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- PDB-9k6j: Crystal structure of SARS-CoV-2 WT RBD bound with P5-1C8 Fab -

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Basic information

Entry
Database: PDB / ID: 9k6j
TitleCrystal structure of SARS-CoV-2 WT RBD bound with P5-1C8 Fab
Components
  • H chain of P5-1C8 Fab
  • L chain of P5-1C8 Fab
  • Spike protein S1
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / Crystal / SARS-CoV-2 / RBD / antibody / VIRAL 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 / viral translation / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion ...symbiont-mediated disruption of host tissue / Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / viral translation / 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 / receptor ligand activity / 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 / 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 / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / 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
Similarity search - Domain/homology
Biological speciesSevere acute respiratory syndrome coronavirus 2
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 Å
AuthorsLv, N.N. / Yang, R.Y.
Funding support2items
OrganizationGrant numberCountry
Other government2022YFA1206400
Other governmentCIFMS 2019-I2M-5-018
CitationJournal: Adv Sci (Weinh) / Year: 2025
Title: IgG-Bridging-Seeded Synergistic Aggregation of SARS-CoV-2 Spikes Underlies Potent Neutralization by a Low-Affinity Antibody.
Authors: Niannian Lv / Peng Chen / Xiaobin Dai / Hu Xu / Ziheng Li / Zelin Shan / Jinqian Li / Fenglin Guo / Yuanfang Chen / Jiayi Li / Yiqian Huang / Guizhi Dong / Yifan Jiang / Liang Chen / Xuanyu ...Authors: Niannian Lv / Peng Chen / Xiaobin Dai / Hu Xu / Ziheng Li / Zelin Shan / Jinqian Li / Fenglin Guo / Yuanfang Chen / Jiayi Li / Yiqian Huang / Guizhi Dong / Yifan Jiang / Liang Chen / Xuanyu Nan / Hanjun Zhao / Kang Zhang / Shilong Fan / Yuanchen Dong / Dongsheng Liu / Xinquan Wang / Deli Huang / Xiaojing Pan / Chunying Chen / Zhihua Liu / Li-Tang Yan / Qi Zhang / Linqi Zhang / Yuliang Zhao / Yuhe Renee Yang /
Abstract: Mechanistic studies of viral neutralization typically prioritize high-affinity antibodies, relegating low-affinity binders to the sidelines. P5‑1C8, a Class 1 SARS-CoV-2 antibody that exemplifies ...Mechanistic studies of viral neutralization typically prioritize high-affinity antibodies, relegating low-affinity binders to the sidelines. P5‑1C8, a Class 1 SARS-CoV-2 antibody that exemplifies this underexplored "low‑affinity yet high‑potency" phenotype is reported, retaining strong neutralization of Omicron JN.1 despite markedly weakened trimer binding (K = 225 nM; IC = 0.06 nM). Structural and biophysical analyses reveal that P5-1C8 engages WT and BA.1 spikes through canonical intra-spike bivalency, but with JN.1 it induces aggregation. Using virion-like nanoparticles displaying multiple spikes, it is shown that IgG remains bound with no detectable dissociation and triggers pronounced aggregation. Coarse-grained molecular dynamics delineate the stepwise pathway in which weak IgG-spike contacts seed aggregation via transient inter-spike bridging. Together, these findings establish the first mechanistic framework demonstrating how weak-binding antibodies can nonetheless achieve potent neutralization through higher-order aggregation, thereby expanding the conceptual landscape of antibody function and opening new directions for antibody evaluation and design.
History
DepositionOct 22, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jan 7, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Spike protein S1
A: H chain of P5-1C8 Fab
B: L chain of P5-1C8 Fab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,9094
Polymers76,6883
Non-polymers2211
Water2,828157
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.306, 115.092, 144.135
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Spike protein S1


Mass: 30512.326 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
#2: Antibody H chain of P5-1C8 Fab


Mass: 23207.910 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 L chain of P5-1C8 Fab


Mass: 22967.486 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.99 Å3/Da / Density % sol: 64.08 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.2 M Ammonium phosphate dibasic,28% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 28, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.39→89.94 Å / Num. obs: 34150 / % possible obs: 100 % / Redundancy: 9 % / Rmerge(I) obs: 0.086 / Rrim(I) all: 0.091 / Net I/σ(I): 10.4
Reflection shellResolution: 2.39→7.55 Å / Num. unique obs: 34150 / CC1/2: 0.951

