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- PDB-7f5g: The crystal structure of RBD-Nanobody complex, DL4 (SA4) -

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Basic information

Entry
Database: PDB / ID: 7f5g
TitleThe crystal structure of RBD-Nanobody complex, DL4 (SA4)
Components
  • Nanobody DL4
  • Spike glycoprotein
KeywordsVIRAL PROTEIN / Nanobody / RBD / neutralizing antibody / 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 / symbiont-mediated-mediated suppression 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 / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell / membrane fusion / Attachment and Entry / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / host cell surface receptor binding / symbiont-mediated suppression of host innate immune response / receptor ligand activity / endocytosis involved in viral entry into host cell / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / Spike glycoprotein
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
Vicugna pacos (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsLi, T. / Lai, Y. / Zhou, Y. / Tan, J. / Li, D.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31870726 China
CitationJournal: Int.J.Biol.Macromol. / Year: 2022
Title: Isolation, characterization, and structure-based engineering of a neutralizing nanobody against SARS-CoV-2.
Authors: Li, T. / Zhou, B. / Li, Y. / Huang, S. / Luo, Z. / Zhou, Y. / Lai, Y. / Gautam, A. / Bourgeau, S. / Wang, S. / Bao, J. / Tan, J. / Lavillette, D. / Li, D.
History
DepositionJun 22, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 25, 2022Provider: repository / Type: Initial release
Revision 2.0Jun 1, 2022Group: Atomic model / Data collection / Derived calculations
Category: atom_site / pdbx_nonpoly_scheme ...atom_site / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.value
Revision 2.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.2Nov 20, 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: Spike glycoprotein
B: Nanobody DL4
C: Spike glycoprotein
D: Nanobody DL4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,33332
Polymers79,8694
Non-polymers3,46428
Water11,043613
1
A: Spike glycoprotein
B: Nanobody DL4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,86019
Polymers39,9342
Non-polymers1,92617
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6070 Å2
ΔGint2 kcal/mol
Surface area15100 Å2
MethodPISA
2
C: Spike glycoprotein
D: Nanobody DL4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,47313
Polymers39,9342
Non-polymers1,53811
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5110 Å2
ΔGint4 kcal/mol
Surface area15640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.818, 95.040, 118.915
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2

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Components

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Protein / Antibody / Sugars , 3 types, 6 molecules ACBD

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


Mass: 23747.643 Da / Num. of mol.: 2 / 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 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P0DTC2
#2: Antibody Nanobody DL4


Mass: 16186.630 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli)
#3: Polysaccharide alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)][alpha-L-fucopyranose-(1- ...alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 716.682 Da / Num. of mol.: 2 / Source method: obtained synthetically
DescriptorTypeProgram
LFucpa1-3[DGlcpNAcb1-4][LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2-1-2/a3-b1_a4-c1_a6-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE

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Non-polymers , 3 types, 639 molecules

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


Mass: 92.094 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 613 / 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: 2.83 Å3/Da / Density % sol: 60.89 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Ammonium sulfate, 0.1 M Sodium acetate trihydrate pH 4.6 and 25% w/v Polyethylene glycol 4,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 28, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.75→36.58 Å / Num. obs: 91752 / % possible obs: 100 % / Redundancy: 12.8 % / Biso Wilson estimate: 20 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.033 / Rrim(I) all: 0.117 / Net I/σ(I): 14
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 11.9 % / Rmerge(I) obs: 1.183 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4455 / CC1/2: 0.898 / Rpim(I) all: 0.522 / Rrim(I) all: 1.288 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6M0J, 5M13

6m0j

5m13


Resolution: 1.75→36.58 Å / SU ML: 0.1796 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.2857
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2172 4580 5.01 %
Rwork0.1879 86921 -
obs0.1894 91501 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.19 Å2
Refinement stepCycle: LAST / Resolution: 1.75→36.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4971 0 230 613 5814
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00715483
X-RAY DIFFRACTIONf_angle_d0.87437435
X-RAY DIFFRACTIONf_chiral_restr0.0568783
X-RAY DIFFRACTIONf_plane_restr0.0049975
X-RAY DIFFRACTIONf_dihedral_angle_d22.0551838
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.770.31031430.28162850X-RAY DIFFRACTION99.87
1.77-1.790.29951570.26922853X-RAY DIFFRACTION99.54
1.79-1.810.2911610.25182834X-RAY DIFFRACTION99.3
1.81-1.840.25751490.23682836X-RAY DIFFRACTION99.27
1.84-1.860.28381660.22742886X-RAY DIFFRACTION99.84
1.86-1.890.24941380.21792865X-RAY DIFFRACTION99.87
1.89-1.910.28191410.22552877X-RAY DIFFRACTION99.83
1.91-1.940.25151820.21242821X-RAY DIFFRACTION99.6
1.94-1.970.24321480.20282875X-RAY DIFFRACTION99.77
1.97-20.28281500.20072877X-RAY DIFFRACTION99.57
2-2.040.24941370.18872858X-RAY DIFFRACTION99.67
2.04-2.070.24731510.19212896X-RAY DIFFRACTION99.87
2.07-2.110.25351690.18942858X-RAY DIFFRACTION99.9
2.11-2.160.19911500.18682893X-RAY DIFFRACTION99.93
2.16-2.20.21131350.18712896X-RAY DIFFRACTION99.77
2.2-2.260.22861530.19532870X-RAY DIFFRACTION99.87
2.26-2.310.23171320.19472918X-RAY DIFFRACTION99.84
2.31-2.370.23361730.19342856X-RAY DIFFRACTION99.7
2.38-2.440.23711500.19462877X-RAY DIFFRACTION99.84
2.44-2.520.23911460.19522912X-RAY DIFFRACTION99.74
2.52-2.610.21231540.18662881X-RAY DIFFRACTION99.9
2.61-2.720.2311700.19052902X-RAY DIFFRACTION99.9
2.72-2.840.22081540.19042897X-RAY DIFFRACTION99.87
2.84-2.990.21861360.18232947X-RAY DIFFRACTION100
2.99-3.180.20711640.18062934X-RAY DIFFRACTION99.94
3.18-3.420.18641500.18282906X-RAY DIFFRACTION100
3.42-3.770.20361500.17162964X-RAY DIFFRACTION99.97
3.77-4.310.18451430.15652988X-RAY DIFFRACTION99.97
4.31-5.430.17371700.15382975X-RAY DIFFRACTION99.9
5.43-36.580.19241580.20493119X-RAY DIFFRACTION99.33

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