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- PDB-6waq: Crystal structure of the SARS-CoV-1 RBD bound by the cross-reacti... -

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Basic information

Entry
Database: PDB / ID: 6waq
TitleCrystal structure of the SARS-CoV-1 RBD bound by the cross-reactive single-domain antibody SARS VHH-72
Components
  • Spike glycoproteinSpike protein
  • nanobody SARS VHH-72
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / SARS-CoV-1 / VHH / nanobody / RBD / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / Attachment and Entry / endocytosis involved in viral entry into host cell / SARS-CoV-1 activates/modulates innate immune responses / suppression by virus of host tetherin activity / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / membrane fusion / positive regulation of viral entry into host cell ...Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / Attachment and Entry / endocytosis involved in viral entry into host cell / SARS-CoV-1 activates/modulates innate immune responses / suppression by virus of host tetherin activity / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / membrane fusion / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / 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 / host cell plasma membrane / virion membrane / membrane / identical protein binding
Similarity search - Function
Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV / 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 / 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 speciesLama glama (llama)
Human SARS coronavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsWrapp, D. / McLellan, J.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01-AI127521 United States
CitationJournal: Cell / Year: 2020
Title: Structural Basis for Potent Neutralization of Betacoronaviruses by Single-Domain Camelid Antibodies.
Authors: Wrapp, D. / De Vlieger, D. / Corbett, K.S. / Torres, G.M. / Wang, N. / Van Breedam, W. / Roose, K. / van Schie, L. / Hoffmann, M. / Pohlmann, S. / Graham, B.S. / Callewaert, N. / Schepens, B. ...Authors: Wrapp, D. / De Vlieger, D. / Corbett, K.S. / Torres, G.M. / Wang, N. / Van Breedam, W. / Roose, K. / van Schie, L. / Hoffmann, M. / Pohlmann, S. / Graham, B.S. / Callewaert, N. / Schepens, B. / Saelens, X. / McLellan, J.S.
History
DepositionMar 25, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2020Provider: repository / Type: Initial release
Revision 1.1May 20, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jun 10, 2020Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Oct 18, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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
A: nanobody SARS VHH-72
D: Spike glycoprotein
C: nanobody SARS VHH-72
B: Spike glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,6817
Polymers71,0174
Non-polymers6643
Water1,838102
1
A: nanobody SARS VHH-72
B: Spike glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7303
Polymers35,5082
Non-polymers2211
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Spike glycoprotein
C: nanobody SARS VHH-72
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9514
Polymers35,5082
Non-polymers4422
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.848, 88.848, 200.887
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Antibody nanobody SARS VHH-72


Mass: 13783.043 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Homo sapiens (human)
#2: Protein Spike glycoprotein / Spike protein / S glycoprotein / E2 / Peplomer protein


Mass: 21725.432 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human SARS coronavirus / Gene: S, 2 / Production host: Homo sapiens (human) / References: UniProt: P59594
#3: 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.: 3
Source method: isolated from a genetically manipulated 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
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 102 / Source method: isolated from a natural source / Formula: H2O
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: 3.26 Å3/Da / Density % sol: 62.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8.5
Details: 0.1 M Tris pH 8.5, 0.2 M LiSO4, 0.1 M LiCl, 8% PEG 8000

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.2→50.513 Å / Num. obs: 47356 / % possible obs: 99.8 % / Redundancy: 8.9 % / CC1/2: 0.993 / Net I/σ(I): 6.2
Reflection shellResolution: 2.2→2.27 Å / Redundancy: 9.1 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 4063 / CC1/2: 0.865 / % possible all: 99.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
PHENIX1.15_3459refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2AJF, 5F1O

2ajf

5f1o


Resolution: 2.2→50.513 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.66
RfactorNum. reflection% reflection
Rfree0.2359 2335 4.94 %
Rwork0.2026 --
obs0.2042 47250 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 180.8 Å2 / Biso mean: 78.4973 Å2 / Biso min: 32.57 Å2
Refinement stepCycle: final / Resolution: 2.2→50.513 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4934 0 42 102 5078
Biso mean--92.54 56.2 -
Num. residues----626
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065115
X-RAY DIFFRACTIONf_angle_d0.7566960
X-RAY DIFFRACTIONf_dihedral_angle_d18.9311817
X-RAY DIFFRACTIONf_chiral_restr0.048734
X-RAY DIFFRACTIONf_plane_restr0.005900
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2-2.2450.3871490.3183254499
2.245-2.29380.39321370.3239262699
2.2938-2.34710.28131350.2789260199
2.3471-2.40580.30971290.2676260799
2.4058-2.47090.31381360.2529261399
2.4709-2.54360.33091590.2659255499
2.5436-2.62570.31191190.2476265099
2.6257-2.71950.26541280.23162612100
2.7195-2.82840.25361240.23792631100
2.8284-2.95710.3191320.23522659100
2.9571-3.1130.22291440.2319259899
3.113-3.3080.26951510.22082644100
3.308-3.56330.23051240.20482678100
3.5633-3.92180.23221260.18822670100
3.9218-4.4890.16231510.1575266999
4.489-5.65450.19041380.15962721100
5.6545-50.5130.22691530.1854283899
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)
14.41580.6067-0.86012.738-1.87641.38160.6318-0.71440.7622-0.8031-0.0564-0.083-1.34790.4521-0.49241.7836-0.08040.29990.5822-0.15810.925643.05560.198-22.827
22.9020.8099-0.2832.69250.38624.03360.132-0.269-0.07260.2511-0.178-0.0405-0.07760.24460.03790.6063-0.1872-0.05830.355-0.01550.332643.8767.908-8.079
32.480.03-1.43214.1497-0.68665.3802-0.02960.1785-0.1142-0.24490.01150.05430.729-0.6440.0010.7633-0.2449-0.01160.36690.02450.359532.656-15.725-17.581
41.727-0.30470.94860.8554-0.63512.42210.41060.11050.3274-0.4601-0.40710.0734-0.9112-0.03330.04831.48750.06320.02630.4103-0.00980.502841.45333.731-34.346
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:115 )A1 - 115
2X-RAY DIFFRACTION2( CHAIN D AND ( RESID 320:503 OR RESID 601:602 ) )D320 - 503
3X-RAY DIFFRACTION2( CHAIN D AND ( RESID 320:503 OR RESID 601:602 ) )D601 - 602
4X-RAY DIFFRACTION3( CHAIN C AND RESID 1:113 )C1 - 113
5X-RAY DIFFRACTION4( CHAIN B AND RESID 321:510 )B321 - 510

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