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- PDB-7msq: Complex between the Fab arm of AB-3467 and the SARS-CoV-2 recepto... -

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Basic information

Entry
Database: PDB / ID: 7msq
TitleComplex between the Fab arm of AB-3467 and the SARS-CoV-2 receptor binding domain (RBD)
Components
  • AB-3467 Fab Heavy Chain
  • AB-3467 Fab Light Chain
  • Spike protein S1
KeywordsVIRAL PROTEIN/ANTIVIRAL PROTEIN / SARS-CoV-2 receptor binding domain AB-3467 / ANTIVIRAL PROTEIN / VIRAL PROTEIN-ANTIVIRAL PROTEIN complex
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 / symbiont-mediated suppression of host innate immune response / 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 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / 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 ...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, 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
Similarity search - Domain/homology
THIOCYANATE ION / Spike glycoprotein
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.29 Å
AuthorsLangley, D.B. / Christ, D.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia) Australia
CitationJournal: Immunity / Year: 2021
Title: Immunizations with diverse sarbecovirus receptor-binding domains elicit SARS-CoV-2 neutralizing antibodies against a conserved site of vulnerability.
Authors: Burnett, D.L. / Jackson, K.J.L. / Langley, D.B. / Aggrawal, A. / Stella, A.O. / Johansen, M.D. / Balachandran, H. / Lenthall, H. / Rouet, R. / Walker, G. / Saunders, B.M. / Singh, M. / Li, H. ...Authors: Burnett, D.L. / Jackson, K.J.L. / Langley, D.B. / Aggrawal, A. / Stella, A.O. / Johansen, M.D. / Balachandran, H. / Lenthall, H. / Rouet, R. / Walker, G. / Saunders, B.M. / Singh, M. / Li, H. / Henry, J.Y. / Jackson, J. / Stewart, A.G. / Witthauer, F. / Spence, M.A. / Hansbro, N.G. / Jackson, C. / Schofield, P. / Milthorpe, C. / Martinello, M. / Schulz, S.R. / Roth, E. / Kelleher, A. / Emery, S. / Britton, W.J. / Rawlinson, W.D. / Karl, R. / Schafer, S. / Winkler, T.H. / Brink, R. / Bull, R.A. / Hansbro, P.M. / Jack, H.M. / Turville, S. / Christ, D. / Goodnow, C.C.
History
DepositionMay 12, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 23, 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
A: Spike protein S1
B: Spike protein S1
D: AB-3467 Fab Heavy Chain
E: AB-3467 Fab Light Chain
H: AB-3467 Fab Heavy Chain
L: AB-3467 Fab Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,71420
Polymers144,1896
Non-polymers1,52514
Water2,954164
1
A: Spike protein S1
H: AB-3467 Fab Heavy Chain
L: AB-3467 Fab Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,2349
Polymers72,0943
Non-polymers1,1406
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Spike protein S1
D: AB-3467 Fab Heavy Chain
E: AB-3467 Fab Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,48011
Polymers72,0943
Non-polymers3868
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)109.764, 115.494, 240.758
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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Antibody , 2 types, 4 molecules DHEL

#2: Antibody AB-3467 Fab Heavy Chain


Mass: 25758.723 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#3: Antibody AB-3467 Fab Light Chain


Mass: 23359.887 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)

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Protein / Sugars , 2 types, 3 molecules AB

#1: Protein Spike protein S1 / Spike glycoprotein


Mass: 22975.688 Da / Num. of mol.: 2 / 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: Cricetulus griseus (Chinese hamster) / References: UniProt: P0DTC2
#4: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-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: 894.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-4/a4-b1_a6-e1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE

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Non-polymers , 4 types, 177 molecules

