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- PDB-7wqv: Crystal structure of a neutralizing monoclonal antibody (Ab08) in... -

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Basic information

Entry
Database: PDB / ID: 7wqv
TitleCrystal structure of a neutralizing monoclonal antibody (Ab08) in complex with SARS-CoV-2 receptor-binding domain (RBD)
Components
  • Ab08
  • Spike protein S1
KeywordsVIRAL PROTEIN / Ab08 / mAb / Coronavirus / Covid-19 / Monoclonal antibody / nAb / Neutralizing antibody / RBD / Receptor-binding domain / SARS-CoV-2
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 / 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: 2.8 Å
AuthorsZha, J. / Meng, L. / Zhang, X. / Li, D.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82151215 China
National Natural Science Foundation of China (NSFC)31870726 China
CitationJournal: Plos Pathog. / Year: 2023
Title: A Spike-destructing human antibody effectively neutralizes Omicron-included SARS-CoV-2 variants with therapeutic efficacy.
Authors: Meng, L. / Zha, J. / Zhou, B. / Cao, L. / Jiang, C. / Zhu, Y. / Li, T. / Lu, L. / Zhang, J. / Yang, H. / Feng, J. / Gu, Z. / Tang, H. / Jiang, L. / Li, D. / Lavillette, D. / Zhang, X.
History
DepositionJan 26, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 25, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 9, 2023Group: 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
Revision 1.2Nov 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
B: Ab08
C: Spike protein S1
D: Ab08
E: Spike protein S1
F: Ab08
G: Spike protein S1
H: Ab08
I: Spike protein S1
J: Ab08
K: Spike protein S1
L: Ab08
M: Spike protein S1
N: Ab08
O: Spike protein S1
P: Ab08
hetero molecules


Theoretical massNumber of molelcules
Total (without water)463,81440
Polymers460,65816
Non-polymers3,15624
Water37821
1
A: Spike protein S1
B: Ab08
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,3808
Polymers57,5822
Non-polymers7976
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3820 Å2
ΔGint-36 kcal/mol
Surface area18970 Å2
MethodPISA
2
C: Spike protein S1
D: Ab08
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,9625
Polymers57,5822
Non-polymers3793
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2750 Å2
ΔGint-11 kcal/mol
Surface area18870 Å2
MethodPISA
3
E: Spike protein S1
F: Ab08
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,9904
Polymers57,5822
Non-polymers4072
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2900 Å2
ΔGint-2 kcal/mol
Surface area19080 Å2
MethodPISA
4
G: Spike protein S1
H: Ab08
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,1035
Polymers57,5822
Non-polymers5213
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3150 Å2
ΔGint-13 kcal/mol
Surface area19230 Å2
MethodPISA
5
I: Spike protein S1
J: Ab08
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,0556
Polymers57,5822
Non-polymers4734
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3220 Å2
ΔGint-32 kcal/mol
Surface area18820 Å2
MethodPISA
6
K: Spike protein S1
L: Ab08
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,6223
Polymers57,5822
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2500 Å2
ΔGint-12 kcal/mol
Surface area18570 Å2
MethodPISA
7
M: Spike protein S1
N: Ab08
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,6223
Polymers57,5822
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2460 Å2
ΔGint-14 kcal/mol
Surface area18560 Å2
MethodPISA
8
O: Spike protein S1
P: Ab08
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,0806
Polymers57,5822
Non-polymers4984
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3220 Å2
ΔGint-18 kcal/mol
Surface area18910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.643, 116.742, 180.720
Angle α, β, γ (deg.)90.000, 90.307, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein / Antibody , 2 types, 16 molecules ACEGIKMOBDFHJLNP

#1: Protein
Spike protein S1


Mass: 26214.709 Da / Num. of mol.: 8 / Fragment: RBD
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: S, 2 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P0DTC2
#2: Antibody
Ab08


Mass: 31367.570 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Details: fusion protein of a pelB signal peptide (SKYLLPTAAAGLLLLAAQPAMA), a linker (GSSS), the variable domain of heavy chain (1-128), a GS linker (15 amino acids), the variable domain of light ...Details: fusion protein of a pelB signal peptide (SKYLLPTAAAGLLLLAAQPAMA), a linker (GSSS), the variable domain of heavy chain (1-128), a GS linker (15 amino acids), the variable domain of light chain (numbered 1001-1110), Myc and hexahistidine tag
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli MC1061 (bacteria)

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Sugars , 3 types, 5 molecules

#3: Polysaccharide alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 2 / Source method: obtained synthetically
DescriptorTypeProgram
LFucpa1-6DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#4: Polysaccharide alpha-L-fucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
LFucpa1-3DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(3+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#8: 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / 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 , 4 types, 40 molecules

