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- PDB-7x4i: Crystal structure of nanobody aSA3 in complex with dimer SARS-CoV... -

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Basic information

Entry
Database: PDB / ID: 7x4i
TitleCrystal structure of nanobody aSA3 in complex with dimer SARS-CoV-1 RBD
Components
  • Spike glycoprotein
  • nanobody aSA3
KeywordsANTIVIRAL PROTEIN / Nanobody / SARS-CoV-1 / RBD
Function / homology
Function and homology information


host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / 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 / host cell plasma membrane / virion membrane / membrane
Similarity search - Function
Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / 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 ...Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / 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
Biological speciesSevere acute respiratory syndrome coronavirus
Vicugna pacos (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.38 Å
AuthorsMa, H. / Zeng, W.H. / Jin, T.C.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31870731 China
National Natural Science Foundation of China (NSFC)32100745 China
CitationJournal: Cell Discov / Year: 2022
Title: A bispecific nanobody dimer broadly neutralizes SARS-CoV-1 & 2 variants of concern and offers substantial protection against Omicron via low-dose intranasal administration.
Authors: Ma, H. / Zhang, X. / Zeng, W. / Zhou, J. / Chi, X. / Chen, S. / Zheng, P. / Wang, M. / Wu, Y. / Zhao, D. / Gong, F. / Lin, H. / Sun, H. / Yu, C. / Shi, Z. / Hu, X. / Zhang, H. / Jin, T. / Chiu, S.
History
DepositionMar 2, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 11, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 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
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Spike glycoprotein
B: Spike glycoprotein
C: Spike glycoprotein
D: Spike glycoprotein
E: nanobody aSA3
F: nanobody aSA3
G: nanobody aSA3
H: nanobody aSA3


Theoretical massNumber of molelcules
Total (without water)145,5558
Polymers145,5558
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12660 Å2
ΔGint-30 kcal/mol
Surface area53890 Å2
Unit cell
Length a, b, c (Å)101.702, 112.006, 151.037
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 320:425 or resid 427:513))
21(chain B and (resid 320 or (resid 321 and (name...
31(chain C and (resid 320 or (resid 321 and (name...
41(chain D and (resid 320 or (resid 321 and (name...
12(chain E and (resid 1:24 or resid 26:31 or (resid...
22(chain F and (resid 1:24 or resid 26:31 or (resid...
32(chain G and (resid 1:24 or resid 26:31 or (resid...
42(chain H and (resid 1:24 or resid 26:38 or resid 40:114 or resid 116:121))

