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- PDB-8cma: SARS-CoV-2 Delta-RBD complexed with BA.4/5-35 Fab -

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Basic information

Entry
Database: PDB / ID: 8cma
TitleSARS-CoV-2 Delta-RBD complexed with BA.4/5-35 Fab
Components
  • BA.4/5-35 heavy chain
  • BA.4/5-35 light chain
  • Spike protein S1
KeywordsVIRAL PROTEIN / SARS-CoV-2 / BA.4 mAb / BA.5 mAb / RBD / BA.4/5-1 / BA.4/5-2 / BA.4/5-5 / Beta-49 / Omi-42 / BA.4/5-35 / 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 / host cell endoplasmic reticulum-Golgi intermediate compartment membrane ...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 / host cell surface receptor binding / 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 / 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 speciesHomo sapiens (human)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.29 Å
AuthorsZhou, D. / 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: Nat Commun / Year: 2024
Title: Emerging variants develop total escape from potent monoclonal antibodies induced by BA.4/5 infection.
Authors: Liu, C. / Das, R. / Dijokaite-Guraliuc, A. / Zhou, D. / Mentzer, A.J. / Supasa, P. / Selvaraj, M. / Duyvesteyn, H.M.E. / Ritter, T.G. / Temperton, N. / Klenerman, P. / Dunachie, S.J. / ...Authors: Liu, C. / Das, R. / Dijokaite-Guraliuc, A. / Zhou, D. / Mentzer, A.J. / Supasa, P. / Selvaraj, M. / Duyvesteyn, H.M.E. / Ritter, T.G. / Temperton, N. / Klenerman, P. / Dunachie, S.J. / Paterson, N.G. / Williams, M.A. / Hall, D.R. / Fry, E.E. / Mongkolsapaya, J. / Ren, J. / Stuart, D.I. / Screaton, G.R.
History
DepositionFeb 18, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 28, 2024Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: BA.4/5-35 heavy chain
E: Spike protein S1
L: BA.4/5-35 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,3524
Polymers70,1303
Non-polymers2211
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5620 Å2
ΔGint-27 kcal/mol
Surface area27720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)195.782, 85.119, 56.974
Angle α, β, γ (deg.)90.000, 102.030, 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

#1: Antibody BA.4/5-35 heavy chain


Mass: 23477.402 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: Protein Spike protein S1


Mass: 22935.734 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
#3: Antibody BA.4/5-35 light chain


Mass: 23717.361 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: 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
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: 3.31 Å3/Da / Density % sol: 62.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Sodium citrate tribasic dihydrate pH 5.5, 18% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 13, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 3.29→48 Å / Num. obs: 13926 / % possible obs: 98.9 % / Redundancy: 7 % / Biso Wilson estimate: 106.69 Å2 / CC1/2: 0.982 / Rmerge(I) obs: 0.298 / Rpim(I) all: 0.121 / Net I/σ(I): 5.6
Reflection shellResolution: 3.29→3.35 Å / Mean I/σ(I) obs: 0.5 / Num. unique obs: 680 / CC1/2: 0.34

