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- PDB-7yi6: bnAb 3D1 in complex with 6-mer HR1 peptide from HCoV-229E S protein -

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Basic information

Entry
Database: PDB / ID: 7yi6
TitlebnAb 3D1 in complex with 6-mer HR1 peptide from HCoV-229E S protein
Components
  • Spike glycoprotein
  • heavy chain of 3D1
  • light chain of 3D1
KeywordsANTIVIRAL PROTEIN/IMMUNE SYSTEM / bnAb / HR1 / 6-mer / ANTIVIRAL PROTEIN / ANTIVIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / endocytosis involved in viral entry into host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion membrane / membrane
Similarity search - Function
Spike glycoprotein, Alphacoronavirus / Spike glycoprotein S1, coronavirus / Coronavirus spike glycoprotein S1 / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 ...Spike glycoprotein, Alphacoronavirus / Spike glycoprotein S1, coronavirus / Coronavirus spike glycoprotein S1 / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-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
DI(HYDROXYETHYL)ETHER / Spike glycoprotein
Similarity search - Component
Biological speciesHuman coronavirus 229E
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å
AuthorsYan, L. / Yang, G.
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
DepositionJul 15, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 30, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 1.2Aug 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
A: Spike glycoprotein
B: light chain of 3D1
D: heavy chain of 3D1
C: Spike glycoprotein
E: light chain of 3D1
F: heavy chain of 3D1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,65713
Polymers93,2056
Non-polymers4527
Water8,251458
1
A: Spike glycoprotein
B: light chain of 3D1
D: heavy chain of 3D1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8868
Polymers46,6033
Non-polymers2845
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4910 Å2
ΔGint-29 kcal/mol
Surface area19140 Å2
MethodPISA
2
C: Spike glycoprotein
E: light chain of 3D1
F: heavy chain of 3D1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7715
Polymers46,6033
Non-polymers1682
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4600 Å2
ΔGint-22 kcal/mol
Surface area18490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.906, 72.703, 86.264
Angle α, β, γ (deg.)90.000, 109.540, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and resid 836 through 841)
21chain C
12(chain B and (resid 3 through 8 or resid 10 through 212))
22(chain E and (resid 3 through 8 or resid 10 through 212))
13(chain D and (resid 1 through 134 or resid 140 through 220))
23chain F

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111VALVALGLYGLY(chain A and resid 836 through 841)AA836 - 8412 - 7
211VALVALGLYGLYchain CCD836 - 8412 - 7
112ALAALAPROPRO(chain B and (resid 3 through 8 or resid 10 through 212))BB3 - 81 - 6
122ALAALAPROPRO(chain B and (resid 3 through 8 or resid 10 through 212))BB10 - 2128 - 210
212ALAALAPROPRO(chain E and (resid 3 through 8 or resid 10 through 212))EE3 - 81 - 6
222ALAALAPROPRO(chain E and (resid 3 through 8 or resid 10 through 212))EE10 - 2128 - 210
113PCAPCASERSER(chain D and (resid 1 through 134 or resid 140 through 220))DC1 - 1341 - 134
123GLYGLYPROPRO(chain D and (resid 1 through 134 or resid 140 through 220))DC140 - 220140 - 220
213PCAPCAPROPROchain FFF1 - 2201 - 220

NCS ensembles :
ID
1
2
3

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Components

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Protein/peptide / Antibody / Protein , 3 types, 6 molecules ACBEDF

#1: Protein/peptide Spike glycoprotein / S glycoprotein / E2 / Peplomer protein


Mass: 758.777 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human coronavirus 229E / Gene: S, 2 / Production host: chemical production metagenome (others) / References: UniProt: P15423
#2: Antibody light chain of 3D1


Mass: 22473.746 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#3: Protein heavy chain of 3D1


Mass: 23370.131 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)

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Non-polymers , 4 types, 465 molecules

#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 458 / 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: 2.35 Å3/Da / Density % sol: 47.57 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Ammonium sulfate, 0.1 M BIS-TRIS buffer at pH 5.5 and 25% (w/v) polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Jan 17, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.28→69.65 Å / Num. obs: 39040 / % possible obs: 99.2 % / Redundancy: 5.6 % / CC1/2: 1 / Net I/σ(I): 11.5
Reflection shellResolution: 2.28→2.34 Å / Num. unique obs: 3986 / CC1/2: 0.91

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Processing

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

6kvf


Resolution: 2.28→45.86 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2204 2000 5.13 %
Rwork0.1927 37006 -
obs0.1941 39006 98.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 85.79 Å2 / Biso mean: 32.46 Å2 / Biso min: 12.73 Å2
Refinement stepCycle: final / Resolution: 2.28→45.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6431 0 28 458 6917
Biso mean--43.57 34.5 -
Num. residues----869
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A42X-RAY DIFFRACTION10.987TORSIONAL
12C42X-RAY DIFFRACTION10.987TORSIONAL
21B1805X-RAY DIFFRACTION10.987TORSIONAL
22E1805X-RAY DIFFRACTION10.987TORSIONAL
31D1922X-RAY DIFFRACTION10.987TORSIONAL
32F1922X-RAY DIFFRACTION10.987TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.28-2.340.30511420.2444262699
2.34-2.40.25671420.2323264499
2.4-2.470.28731430.2211262199
2.47-2.550.28071400.2343261399
2.55-2.640.27771430.2222263199
2.64-2.750.26831430.22512660100
2.75-2.870.24651430.2109265799
2.87-3.030.24591430.2103263699
3.03-3.220.24341410.2185263099
3.22-3.460.19811440.1926265499
3.46-3.810.18951420.1848264399
3.81-4.360.18251450.1592266399
4.36-5.490.16211430.1427266299
5.5-60.21611460.1829266697

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