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- PDB-8dce: SARS-CoV-2 Receptor-Binding Domain SPEEDesign Immunogen 1 Bound t... -

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Basic information

Entry
Database: PDB / ID: 8dce
TitleSARS-CoV-2 Receptor-Binding Domain SPEEDesign Immunogen 1 Bound to C144 scFv
Components
  • C144 scFv
  • Spike protein S1
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / Immunogen / antigen / design / vaccine / VIRAL PROTEIN-IMMUNE SYSTEM complex
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 / host extracellular space / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / membrane fusion ...symbiont-mediated disruption of host tissue / Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / 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 / endocytosis involved in viral entry into host cell / receptor ligand activity / 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 / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus spike glycoprotein S1, receptor binding / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsTang, W.K. / Tolia, N.H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Sci Adv / Year: 2022
Title: Design of the SARS-CoV-2 RBD vaccine antigen improves neutralizing antibody response.
Authors: Dickey, T.H. / Tang, W.K. / Butler, B. / Ouahes, T. / Orr-Gonzalez, S. / Salinas, N.D. / Lambert, L.E. / Tolia, N.H.
History
DepositionJun 16, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: C144 scFv
A: Spike protein S1


Theoretical massNumber of molelcules
Total (without water)52,5692
Polymers52,5692
Non-polymers00
Water4,071226
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)81.630, 97.310, 141.180
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Antibody C144 scFv


Mass: 28929.312 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pHLsec / Cell line (production host): Expi293F / Production host: Homo sapiens (human)
#2: Protein Spike protein S1


Mass: 23639.318 Da / Num. of mol.: 1 / Fragment: RBD SPEEDesign Immunogen 1 (UNP residues 333-526)
Mutation: T333M,A348P,V362Y,A363Y,N394Q,Y396F,I468T,H519D,A522P
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): Expi293F / Production host: Homo sapiens (human) / References: UniProt: P0DTC2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 226 / Source method: isolated from a natural source / Formula: H2O
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: 2.91 Å3/Da / Density % sol: 57.78 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.04 M potassium dihydrogen phosphate, 16% PEG8000, 20% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Nov 24, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→19.78 Å / Num. obs: 38255 / % possible obs: 99.68 % / Redundancy: 5.73 % / Biso Wilson estimate: 30.9 Å2 / CC1/2: 0.997 / Rrim(I) all: 0.125 / Net I/σ(I): 12.83
Reflection shellResolution: 2→2.05 Å / Num. unique obs: 2688 / CC1/2: 0.793 / Rrim(I) all: 0.845

