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- PDB-7zf6: Omi-12 Fab -

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Basic information

Entry
Database: PDB / ID: 7zf6
TitleOmi-12 Fab
Components
  • Omi-12 heavy chain
  • Omi-12 light chain
KeywordsIMMUNE SYSTEM / SARS-CoV-2 / Omicron / RBD / antibody / Fab / Omi-12
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / CITRIC ACID
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 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
Revision 1.4Nov 20, 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: Omi-12 heavy chain
L: Omi-12 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,68917
Polymers48,0392
Non-polymers1,65015
Water68538
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6660 Å2
ΔGint-151 kcal/mol
Surface area19420 Å2
Unit cell
Length a, b, c (Å)64.996, 209.624, 86.137
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
Components on special symmetry positions
IDModelComponents
11L-312-

SO4

21L-419-

HOH

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Components

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Antibody , 2 types, 2 molecules HL

#1: Antibody Omi-12 heavy chain


Mass: 24514.531 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-12 light chain


Mass: 23524.197 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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Sugars , 1 types, 1 molecules

#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 52 molecules

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


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / Source method: isolated from a natural source / Formula: H2O

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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: 3.05 Å3/Da / Density % sol: 59.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 2.4 M (NH4)2SO4, 0.1 M citric acid pH 5.0

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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: Feb 7, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.2→67 Å / Num. obs: 29897 / % possible obs: 98.1 % / Redundancy: 25.3 % / Biso Wilson estimate: 51.89 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.316 / Rpim(I) all: 0.063 / Net I/σ(I): 4.5
Reflection shellResolution: 2.2→2.23 Å / Mean I/σ(I) obs: 0.2 / Num. unique obs: 1154 / CC1/2: 0.453

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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: 7PS5

7ps5


Resolution: 2.21→66.55 Å / SU ML: 0.4083 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 35.611
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2653 1391 5.15 %
Rwork0.2354 25609 -
obs0.2369 27000 90.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 64.91 Å2
Refinement stepCycle: LAST / Resolution: 2.21→66.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3318 0 95 38 3451
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023480
X-RAY DIFFRACTIONf_angle_d0.50494734
X-RAY DIFFRACTIONf_chiral_restr0.0423524
X-RAY DIFFRACTIONf_plane_restr0.0041599
X-RAY DIFFRACTIONf_dihedral_angle_d12.4991247
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.21-2.290.4758290.4466748X-RAY DIFFRACTION26.33
2.29-2.380.42141070.41192104X-RAY DIFFRACTION74.95
2.38-2.490.41671550.3842788X-RAY DIFFRACTION98.79
2.49-2.620.39441670.36342771X-RAY DIFFRACTION99.83
2.62-2.780.3481500.3342809X-RAY DIFFRACTION99.7
2.78-30.29941630.28332806X-RAY DIFFRACTION99.9
3-3.30.30851450.24622841X-RAY DIFFRACTION99.9
3.3-3.780.22831450.21032868X-RAY DIFFRACTION99.87
3.78-4.760.19711650.17532870X-RAY DIFFRACTION99.97
4.76-66.550.24141650.20023004X-RAY DIFFRACTION99.97
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)
13.36145351477-0.3179391560562.043281024316.36244762091-1.036639498485.370968331950.07489278984990.316832210559-0.384458532483-0.3910228975650.0274603596158-0.07371602142260.1820267525270.269537629236-0.1563194392960.407207798908-0.08892427243190.07647228750470.416055786162-0.1372366238620.6902466986918.746462717915.097441419-3.61201418623
22.024486999841.119517277910.5550744273253.728373586881.027950320323.44762022063-0.09576213130870.0231060816170.0901177245624-0.2657185908760.0398547301872-0.379857820742-0.2322829299240.122054834240.03048403144710.2155776203760.01672235408260.02547070445150.3000030528220.04513438604070.55001815345223.453642990645.17839214193.15639478799
31.79169591042-0.984889604331-1.078534073136.296444351472.442815257642.81483634963-0.33303996166-0.0577513283153-0.6391790264450.6240159824710.1270780468130.2504346178090.599368007962-0.08358958204780.1923506371320.489690097164-0.03683455487910.06126645996510.3754383547450.01408475629270.58583625968710.639429519817.002350994116.7919449532
41.68516401208-0.5309714208010.006863329947073.93775397551-1.841353918263.959700227790.02942129481720.09035055642710.441820676367-0.118762843381-0.06313320667890.15339024593-0.301589717573-0.05853749442740.0392175118860.333115532335-0.0237054693-0.04405127275810.367599231405-0.04793638151380.64476139190611.23105481453.06875388539.44103089501
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 121 )HA1 - 1211 - 121
22chain 'H' and (resid 122 through 224 )HA122 - 224122 - 224
33chain 'L' and (resid 1 through 114 )LD1 - 1141 - 114
44chain 'L' and (resid 115 through 212 )LD115 - 212115 - 212

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