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- PDB-7kfx: Structural basis for a germline-biased antibody response to SARS-... -

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Basic information

Entry
Database: PDB / ID: 7kfx
TitleStructural basis for a germline-biased antibody response to SARS-CoV-2 (RBD:C1A-C2 Fab)
Components
  • Spike glycoprotein
  • heavy chain of human antibody C1A-C2 Fab
  • light chain of human antibody C1A-C2 Fab
KeywordsIMMUNE SYSTEM/Viral protein / COVID-19 / SARS-CoV-2 / neutralizing antibody / affinity maturation / IMMUNE SYSTEM / IMMUNE SYSTEM-Viral 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
Biological speciesSevere acute respiratory syndrome coronavirus 2
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.226 Å
AuthorsPan, J. / Abraham, J. / Clark, L. / Clark, S.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: Biorxiv / Year: 2020
Title: Molecular basis for a germline-biased neutralizing antibody response to SARS-CoV-2.
Authors: Clark, S.A. / Clark, L.E. / Pan, J. / Coscia, A. / McKay, L.G.A. / Shankar, S. / Johnson, R.I. / Griffiths, A. / Abraham, J.
History
DepositionOct 15, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 2, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 20, 2021Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / struct / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity_src_gen.pdbx_gene_src_gene ..._entity.pdbx_description / _entity_src_gen.pdbx_gene_src_gene / _struct.pdbx_descriptor / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.pdbx_seq_db_accession_code
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.journal_id_ISSN / _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
A: Spike glycoprotein
H: heavy chain of human antibody C1A-C2 Fab
L: light chain of human antibody C1A-C2 Fab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,8654
Polymers72,6443
Non-polymers2211
Water5,855325
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.455, 149.192, 146.143
Angle α, β, γ (deg.)90, 90, 90
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 25467.650 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: S, 2 / Plasmid: pHLSec / Cell line (production host): HEK-293T / Production host: Homo sapiens (human) / References: UniProt: P0DTC2
#2: Antibody heavy chain of human antibody C1A-C2 Fab


Mass: 23909.711 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pVRC-8400 / Cell line (production host): HEK-293T / Production host: Homo sapiens (human)
#3: Antibody light chain of human antibody C1A-C2 Fab


Mass: 23266.734 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pVRC-8400 / Cell line (production host): HEK-293T / Production host: Homo sapiens (human)
#4: 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: obtained synthetically / 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 325 / Source method: isolated from a natural source / Formula: H2O
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: 3.13 Å3/Da / Density % sol: 60.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: protein sample: 13 mg/mL in 150mM NaCl, 25 mM Tris-HCl pH 7.5 mother liquor composition (equal volume): 0.03 M Citric acid, 0.07M BIS-TRIS propane/pH 7.6, 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 5, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.22→200 Å / Num. obs: 44541 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 3.58 % / CC1/2: 0.995 / Rmerge(I) obs: 0.136 / Rrim(I) all: 0.159 / Χ2: 0.89 / Net I/σ(I): 6.86
Reflection shellResolution: 2.22→2.36 Å / Redundancy: 3.56 % / Mean I/σ(I) obs: 0.61 / Num. unique obs: 13624 / CC1/2: 0.251 / % possible all: 97.1

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
PHENIX1.18.2-3874data processing
O15.1.0model building
XDS20200131data reduction
XDS20200131data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7KFV

7kfv


Resolution: 2.226→74.6 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.926 / SU R Cruickshank DPI: 0.201 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.207 / SU Rfree Blow DPI: 0.174 / SU Rfree Cruickshank DPI: 0.173
RfactorNum. reflection% reflectionSelection details
Rfree0.2261 2121 -RANDOM
Rwork0.1909 ---
obs0.1926 44541 98.9 %-
Displacement parametersBiso mean: 63.35 Å2
Baniso -1Baniso -2Baniso -3
1--8.7707 Å20 Å20 Å2
2---4.8075 Å20 Å2
3---13.5782 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: LAST / Resolution: 2.226→74.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4861 0 14 325 5200
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0085065HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.016907HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1687SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes865HARMONIC5
X-RAY DIFFRACTIONt_it5065HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion658SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies9HARMONIC1
X-RAY DIFFRACTIONt_ideal_dist_contact3927SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.56
X-RAY DIFFRACTIONt_other_torsion16.82
LS refinement shellResolution: 2.23→2.25 Å
RfactorNum. reflection% reflection
Rfree0.2642 44 -
Rwork0.2603 --
obs0.2605 891 74.4 %
Refinement TLS params.

