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- PDB-7f5h: The crystal structure of RBD-Nanobody complex, DL28 (SC4) -

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Basic information

Entry
Database: PDB / ID: 7f5h
TitleThe crystal structure of RBD-Nanobody complex, DL28 (SC4)
Components
  • Nanobody DL28
  • SARS-CoV-2 Spike Receptor-Binding Domain (RBD)
KeywordsVIRAL PROTEIN / Nanobody / RBD / neutralizing antibody / SARS-CoV-2 / receptor-binding domain / receptor-binding motif / RBM distortion
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
PHOSPHATE ION / Spike glycoprotein
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
Vicugna pacos (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsLuo, Z.P. / Li, 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: Front Microbiol / Year: 2022
Title: Structural Characterization of a Neutralizing Nanobody With Broad Activity Against SARS-CoV-2 Variants.
Authors: Li, T. / Zhou, B. / Luo, Z. / Lai, Y. / Huang, S. / Zhou, Y. / Li, 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 1.0Jun 29, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 11, 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 ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SARS-CoV-2 Spike Receptor-Binding Domain (RBD)
B: SARS-CoV-2 Spike Receptor-Binding Domain (RBD)
C: Nanobody DL28
D: Nanobody DL28
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,47611
Polymers78,5474
Non-polymers1,9297
Water37821
1
A: SARS-CoV-2 Spike Receptor-Binding Domain (RBD)
C: Nanobody DL28
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,1905
Polymers39,2732
Non-polymers9173
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3320 Å2
ΔGint6 kcal/mol
Surface area14950 Å2
MethodPISA
2
B: SARS-CoV-2 Spike Receptor-Binding Domain (RBD)
D: Nanobody DL28
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2856
Polymers39,2732
Non-polymers1,0124
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3210 Å2
ΔGint6 kcal/mol
Surface area16060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)177.463, 177.463, 133.130
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11B-602-

PO4

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASNASNPROPROAA334 - 5278 - 201
21ASNASNPROPROBB334 - 5278 - 201
12GLNGLNSERSERCC1 - 1135 - 117
22GLNGLNSERSERDD1 - 1135 - 117

NCS ensembles :
ID
1
2

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Components

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

#1: Protein SARS-CoV-2 Spike Receptor-Binding Domain (RBD) / 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 DL28


Mass: 15525.795 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 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-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[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1221m-1a_1-5]/1-1-2-3/a4-b1_a6-d1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE

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Non-polymers , 3 types, 26 molecules

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


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / 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: 3.85 Å3/Da / Density % sol: 68.07 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Potassium phosphate dibasic, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 31, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 25343 / % possible obs: 100 % / Redundancy: 9.2 % / CC1/2: 0.99 / CC star: 0.997 / Rmerge(I) obs: 0.174 / Rpim(I) all: 0.057 / Rrim(I) all: 0.184 / Net I/σ(I): 14.1
Reflection shellResolution: 3→3.11 Å / Redundancy: 9.7 % / Rmerge(I) obs: 1.565 / Mean I/σ(I) obs: 1.35 / Num. unique obs: 2472 / CC1/2: 0.569 / CC star: 0.852 / Rpim(I) all: 0.509 / Rrim(I) all: 1.652 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6M0J, 5M13

6m0j

5m13


Resolution: 3→47.81 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.903 / SU B: 17.886 / SU ML: 0.293 / Cross valid method: THROUGHOUT / ESU R: 0.785 / ESU R Free: 0.346 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2476 1307 5.2 %RANDOM
Rwork0.22643 ---
obs0.22751 24003 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 90.627 Å2
Baniso -1Baniso -2Baniso -3
1-1.26 Å20.63 Å20 Å2
2--1.26 Å20 Å2
3----4.08 Å2
Refinement stepCycle: 1 / Resolution: 3→47.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4878 0 127 21 5026
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0135140
X-RAY DIFFRACTIONr_bond_other_d0.0030.0184571
X-RAY DIFFRACTIONr_angle_refined_deg1.5821.6726975
X-RAY DIFFRACTIONr_angle_other_deg1.571.60510497
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0565622
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.71522.246276
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.00315749
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1641531
X-RAY DIFFRACTIONr_chiral_restr0.0810.2652
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025913
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021311
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it7.9699.3472500
X-RAY DIFFRACTIONr_mcbond_other7.9469.3462499
X-RAY DIFFRACTIONr_mcangle_it12.121143118
X-RAY DIFFRACTIONr_mcangle_other12.12314.0023119
X-RAY DIFFRACTIONr_scbond_it8.44310.0992640
X-RAY DIFFRACTIONr_scbond_other8.44210.0992641
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other12.93314.9183858
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A53240.2
12B53240.2
21C30860.18
22D30860.18
LS refinement shellResolution: 3→3.074 Å
RfactorNum. reflection% reflection
Rfree0.426 103 -
Rwork0.374 1689 -
obs--97.76 %

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