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- PDB-7fcp: Crystallographic structure of two neutralizing antibodies in comp... -

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Basic information

Entry
Database: PDB / ID: 7fcp
TitleCrystallographic structure of two neutralizing antibodies in complex with SARS-CoV-2 spike receptor-binding Domain (RBD)
Components
  • (P14-44 antibody Fab fragment ...) x 2
  • (P5-22 antibody Fab fragment ...) x 2
  • Spike protein S1
KeywordsANTIVIRAL PROTEIN / SARS-CoV-2 / RBD / neutralizing antibodies
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 / host cell endoplasmic reticulum-Golgi intermediate compartment membrane ...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 / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / entry receptor-mediated virion attachment to host cell / 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 / 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 / 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 speciesSevere acute respiratory syndrome coronavirus 2
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsZheng, P. / Jin, T.
CitationJournal: J.Clin.Invest. / Year: 2022
Title: Ultrapotent neutralizing antibodies against SARS-CoV-2 with a high degree of mutation resistance.
Authors: Zou, J. / Li, L. / Zheng, P. / Liang, W. / Hu, S. / Zhou, S. / Wang, Y. / Zhao, J. / Yuan, D. / Liu, L. / Wu, D. / Xu, M. / Zhang, F. / Zhu, M. / Wu, Z. / Cao, X. / Ni, M. / Ling, X. / Wu, Y. ...Authors: Zou, J. / Li, L. / Zheng, P. / Liang, W. / Hu, S. / Zhou, S. / Wang, Y. / Zhao, J. / Yuan, D. / Liu, L. / Wu, D. / Xu, M. / Zhang, F. / Zhu, M. / Wu, Z. / Cao, X. / Ni, M. / Ling, X. / Wu, Y. / Kuang, Z. / Hu, M. / Li, J. / Li, X. / Guo, X. / Xu, T. / Jiang, H. / Gao, C. / Yu, M. / Liu, J. / Zhong, N. / Zhou, J. / Huang, J.A. / Jin, T. / He, J.
History
DepositionJul 15, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 15, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Spike protein S1
H: P14-44 antibody Fab fragment heavy chain
L: P14-44 antibody Fab fragment light chain
B: P5-22 antibody Fab fragment heavy chain
D: P5-22 antibody Fab fragment light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,6559
Polymers127,1285
Non-polymers5284
Water10,611589
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)223.007, 80.414, 72.746
Angle α, β, γ (deg.)90.000, 106.230, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Antibody , 4 types, 4 molecules HLBD

#2: Antibody P14-44 antibody Fab fragment heavy chain


Mass: 25477.451 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 P14-44 antibody Fab fragment light chain


Mass: 22858.178 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: Antibody P5-22 antibody Fab fragment heavy chain


Mass: 24304.221 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#5: Antibody P5-22 antibody Fab fragment light chain


Mass: 23547.059 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: 30940.680 Da / Num. of mol.: 1
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
#7: 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

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Non-polymers , 3 types, 592 molecules

#6: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#8: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 589 / 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: 2.59 Å3/Da / Density % sol: 52.5 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.05 M HEPES pH 7.0 20%(w/v) PEG3350 1%(w/v) Tryptone

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.97852 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 8, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 2.4→107.06 Å / Num. obs: 48529 / % possible obs: 100 % / Redundancy: 6.3 % / CC1/2: 0.981 / Rmerge(I) obs: 0.08 / Rrim(I) all: 0.088 / Net I/σ(I): 22.4
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.719 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2422 / CC1/2: 0.751 / Rrim(I) all: 0.795 / % possible all: 99.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.48 Å48.86 Å
Translation6.48 Å48.86 Å

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0155refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASER2.6.1phasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6XDG, 7JMW

6xdg

7jmw


Resolution: 2.4→50 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.91 / SU R Cruickshank DPI: 0.4645 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.465 / ESU R Free: 0.27 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2446 2243 4.8 %RANDOM
Rwork0.191 ---
obs0.1935 44351 95.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 110.66 Å2 / Biso mean: 40.402 Å2 / Biso min: 18.11 Å2
Baniso -1Baniso -2Baniso -3
1-0.53 Å2-0 Å20.26 Å2
2---0.71 Å2-0 Å2
3---0.03 Å2
Refinement stepCycle: final / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8170 0 34 589 8793
Biso mean--43.61 39.15 -
Num. residues----1069
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.028435
X-RAY DIFFRACTIONr_bond_other_d00.027649
X-RAY DIFFRACTIONr_angle_refined_deg1.3891.94911473
X-RAY DIFFRACTIONr_angle_other_deg3.853317702
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.42451068
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.44224.186344
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.186151313
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4091535
X-RAY DIFFRACTIONr_chiral_restr0.2580.21270
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0219588
X-RAY DIFFRACTIONr_gen_planes_other0.0250.021931
LS refinement shellResolution: 2.4→2.461 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.341 112 -
Rwork0.291 2445 -
obs--71.07 %

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