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-2000data collection
autoPROCdata processing
Cootmodel building
PHASERphasing
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7cdi

7cdi


Resolution: 2.39→53.44 Å / SU ML: 0.38 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 25.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2829 1686 4.94 %
Rwork0.2358 --
obs0.2381 34149 91.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.39→53.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4625 0 0 157 4782
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044738
X-RAY DIFFRACTIONf_angle_d0.7776448
X-RAY DIFFRACTIONf_dihedral_angle_d16.531673
X-RAY DIFFRACTIONf_chiral_restr0.056712
X-RAY DIFFRACTIONf_plane_restr0.004833
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.39-2.460.3971450.35952828X-RAY DIFFRACTION97
2.46-2.540.34311550.29842917X-RAY DIFFRACTION100
2.54-2.630.35311470.29042927X-RAY DIFFRACTION100
2.63-2.730.35111330.29542912X-RAY DIFFRACTION100
2.73-2.860.33931620.27132931X-RAY DIFFRACTION100
2.86-3.010.30871430.25142944X-RAY DIFFRACTION100
3.01-3.20.25131700.22682946X-RAY DIFFRACTION100
3.2-3.440.27681400.24132882X-RAY DIFFRACTION97
3.44-3.560.3576460.2512820X-RAY DIFFRACTION74
3.82-4.340.25541340.20392267X-RAY DIFFRACTION82
4.34-5.460.20381460.1622922X-RAY DIFFRACTION96
5.46-53.440.24431650.20323167X-RAY DIFFRACTION100
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)
12.54090.03611.21831.417-0.04321.78540.2104-0.41330.15270.1663-0.3074-0.23870.16460.22380.03520.1749-0.0867-0.02920.24460.00280.289131.003812.652959.1863
22.66940.31351.52340.76491.39532.8514-0.1517-0.3354-0.060.8496-0.2417-0.66930.10860.3547-0.62780.4268-0.0476-0.1590.3830.09270.230930.6358.649470.7683
30.6870.0860.84740.00710.1011.0515-0.1382-0.26930.29450.30380.0303-0.1776-0.29960.27270.06510.7777-0.2399-0.28330.4629-0.0693-0.334931.926324.985468.8982
40.5522-0.54850.50791.1353-1.48632.3435-0.1357-0.61020.24791.02960.0871-0.2042-0.0919-0.42350.02960.7117-0.0935-0.08230.3955-0.0231-0.090223.666120.318374.803
51.5803-0.49250.52280.9613-0.06361.3723-0.1057-0.04440.04960.2028-0.07440.1876-0.0182-0.1293-0.12550.1953-0.0416-0.00050.23230.03960.174118.403617.503557.6719
61.1529-0.45580.61271.3328-0.32431.85490.114-0.22930.04680.034-0.02830.0440.12530.05780.00760.1673-0.0367-0.02390.1430.04860.182921.032114.404254.1642
72.5642-0.05440.92351.1936-0.16531.65630.17860.3207-0.3337-0.4438-0.08530.2410.344-0.151-0.20870.2938-0.0189-0.05550.2233-0.00620.281512.21354.583538.0985
81.3535-0.33630.86291.2442-0.58911.75740.03650.10840.28640.1932-0.02210.1449-0.0161-0.15380.12080.2713-0.0744-0.00560.2030.02780.23926.519821.92953.1017
91.9866-0.90110.92941.6199-1.1771.03950.0131-0.1311-0.3894-0.170.15910.26230.1553-0.5878-0.13690.1217-0.0655-0.00910.31840.0630.2273-11.577823.568237.6244
101.5906-0.9930.55540.6816-0.27281.43490.1133-0.1297-0.16470.05160.03540.13680.1439-0.1464-0.13050.158-0.03790.02780.20660.03660.1917-2.360620.786543.3816
111.7429-1.00310.48121.1551-0.67730.98910.07-0.0198-0.2130.1238-0.01910.1242-0.0199-0.0543-0.08310.1408-0.05380.00060.19160.0270.1739-1.080724.81737.8948
