[English] 日本語
Yorodumi
- PDB-8dce: SARS-CoV-2 Receptor-Binding Domain SPEEDesign Immunogen 1 Bound t... -

+
Open data


ID or keywords:

Loading...

-
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


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 / 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 / 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 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more