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)
13.3651-1.8087-2.53142.87293.122310.41240.2276-0.806-1.6326-0.8060.2437-0.1202-1.6326-0.1202-0.4713-0.18940.03160.0508-0.360.0105-0.3569-0.016172.019214.8805
26.7154-4.1073-2.26663.72154.59515.0866-0.02550.0827-0.23010.0827-0.4396-1.6015-0.2301-1.60150.4651-0.60920.2305-0.01560.0365-0.0189-0.3103-12.963765.302117.3277
32.2539-1.6787-3.66655.67036.995613.88960.1854-0.1545-0.3306-0.1545-0.2927-1.0208-0.3306-1.02080.1073-0.51210.0606-0.0191-0.18380.0415-0.3643-5.000462.444618.8834
42.0758-1.6407-1.64574.17062.91222.96730.0791-0.2679-0.3085-0.2679-0.2024-0.1207-0.3085-0.12070.1233-0.3798-0.06330.0064-0.1956-0.0639-0.34462.120456.49948.7049
51.8756-2.6732-1.06555.40232.55132.07460.2444-0.6061-0.5338-0.60610.0046-0.1028-0.5338-0.1028-0.249-0.397-0.13510.0589-0.3029-0.0665-0.38678.383155.01394.794
66.49943.21234.976502.082616.91030.34830.4353-0.6210.4353-0.2979-0.551-0.621-0.551-0.0504-0.36470.15410.0946-0.1996-0.1366-0.4571-1.357673.031832.739
70.58661.3130.28334.5770.1571.28310.0964-0.02660.1629-0.02660.01950.06080.16290.0608-0.1159-0.3852-0.0763-0.0314-0.282-0.0082-0.31655.756930.49983.7107
80.2960.1803-0.9490.91050.1145.7919-0.1013-0.15040.1719-0.1504-0.1135-0.03370.1719-0.03370.2149-0.31530.03320.0394-0.33720.01-0.2744-4.82060.684-18.45
93.6359-1.5676-2.70565.84928.731217.8427-0.4791-0.9186-0.2576-0.9186-0.141-0.6123-0.2576-0.61230.6201-0.061-0.0569-0.0887-0.51130.0098-0.563-3.973636.7323-20.9816
100.21610.7207-0.09452.62211.20955.3444-0.2093-0.7787-0.3901-0.77870.2457-0.133-0.3901-0.133-0.0364-0.1258-0.09730.0198-0.3609-0.011-0.38512.597839.9133-14.8055
112.82743.36050.89591.25150.47046.81530.1445-0.3568-0.6532-0.3568-0.1392-0.5899-0.6532-0.5899-0.0053-0.0296-0.04060.0164-0.43620.0241-0.3772-4.365124.4259-30.8522
121.86451.5793-1.86210.4675-1.19713.17240.2023-0.17160.086-0.1716-0.3220.03750.0860.03750.1196-0.27870.0245-0.0082-0.3019-0.0016-0.2969-15.25597.9057-21.8043
131.18570.41040.46530.5064-1.22951.00630.0157-0.24780.0263-0.2478-0.0579-0.05090.0263-0.05090.0421-0.27490.1109-0.0457-0.2503-0.0568-0.2722-21.001912.8973-17.2534
143.14982.776-1.69482.9652-1.72772.9650.0574-0.2182-0.1578-0.2182-0.0746-0.2862-0.1578-0.28620.0173-0.34050.0901-0.0114-0.3553-0.0384-0.2957-17.60929.0808-23.863
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|334 - A|364 }A334 - 364
2X-RAY DIFFRACTION2{ A|365 - A|380 }A365 - 380
3X-RAY DIFFRACTION3{ A|381 - A|409 }A381 - 409
4X-RAY DIFFRACTION4{ A|410 - A|459 }A410 - 459
5X-RAY DIFFRACTION5{ A|460 - A|516 }A460 - 516
6X-RAY DIFFRACTION6{ A|517 - A|528 }A517 - 528
7X-RAY DIFFRACTION7{ H|1 - H|111 }H1 - 111
8X-RAY DIFFRACTION8{ H|112 - H|218 }H112 - 218
9X-RAY DIFFRACTION9{ L|1 - L|18 }L1 - 18
10X-RAY DIFFRACTION10{ L|19 - L|102 }L19 - 102
11X-RAY DIFFRACTION11{ L|103 - L|113 }L103 - 113
12X-RAY DIFFRACTION12{ L|114 - L|150 }L114 - 150
13X-RAY DIFFRACTION13{ L|151 - L|163 }L151 - 163
14X-RAY DIFFRACTION14{ L|164 - L|214 }L164 - 214

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