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- PDB-8r80: SARS-CoV-2 Delta RBD in complex with XBB-9 Fab and an anti-Fab na... -

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Basic information

Entry
Database: PDB / ID: 8r80
TitleSARS-CoV-2 Delta RBD in complex with XBB-9 Fab and an anti-Fab nanobody
Components
  • Spike protein S1
  • XBB-9 Fab heavy chain
  • XBB-9 Fab light chain
  • anti-Fab nanobody
KeywordsVIRAL PROTEIN / SARS-CoV-2 / RBD / BA.2.86 / XBB.1.5 / XBB.1.5.10 / XBB.1.5.70
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 / 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 speciesHomo sapiens (human)
Severe acute respiratory syndrome coronavirus 2
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.03 Å
AuthorsZhou, D. / Ren, J. / Stuart, D.I.
Funding support United Kingdom, 3items
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
Wellcome Trust090532/Z/09/Z United Kingdom
CitationJournal: Cell Rep Med / Year: 2024
Title: A structure-function analysis shows SARS-CoV-2 BA.2.86 balances antibody escape and ACE2 affinity.
Authors: Chang Liu / Daming Zhou / Aiste Dijokaite-Guraliuc / Piyada Supasa / Helen M E Duyvesteyn / Helen M Ginn / Muneeswaran Selvaraj / Alexander J Mentzer / Raksha Das / Thushan I de Silva / ...Authors: Chang Liu / Daming Zhou / Aiste Dijokaite-Guraliuc / Piyada Supasa / Helen M E Duyvesteyn / Helen M Ginn / Muneeswaran Selvaraj / Alexander J Mentzer / Raksha Das / Thushan I de Silva / Thomas G Ritter / Megan Plowright / Thomas A H Newman / Lizzie Stafford / Barbara Kronsteiner / Nigel Temperton / Yuan Lui / Martin Fellermeyer / Philip Goulder / Paul Klenerman / Susanna J Dunachie / Michael I Barton / Mikhail A Kutuzov / Omer Dushek / / Elizabeth E Fry / Juthathip Mongkolsapaya / Jingshan Ren / David I Stuart / Gavin R Screaton /
Abstract: BA.2.86, a recently described sublineage of SARS-CoV-2 Omicron, contains many mutations in the spike gene. It appears to have originated from BA.2 and is distinct from the XBB variants responsible ...BA.2.86, a recently described sublineage of SARS-CoV-2 Omicron, contains many mutations in the spike gene. It appears to have originated from BA.2 and is distinct from the XBB variants responsible for many infections in 2023. The global spread and plethora of mutations in BA.2.86 has caused concern that it may possess greater immune-evasive potential, leading to a new wave of infection. Here, we examine the ability of BA.2.86 to evade the antibody response to infection using a panel of vaccinated or naturally infected sera and find that it shows marginally less immune evasion than XBB.1.5. We locate BA.2.86 in the antigenic landscape of recent variants and look at its ability to escape panels of potent monoclonal antibodies generated against contemporary SARS-CoV-2 infections. We demonstrate, and provide a structural explanation for, increased affinity of BA.2.86 to ACE2, which may increase transmissibility.
History
DepositionNov 27, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 8, 2024Provider: repository / Type: Initial release
Revision 1.1May 22, 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.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jun 5, 2024Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: XBB-9 Fab heavy chain
L: XBB-9 Fab light chain
E: Spike protein S1
R: Spike protein S1
N: anti-Fab nanobody
J: anti-Fab nanobody
A: XBB-9 Fab heavy chain
B: XBB-9 Fab light chain


Theoretical massNumber of molelcules
Total (without water)169,5738
Polymers169,5738
Non-polymers00
Water0
1
H: XBB-9 Fab heavy chain
L: XBB-9 Fab light chain
R: Spike protein S1
N: anti-Fab nanobody


Theoretical massNumber of molelcules
Total (without water)84,7874
Polymers84,7874
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Spike protein S1
J: anti-Fab nanobody
A: XBB-9 Fab heavy chain
B: XBB-9 Fab light chain


Theoretical massNumber of molelcules
Total (without water)84,7874
Polymers84,7874
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)108.538, 126.398, 164.824
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 2 through 122 or resid 124 through 221))
d_2ens_1(chain "H" and (resid 2 through 122 or resid 124 through 221))
d_1ens_2chain "B"
d_2ens_2(chain "L" and resid 1 through 213)
d_1ens_3(chain "E" and (resid 333 through 442 or resid 444 through 518))
d_2ens_3(chain "R" and (resid 333 through 442 or resid 444 through 518))
d_1ens_4(chain "J" and (resid 1 through 2 or resid 4 through 120))
d_2ens_4(chain "N" and (resid 1 through 2 or resid 4 through 120))

