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- PDB-7y8j: 3D1 in complex with 6-mer HR1 peptide from SARS-CoV-2 -

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Basic information

Entry
Database: PDB / ID: 7y8j
Title3D1 in complex with 6-mer HR1 peptide from SARS-CoV-2
Components
  • Spike protein S2'
  • heavy chain of 3D1
  • light chain of 3D1
KeywordsANTIMICROBIAL PROTEIN/IMMUNE SYSTEM / human antibody / broad / coronavirus / ANTIMICROBIAL PROTEIN / ANTIMICROBIAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


symbiont-mediated disruption of host tissue / Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / membrane fusion ...symbiont-mediated disruption of host tissue / Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / membrane fusion / entry receptor-mediated virion attachment to host cell / Attachment and Entry / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / host cell surface receptor binding / symbiont-mediated suppression of host innate immune response / endocytosis involved in viral entry into host cell / receptor ligand activity / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / symbiont entry into host cell / 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 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, N-terminal domain superfamily / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein, betacoronavirus / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / 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 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, N-terminal domain superfamily / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein, betacoronavirus / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus spike glycoprotein S1, receptor binding / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.03 Å
AuthorsLei, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nat Commun / Year: 2025
Title: A broadly neutralizing antibody recognizes a unique epitope with a signature motif common across coronaviruses.
Authors: Yan, L. / Wang, F. / Hill, M. / Brun, J. / Liang, Z. / Shi, X. / Zhang, L. / He, X. / Li, Y. / Huang, Q. / Dong, X. / Liu, H. / Zhang, Y. / Liu, L. / Dwek, R.A. / Zitzmann, N. / Liang, A. / Yang, G.
History
DepositionJun 24, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 12, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 1.3Aug 27, 2025Group: 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: heavy chain of 3D1
A: Spike protein S2'
L: light chain of 3D1


Theoretical massNumber of molelcules
Total (without water)25,5023
Polymers25,5023
Non-polymers00
Water7,746430
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2560 Å2
ΔGint-17 kcal/mol
Surface area10350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.965, 69.810, 51.058
Angle α, β, γ (deg.)90.000, 110.460, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein heavy chain of 3D1


Mass: 13138.580 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#2: Protein/peptide Spike protein S2'


Mass: 744.751 Da / Num. of mol.: 1 / Fragment: HR1 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: S, 2 / Production host: synthetic construct (others) / References: UniProt: P0DTC2
#3: Antibody light chain of 3D1


Mass: 11618.550 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 430 / Source method: isolated from a natural source / Formula: H2O
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: 2.42 Å3/Da / Density % sol: 49.18 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: 0.1 M HEPES pH7.5, 25% PEG8000

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Data collection

DiffractionMean temperature: 77 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 6, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.03→69.81 Å / Num. obs: 85307 / % possible obs: 98.1 % / Redundancy: 3.4 % / CC1/2: 0.999 / Net I/σ(I): 17.4
Reflection shellResolution: 1.03→1.09 Å / Num. unique obs: 3761 / CC1/2: 0.998

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Processing

Software
NameVersionClassification
Aimlessdata scaling
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6kvf

6kvf


Resolution: 1.03→24.59 Å / SU ML: 0.05 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 18.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1446 1989 2.33 %
Rwork0.1335 83211 -
obs0.1338 85200 71.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 82.88 Å2 / Biso mean: 16.6095 Å2 / Biso min: 8.23 Å2
Refinement stepCycle: final / Resolution: 1.03→24.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1790 0 0 430 2220
Biso mean---31.44 -
Num. residues----243
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.03-1.060.3076140.30786616758
1.06-1.090.2711400.22441624166420
1.09-1.120.24520.18592516256830
1.12-1.160.1808980.163481357942
1.16-1.20.17851070.14654914502160
1.2-1.250.14511790.14397151733087
1.25-1.30.14871750.13917666784193
1.3-1.370.15751820.14027713789593
1.37-1.460.15031900.1437766795694
1.46-1.570.151890.13487771796094
1.57-1.730.14611880.12987872806095
1.73-1.980.13831910.13057924811595
1.98-2.490.13971930.12927978817196
2.49-24.590.13831910.12918174836597

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