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- PDB-7d30: Structure of sybody MR17-SR31 fusion in complex with the SARS-CoV... -

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Basic information

Entry
Database: PDB / ID: 7d30
TitleStructure of sybody MR17-SR31 fusion in complex with the SARS-CoV-2 S Receptor Binding domain (RBD)
Components
  • Spike protein S1
  • sybody fusion of MR17-SR31 with a GS linker
KeywordsPROTEIN BINDING / coronavirus / Covid-19 / nanobody / neutralizing antibody / receptor binding protein / SARS-CoV-2 / S protein / synthetic antibody / VHH.
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 / entry receptor-mediated virion attachment to host cell ...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 / entry receptor-mediated virion attachment to host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated endocytosis of virus by host cell / membrane fusion / Attachment and Entry / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / host cell surface receptor binding / symbiont-mediated suppression of host innate immune response / 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 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / 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 S1 subunit, receptor binding domain superfamily, 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, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / 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 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 1 (HR1) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2
Similarity search - Domain/homology
ACETATE ION / 1,3-BUTANEDIOL / : / Spike glycoprotein
Similarity search - Component
Biological speciessynthetic construct (others)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsLi, T. / Yao, H. / Cai, H. / Qin, W. / Li, D.
Funding support China, 2items
OrganizationGrant numberCountry
Chinese Academy of SciencesQYZDB-SSW-SMC037, XDB37020204 China
National Science Foundation (NSF, China)31870726 China
CitationJournal: Plos Pathog. / Year: 2021
Title: A high-affinity RBD-targeting nanobody improves fusion partner's potency against SARS-CoV-2.
Authors: Yao, H. / Cai, H. / Li, T. / Zhou, B. / Qin, W. / Lavillette, D. / Li, D.
History
DepositionSep 17, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 17, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 1, 2021Group: Database references / Category: citation / citation_author / database_2
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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: sybody fusion of MR17-SR31 with a GS linker
B: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,13446
Polymers54,9682
Non-polymers5,16644
Water3,945219
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.384, 73.384, 478.363
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Space group name HallP652(x,y,z+1/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z+1/2
#9: y,x,-z+2/3
#10: -y,-x,-z+1/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+5/6

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Components

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Antibody / Protein / Sugars , 3 types, 3 molecules AB

#1: Antibody sybody fusion of MR17-SR31 with a GS linker


Mass: 31220.143 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Protein Spike protein S1 / S glycoprotein / E2 / Peplomer protein


Mass: 23747.643 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 / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P0DTC2
#3: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1040.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4[LFucpa1-3][LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5][a1122h-1b_1-5][a1122h-1a_1-5]/1-2-1-3-4-2/a3-b1_a4-c1_a6-f1_c4-d1_d3-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE

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Non-polymers , 6 types, 262 molecules

#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#7: Chemical
ChemComp-BU2 / 1,3-BUTANEDIOL


Mass: 90.121 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O2 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 17
Source method: isolated from a genetically manipulated source
Formula: Cd
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 219 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.38 Å3/Da / Density % sol: 68.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.1M cadmium chloride, 30% (v/v) PEG 400, 4%(v/v) 1,3-butanediol, 0.1M sodium acetate pH 4.5
Temp details: in a Rockmaker Imager with temp. control

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97854 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 17, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97854 Å / Relative weight: 1
ReflectionResolution: 2.1→49.7 Å / Num. obs: 46317 / % possible obs: 99.7 % / Redundancy: 18.6 % / Biso Wilson estimate: 42.37 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.14 / Rpim(I) all: 0.034 / Net I/σ(I): 12.6
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 14.5 % / Rmerge(I) obs: 1.409 / Mean I/σ(I) obs: 2 / Num. unique obs: 3572 / CC1/2: 0.872 / Rpim(I) all: 0.373 / % possible all: 96.6

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6M0J, 5m13

6m0j

5m13


Resolution: 2.1→49.7 Å / SU ML: 0.242 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.4641
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2359 4611 10.01 %
Rwork0.1949 41466 -
obs0.1991 46077 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.52 Å2
Refinement stepCycle: LAST / Resolution: 2.1→49.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3366 0 235 220 3821
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00773723
X-RAY DIFFRACTIONf_angle_d0.82445025
X-RAY DIFFRACTIONf_chiral_restr0.0501545
X-RAY DIFFRACTIONf_plane_restr0.0049643
X-RAY DIFFRACTIONf_dihedral_angle_d22.2915604
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.120.32561320.29611242X-RAY DIFFRACTION93.03
2.12-2.150.36751620.29271302X-RAY DIFFRACTION97.15
2.15-2.180.33841420.26221327X-RAY DIFFRACTION97.93
2.18-2.20.29541460.24751335X-RAY DIFFRACTION98.41
2.2-2.230.31551730.2341346X-RAY DIFFRACTION98.89
2.23-2.260.27191540.22611297X-RAY DIFFRACTION99.66
2.26-2.290.27641540.22961390X-RAY DIFFRACTION99.55
2.29-2.330.29951420.21791318X-RAY DIFFRACTION99.52
2.33-2.370.28871610.21821388X-RAY DIFFRACTION99.87
2.37-2.40.26321570.20121313X-RAY DIFFRACTION100
2.4-2.450.25181560.22051405X-RAY DIFFRACTION99.81
2.45-2.490.25431390.20711344X-RAY DIFFRACTION99.87
2.49-2.540.31681450.19861369X-RAY DIFFRACTION99.8
2.54-2.590.2661510.20391366X-RAY DIFFRACTION99.8
2.59-2.650.27431530.20631379X-RAY DIFFRACTION99.87
2.65-2.710.23161460.1981373X-RAY DIFFRACTION99.87
2.71-2.780.25061440.20551367X-RAY DIFFRACTION99.67
2.78-2.850.271470.2141379X-RAY DIFFRACTION99.93
2.85-2.930.26781570.21441397X-RAY DIFFRACTION100
2.93-3.030.25391430.20561393X-RAY DIFFRACTION99.93
3.03-3.140.27821400.20821374X-RAY DIFFRACTION99.93
3.14-3.260.24351780.20171372X-RAY DIFFRACTION99.94
3.26-3.410.25871650.18931393X-RAY DIFFRACTION100
3.41-3.590.21631390.18591421X-RAY DIFFRACTION100
3.59-3.820.22821440.17741437X-RAY DIFFRACTION99.94
3.82-4.110.19571500.16381437X-RAY DIFFRACTION100
4.11-4.520.17821520.15021440X-RAY DIFFRACTION100
4.52-5.180.18471840.15541431X-RAY DIFFRACTION100
5.18-6.520.22131690.20261494X-RAY DIFFRACTION100
6.52-49.70.24941860.22871637X-RAY DIFFRACTION99.62

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