#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#6: Chemical
ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: CNS
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / 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: 2.65 Å3/Da / Density % sol: 53.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.9
Details: Protein complex (5 mg/mL in 25 mM Tris (pH 8.0), 200 mM NaCl) was mixed with an equal volume (2 uL) of well solution comprising 100 mM BisTrisPropane (pH 6.9), 800 mM KSCN, 10% (v/v) ...Details: Protein complex (5 mg/mL in 25 mM Tris (pH 8.0), 200 mM NaCl) was mixed with an equal volume (2 uL) of well solution comprising 100 mM BisTrisPropane (pH 6.9), 800 mM KSCN, 10% (v/v) glycerol, and 18%(m/v) PEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 29, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.29→48.15 Å / Num. obs: 68595 / % possible obs: 99.8 % / Redundancy: 13.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.021 / Rrim(I) all: 0.078 / Net I/σ(I): 22.5 / Num. measured all: 938116 / Scaling rejects: 3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.29-2.3513.40.7475988044600.8820.2080.776497.5
10.76-48.15120.03590117540.9990.010.03656.498.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.93 Å48 Å

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0267refinement
XDSdata reduction
Aimless0.7.4data scaling
PHASER2.8.3phasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7kzb (RBD) and 7czx

7kzb

7czx


Resolution: 2.29→48 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.926 / WRfactor Rfree: 0.2446 / WRfactor Rwork: 0.1942 / FOM work R set: 0.8314 / SU B: 13.529 / SU ML: 0.16 / SU R Cruickshank DPI: 0.2843 / SU Rfree: 0.2233 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.284 / ESU R Free: 0.223 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2447 3368 4.9 %RANDOM
Rwork0.1942 ---
obs0.1966 65175 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 156.23 Å2 / Biso mean: 50.259 Å2 / Biso min: 22.15 Å2
Baniso -1Baniso -2Baniso -3
1--0.43 Å20 Å20 Å2
2--1.63 Å2-0 Å2
3----1.19 Å2
Refinement stepCycle: final / Resolution: 2.29→48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9674 0 88 164 9926
Biso mean--76.33 43.78 -
Num. residues----1253
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01310058
X-RAY DIFFRACTIONr_bond_other_d0.0010.0159062
X-RAY DIFFRACTIONr_angle_refined_deg1.7221.65413700
X-RAY DIFFRACTIONr_angle_other_deg1.3231.58220925
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.18851254
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.40122.922462
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.177151524
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4451540
X-RAY DIFFRACTIONr_chiral_restr0.0760.21320
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211479
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022371
LS refinement shellResolution: 2.294→2.353 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 239 -
Rwork0.256 4650 -
all-4889 -
obs--97.55 %
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)
12.5227-0.126-1.28730.8927-0.85752.08710.10830.49240.13810.12580.1034-0.02010.0995-0.4146-0.21170.2330.0202-0.03650.2210.04970.1642-21.588-16.41255.767
20.7671-0.4225-0.23182.3814-0.59412.0950.0120.0305-0.08490.23920.10960.0932-0.32570.2643-0.12170.192-0.05930.00830.10650.04020.130119.2979.9024.714
30.66580.5887-0.52190.6785-0.58730.7027-0.0271-0.099-0.1145-0.0234-0.0959-0.0521-0.04010.11680.1230.11640.07280.06460.08610.0920.1322.76444.87329.029
41.25670.6978-0.96320.399-0.50250.8418-0.02450.08510.1167-0.01660.0330.07830.0359-0.0916-0.00850.12660.06890.06740.10160.07260.1488-16.16947.85727.325
51.07620.7476-0.84840.7217-0.46930.7627-0.11680.0613-0.1003-0.08390.0501-0.10230.065-0.080.06680.10690.06980.05870.10630.08040.138713.3030.04830.982
60.35290.5357-0.41550.9863-0.79650.69530.06590.0130.08730.11760.00330.1352-0.12610.0121-0.06920.14760.09160.0910.08870.09350.129111.59119.132.779
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A334 - 528
2X-RAY DIFFRACTION2B334 - 528
3X-RAY DIFFRACTION3D1 - 228
4X-RAY DIFFRACTION4E1 - 213
5X-RAY DIFFRACTION5H1 - 228
6X-RAY DIFFRACTION6L1 - 214

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