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- PDB-7ldj: SARS-CoV-2 receptor binding domain in complex with WNb-2 -

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Basic information

Entry
Database: PDB / ID: 7ldj
TitleSARS-CoV-2 receptor binding domain in complex with WNb-2
Components
  • Nanobody 2Single-domain antibody
  • Spike glycoproteinSpike protein
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / Nanobody / Complex / SARS-CoV-2 / 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
alpha-D-mannopyranose / Spike glycoprotein
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
Vicugna pacos (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.36 Å
AuthorsPymm, P. / Dietrich, M.H. / Tan, L.L. / Adair, A. / Tham, W.H.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)GNT2002073 Australia
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2021
Title: SARS-CoV-2 receptor binding domain in complex with WNb-2
Authors: Pymm, P. / Adair, A. / Chan, L.J. / Cooney, J.P. / Mordant, F.L. / Allison, C.C. / Lopez, E. / Haycroft, E. / O'Neill, M.T. / Tan, L.L. / Dietrich, M.H. / Drew, D. / Doerflinger, M. / ...Authors: Pymm, P. / Adair, A. / Chan, L.J. / Cooney, J.P. / Mordant, F.L. / Allison, C.C. / Lopez, E. / Haycroft, E. / O'Neill, M.T. / Tan, L.L. / Dietrich, M.H. / Drew, D. / Doerflinger, M. / Dengler, M. / Scott, N.E. / Wheatley, A.K. / Gherardin, N.A. / Venugopal, H. / Cromer, D. / Davenport, M.P. / Pickering, R. / Godfrey, D.I. / Purcell, D.J. / Kent, S.J. / Chung, A.W. / Subbarao, K. / Pellegrini, M. / Glukhova, A. / Tham, W.H.
History
DepositionJan 13, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 5, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Spike glycoprotein
A: Spike glycoprotein
C: Spike glycoprotein
D: Spike glycoprotein
E: Nanobody 2
F: Nanobody 2
G: Nanobody 2
H: Nanobody 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,11714
Polymers145,9588
Non-polymers3,1596
Water2,954164
1
B: Spike glycoprotein
E: Nanobody 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4174
Polymers36,4902
Non-polymers9272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Spike glycoprotein
F: Nanobody 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7684
Polymers36,4902
Non-polymers1,2782
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Spike glycoprotein
G: Nanobody 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2223
Polymers36,4902
Non-polymers7331
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Spike glycoprotein
H: Nanobody 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7113
Polymers36,4902
Non-polymers2211
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.120, 88.508, 107.488
Angle α, β, γ (deg.)90.000, 90.400, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Antibody , 2 types, 8 molecules BACDEFGH

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


Mass: 22244.885 Da / Num. of mol.: 4 / Fragment: receptor binding domain (UNP residues 331-527)
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
Nanobody 2 / Single-domain antibody


Mass: 14244.712 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Homo sapiens (human)

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Sugars , 4 types, 5 molecules

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


Type: oligosaccharide / Mass: 732.682 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4[LFucpb1-6]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-1b_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)][b-L-Fucp]{}}LINUCSPDB-CARE
#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1098.016 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DManpa1-6DManpa1-4DGlcpNAcb1-4[LFucpb1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5][a1221m-1b_1-5]/1-1-2-2-1-3/a4-b1_a6-f1_b4-c1_c6-d1_d4-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{[(6+1)][a-D-Manp]{[(4+1)][b-D-GlcpNAc]{}}}}[(6+1)][b-L-Fucp]{}}LINUCSPDB-CARE
#5: Sugar ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose / Mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#6: 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.: 1 / Source method: isolated from a natural source / 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 , 2 types, 165 molecules

#7: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C8H18O5 / Comment: precipitant*YM
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 164 / 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: 2.38 Å3/Da / Density % sol: 48.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: PEG4000, potassium thiocyanate, sodium cacodylate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953732 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 10, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953732 Å / Relative weight: 1
ReflectionResolution: 2.36→45.94 Å / Num. obs: 56518 / % possible obs: 100 % / Redundancy: 7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.034 / Rrim(I) all: 0.091 / Net I/σ(I): 12.8 / Num. measured all: 398095
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
2.36-2.437.31.0523336946010.790.4181.1331.8100
10.01-45.946.90.03853277760.9990.0160.04140.898.9

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata reduction
Aimless0.5.23data scaling
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 5TP3 & 6W41

5tp3

6w41


Resolution: 2.36→45.937 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 31.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2681 2750 4.87 %
Rwork0.2103 53716 -
obs0.213 56466 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 158.92 Å2 / Biso mean: 59.2779 Å2 / Biso min: 29.85 Å2
Refinement stepCycle: final / Resolution: 2.36→45.937 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10021 0 205 164 10390
Biso mean--81.82 54.22 -
Num. residues----1287
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.36-2.40070.37131490.31252646
2.4007-2.44430.33021390.31322709
2.4443-2.49140.35821190.31382657
2.4914-2.54220.35931340.30012661
2.5422-2.59750.36821490.2872665
2.5975-2.65790.34251370.26742665
2.6579-2.72440.36331580.27182659
2.7244-2.7980.32221630.26862653
2.798-2.88030.30821470.25682656
2.8803-2.97330.34281580.25622662
2.9733-3.07950.2961160.25242692
3.0795-3.20280.29221280.2472703
3.2028-3.34850.34681250.23492702
3.3485-3.5250.28181310.23032678
3.525-3.74580.27061550.21222668
3.7458-4.03480.29291230.19862709
4.0348-4.44060.22421110.16352722
4.4406-5.08240.19131430.15562691
5.0824-6.40050.2141400.17712729
6.4005-45.9370.21151250.17982789

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