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- PDB-7mzf: SARS-CoV-2 receptor binding domain bound to Fab PDI 37 -

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Basic information

Entry
Database: PDB / ID: 7mzf
TitleSARS-CoV-2 receptor binding domain bound to Fab PDI 37
Components
  • PDI 37 heavy chain
  • PDI 37 light chain
  • Spike protein S1
KeywordsVIRAL PROTEIN / SARS-CoV-2 / spike / RBD / human antibody
Function / homology
Function and homology information


Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / suppression by virus of host tetherin activity / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / Attachment and Entry / receptor-mediated virion attachment to host cell / viral translation / endoplasmic reticulum-Golgi intermediate compartment / host cell surface receptor binding ...Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / suppression by virus of host tetherin activity / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / Attachment and Entry / receptor-mediated virion attachment to host cell / viral translation / endoplasmic reticulum-Golgi intermediate compartment / host cell surface receptor binding / endocytosis involved in viral entry into host cell / endocytic vesicle membrane / fusion of virus membrane with host plasma membrane / viral protein processing / suppression by virus of host type I interferon-mediated signaling pathway / fusion of virus membrane with host endosome membrane / : / viral entry into host cell / viral envelope / endoplasmic reticulum lumen / host cell plasma membrane / virion membrane / integral component of membrane / identical protein binding
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 C-terminal (CTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / : / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Spike glycoprotein, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike receptor binding domain superfamily, coronavirus / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus ...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 C-terminal (CTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / : / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Spike glycoprotein, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike receptor binding domain superfamily, coronavirus / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S2 superfamily, coronavirus / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S2 / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein S2, coronavirus
Similarity search - Domain/homology
Biological speciesSevere acute respiratory syndrome coronavirus 2
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.493 Å
AuthorsPymm, P. / Chan, L.J. / Dietrich, M.H. / Tan, L.L. / Tham, W.H.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)GNT2002073 Australia
CitationJournal: Cell Rep / Year: 2021
Title: Landscape of human antibody recognition of the SARS-CoV-2 receptor binding domain.
Authors: Adam K Wheatley / Phillip Pymm / Robyn Esterbauer / Melanie H Dietrich / Wen Shi Lee / Damien Drew / Hannah G Kelly / Li-Jin Chan / Francesca L Mordant / Katrina A Black / Amy Adair / Hyon- ...Authors: Adam K Wheatley / Phillip Pymm / Robyn Esterbauer / Melanie H Dietrich / Wen Shi Lee / Damien Drew / Hannah G Kelly / Li-Jin Chan / Francesca L Mordant / Katrina A Black / Amy Adair / Hyon-Xhi Tan / Jennifer A Juno / Kathleen M Wragg / Thakshila Amarasena / Ester Lopez / Kevin J Selva / Ebene R Haycroft / James P Cooney / Hariprasad Venugopal / Li Lynn Tan / Matthew T O Neill / Cody C Allison / Deborah Cromer / Miles P Davenport / Richard A Bowen / Amy W Chung / Marc Pellegrini / Mark T Liddament / Alisa Glukhova / Kanta Subbarao / Stephen J Kent / Wai-Hong Tham /
Abstract: Potent neutralizing monoclonal antibodies are one of the few agents currently available to treat COVID-19. SARS-CoV-2 variants of concern (VOCs) that carry multiple mutations in the viral spike ...Potent neutralizing monoclonal antibodies are one of the few agents currently available to treat COVID-19. SARS-CoV-2 variants of concern (VOCs) that carry multiple mutations in the viral spike protein can exhibit neutralization resistance, potentially affecting the effectiveness of some antibody-based therapeutics. Here, the generation of a diverse panel of 91 human, neutralizing monoclonal antibodies provides an in-depth structural and phenotypic definition of receptor binding domain (RBD) antigenic sites on the viral spike. These RBD antibodies ameliorate SARS-CoV-2 infection in mice and hamster models in a dose-dependent manner and in proportion to in vitro, neutralizing potency. Assessing the effect of mutations in the spike protein on antibody recognition and neutralization highlights both potent single antibodies and stereotypic classes of antibodies that are unaffected by currently circulating VOCs, such as B.1.351 and P.1. These neutralizing monoclonal antibodies and others that bind analogous epitopes represent potentially useful future anti-SARS-CoV-2 therapeutics.
History
DepositionMay 24, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 6, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 20, 2021Group: 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 1.2Oct 27, 2021Group: 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
A: Spike protein S1
H: PDI 37 heavy chain
L: PDI 37 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,4627
Polymers70,6683
Non-polymers7944
Water2,918162
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7030 Å2
ΔGint-38 kcal/mol
Surface area26890 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)83.919, 147.665, 146.099
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
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

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Antibody , 2 types, 2 molecules HL

#2: Antibody PDI 37 heavy chain


Mass: 23979.836 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 PDI 37 light chain


Mass: 23614.252 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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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Spike protein S1


Mass: 23073.766 Da / Num. of mol.: 1 / Fragment: Receptor Binding Domain (RBD)
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: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE

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Non-polymers , 4 types, 165 molecules

#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Cl
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 162 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.2 Å3/Da / Density % sol: 61.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M ammonium sulphate, 20% PEG3350, 0.1 M Tris chloride pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953725 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 5, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953725 Å / Relative weight: 1
ReflectionResolution: 2.49→48.7 Å / Num. obs: 31884 / % possible obs: 99.5 % / Redundancy: 10.207 % / Biso Wilson estimate: 55.35 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.171 / Rrim(I) all: 0.18 / Χ2: 0.746 / Net I/σ(I): 11.33 / Num. measured all: 325436
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.49-2.6410.2881.5861.4450938510749510.6411.66896.9
2.64-2.8310.5411.0122.4950554479747960.841.063100
2.83-3.0510.2190.6174.245708447344730.9190.65100
3.05-3.349.9980.3417.2641310413241320.9730.36100
3.34-3.7310.6040.18613.0639924376537650.9920.195100
3.73-4.310.170.11220.0233967334033400.9960.118100
4.3-5.269.7720.07626.6127879285328530.9970.081100
5.26-7.3810.2990.08125.4423049223822380.9970.085100
7.38-48.79.0620.05233.2312107134613360.9980.05699.3

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Processing

Software
NameVersionClassification
PHENIX1.15_3459refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6W41
Resolution: 2.493→42.457 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 25.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2272 1593 5 %
Rwork0.1851 30280 -
obs0.1872 31873 99.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 130.88 Å2 / Biso mean: 54.7287 Å2 / Biso min: 31.01 Å2
Refinement stepCycle: final / Resolution: 2.493→42.457 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4739 0 58 162 4959
Biso mean--93.5 52.92 -
Num. residues----624
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.493-2.57310.43191360.376256894
2.5731-2.66510.32911430.28152718100
2.6651-2.77180.28341440.25112747100
2.7718-2.89790.28091450.22522740100
2.8979-3.05060.27231440.22572739100
3.0506-3.24170.25861450.21512762100
3.2417-3.49190.24941440.1922740100
3.4919-3.84310.23441470.17912782100
3.8431-4.39870.19161450.14922765100
4.3987-5.53990.16961480.13742800100
5.5399-42.4570.19981520.1772919100

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