121.3085-0.50810.77520.8357-0.16440.9825-0.059-0.1552-0.0403-0.11170.05210.18870.2665-0.4726-0.1240.1729-0.0879-0.02140.3040.03340.2504-22.811536.866720.512
131.6175-0.36120.59150.6977-0.69341.81760.0328-0.052-0.2398-0.02950.0674-0.03240.2268-0.297-0.10260.1626-0.05720.02170.1532-0.02170.2015-17.691634.013615.4918
140.9518-0.59930.40060.7026-0.03913.81180.0428-0.3212-0.73290.1772-0.0895-0.07060.5956-0.2641-0.26160.2985-0.1652-0.05060.35150.07660.3255-24.953828.02414.891
150.9799-0.2430.80280.9827-0.7061.78710.26030.09910.26750.1823-0.0826-0.1728-0.17430.05480.19060.2724-0.01630.03910.22460.02460.261213.416937.469124.2341
160.5139-0.14611.54383.0991-1.25074.93710.10510.3875-0.02910.4562-0.2529-0.4674-0.47190.2130.22970.0863-0.01750.00620.34790.01690.10118.810435.092634.1122
172.3846-1.22221.23781.1405-1.30071.75730.31660.2873-0.3997-0.17920.0260.00370.3959-0.14110.12830.10030.05320.00240.21110.00610.17028.663725.839728.6781
181.7269-0.65390.48621.323-1.4421.92530.0890.3613-0.1472-0.2447-0.0525-0.29120.0290.42940.09050.20830.01190.02050.2231-0.00880.217317.972825.316325.9292
190.975-0.56510.55230.637-1.13762.1840.13780.08970.0343-0.04380.0437-0.10820.0597-0.07030.07280.13450.01250.01820.1470.02020.22339.734129.836927.6765
201.2412-0.68610.82320.7549-0.18971.35950.1221-0.0355-0.10580.0062-0.06590.0382-0.0684-0.0510.02340.138-0.03050.01110.137-0.05620.18-12.516341.710512.3203
212.3214-2.0172-0.15893.433-0.94731.2841-0.0088-0.27710.284-0.1496-0.1399-0.4181-0.01980.1629-0.45590.16290.01170.0030.1587-0.03040.1366-7.202848.2689.9313
220.9497-1.08650.79082.0514-1.25461.2361-0.0535-0.02690.05270.1964-0.16780.0714-0.0874-0.2780.10330.24590.0108-0.02460.141-0.04380.1713-16.131853.635314.2018
231.8182-0.29160.76850.8671-0.67151.84140.0290.00810.1589-0.1061-0.04730.0015-0.2166-0.06390.05690.15070.0182-0.00950.18-0.02460.1779-14.87347.51098.7242
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'C' and (resid 336 through 353 )
2X-RAY DIFFRACTION2chain 'C' and (resid 354 through 364 )
3X-RAY DIFFRACTION3chain 'C' and (resid 365 through 375 )
4X-RAY DIFFRACTION4chain 'C' and (resid 376 through 393 )
5X-RAY DIFFRACTION5chain 'C' and (resid 394 through 421 )
6X-RAY DIFFRACTION6chain 'C' and (resid 422 through 469 )
7X-RAY DIFFRACTION7chain 'C' and (resid 470 through 494 )
8X-RAY DIFFRACTION8chain 'C' and (resid 495 through 516 )
9X-RAY DIFFRACTION9chain 'A' and (resid 1 through 17 )
10X-RAY DIFFRACTION10chain 'A' and (resid 18 through 82 )
11X-RAY DIFFRACTION11chain 'A' and (resid 83 through 113 )
12X-RAY DIFFRACTION12chain 'A' and (resid 114 through 138 )
13X-RAY DIFFRACTION13chain 'A' and (resid 139 through 194 )
14X-RAY DIFFRACTION14chain 'A' and (resid 195 through 217 )
15X-RAY DIFFRACTION15chain 'B' and (resid 1 through 18 )
16X-RAY DIFFRACTION16chain 'B' and (resid 19 through 30 )
17X-RAY DIFFRACTION17chain 'B' and (resid 31 through 49 )
18X-RAY DIFFRACTION18chain 'B' and (resid 50 through 76 )
19X-RAY DIFFRACTION19chain 'B' and (resid 77 through 98 )
20X-RAY DIFFRACTION20chain 'B' and (resid 99 through 137 )
21X-RAY DIFFRACTION21chain 'B' and (resid 138 through 150 )
22X-RAY DIFFRACTION22chain 'B' and (resid 151 through 163 )
23X-RAY DIFFRACTION23chain 'B' and (resid 164 through 211 )

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