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 7BWJ

7bwj


Resolution: 2→19.78 Å / SU ML: 0.1724 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.1732
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.203 2000 5.23 %
Rwork0.1772 36247 -
obs0.1786 38247 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.24 Å2
Refinement stepCycle: LAST / Resolution: 2→19.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3390 0 0 226 3616
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00243477
X-RAY DIFFRACTIONf_angle_d0.53044724
X-RAY DIFFRACTIONf_chiral_restr0.0442497
X-RAY DIFFRACTIONf_plane_restr0.0038614
X-RAY DIFFRACTIONf_dihedral_angle_d12.30961227
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.30411410.26552554X-RAY DIFFRACTION98.94
2.05-2.110.28611420.21152562X-RAY DIFFRACTION99.93
2.11-2.170.25081410.19692562X-RAY DIFFRACTION99.96
2.17-2.240.21181400.1852531X-RAY DIFFRACTION100
2.24-2.320.24631430.18952606X-RAY DIFFRACTION100
2.32-2.410.22541400.18812538X-RAY DIFFRACTION100
2.41-2.520.23331420.18322564X-RAY DIFFRACTION100
2.52-2.650.211430.18642596X-RAY DIFFRACTION99.96
2.65-2.820.20671420.17762584X-RAY DIFFRACTION99.96
2.82-3.030.18131430.17272594X-RAY DIFFRACTION99.93
3.03-3.340.18171430.17552587X-RAY DIFFRACTION99.93
3.34-3.820.1721450.16722619X-RAY DIFFRACTION99.71
3.82-4.80.17271450.14842628X-RAY DIFFRACTION99.93
4.8-19.780.2211500.18682722X-RAY DIFFRACTION99.48
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)
12.967303418380.001502285093951.229636959972.10852615137-0.460964437564.852101012720.1036203432040.02311028058930.125282420082-0.100496281867-0.05268858930110.279173252772-0.164283502293-0.562264884615-0.08689951993910.2302730376540.04241361533350.01180582027380.209973628962-0.02876974224820.296973282546-33.27709838125.31673791984-33.8677509675
22.457880145341.523912248391.006594381222.873785002380.302734447762.27627813456-0.05603078225960.0345989565458-0.0177968186431-0.3025917452820.00997176522808-0.0856682158979-0.212066875007-0.0901786808305-0.01508969351870.254978545210.02588297031740.03029549886160.2248055294390.01094753749830.241868908843-23.7993849461.85518344918-38.6493201372
33.30374153276-0.361131981358-0.8531761930463.387840037710.9008699996267.22410002498-0.189082124007-0.02292885083350.334479659257-0.09666214889780.01657700290810.127325755113-0.434153355642-0.1138933311760.06286260511370.286299070853-0.00127344499996-0.02533161505560.1920652806870.008505642684670.29254284825-27.40552621039.98405778755-37.2507605299
44.10428989855-1.007122695162.652080748084.86501552521-1.727937183834.46457293437-0.04141027605410.3136573617360.182586157827-0.483009778924-0.0643810880474-0.136654755482-0.3725901133360.04303089698150.05245912414890.2644481850040.009889235280390.03302342005440.196514673236-0.002961965239260.198774289622-30.10237699763.09491645701-44.623516633
53.2359356291-0.163826879472.10646472761.8010601512-1.202701143153.99635636976-0.0578310058704-0.353161803383-0.2574707150460.1843773122260.0366093341679-0.120417486331-0.142768182898-0.2400389249860.07844989284810.2928825293820.01864870467780.008791536052470.276495809829-0.01097354120070.316962553819-17.7794466966-4.52305636813-20.3930563584
64.6852398078-2.37099775272.281640774264.51897040919-0.08751358978821.148446201490.04714254388030.1862591599210.172794267827-0.237843840825-0.143229147495-0.0299982495519-0.00209383669224-0.338652036730.03308881974980.213128347631-0.04574592544820.03229293192410.2081378667840.03628932084320.164350294547-28.9715127318-5.06726273586-40.9505303092
72.478838507691.993977398530.333621530924.490784824820.7099121812730.92532349011-0.0145300656123-0.0229903012388-0.113145033760.1882593568750.0550256775808-0.3274422398440.1762247797040.0845350332534-0.0294499036510.2380932211340.0463497111199-0.003474813276140.2024350245580.0049096868390.235496857438-20.3956568043-17.1158839811-33.9406798237
82.386400073971.959282617231.624680556758.198434480271.495079056571.941480942060.0967145178623-0.06752650541380.03168209200140.2611224951810.03155813111460.479077197450.0505471454898-0.167577466745-0.1230610117260.2280899639650.05941860229920.037308319740.230745268907-0.01913024315040.226300294679-26.4926635605-18.4449402812-36.1929170343
90.03679512702380.317170853842-0.3214129856076.05252063559-0.5859261226151.16983809061-0.1112044029360.0355641859915-0.0203662406426-0.3290187038490.09885977981840.2159394546690.03990430059720.0435988120214-0.02289829453680.2084286792080.02454091643930.04550815873440.219672153545-0.008150073320660.230360028142-22.6795134275-13.1613853368-40.6143256847
101.13330967765-0.258576772117-0.684564880532.121440876322.572686062344.025580199450.106239138286-0.03754816832250.361963007886-0.237861387686-0.1615604306480.221985003802-1.87535954905-1.096009733720.230018723270.8458037611720.253866278971-0.05566596852790.417064810062-0.08130151902510.370988497387-23.304670737325.25381428682.78414493321
112.00253943428-1.1094409971-0.4474463283031.924142879271.69579127667.22528519667-0.0963583695135-0.139881153357-0.0249532262020.300263500678-0.157761612151-0.0325184559407-0.412876977396-0.356600352320.2232589629490.3960469355410.00194082490218-0.002457628129620.231084214724-0.03204408056930.233071975377-17.946056101614.86481541332.95680078333
124.105815743930.013953207248-0.05669014835222.809645723270.9802475282677.09061841982-0.3177002021690.301015904513-0.147308137769-0.286734901405-0.1207077988020.30338736063-0.205577294069-1.110072765630.3447952368770.3133901856830.0247432141553-0.03581047324960.432505977125-0.1008869769920.263425668982-21.785256956410.7669106425-15.1050119088
131.52219325880.125928736001-1.269762905522.613545753861.81748361897.699290655220.009668172515270.02420030740520.01002359317130.0591488544879-0.049210474452-0.300639829156-0.4047988869270.2777340153730.07517344323880.212198562943-0.0193841838748-0.03438523830960.1762716810380.01358005040570.323786647216-9.0415389072210.460791842-19.7617376611
142.667476757141.8744809451-2.03330887481.34038541272-1.416162953561.56877830705-0.2534865224840.12857157635-0.629522836509-0.0375951175941-0.5316792547750.6293799484430.500829049381-2.19720702270.660628774170.454462992132-0.1976340135670.1562526024360.952261589527-0.3435884895650.563672328803-31.12473332835.5577530456-9.21460680753
152.809070963250.37232697749-0.3094621605883.569256817592.596423999226.592980165150.209700128663-0.133370789370.02178147436870.2021620700550.0228931711781-0.518667713592-1.162537252450.2491907391610.0483822781140.7470194050440.0105600143889-0.05983174187940.298050421003-0.02298625876820.314220844748-15.603275610924.60305048226.59055734083
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'H' and (resid 1 through 33 )HA1 - 331 - 33
22chain 'H' and (resid 34 through 59 )HA34 - 5934 - 59
33chain 'H' and (resid 60 through 82 )HA60 - 8260 - 82
44chain 'H' and (resid 83 through 97 )HA83 - 9783 - 97
55chain 'H' and (resid 98 through 117 )HA98 - 11798 - 117
66chain 'H' and (resid 118 through 164 )HA118 - 164118 - 138
77chain 'H' and (resid 165 through 233 )HA165 - 233139 - 207
88chain 'H' and (resid 234 through 249 )HA234 - 249208 - 223
99chain 'H' and (resid 250 through 268 )HA250 - 268224 - 242
1010chain 'A' and (resid 334 through 375 )AB334 - 3751 - 42
1111chain 'A' and (resid 376 through 442 )AB376 - 44243 - 109
1212chain 'A' and (resid 443 through 459 )AB443 - 459110 - 126
1313chain 'A' and (resid 460 through 494 )AB460 - 494127 - 161
1414chain 'A' and (resid 495 through 506 )AB495 - 506162 - 173
1515chain 'A' and (resid 507 through 527 )AB507 - 527174 - 194

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