614683690.378719372463-23.0437379288-9.5287807180924.9933506573
72.000046508982.000439870447.823628538841.99989747171-4.57029011573.02095255383-1.69230103847-0.8719628053830.1540997775460.8923612723910.9230840773513.12380848265-1.42389350869-1.061351784030.6315736735750.7947561936250.4292347950930.1390817189411.34868269156-0.2848574032340.24794570665-19.50221388540.38793364561135.8095689799
84.158718810990.157007319676-0.2437270363443.11604532215-1.903180884843.542157635170.442913895886-0.355407582930.2805351229460.476179077343-0.23037240177-0.178549094572-0.705173032441-0.138178332265-0.168158435730.688713257912-0.103689182541-0.03880623348350.425804702293-0.01422855487280.359557803617-8.7022917226213.4839259189-11.9234225682
95.91363999549-0.406692735965-1.906156848956.4418563908-2.803708971126.835627934180.1094466869710.3372632319760.04273494696630.3921505444320.3214206262680.575439923943-0.496552078893-0.813061944224-0.1753984018610.3974471810570.0882445214214-0.02572123188510.360601064159-0.022711635750.332772402896-13.74789507098.25079960963-19.8830582235
104.058811467560.117369428484-1.413533854545.66340869318-1.377852331293.699291416070.07611072580060.2038031333670.3013642404050.5992981534420.1464987618480.244231923435-0.445360197543-0.244431915299-0.2376599728850.4493075303450.00754637121908-0.01014190201430.372438328234-0.01243907006750.286772422276-12.21782897259.75702865393-17.8978520263
110.728106299635-1.13261997943-1.430694578972.660768543073.659807197915.426006140190.5010551567120.3648015830180.210618989802-0.958483327165-0.580919772081-0.08433176221760.280865051618-1.30777664977-0.2243283669750.7985221076980.0183774647047-0.03053287684250.5357369423360.1435183293510.710457338679-25.972481787215.14469404060.0118959390702
125.26817316523-0.631993609633-3.125848518115.418870289932.697273795043.6265092969-0.358645970004-0.00876649800768-0.5078241146890.7880732705970.5776734959990.657979919958-0.327433169104-0.3882742542080.5190543265820.432706502513-0.0276080589460.01903342220750.2111522121790.02480344212590.477789370615-17.21377973627.0288229848419.6843235931
137.66577022821.899014026740.9985511348141.868528305660.480060507391.39146683715-0.08504846282380.4082221531620.6791270664380.0868386490570.101905897257-0.0267229194601-0.177975635670.3591331281690.01221332377550.412757623413-0.0342855120469-0.01241603408160.3690702440290.002058251742780.397731365587-14.75025605618.8710862436413.7233287933
143.697570353691.540253393721.823568107152.370110680362.385157714832.452590249330.2632217712031.02911534522-1.090764088040.8020500682432.69589146445-2.942036704641.130732548762.46486493856-2.645212552181.770106705480.313928761550.1752177423660.639713446594-0.102279237980.705434945738-14.20632877895.7752287562636.4791371806
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'L' and (resid 2 through 23 )LA2 - 231 - 22
22chain 'L' and (resid 24 through 104 )LA24 - 10423 - 103
33chain 'L' and (resid 105 through 153 )LA105 - 153104 - 152
44chain 'L' and (resid 154 through 164 )LA154 - 164153 - 163
55chain 'L' and (resid 165 through 200 )LA165 - 200164 - 199
66chain 'L' and (resid 201 through 212 )LA201 - 212200 - 211
77chain 'L' and (resid 213 through 213 )LA213212
88chain 'H' and (resid 1 through 33 )HH1 - 331 - 33
99chain 'H' and (resid 34 through 60 )HH34 - 6034 - 60
1010chain 'H' and (resid 61 through 118 )HH61 - 11861 - 118
1111chain 'H' and (resid 119 through 131 )HH119 - 131119 - 131
1212chain 'H' and (resid 132 through 157 )HH132 - 157132 - 152
1313chain 'H' and (resid 158 through 227 )HH158 - 227153 - 222
1414chain 'H' and (resid 228 through 228 )HH228223

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