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111THRTHRTHRTHR(chain A and (resid 320:425 or resid 427:513))AA320 - 4251 - 106
121ASNASNPROPRO(chain A and (resid 320:425 or resid 427:513))AA427 - 513108 - 194
211THRTHRTHRTHR(chain B and (resid 320 or (resid 321 and (name...BB3201
221ASNASNASNASN(chain B and (resid 320 or (resid 321 and (name...BB3212
231THRTHRPROPRO(chain B and (resid 320 or (resid 321 and (name...BB320 - 5131 - 194
241THRTHRPROPRO(chain B and (resid 320 or (resid 321 and (name...BB320 - 5131 - 194
251THRTHRPROPRO(chain B and (resid 320 or (resid 321 and (name...BB320 - 5131 - 194
261THRTHRPROPRO(chain B and (resid 320 or (resid 321 and (name...BB320 - 5131 - 194
311THRTHRTHRTHR(chain C and (resid 320 or (resid 321 and (name...CC3201
321ASNASNASNASN(chain C and (resid 320 or (resid 321 and (name...CC3212
331THRTHRPROPRO(chain C and (resid 320 or (resid 321 and (name...CC320 - 5131 - 194
341THRTHRPROPRO(chain C and (resid 320 or (resid 321 and (name...CC320 - 5131 - 194
351THRTHRPROPRO(chain C and (resid 320 or (resid 321 and (name...CC320 - 5131 - 194
361THRTHRPROPRO(chain C and (resid 320 or (resid 321 and (name...CC320 - 5131 - 194
411THRTHRTHRTHR(chain D and (resid 320 or (resid 321 and (name...DD3201
421ASNASNASNASN(chain D and (resid 320 or (resid 321 and (name...DD3212
431THRTHRPROPRO(chain D and (resid 320 or (resid 321 and (name...DD320 - 5131 - 194
441THRTHRPROPRO(chain D and (resid 320 or (resid 321 and (name...DD320 - 5131 - 194
451THRTHRPROPRO(chain D and (resid 320 or (resid 321 and (name...DD320 - 5131 - 194
461THRTHRPROPRO(chain D and (resid 320 or (resid 321 and (name...DD320 - 5131 - 194
112GLNGLNALAALA(chain E and (resid 1:24 or resid 26:31 or (resid...EE1 - 241 - 24
122GLYGLYHISHIS(chain E and (resid 1:24 or resid 26:31 or (resid...EE26 - 3126 - 31
132TYRTYRALAALA(chain E and (resid 1:24 or resid 26:31 or (resid...EE32 - 3332 - 33
142GLNGLNSERSER(chain E and (resid 1:24 or resid 26:31 or (resid...EE1 - 1231 - 123
152GLNGLNSERSER(chain E and (resid 1:24 or resid 26:31 or (resid...EE1 - 1231 - 123
162GLNGLNSERSER(chain E and (resid 1:24 or resid 26:31 or (resid...EE1 - 1231 - 123
172GLNGLNSERSER(chain E and (resid 1:24 or resid 26:31 or (resid...EE1 - 1231 - 123
212GLNGLNALAALA(chain F and (resid 1:24 or resid 26:31 or (resid...FF1 - 241 - 24
222GLYGLYHISHIS(chain F and (resid 1:24 or resid 26:31 or (resid...FF26 - 3126 - 31
232TYRTYRALAALA(chain F and (resid 1:24 or resid 26:31 or (resid...FF32 - 3332 - 33
242GLNGLNSERSER(chain F and (resid 1:24 or resid 26:31 or (resid...FF1 - 1231 - 123
252GLNGLNSERSER(chain F and (resid 1:24 or resid 26:31 or (resid...FF1 - 1231 - 123
262GLNGLNSERSER(chain F and (resid 1:24 or resid 26:31 or (resid...FF1 - 1231 - 123
272GLNGLNSERSER(chain F and (resid 1:24 or resid 26:31 or (resid...FF1 - 1231 - 123
312GLNGLNALAALA(chain G and (resid 1:24 or resid 26:31 or (resid...GG1 - 241 - 24
322GLYGLYHISHIS(chain G and (resid 1:24 or resid 26:31 or (resid...GG26 - 3126 - 31
332TYRTYRALAALA(chain G and (resid 1:24 or resid 26:31 or (resid...GG32 - 3332 - 33
342GLNGLNSERSER(chain G and (resid 1:24 or resid 26:31 or (resid...GG1 - 1231 - 123
352GLNGLNSERSER(chain G and (resid 1:24 or resid 26:31 or (resid...GG1 - 1231 - 123
362GLNGLNSERSER(chain G and (resid 1:24 or resid 26:31 or (resid...GG1 - 1231 - 123
372GLNGLNSERSER(chain G and (resid 1:24 or resid 26:31 or (resid...GG1 - 1231 - 123
412GLNGLNALAALA(chain H and (resid 1:24 or resid 26:38 or resid 40:114 or resid 116:121))HH1 - 241 - 24
422GLYGLYARGARG(chain H and (resid 1:24 or resid 26:38 or resid 40:114 or resid 116:121))HH26 - 3826 - 38
432ALAALAGLYGLY(chain H and (resid 1:24 or resid 26:38 or resid 40:114 or resid 116:121))HH40 - 11440 - 114
442GLYGLYVALVAL(chain H and (resid 1:24 or resid 26:38 or resid 40:114 or resid 116:121))HH116 - 121116 - 121