#5: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#7: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 2.21 Å3/Da / Density % sol: 44.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Magnesium chloride hexahydrate, calcium chloride dihydrate, sodium HEPES, MOPS (acid), MPD, PEG 1000, PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 3, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.8→49.39 Å / Num. obs: 94140 / % possible obs: 99.3 % / Redundancy: 6.9 % / Biso Wilson estimate: 48.27 Å2 / Rmerge(I) obs: 0.161 / Rpim(I) all: 0.071 / Net I/σ(I): 9.4
Reflection shellResolution: 2.8→2.85 Å / Rmerge(I) obs: 0.945 / Num. unique obs: 9381

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7CYV

7cyv


Resolution: 2.8→44.93 Å / SU ML: 0.3522 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.7844
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.251 4716 5.01 %
Rwork0.2198 89357 -
obs0.2213 94073 99.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 56.4 Å2
Refinement stepCycle: LAST / Resolution: 2.8→44.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26369 0 196 21 26586
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002427218
X-RAY DIFFRACTIONf_angle_d0.543537033
X-RAY DIFFRACTIONf_chiral_restr0.04474004
X-RAY DIFFRACTIONf_plane_restr0.00374781
X-RAY DIFFRACTIONf_dihedral_angle_d15.50059496
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.830.36851660.31882935X-RAY DIFFRACTION97.92
2.83-2.870.32261680.29652960X-RAY DIFFRACTION99.4
2.87-2.90.39561480.28022992X-RAY DIFFRACTION99.59
2.9-2.940.2991720.28212924X-RAY DIFFRACTION99.68
2.94-2.980.36411670.27733009X-RAY DIFFRACTION99.5
2.98-3.020.28771380.27712965X-RAY DIFFRACTION99.46
3.02-3.060.30481950.2712923X-RAY DIFFRACTION99.27
3.06-3.10.31221470.26733019X-RAY DIFFRACTION99.28
3.1-3.150.28781190.26532961X-RAY DIFFRACTION99.23
3.15-3.210.31751670.26112985X-RAY DIFFRACTION99.46
3.21-3.260.29291720.26082978X-RAY DIFFRACTION99.56
3.26-3.320.3041900.24272961X-RAY DIFFRACTION99.43
3.32-3.380.29431630.2412912X-RAY DIFFRACTION99.13
3.38-3.450.28711520.24172943X-RAY DIFFRACTION97.27
3.45-3.530.27281590.23932947X-RAY DIFFRACTION98.85
3.53-3.610.23671560.23012969X-RAY DIFFRACTION99.52
3.61-3.70.2811480.22263026X-RAY DIFFRACTION99.5
3.7-3.80.26251510.2222954X-RAY DIFFRACTION99.52
3.8-3.910.25761310.21453055X-RAY DIFFRACTION99.53
3.91-4.040.22371600.20192994X-RAY DIFFRACTION99.53
4.04-4.180.19781580.18382968X-RAY DIFFRACTION99.55
4.18-4.350.1971540.17222975X-RAY DIFFRACTION99.3
4.35-4.550.17521470.16672954X-RAY DIFFRACTION97.98
4.55-4.790.18971200.16483034X-RAY DIFFRACTION99.34
4.79-5.090.20821280.17253051X-RAY DIFFRACTION99.81
5.09-5.480.22161810.18012987X-RAY DIFFRACTION99.47
5.48-6.030.25441620.2112988X-RAY DIFFRACTION99.4
6.03-6.90.23991740.2322939X-RAY DIFFRACTION97.65
6.9-8.680.23131670.22073033X-RAY DIFFRACTION99.63
8.68-44.930.22331560.23643016X-RAY DIFFRACTION96.85
Refinement TLS params.Method: refined / Origin x: 75.530723901 Å / Origin y: 75.3725651428 Å / Origin z: 136.164682058 Å
111213212223313233
T0.194583492404 Å20.00677324032783 Å2-0.00316308890049 Å2-0.221368187607 Å2-0.00320751977239 Å2--0.222847362106 Å2
L-0.0398160215465 °20.0161915904928 °2-0.00801003424961 °2-0.0186084631416 °2-0.00887453573958 °2--0.087332713135 °2
S0.0192599070114 Å °-0.0102849288311 Å °0.00631578247642 Å °-0.00323560680636 Å °0.00714457764102 Å °0.000794706380352 Å °-0.00260486233182 Å °-0.0168885984232 Å °7.82758798245E-7 Å °
Refinement TLS groupSelection details: all

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