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- PDB-7kgj: Crystal structure of synthetic nanobody (Sb45) complexes with SAR... -

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Basic information

Entry
Database: PDB / ID: 7kgj
TitleCrystal structure of synthetic nanobody (Sb45) complexes with SARS-CoV-2 receptor binding domain
Components
  • Sb45, Sybody-45, Synthetic Nanobody
  • Spike glycoprotein
KeywordsVIRAL PROTEIN / SARS-CoV-2 / Spike Protein / RBD / Antibody / Nanobody / Sybody / epitopes / neutralization
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 / 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
Biological speciesSevere acute respiratory syndrome coronavirus 2
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsJiang, J. / Ahmad, J. / Natarajan, K. / Boyd, L.F. / Margulies, D.H.
Citation
Journal: J Biol Chem / Year: 2021
Title: Structures of synthetic nanobody-SARS-CoV-2 receptor-binding domain complexes reveal distinct sites of interaction.
Authors: Javeed Ahmad / Jiansheng Jiang / Lisa F Boyd / Allison Zeher / Rick Huang / Di Xia / Kannan Natarajan / David H Margulies /
Abstract: Combating the worldwide spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the emergence of new variants demands understanding of the structural basis of the interaction of ...Combating the worldwide spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the emergence of new variants demands understanding of the structural basis of the interaction of antibodies with the SARS-CoV-2 receptor-binding domain (RBD). Here, we report five X-ray crystal structures of sybodies (synthetic nanobodies) including those of binary and ternary complexes of Sb16-RBD, Sb45-RBD, Sb14-RBD-Sb68, and Sb45-RBD-Sb68, as well as unliganded Sb16. These structures reveal that Sb14, Sb16, and Sb45 bind the RBD at the angiotensin-converting enzyme 2 interface and that the Sb16 interaction is accompanied by a large conformational adjustment of complementarity-determining region 2. In contrast, Sb68 interacts at the periphery of the SARS-CoV-2 RBD-angiotensin-converting enzyme 2 interface. We also determined cryo-EM structures of Sb45 bound to the SARS-CoV-2 spike protein. Superposition of the X-ray structures of sybodies onto the trimeric spike protein cryo-EM map indicates that some sybodies may bind in both "up" and "down" configurations, but others may not. Differences in sybody recognition of several recently identified RBD variants are explained by these structures.
#1: Journal: Biorxiv / Year: 2021
Title: Synthetic nanobody-SARS-CoV-2 receptor-binding domain structures identify distinct epitopes.
Authors: Ahmad, J. / Jiang, J. / Boyd, L.F. / Natarajan, K. / Margulies, D.H.
History
DepositionOct 16, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 10, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Sep 29, 2021Group: Advisory / Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_unobs_or_zero_occ_atoms / struct
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct.title
Revision 1.3Oct 20, 2021Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.4Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / pdbx_initial_refinement_model
Item: _citation.journal_id_ISSN

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Spike glycoprotein
B: Sb45, Sybody-45, Synthetic Nanobody


Theoretical massNumber of molelcules
Total (without water)35,5772
Polymers35,5772
Non-polymers00
Water2,540141
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1950 Å2
ΔGint-5 kcal/mol
Surface area14650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.552, 62.552, 168.815
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

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Components

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


Mass: 22002.676 Da / Num. of mol.: 1 / Fragment: receptor binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: S, 2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0DTC2
#2: Antibody Sb45, Sybody-45, Synthetic Nanobody


Mass: 13574.048 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Plasmid: pET21b / Production host: Escherichia coli MC1061 (bacteria)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / Source method: isolated from a natural source / Formula: H2O

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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: 2.69 Å3/Da / Density % sol: 54.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 12% PEG 8000, 0.1M Hepes pH 7.5, 0.2M NaCl / PH range: 5.5 -7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 19, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→45.59 Å / Num. obs: 17592 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.9 % / Biso Wilson estimate: 26.94 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.038 / Net I/σ(I): 14.9
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.849 / Mean I/σ(I) obs: 3.4 / Num. unique obs: 1687 / CC1/2: 0.919 / Rpim(I) all: 0.293 / % possible all: 98.3

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PHENIX1.18.2_3874refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7BZ5

