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- PDB-7ycn: Crystal structure of SARS-CoV-2 Spike RBD in complex with IY-2A Fab -

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Basic information

Entry
Database: PDB / ID: 7ycn
TitleCrystal structure of SARS-CoV-2 Spike RBD in complex with IY-2A Fab
Components
  • IY-2A Fab heavy chain
  • IY-2A 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 / 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 / Resolution: 2.85 Å
AuthorsMohapatra, A. / 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
J: Spike protein S1
K: IY-2A Fab heavy chain
L: IY-2A Fab light chain
A: Spike protein S1
E: IY-2A Fab heavy chain
F: IY-2A Fab light chain
B: Spike protein S1
C: IY-2A Fab heavy chain
D: IY-2A Fab light chain
G: Spike protein S1
H: IY-2A Fab heavy chain
I: IY-2A Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)276,42614
Polymers275,98312
Non-polymers4422
Water00
1
J: Spike protein S1
K: IY-2A Fab heavy chain
L: IY-2A Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,2174
Polymers68,9963
Non-polymers2211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5580 Å2
ΔGint-33 kcal/mol
Surface area28390 Å2
MethodPISA
2
A: Spike protein S1
E: IY-2A Fab heavy chain
F: IY-2A Fab light chain


Theoretical massNumber of molelcules
Total (without water)68,9963
Polymers68,9963
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5510 Å2
ΔGint-35 kcal/mol
Surface area28360 Å2
MethodPISA
3
B: Spike protein S1
C: IY-2A Fab heavy chain
D: IY-2A Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,2174
Polymers68,9963
Non-polymers2211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5730 Å2
ΔGint-31 kcal/mol
Surface area28360 Å2
MethodPISA
4
G: Spike protein S1
H: IY-2A Fab heavy chain
I: IY-2A Fab light chain


Theoretical massNumber of molelcules
Total (without water)68,9963
Polymers68,9963
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5510 Å2
ΔGint-37 kcal/mol
Surface area28170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)193.019, 225.150, 95.520
Angle α, β, γ (deg.)90.000, 96.160, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 334 through 345 or (resid 346...
21(chain B and resid 334 through 527)
31chain G
41(chain J and (resid 334 through 345 or (resid 346...
12(chain C and (resid 1 through 74 or (resid 75...
22(chain E and (resid 1 through 131 or resid 137 through 219))
32(chain H and (resid 1 through 74 or (resid 75...
42(chain K and (resid 1 through 74 or (resid 75...
13chain D
23(chain F and resid 2 through 212)
33(chain I and resid 2 through 212)
43chain L

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 334 through 345 or (resid 346...A334 - 345
121(chain A and (resid 334 through 345 or (resid 346...A346
131(chain A and (resid 334 through 345 or (resid 346...A334 - 527
141(chain A and (resid 334 through 345 or (resid 346...A334 - 527
151(chain A and (resid 334 through 345 or (resid 346...A334 - 527
161(chain A and (resid 334 through 345 or (resid 346...A334 - 527
211(chain B and resid 334 through 527)B334 - 527
311chain GG334 - 527
411(chain J and (resid 334 through 345 or (resid 346...J334 - 345
421(chain J and (resid 334 through 345 or (resid 346...J346
431(chain J and (resid 334 through 345 or (resid 346...J334 - 528
441(chain J and (resid 334 through 345 or (resid 346...J334 - 528
451(chain J and (resid 334 through 345 or (resid 346...J334 - 528
461(chain J and (resid 334 through 345 or (resid 346...J334 - 528
112(chain C and (resid 1 through 74 or (resid 75...C1 - 74
122(chain C and (resid 1 through 74 or (resid 75...C75
132(chain C and (resid 1 through 74 or (resid 75...C1 - 219
142(chain C and (resid 1 through 74 or (resid 75...C1 - 219
152(chain C and (resid 1 through 74 or (resid 75...C1 - 219
162(chain C and (resid 1 through 74 or (resid 75...C1 - 219
212(chain E and (resid 1 through 131 or resid 137 through 219))E1 - 131
222(chain E and (resid 1 through 131 or resid 137 through 219))E137 - 219
312(chain H and (resid 1 through 74 or (resid 75...H1 - 74
322(chain H and (resid 1 through 74 or (resid 75...H75
332(chain H and (resid 1 through 74 or (resid 75...H1 - 219
342(chain H and (resid 1 through 74 or (resid 75...H1 - 219
352(chain H and (resid 1 through 74 or (resid 75...H1 - 219
362(chain H and (resid 1 through 74 or (resid 75...H1 - 219
412(chain K and (resid 1 through 74 or (resid 75...K1 - 74
422(chain K and (resid 1 through 74 or (resid 75...K75
432(chain K and (resid 1 through 74 or (resid 75...K1 - 214
442(chain K and (resid 1 through 74 or (resid 75...K1 - 214
452(chain K and (resid 1 through 74 or (resid 75...K1 - 214
462(chain K and (resid 1 through 74 or (resid 75...K1 - 214
113chain DD2 - 208
213(chain F and resid 2 through 212)F2 - 212
313(chain I and resid 2 through 212)I2 - 212
413chain LL2 - 208

