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- PDB-6yz5: H11-D4 complex with SARS-CoV-2 RBD -

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Basic information

Entry
Database: PDB / ID: 6yz5
TitleH11-D4 complex with SARS-CoV-2 RBD
Components
  • Nanobody H11-D4
  • Spike glycoprotein
KeywordsVIRAL PROTEIN / nanobody / complex / SARS-Cov-2
Function / homology
Function and homology information


symbiont-mediated disruption of host tissue / Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / viral translation / host extracellular space / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion ...symbiont-mediated disruption of host tissue / Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / viral translation / host extracellular space / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / membrane fusion / entry receptor-mediated virion attachment to host cell / 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 / symbiont entry into host cell / 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, N-terminal domain superfamily / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein, betacoronavirus / 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 (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, N-terminal domain superfamily / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein, betacoronavirus / 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 / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S2 superfamily, coronavirus / 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, coronavirus / Coronavirus spike glycoprotein S2
Similarity search - Domain/homology
ACETATE ION / Spike glycoprotein
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsNaismith, J.H. / Huo, J. / Mikolajek, H. / Ward, P. / Dumoux, M. / Owens, R.J. / Le Bas, A.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Wellcome Trust100209/Z/12/Z United Kingdom
Engineering and Physical Sciences Research CouncilEP/S025243/1. United Kingdom
CitationJournal: To Be Published
Title: H11-D4 complex with SARS-CoV-2 RBD
Authors: Naismith, J.H.
History
DepositionMay 6, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 3, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 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_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Jan 24, 2024Group: 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
Revision 1.3Nov 13, 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
E: Spike glycoprotein
F: Nanobody H11-D4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,93019
Polymers38,7272
Non-polymers1,20217
Water4,342241
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Complex
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4550 Å2
ΔGint37 kcal/mol
Surface area15620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.280, 78.280, 127.090
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

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Protein / Antibody / Sugars , 3 types, 3 molecules EF

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


Mass: 23716.580 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Truncated version expressed
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: S, 2 / Production host: Escherichia coli (E. coli) / References: UniProt: P0DTC2
#2: Antibody Nanobody H11-D4


Mass: 15010.732 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)
#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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
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

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Non-polymers , 3 types, 257 molecules

#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 241 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 2.9 Å3/Da / Density % sol: 57.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: the crystallization buffer containing 0.2 M Sodium acetate trihydrate, 0.1 M MES pH 6.0, 20 % w/v PEG 8000. The crystals grew overnight and were flash cooled in a solution containing the ...Details: the crystallization buffer containing 0.2 M Sodium acetate trihydrate, 0.1 M MES pH 6.0, 20 % w/v PEG 8000. The crystals grew overnight and were flash cooled in a solution containing the mother liquor with 30 % (v/v) ethylene glycol.

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: liquid nitrogen / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97623 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 30, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97623 Å / Relative weight: 1
ReflectionResolution: 1.8→46.41 Å / Num. obs: 40120 / % possible obs: 99 % / Redundancy: 19.7 % / CC1/2: 1 / Rmerge(I) obs: 0.109 / Net I/σ(I): 20.6
Reflection shellResolution: 1.8→1.85 Å / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 3066 / CC1/2: 0.7 / % possible all: 99

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Processing

Software
NameVersionClassification
XDSdata reduction
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6YLA

6yla


Resolution: 1.8→46.41 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.963 / SU B: 4.394 / SU ML: 0.067 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.097 / ESU R Free: 0.096
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1933 2158 5.1 %RANDOM
Rwork0.1658 ---
obs0.1672 40120 99.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 108.22 Å2 / Biso mean: 35.176 Å2 / Biso min: 15.44 Å2
Baniso -1Baniso -2Baniso -3
1-0.58 Å20.29 Å20 Å2
2--0.58 Å20 Å2
3----1.89 Å2
Refinement stepCycle: final / Resolution: 1.8→46.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2533 0 78 241 2852
Biso mean--52.22 45.33 -
Num. residues----322
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0132748
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172438
X-RAY DIFFRACTIONr_angle_refined_deg1.4411.6643727
X-RAY DIFFRACTIONr_angle_other_deg1.3531.5785647
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0595344
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.92321.486148
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.84815413
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.051519
X-RAY DIFFRACTIONr_chiral_restr0.0650.2340
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023128
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02647
LS refinement shellResolution: 1.8→1.847 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 171 -
Rwork0.305 2895 -
all-3066 -
obs--99.61 %
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)
11.17230.52040.18831.60770.68141.42790.0479-0.17070.009-0.0042-0.0154-0.06360.00940.0622-0.03250.00680.00280.00250.0551-0.00330.089860.15619.09931.893
23.15270.8861.86061.65510.34312.99280.0527-0.39010.06780.0058-0.12030.18090.2024-0.43440.06760.0802-0.060.00690.0921-0.0010.13332.310.6617.05
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1E334 - 528
2X-RAY DIFFRACTION2F1 - 127

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