NCS ensembles :
ID
1
2

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Components

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


Mass: 23006.984 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus
Plasmid: pTT5 / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: Q19QX0
#2: Antibody
nanobody aSA3


Mass: 13381.655 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Plasmid: pTT5 / Cell line (production host): HEK293F / Production host: Homo sapiens (human)
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: 2.96 Å3/Da / Density % sol: 58.38 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20%(v/v) PEG 400, 0.1 M Lithium chloride, 0.1 M HEPES pH 7.5

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Data collection

DiffractionMean temperature: 190 K / Ambient temp details: Liquid nitrogen steam / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97911 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 4, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97911 Å / Relative weight: 1
ReflectionResolution: 3.38→151.04 Å / Num. obs: 24667 / % possible obs: 99.5 % / Redundancy: 7.03 % / Biso Wilson estimate: 85.05 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.2 / Rrim(I) all: 0.263 / Net I/σ(I): 8.7
Reflection shellResolution: 3.38→3.56 Å / Redundancy: 7.47 % / Rmerge(I) obs: 1.334 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 3528 / CC1/2: 0.872 / Rpim(I) all: 0.516 / Rrim(I) all: 1.4 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIXdev_2481refinement
PDB_EXTRACT3.27data extraction
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7LM9, 70LZ

7lm9

70lz


Resolution: 3.38→75.519 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 37.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3209 1213 4.94 %
Rwork0.267 23325 -
obs0.2697 24538 99.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 157.28 Å2 / Biso mean: 100.6298 Å2 / Biso min: 69.49 Å2
Refinement stepCycle: final / Resolution: 3.38→75.519 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9747 0 0 0 9747
Num. residues----1245
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00510081
X-RAY DIFFRACTIONf_angle_d0.73113740
X-RAY DIFFRACTIONf_chiral_restr0.0471433
X-RAY DIFFRACTIONf_plane_restr0.0061785
X-RAY DIFFRACTIONf_dihedral_angle_d4.7596726
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3501X-RAY DIFFRACTION13.486TORSIONAL
12B3501X-RAY DIFFRACTION13.486TORSIONAL
13C3501X-RAY DIFFRACTION13.486TORSIONAL
14D3501X-RAY DIFFRACTION13.486TORSIONAL
21E2071X-RAY DIFFRACTION13.486TORSIONAL
22F2071X-RAY DIFFRACTION13.486TORSIONAL
23G2071X-RAY DIFFRACTION13.486TORSIONAL
24H2071X-RAY DIFFRACTION13.486TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.3804-3.51580.44541500.3748252599
3.5158-3.67580.37261330.3329254199
3.6758-3.86960.3341450.305255499
3.8696-4.1120.30311310.2692255899
4.112-4.42940.32541160.2525260099
4.4294-4.87510.34291240.2328259299
4.8751-5.58040.31671350.2448259199
5.5804-7.02990.31961390.2648263899
7.0299-75.5190.26491400.2485272698
Refinement TLS params.Method: refined / Origin x: 0.1381 Å / Origin y: 0.2249 Å / Origin z: -1.3622 Å
111213212223313233
T0.4785 Å20.0109 Å20.0091 Å2-0.6257 Å2-0.012 Å2--0.6501 Å2
L0.9885 °2-0.0322 °20.1396 °2-1.3874 °20.0295 °2--0.637 °2
S0.1321 Å °-0.0094 Å °0.0293 Å °-0.0404 Å °-0.0725 Å °-0.1557 Å °0.1258 Å °0.1041 Å °-0.0589 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA320 - 513
2X-RAY DIFFRACTION1allB320 - 513
3X-RAY DIFFRACTION1allC320 - 513
4X-RAY DIFFRACTION1allD320 - 513
5X-RAY DIFFRACTION1allE1 - 123
6X-RAY DIFFRACTION1allF1 - 123
7X-RAY DIFFRACTION1allG1 - 123
8X-RAY DIFFRACTION1allH1 - 121

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