NCS ensembles :
ID
1
2
3

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Components

#1: Protein
Spike protein S1 / S glycoprotein / E2 / Peplomer protein


Mass: 21873.496 Da / Num. of mol.: 4
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
IY-2A Fab heavy chain


Mass: 24060.084 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody
IY-2A Fab light chain


Mass: 23062.277 Da / Num. of mol.: 4
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.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
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
Has ligand of interestY

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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: 3.54 Å3/Da / Density % sol: 65.28 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.2M Ammonium citrate tribasic pH 7.0, 0.1M Imidazole pH 7.0, 20% w/v Polyethylene glycol monomethyl ether

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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 14, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.85→34.05 Å / Num. obs: 94154 / % possible obs: 99.9 % / Redundancy: 3.8 % / Biso Wilson estimate: 55.01 Å2 / CC1/2: 0.984 / Rmerge(I) obs: 0.151 / Rpim(I) all: 0.091 / Rrim(I) all: 0.177 / Net I/σ(I): 6.6 / Num. measured all: 353905 / Scaling rejects: 209
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
2.85-2.93.70.7121710946550.3260.4310.8331.7100
15.61-34.053.30.05317825360.9920.0340.06317.689.9

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.27data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ZER

6zer


Resolution: 2.85→33.64 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2499 4687 4.98 %
Rwork0.2114 89430 -
obs0.2133 94117 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 168.14 Å2 / Biso mean: 64.1493 Å2 / Biso min: 1.93 Å2
Refinement stepCycle: final / Resolution: 2.85→33.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19066 0 28 0 19094
Biso mean--79.47 --
Num. residues----2511
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3651X-RAY DIFFRACTION16.537TORSIONAL
12B3651X-RAY DIFFRACTION16.537TORSIONAL
13G3651X-RAY DIFFRACTION16.537TORSIONAL
14J3651X-RAY DIFFRACTION16.537TORSIONAL
21C3858X-RAY DIFFRACTION16.537TORSIONAL
22E3858X-RAY DIFFRACTION16.537TORSIONAL
23H3858X-RAY DIFFRACTION16.537TORSIONAL
24K3858X-RAY DIFFRACTION16.537TORSIONAL
31D3904X-RAY DIFFRACTION16.537TORSIONAL
32F3904X-RAY DIFFRACTION16.537TORSIONAL
33I3904X-RAY DIFFRACTION16.537TORSIONAL
34L3904X-RAY DIFFRACTION16.537TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.85-2.880.36661630.324329623125
2.88-2.920.3631630.331429533116
2.92-2.950.34561500.333229903140
2.95-2.990.33341560.322229963152
2.99-3.030.35871550.315729423097
3.03-3.070.32531720.308129543126
3.07-3.110.36861560.317329603116
3.11-3.160.32581650.296630093174
3.16-3.210.30231380.290629713109
3.21-3.260.30091520.276629493101
3.26-3.320.30411450.272130083153
3.32-3.380.31561460.267430123158
3.38-3.440.29621580.276129683126
3.44-3.510.33141530.273229593112
3.51-3.590.31651350.242729803115
3.59-3.670.31431540.256529883142
3.67-3.770.27561780.239629423120
3.77-3.870.30331510.227130053156
3.87-3.980.29661630.230629723135
3.98-4.110.21831420.19229823124
4.11-4.260.20461670.172929653132
4.26-4.430.20441910.159129523143
4.43-4.630.19551530.153930033156
4.63-4.870.181870.148929503137
4.87-5.170.19881690.143429783147
5.17-5.570.18341300.147530163146
5.57-6.130.18361490.154629983147
6.13-7.010.19131530.165230043157
7.01-8.80.20231540.155730073161
8.81-33.640.20521390.171430553194
Refinement TLS params.Method: refined / Origin x: 45.2613 Å / Origin y: 33.1567 Å / Origin z: -0.7999 Å
111213212223313233
T0.3385 Å2-0.0577 Å2-0.0213 Å2-0.3591 Å20.0166 Å2--0.3931 Å2
L0.057 °2-0.0654 °2-0.0667 °2-0.1319 °20.1173 °2--0.5516 °2
S-0.0307 Å °0.0307 Å °0.015 Å °-0.0609 Å °-0.0008 Å °0.0022 Å °0.0236 Å °-0.1683 Å °0.0231 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allJ334 - 528
2X-RAY DIFFRACTION1allK1 - 214
3X-RAY DIFFRACTION1allL2 - 208
4X-RAY DIFFRACTION1allA334 - 527
5X-RAY DIFFRACTION1allE1 - 219
6X-RAY DIFFRACTION1allF2 - 215
7X-RAY DIFFRACTION1allB334 - 528
8X-RAY DIFFRACTION1allC1 - 219
9X-RAY DIFFRACTION1allD2 - 208
10X-RAY DIFFRACTION1allG334 - 527
11X-RAY DIFFRACTION1allH1 - 219
12X-RAY DIFFRACTION1allI2 - 211

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