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

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Basic information

Entry
Database: PDB / ID: 7kfy
TitleStructural basis for a germline-biased antibody response to SARS-CoV-2 (RBD:C1A-F10 Fab)
Components
  • Spike glycoproteinSpike protein
  • heavy chain of human antibody C1A-F10 Fab
  • light chain of human antibody C1A-F10 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 / host cell endoplasmic reticulum-Golgi intermediate compartment membrane ...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 / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / entry receptor-mediated virion attachment to host cell / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / membrane fusion / 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 / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / membrane / identical protein binding / 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
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.157 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

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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-F10 Fab
L: light chain of human antibody C1A-F10 Fab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,7914
Polymers72,5703
Non-polymers2211
Water9,584532
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)85.74, 146.801, 144.593
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 / Spike protein / 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-F10 Fab


Mass: 23854.633 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-F10 Fab


Mass: 23247.756 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 / N-Acetylglucosamine


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 / Water


Mass: 18.015 Da / Num. of mol.: 532 / 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: 3.3 Å3/Da / Density % sol: 62.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: protein sample: 13 mg/mL in 150mM NaCl, 25 mM Tris-HCl, pH 7.5 mother liquor composition (equal volume): 0.10% (w/v) n-Octyl-B-glucoside, 0.1 M Sodium citrate tribasic dihydrate pH 4.5, 22% (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: 2.157→200 Å / Num. obs: 48373 / % possible obs: 94 % / Observed criterion σ(I): -3 / Redundancy: 2.06 % / CC1/2: 0.991 / Rmerge(I) obs: 0.118 / Rrim(I) all: 0.157 / Χ2: 0.99 / Net I/σ(I): 6.17
Reflection shellResolution: 2.157→2.29 Å / Redundancy: 1.96 % / Mean I/σ(I) obs: 0.71 / Num. unique obs: 27507 / CC1/2: 0.37 / % possible all: 89.4

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
PHENIX1.18.2-3874data processing
O15.1.0model building
XDS20200131data reduction
XDS20200131data scaling
PARROT2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7KFV