7bz5


Resolution: 2.3→45.59 Å / SU ML: 0.1956 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.7864
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2163 879 5 %
Rwork0.1859 16713 -
obs0.1874 17592 99.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.94 Å2
Refinement stepCycle: LAST / Resolution: 2.3→45.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2500 0 0 141 2641
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00512567
X-RAY DIFFRACTIONf_angle_d0.743490
X-RAY DIFFRACTIONf_chiral_restr0.0483363
X-RAY DIFFRACTIONf_plane_restr0.0044457
X-RAY DIFFRACTIONf_dihedral_angle_d21.737908
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.450.28871420.22562695X-RAY DIFFRACTION98.4
2.45-2.630.23871430.20712727X-RAY DIFFRACTION99.1
2.63-2.90.24831450.20392743X-RAY DIFFRACTION99.28
2.9-3.320.22591460.18762777X-RAY DIFFRACTION99.73
3.32-4.180.19281480.17332825X-RAY DIFFRACTION99.46
4.18-45.590.19281550.17122946X-RAY DIFFRACTION99.58
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.83279528457-0.8815064529951.102069847052.4587590963-0.629047296071.44740163251-0.215794246272-0.1351381654570.241756267774-0.02639702938130.1672341675850.465653639691-0.402561307393-0.4457729159570.04375135599060.2439452778240.0784573333293-0.04327460588440.284862203405-0.01699106008730.28128415236116.8363103619-3.59044108559-15.5134088439
21.94641654633-1.294714353311.044783065964.05794618147-2.459056317573.61446231801-0.002819283154-0.0636328228559-0.123505438427-0.0360487913851-0.0788286264232-0.07398410587660.1235701708820.1211634726430.07456862952610.1490438315360.07341519871940.01205068957420.2440585761980.006102057803360.14307602311229.556341178-15.4938570626-6.79952732651
34.583382084683.161128633941.446351817488.292609030096.355290578888.143809664060.147964265444-0.219054939548-0.620190511375-0.757593735307-0.07718683716541.480891908960.405972988371-1.40858152262-0.08700570296490.340801687082-0.0787447888247-0.12149961230.494636189722-0.007755158035940.5727510594734.82181126919-9.0444757193-23.291342614
45.146051340710.510408244701-0.7232406647127.9700023924-4.565625969612.650805316310.2192363937430.4647014573270.53390654763-0.0325475650543-0.0352499266756-0.982638453019-0.4788440790390.919742174297-0.1653392654250.309531160692-0.02154758811950.01385449989760.4472871074780.04013107820110.3582263851646.6339173212-12.069055591615.4022235195
57.266793146251.14278999082-2.780926947398.3998383857-1.167531521251.13409679841-0.101270135405-0.650615207993-0.3046033518250.6651296942550.467945608288-0.04674678650170.100943286541-0.939162697269-0.2951214089390.294505747344-0.0712623292454-0.05022404891240.3440941108810.06566163253080.15020563363443.1044854817-25.913394200933.4275573384
62.64913653077-0.1417928377921.479393243443.53310590327-1.110856530544.36045852688-0.00883096744220.5737275888270.2710463857760.0821409685361-0.208277579980.00659833029406-0.520314569421-0.126763131560.1691354560470.2736568711740.107373808868-0.006318931856410.2780697918650.05873654697550.20128465506638.3058178892-12.965800675715.6397964326
77.74430567645-0.2755635675372.764579144641.59994027618-0.4700389225783.163150744310.2142078391490.271368836091-0.448054283581-0.203618562852-0.210046667248-0.1679848087180.3490965867820.713517561154-0.003877607819180.145119445380.05411992496040.0238886955960.4161489834970.03913895075680.1684213052841.9587971568-26.1385462314.7210310611
84.013655831940.2302141786530.1211640026355.14390732198-0.9615504755794.638681230030.160932843756-0.2742406649610.04777508361020.103586952829-0.164130531323-0.000328558869798-0.0751422836982-0.772238044368-0.0001614172099370.1486287122240.003422221347720.003402890466780.32135560324-0.004579952294230.11860892675331.4148022807-24.113787839517.5580056547
92.962082282141.61651577359-0.5896938433328.27306845314-4.541442351359.65928130155-0.22000330175-0.06302653537620.279213528390.331476705658-0.4876550959610.156913942505-1.14052006638-0.181611537870.6678953169230.2607703857540.0288653092679-0.1148374894660.282929457215-0.01462732558350.25371016233836.1770052297-13.747325297921.3297923968
103.48447843898-0.5188868363891.389690315442.26813165633-0.9541789163627.454806580540.1334945678230.1470454862740.0607287187718-0.0456700276770.09025518795030.1312941049820.3182097933720.0649862619616-0.206541069460.110382255223-0.0212883645569-0.00478185878960.1414563993370.01174495420210.23197503516242.6181327396-25.196126185119.2290027001
110.0149646529801-0.01268230047310.06898540097963.15004517036-1.960765607676.138900016020.3152258205361.126819181270.90911752953-0.849921023976-0.176483340846-0.0646615641007-0.1696325795050.619375295639-0.07562818626920.4663381476070.106781326170.1005405897090.9289291766390.2438849894550.40223829173346.1969481989-15.94478690152.36579348623
128.990757200192.36381037693-3.898775755453.12600169453-5.451903640899.517826082010.143740634661-0.334875574395-0.2663589015490.516855278959-0.578481686143-0.6839149460340.2502658991830.8098483647970.4650194448510.215167771061-0.0467536711303-0.03882289629240.2162333124590.06965666453830.30410052838947.4748209819-27.301481662129.0115146001
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 334 through 393 )AA334 - 3932 - 61
22chain 'A' and (resid 394 through 516 )AA394 - 51662 - 184
33chain 'A' and (resid 517 through 527 )AA517 - 527185 - 195
44chain 'B' and (resid 1 through 7 )BB1 - 71 - 7
55chain 'B' and (resid 8 through 17 )BB8 - 178 - 17
66chain 'B' and (resid 18 through 32 )BB18 - 3218 - 32
77chain 'B' and (resid 33 through 52 )BB33 - 5233 - 52
88chain 'B' and (resid 53 through 73 )BB53 - 7353 - 73
99chain 'B' and (resid 74 through 83 )BB74 - 8374 - 83
1010chain 'B' and (resid 84 through 101 )BB84 - 10184 - 101
1111chain 'B' and (resid 102 through 114 )BB102 - 114102 - 114
1212chain 'B' and (resid 115 through 121 )BB115 - 121115 - 121

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