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- PDB-7yck: Crystal structure of SARS-CoV-2 Spike RBD in complex with FP-12A Fab -

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Basic information

Entry
Database: PDB / ID: 7yck
TitleCrystal structure of SARS-CoV-2 Spike RBD in complex with FP-12A Fab
Components
  • FP-12A Fab heavy chain
  • FP-12A Fab light chain
  • Spike protein S1
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / antibody / SARS-CoV-2 / Spike / RBD / class 4 / VIRAL PROTEIN-IMMUNE SYSTEM complex
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 / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / membrane / identical protein binding / 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 / Resolution: 2.6 Å
AuthorsNguyen, V.H.T. / Chen, X.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan) Taiwan
CitationJournal: Nat Commun / Year: 2023
Title: Structural basis for a conserved neutralization epitope on the receptor-binding domain of SARS-CoV-2.
Authors: Kuan-Ying A Huang / Xiaorui Chen / Arpita Mohapatra / Hong Thuy Vy Nguyen / Lisa Schimanski / Tiong Kit Tan / Pramila Rijal / Susan K Vester / Rory A Hills / Mark Howarth / Jennifer R Keeffe ...Authors: Kuan-Ying A Huang / Xiaorui Chen / Arpita Mohapatra / Hong Thuy Vy Nguyen / Lisa Schimanski / Tiong Kit Tan / Pramila Rijal / Susan K Vester / Rory A Hills / Mark Howarth / Jennifer R Keeffe / Alexander A Cohen / Leesa M Kakutani / Yi-Min Wu / Md Shahed-Al-Mahmud / Yu-Chi Chou / Pamela J Bjorkman / Alain R Townsend / Che Ma /
Abstract: Antibody-mediated immunity plays a crucial role in protection against SARS-CoV-2 infection. We isolated a panel of neutralizing anti-receptor-binding domain (RBD) antibodies elicited upon natural ...Antibody-mediated immunity plays a crucial role in protection against SARS-CoV-2 infection. We isolated a panel of neutralizing anti-receptor-binding domain (RBD) antibodies elicited upon natural infection and vaccination and showed that they recognize an immunogenic patch on the internal surface of the core RBD, which faces inwards and is hidden in the "down" state. These antibodies broadly neutralize wild type (Wuhan-Hu-1) SARS-CoV-2, Beta and Delta variants and some are effective against other sarbecoviruses. We observed a continuum of partially overlapping antibody epitopes from lower to upper part of the inner face of the RBD and some antibodies extend towards the receptor-binding motif. The majority of antibodies are substantially compromised by three mutational hotspots (S371L/F, S373P and S375F) in the lower part of the Omicron BA.1, BA.2 and BA.4/5 RBD. By contrast, antibody IY-2A induces a partial unfolding of this variable region and interacts with a conserved conformational epitope to tolerate all antigenic variations and neutralize diverse sarbecoviruses as well. This finding establishes that antibody recognition is not limited to the normal surface structures on the RBD. In conclusion, the delineation of functionally and structurally conserved RBD epitopes highlights potential vaccine and therapeutic candidates for COVID-19.
History
DepositionJul 1, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 1, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Spike protein S1
C: FP-12A Fab heavy chain
D: FP-12A Fab light chain
B: Spike protein S1
E: FP-12A Fab heavy chain
F: FP-12A Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,4998
Polymers140,1966
Non-polymers1,3032
Water2,288127
1
A: Spike protein S1
C: FP-12A Fab heavy chain
D: FP-12A Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,8314
Polymers70,0983
Non-polymers7331
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Spike protein S1
E: FP-12A Fab heavy chain
F: FP-12A Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,6684
Polymers70,0983
Non-polymers5711
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.830, 79.124, 92.539
Angle α, β, γ (deg.)76.260, 81.160, 71.130
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and resid 333 through 535)
21chain B

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and resid 333 through 535)A333 - 535
211chain BB333 - 535

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Components

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Antibody , 2 types, 4 molecules CEDF

#2: Antibody FP-12A Fab heavy chain


Mass: 23925.725 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody FP-12A Fab light chain


Mass: 23124.326 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Protein / Non-polymers , 2 types, 129 molecules AB

#1: Protein Spike protein S1


Mass: 23047.816 Da / Num. of mol.: 2
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
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 127 / Source method: isolated from a natural source / Formula: H2O

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Sugars , 2 types, 2 molecules

#4: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 732.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1221m-1a_1-5]/1-1-2-3/a4-b1_a6-d1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#5: 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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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: 2.7 Å3/Da / Density % sol: 54.42 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 0.2M Ammonium sulfate; 0.05 M Magnesium sulfate heptahydrate, 0.1M BICINE pH 9.0, 2.5% w/v PEG 3350, 2.5%w/v PEG 4000, 2.5% w/v PEG 2000, 2.5% w/v PEG 5000 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Mar 8, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→45.51 Å / Num. obs: 46056 / % possible obs: 97.8 % / Redundancy: 4 % / Biso Wilson estimate: 53.44 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.054 / Rrim(I) all: 0.107 / Net I/σ(I): 5.6 / Num. measured all: 183621 / Scaling rejects: 164
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.6-2.6940.9171800345150.6590.531.0591.497.1
10.07-45.513.90.05130287820.9870.030.0599.896.5

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
Aimlessdata scaling
PDB_EXTRACT3.27data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ZER

6zer


Resolution: 2.6→32.25 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 27.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2644 2206 4.8 %
Rwork0.2285 43753 -
obs0.2302 45959 97.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 163.61 Å2 / Biso mean: 71.7975 Å2 / Biso min: 23 Å2
Refinement stepCycle: final / Resolution: 2.6→32.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8101 0 87 127 8315
Biso mean--95.56 51.03 -
Num. residues----1053
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1906X-RAY DIFFRACTION7.738TORSIONAL
12B1906X-RAY DIFFRACTION7.738TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6-2.660.34581450.31862746289197
2.66-2.720.36481510.29752695284697
2.72-2.790.29721440.2762684282897
2.79-2.860.32151230.2692722284597
2.86-2.950.31491400.28142763290397
2.95-3.040.3241510.27032702285398
3.04-3.150.3291290.26462750287998
3.15-3.280.33291360.25552742287898
3.28-3.420.31871380.24742739287798
3.42-3.60.26131510.23542690284198
3.6-3.830.24491380.22922736287498
3.83-4.130.22321360.20812761289798
4.13-4.540.21911070.18832786289398
4.54-5.190.20941410.19222738287998
5.19-6.530.26431420.21312771291399
6.54-32.250.23091340.21732728286298

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