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1VALVALTHRTHRAG2 - 1222 - 122
d_12ens_1GLYGLYSERSERAG124 - 221124 - 221
d_21ens_1VALVALTHRTHRHA2 - 1222 - 122
d_22ens_1GLYGLYSERSERHA124 - 221124 - 221
d_11ens_2ALAALAGLUGLUBH1 - 2131 - 213
d_21ens_2ALAALAGLUGLULB1 - 2131 - 213
d_11ens_3THRTHRASPASPEC333 - 4427 - 116
d_12ens_3LYSLYSLEULEUEC444 - 518118 - 192
d_21ens_3THRTHRASPASPRD333 - 4427 - 116
d_22ens_3LYSLYSLEULEURD444 - 518118 - 192
d_11ens_4GLNGLNVALVALJF1 - 25 - 6
d_12ens_4LEULEUSERSERJF4 - 1208 - 124
d_21ens_4GLNGLNVALVALNE1 - 25 - 6
d_22ens_4LEULEUSERSERNE4 - 1208 - 124

NCS ensembles :
ID
ens_1
ens_2
ens_3
ens_4

NCS oper:
IDCodeMatrixVector
1given(-0.103809731524, -0.26522270915, -0.958582523412), (-0.27205686683, -0.919460762598, 0.28386082374), (-0.956665354684, 0.29025647382, 0.0232933156485)-22.9689002113, -38.8452283628, -8.69547404427
2given(-0.165764139906, -0.266070769208, -0.94959391094), (-0.276528143495, -0.91174342488, 0.303736914192), (-0.946601519002, 0.312938129605, 0.0775583087932)-24.1700651996, -39.7385970184, -9.49172375932
3given(-0.129920209273, -0.378736862284, -0.916340072446), (-0.199086164503, -0.895387570693, 0.398303649685), (-0.971331785914, 0.234178323924, 0.0409276712966)-23.1105528616, -39.5314266344, -8.072668912
4given(-0.184397232356, -0.240665770939, -0.952931082187), (-0.30721936928, -0.906860557435, 0.288479095445), (-0.933602656294, 0.345953632829, 0.0932853905692)-23.6487945086, -39.9239229004, -8.97020887555

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Components

#1: Antibody XBB-9 Fab heavy chain


Mass: 23516.543 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody XBB-9 Fab light chain


Mass: 23486.170 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Protein Spike protein S1


Mass: 22935.734 Da / Num. of mol.: 2
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
#4: Antibody anti-Fab nanobody


Mass: 14848.221 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)

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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: 3.33 Å3/Da / Density % sol: 63.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Calcium acetate hydrate, 0.1 M sodium cacodylate pH 6.5, 40% PEG 300.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97629 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Nov 13, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97629 Å / Relative weight: 1
ReflectionResolution: 4.03→66 Å / Num. obs: 19426 / % possible obs: 100 % / Redundancy: 13.4 % / Biso Wilson estimate: 166.91 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.386 / Rpim(I) all: 0.109 / Net I/σ(I): 5.4
Reflection shellResolution: 4.03→4.09 Å / Mean I/σ(I) obs: 0.4 / Num. unique obs: 923 / CC1/2: 0.25 / % possible all: 99.1

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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: 4.03→65.64 Å / SU ML: 0.7264 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.232
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3133 944 4.9 %
Rwork0.2684 18334 -
obs0.2706 19278 99.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 203.78 Å2
Refinement stepCycle: LAST / Resolution: 4.03→65.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11360 0 0 0 11360
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00211632
X-RAY DIFFRACTIONf_angle_d0.465615810
X-RAY DIFFRACTIONf_chiral_restr0.04111745
X-RAY DIFFRACTIONf_plane_restr0.00392049
X-RAY DIFFRACTIONf_dihedral_angle_d10.60864168
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2GAX-RAY DIFFRACTIONTorsion NCS1.20883263007
ens_2d_2HBX-RAY DIFFRACTIONTorsion NCS0.877084371592
ens_3d_2CEX-RAY DIFFRACTIONTorsion NCS0.282325491752
ens_4d_2FJX-RAY DIFFRACTIONTorsion NCS0.26122960886
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.03-4.240.38241370.36312479X-RAY DIFFRACTION96.53
4.24-4.50.3591400.3162595X-RAY DIFFRACTION99.89
4.5-4.850.28161350.26892581X-RAY DIFFRACTION100
4.85-5.340.3021290.2582618X-RAY DIFFRACTION99.96
5.34-6.110.31021440.2652613X-RAY DIFFRACTION99.93
6.11-7.70.36451130.29512673X-RAY DIFFRACTION99.93
7.7-65.640.28871460.23712775X-RAY DIFFRACTION99.76
Refinement TLS params.Method: refined / Origin x: -29.2594010336 Å / Origin y: -14.4402221066 Å / Origin z: 14.5315721748 Å
111213212223313233
T1.59255810148 Å2-0.0908659761075 Å20.0347082285296 Å2-1.76696350102 Å2-0.0194851011771 Å2--1.59906000835 Å2
L1.25520441474 °2-0.178496502739 °2-0.589689161334 °2-0.830413008124 °20.526557152051 °2--1.07878307003 °2
S-0.25556543646 Å °0.149794734972 Å °-0.034237135674 Å °0.177200817268 Å °0.118165850701 Å °-0.081819087866 Å °0.0644083214135 Å °0.381978992398 Å °0.0726417218434 Å °
Refinement TLS groupSelection details: all

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