7kfv


Resolution: 2.157→74.04 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.894 / SU R Cruickshank DPI: 0.201 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.216 / SU Rfree Blow DPI: 0.186 / SU Rfree Cruickshank DPI: 0.18
RfactorNum. reflection% reflectionSelection details
Rfree0.2486 2585 -RANDOM
Rwork0.2054 ---
obs0.2078 48373 97.9 %-
Displacement parametersBiso mean: 52.24 Å2
Baniso -1Baniso -2Baniso -3
1--8.2057 Å20 Å20 Å2
2--6.038 Å20 Å2
3---2.1677 Å2
Refine analyzeLuzzati coordinate error obs: 0.29 Å
Refinement stepCycle: LAST / Resolution: 2.157→74.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4836 0 14 532 5382
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0085019HARMONIC2
X-RAY DIFFRACTIONt_angle_deg16839HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1660SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes851HARMONIC5
X-RAY DIFFRACTIONt_it5018HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion652SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies5HARMONIC1
X-RAY DIFFRACTIONt_ideal_dist_contact4287SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.74
X-RAY DIFFRACTIONt_other_torsion16.81
LS refinement shellResolution: 2.16→2.17 Å
RfactorNum. reflection% reflection
Rfree0.2512 54 -
Rwork0.2316 --
obs0.2327 968 89.33 %
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)
10.5449-0.41681.02191.5439-0.59732.0739-0.0351-0.3570.5442-0.3570.2597-0.3210.5442-0.321-0.2246-0.0905-0.0066-0.0093-0.3040.0371-0.2348-1.5432-70.357412.6903
20-0.6219-2.91045.7087-1.95765.83870.00690.34740.54420.34740.17860.54420.54420.5442-0.1855-0.22180.152-0.0583-0.24920.0783-0.24678.5821-73.181921.7808
31.2368-1.08360.63430.6933-1.63743.1620.0421-0.23240.2486-0.2324-0.13590.22850.24860.22850.0938-0.27630.03550.0032-0.1740.0308-0.20346.5581-62.457617.6893
400.1715-0.63150.5362-0.869300.014-0.07450.1639-0.07450.038-0.07610.1639-0.0761-0.052-0.2039-0.0135-0.0338-0.2140.0316-0.1722-3.6636-56.53129.2154
51.6537-2.91041.16853.7769-2.48750.68560.0629-0.51240.4564-0.51240.4185-0.01280.4564-0.0128-0.4814-0.2689-0.1343-0.1337-0.24750.1146-0.0353-19.7867-48.8162-0.5538
61.0394-0.2402-1.06420.6466-1.08390-0.0631-0.19890.1363-0.1989-0.1164-0.08670.1363-0.08670.1794-0.18030.04420.0323-0.22190.0626-0.20813.777-59.81994.7573
70-1.8199-2.91040-2.91048.3140.12550.4120.26910.412-0.2250.08840.26910.08840.0995-0.13730.105-0.0578-0.21970.0312-0.3041.3208-72.2632.2148
81.71421.29410.02450.5814-0.76670.5350.03240.1402-0.10790.14020.0362-0.0568-0.1079-0.0568-0.0686-0.24610.01480.055-0.25670.0103-0.116-10.5614-26.50083.9673
90.15770.42010.22321.1743-0.206100.0367-0.0096-0.0729-0.0096-0.00180.0114-0.07290.0114-0.0349-0.2323-0.0430.0307-0.21560.0088-0.1379-3.3773-29.37862.849
100-0.08841.96030.1355-1.12990.0883-0.0087-0.17470.0559-0.17470.19830.33820.05590.3382-0.1896-0.0604-0.0380.0573-0.25660.0014-0.213112.39232.3931-26.1016
110-0.01360.226600.04881.60610.0182-0.04670.0031-0.0467-0.0813-0.11340.0031-0.11340.0631-0.17660.0137-0.0213-0.1907-0.0062-0.23123.2174-2.862-18.2381
120.26490.1162-1.44640.0082-2.21075.6802-0.0505-0.0058-0.3879-0.0058-0.00420.076-0.38790.0760.0547-0.15520.00950.0094-0.22030.0406-0.18695.33767.3947-18.4785
130.09620.07520.14932.4793-2.63512.58-0.1942-0.2415-0.1505-0.2415-0.13390.4181-0.15050.41810.3281-0.095-0.0345-0.0051-0.3040.0072-0.2754.5508-36.8781-20.7224
1400.0744-0.01350-1.07691.5493-0.0184-0.29320.0818-0.29320.11010.04150.08180.0415-0.0917-0.105-0.0528-0.0447-0.28140.0148-0.2094-4.2159-39.8763-14.5564
1500.454-0.02170.0242-0.14280.6987-0.164-0.20160.0463-0.20160.00220.08530.04630.08530.1618-0.0807-0.0205-0.0157-0.27090.0072-0.2182-0.9344-38.7812-15.9562
162.77631.33370.14814.8828-2.91041.65790.0356-0.25790.25-0.25790.06980.07760.250.0776-0.1054-0.08390.0134-0.0474-0.304-0.0605-0.28924.7934-23.8697-31.1998
170.45230.57990.31720.95150.57030.16520.2216-0.2318-0.1379-0.2318-0.1947-0.0457-0.1379-0.0457-0.0269-0.1651-0.0030.0219-0.2262-0.0538-0.190416.13781.2518-19.031
180.43971.12560.954400.43351.34690.07-0.08880.1798-0.0888-0.1596-0.04310.1798-0.04310.0896-0.15220.0356-0.0195-0.2427-0.0227-0.17415.355-13.6717-23.8841
193.39640.90651.307801.47970.6809-0.0352-0.16480.098-0.1648-0.0804-0.04290.098-0.04290.1156-0.20110.05430.0219-0.20810.0485-0.202922.1529-12.3977-17.1938
200.77941.07760.95710.9650.65421.42830.1167-0.11710.0483-0.1171-0.15290.05950.04830.05950.0362-0.24420.0399-0.0149-0.2802-0.024-0.156317.6321-8.8233-24.1527
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|334 - A|358 }A334 - 358
2X-RAY DIFFRACTION2{ A|359 - A|369 }A359 - 369
3X-RAY DIFFRACTION3{ A|370 - A|409 }A370 - 409
4X-RAY DIFFRACTION4{ A|410 - A|469 }A410 - 469
5X-RAY DIFFRACTION5{ A|470 - A|494 }A470 - 494
6X-RAY DIFFRACTION6{ A|495 - A|516 }A495 - 516
7X-RAY DIFFRACTION7{ A|517 - A|528 }A517 - 528
8X-RAY DIFFRACTION8{ H|1 - H|33 }H1 - 33
9X-RAY DIFFRACTION9{ H|34 - H|119 }H34 - 119
10X-RAY DIFFRACTION10{ H|120 - H|134 }H120 - 134
11X-RAY DIFFRACTION11{ H|135 - H|203 }H135 - 203
12X-RAY DIFFRACTION12{ H|204 - H|216 }H204 - 216
13X-RAY DIFFRACTION13{ L|1 - L|18 }L1 - 18
14X-RAY DIFFRACTION14{ L|19 - L|61 }L19 - 61
15X-RAY DIFFRACTION15{ L|62 - L|102 }L62 - 102
16X-RAY DIFFRACTION16{ L|103 - L|113 }L103 - 113
17X-RAY DIFFRACTION17{ L|114 - L|128 }L114 - 128
18X-RAY DIFFRACTION18{ L|129 - L|150 }L129 - 150
19X-RAY DIFFRACTION19{ L|151 - L|163 }L151 - 163
20X-RAY DIFFRACTION20{ L|164 - L|214 }L164 - 214

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