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Processing

Software
NameVersionClassification
GDA1.20.1_4487data collection
PHENIX1.20.1_4487refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.29→47.87 Å / SU ML: 0.5483 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.5501
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2679 680 4.91 %
Rwork0.2306 13160 -
obs0.2325 13840 98.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 124.98 Å2
Refinement stepCycle: LAST / Resolution: 3.29→47.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4715 0 14 0 4729
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00194848
X-RAY DIFFRACTIONf_angle_d0.43736597
X-RAY DIFFRACTIONf_chiral_restr0.0405732
X-RAY DIFFRACTIONf_plane_restr0.0051851
X-RAY DIFFRACTIONf_dihedral_angle_d10.5691729
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.29-3.540.36511140.3452550X-RAY DIFFRACTION94.91
3.54-3.90.30281420.2912615X-RAY DIFFRACTION99.53
3.9-4.460.28491510.24192667X-RAY DIFFRACTION99.72
4.46-5.620.25351410.20142626X-RAY DIFFRACTION98.79
5.62-47.870.23611320.19882702X-RAY DIFFRACTION98.92
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)
14.98958925586-3.816001079262.014113422635.703892142290.1095078617941.77932909946-0.5984755759311.09775040234-1.26969386143-1.51289896166-0.00719230581206-0.1742502864070.708019551630.599076232119-0.450392932870.935167204288-0.2206749553070.1239488260431.59665508886-0.181978338491.49123096642-41.4398094679-16.5653706427-11.9572550848
26.175165404792.45616226302-2.046072594842.75504816082-0.6053491723850.882087234997-1.017653912350.613618236368-1.13254982716-0.8220679532620.935375514057-0.09604845582810.293872276340.6838646485320.2464438082761.07160505653-0.3424135071110.09145396623531.0054486343-0.2857416991161.09964597524-48.6245658275-17.9761693779-5.28275520538
33.700846868430.824391327276-2.250356536211.32333271016-0.9070579493132.94193364321-0.7396603143321.09322540720.97577396875-0.3364741669550.603628255060.176282849686-0.554485588482-0.05621289790170.06832738240761.3251541005-0.0914293458956-0.01681109509220.9569960018090.01839157564380.751952014232-51.2217499087-7.33568635632-4.20014150135
45.705538595960.6406922086531.376169807540.8026133560640.6374329023152.13135584646-0.5505816734960.896734834355-0.936263734015-0.5064122959031.015425258940.8051586544280.3100014725490.1706685797010.1652181632840.881476095404-0.3070806792010.05145347752060.92917601612-0.1284427802011.0305599812-47.5647923818-14.5730782865-5.88318729208
50.2497764297830.628286637673-0.4214599963031.59699614603-1.181998980370.816609964175-1.170008493041.97741947444-0.870797103617-0.3981638564751.18118069143-0.616883658168-0.0984500553515-0.5415599459120.1220162139531.16462011764-0.5835384777670.2122240408921.69616776712-0.4966446754250.943272014789-18.6676424769-1.87464149971-16.9570492486
62.107941231333.23439639861-1.428548397867.5567115685-3.141168196383.24397414602-1.765410743551.70709862603-2.66646223953-1.276161743290.21237832373-1.139973753791.99377743431-0.566729550817-4.038693888521.12081427759-0.5036741328220.2501066534431.26738163721-0.8293596435460.991861524178-12.5969314344-6.61447797318-15.1753465927
76.113250139270.990457017444-3.207317183643.706781063950.9486745068033.25612266270.6130191049421.064783159182.453883331730.572350362106-0.4914027104450.748642570061-0.16214232148-0.7330802746560.0122061088471.262731341220.03417807742010.0703423944961.43591697898-0.218700646642.15237874737-82.9460450494-6.9190585531820.5997746068
87.090526445090.221621070714-0.1767681020133.456374231360.0036557767065-0.02583598585210.587166666805-0.822616916290.641160190811-0.664136088808-1.318195971711.71580732061-0.363598668966-0.4742103320620.08301635435380.9820621136140.107169640634-0.167692533551.35009324735-0.3600339327981.95318779504-85.0275943822-7.2496375863913.0876931881
96.621521036361.92995641587-0.01689269205553.488112724911.398192576437.29420884876-0.368748063637-0.5634455551641.256934487720.119801418149-1.336215073650.458815098035-0.46690795401-1.398195881950.1394693786411.848531055450.1496152360530.04741708029231.24096977559-0.07817936560732.01776802547-78.50965337983.727275301910.2634520783
101.959058165710.4153410253421.525069616780.1002395069580.1172614845984.07863979678-0.8146871351-0.0404651627991-0.487008216374-0.3080667429510.0910319885711.69604260423-1.186853065-0.08116804849590.4863192546671.361977707770.0739381449053-1.137792961021.088360674640.2802206163773.0327913105-91.593355554-0.3869524150494.48785381539
114.953044640970.690286291268-1.36343166674.396506366470.05993009674832.774617294980.1530743348810.7397648377020.553502564905-0.908660293783-0.5006106177420.834466516895-0.470057042449-0.2134788099570.06189086526620.977677215702-0.0615170605454-0.3153487090220.96872004681-0.1667499211530.924542322473-70.9810116406-8.700408493697.59165121525
126.177680836562.182444383041.10382691523.59431722021-0.1268317703653.01920929205-0.237727599489-0.809151808683-0.446689926308-0.415848113357-0.2614263503170.35926870715-0.0280498809392-0.3268476200020.1592033736050.703360823773-0.0315792113906-0.1052755182570.913101764498-0.002566278246021.00709847581-66.3015731031-16.345047607711.3819406819
135.891443768491.63867563876-1.071472024514.1166634497-0.3868226986222.57955447267-0.0250463524741-0.9561180304940.620953740070.154415877726-0.9074452049810.593336345079-0.6894056194410.5426458358050.09905015725890.8839636103720.0215519720396-0.1571979848381.11165755131-0.02133713642451.20487871344-67.1261291032-8.7534525282314.726262877
145.025691651131.13935256019-0.1998665560535.37952722565-0.4075188568163.48970201363-0.110358263657-0.864727078723-0.709276418754-0.234114558711-0.00698323016724-0.2790876672360.0878412374097-0.113624169509-0.02905740175760.66603620015-0.0724970058732-0.001913785338780.451813126909-0.03251918729170.443316047134-36.3417611328-8.6434383788512.7510163655
154.208046317180.3718970448390.2718855232914.97241999308-2.492061110433.92455401912-0.56183735380.4391535223660.409935826779-0.1610264387860.452160746285-0.02101177634410.0195199067964-0.346182369910.1053573907260.799094320152-0.1296569984990.008998022056010.879427863249-0.1477004727180.963543596697-14.17769940148.99261527345-7.39041189377
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 16 )HA1 - 161 - 16
22chain 'H' and (resid 17 through 39 )HA17 - 3917 - 39
33chain 'H' and (resid 40 through 66 )HA40 - 6640 - 66
44chain 'H' and (resid 67 through 111 )HA67 - 11167 - 111
55chain 'H' and (resid 112 through 150 )HA112 - 150112 - 145
66chain 'H' and (resid 151 through 219 )HA151 - 219146 - 214
77chain 'E' and (resid 334 through 349 )EB334 - 3491 - 16
88chain 'E' and (resid 350 through 369 )EB350 - 36917 - 36
99chain 'E' and (resid 370 through 380 )EB370 - 38037 - 47
1010chain 'E' and (resid 381 through 393 )EB381 - 39348 - 60
1111chain 'E' and (resid 394 through 421 )EB394 - 42161 - 88
1212chain 'E' and (resid 422 through 487 )EB422 - 48789 - 154
1313chain 'E' and (resid 488 through 517 )EB488 - 517155 - 184
1414chain 'L' and (resid 1 through 115 )LD1 - 1151 - 115
1515chain 'L' and (resid 116 through 215 )LD116 - 215116 - 215

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