[English] 日本語
Yorodumi
- PDB-7u8e: Crystal structure of antibody Ab246 in complex with SARS-CoV-2 re... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7u8e
TitleCrystal structure of antibody Ab246 in complex with SARS-CoV-2 receptor binding domain
Components
  • (Antibody Ab246 Fab ...) x 2
  • Spike protein S1
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / Neutralizing antibody / SARS-CoV-2 / Ab246 / receptor binding domain / ANTIVIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex / VIRAL PROTEIN
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 / viral translation / host extracellular space / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion ...symbiont-mediated disruption of host tissue / Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / viral translation / 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 / receptor ligand activity / endocytosis involved in viral entry into host cell / 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 / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / 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 speciesSevere acute respiratory syndrome coronavirus 2
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å
AuthorsSankhala, R.S. / Joyce, M.G.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Defense (DOD, United States)W81XWH-18-2-0040 United States
CitationJournal: Structure / Year: 2024
Title: Antibody targeting of conserved sites of vulnerability on the SARS-CoV-2 spike receptor-binding domain.
Authors: Sankhala, R.S. / Dussupt, V. / Chen, W.H. / Bai, H. / Martinez, E.J. / Jensen, J.L. / Rees, P.A. / Hajduczki, A. / Chang, W.C. / Choe, M. / Yan, L. / Sterling, S.L. / Swafford, I. / Kuklis, ...Authors: Sankhala, R.S. / Dussupt, V. / Chen, W.H. / Bai, H. / Martinez, E.J. / Jensen, J.L. / Rees, P.A. / Hajduczki, A. / Chang, W.C. / Choe, M. / Yan, L. / Sterling, S.L. / Swafford, I. / Kuklis, C. / Soman, S. / King, J. / Corbitt, C. / Zemil, M. / Peterson, C.E. / Mendez-Rivera, L. / Townsley, S.M. / Donofrio, G.C. / Lal, K.G. / Tran, U. / Green, E.C. / Smith, C. / de Val, N. / Laing, E.D. / Broder, C.C. / Currier, J.R. / Gromowski, G.D. / Wieczorek, L. / Rolland, M. / Paquin-Proulx, D. / van Dyk, D. / Britton, Z. / Rajan, S. / Loo, Y.M. / McTamney, P.M. / Esser, M.T. / Polonis, V.R. / Michael, N.L. / Krebs, S.J. / Modjarrad, K. / Joyce, M.G.
History
DepositionMar 8, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 15, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Jan 10, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.3Jan 17, 2024Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.4Feb 14, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Spike protein S1
H: Antibody Ab246 Fab heavy chain
L: Antibody Ab246 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,66311
Polymers70,8543
Non-polymers8098
Water3,603200
1
H: Antibody Ab246 Fab heavy chain
L: Antibody Ab246 Fab light chain
hetero molecules

A: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,66311
Polymers70,8543
Non-polymers8098
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455x-1/2,y+1/2,z1
Buried area5610 Å2
ΔGint-30 kcal/mol
Surface area30490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)194.797, 41.603, 98.991
Angle α, β, γ (deg.)90.000, 107.030, 90.000
Int Tables number5
Space group name H-MC121

-
Components

-
Antibody , 2 types, 2 molecules HL

#2: Antibody Antibody Ab246 Fab heavy chain


Mass: 24152.074 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: fragment antigen-binding (Fab) heavy chain / Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody Antibody Ab246 Fab light chain


Mass: 23628.334 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: fragment antigen-binding (Fab) light chain / Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

-
Protein / Sugars , 2 types, 2 molecules A

#1: Protein Spike protein S1


Mass: 23073.766 Da / Num. of mol.: 1 / Fragment: receptor binding domain (RBD)
Source method: isolated from a genetically manipulated source
Details: Viral protein
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: S, 2 / Production host: Homo sapiens (human) / References: UniProt: P0DTC2
#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

-
Non-polymers , 3 types, 207 molecules

#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 200 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.75 Å3/Da / Density % sol: 55.22 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 4.6
Details: 0.1 M Sodium acetate trihydrate pH 4.6, 2.0 M Ammonium sulfate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 26, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.29→50 Å / Num. obs: 33571 / % possible obs: 96.3 % / Redundancy: 3.2 % / Biso Wilson estimate: 26.02 Å2 / CC1/2: 0.98 / Rpim(I) all: 0.08 / Rrim(I) all: 0.148 / Rsym value: 0.124 / Χ2: 0.92 / Net I/av σ(I): 9.78 / Net I/σ(I): 9.78
Reflection shellResolution: 2.29→2.38 Å / Num. unique obs: 3156 / CC1/2: 0.897 / % possible all: 91

-
Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6H0E

6h0e


Resolution: 2.29→19.899 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 26.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2475 1433 5 %
Rwork0.204 27223 -
obs0.2062 28656 82.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 139.62 Å2 / Biso mean: 44.9468 Å2 / Biso min: 11.18 Å2
Refinement stepCycle: final / Resolution: 2.29→19.899 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4841 0 51 200 5092
Biso mean--52.07 38.67 -
Num. residues----636
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045031
X-RAY DIFFRACTIONf_angle_d0.6776852
X-RAY DIFFRACTIONf_chiral_restr0.044754
X-RAY DIFFRACTIONf_plane_restr0.004871
X-RAY DIFFRACTIONf_dihedral_angle_d13.932983
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.29-2.37160.3366910.2457171652
2.3716-2.46640.28381040.2392198061
2.4664-2.57840.31561190.2388225769
2.5784-2.7140.31381280.2398244875
2.714-2.88360.26521470.239277884
2.8836-3.10550.30531630.2294310694
3.1055-3.41660.25181700.2111323898
3.4166-3.90770.2331670.1891318096
3.9077-4.9110.18091720.1638326298
4.911-19.8990.24091720.1959325895
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)
12.70960.0007-0.69892.39851.28080.86120.09530.2350.0199-0.71520.0092-0.7048-0.40660.8144-0.17180.38310.09050.19810.89870.11220.5102-9.572514.602821.2964
22.8215-1.5163-2.6642.75622.67483.36110.24950.52340.2998-0.86060.2142-0.4542-0.55570.7393-0.44110.73710.08420.36470.78770.16590.6578-14.026416.486612.954
31.9699-1.04611.99025.2783-4.49844.51840.22760.9169-0.8238-0.9929-0.1102-0.70621.4531.2077-0.06760.53550.30650.17061.01960.05590.7285-11.54110.658716.2828
46.4873-0.02931.88718.7212-2.20028.7821-0.13940.7722-0.6298-1.02810.136-0.75950.87950.80430.01830.37920.12880.09080.5364-0.04440.4347-21.86064.172512.7203
54.5529-0.3775-0.96791.6886-0.43642.37140.1267-0.0984-0.0036-0.030.0746-0.0011-0.0775-0.20980.08660.05930.14460.10550.80910.08320.4573-18.131910.2128.2807
61.4883-0.3709-0.00430.518-0.09810.0378-0.0341-0.64010.3307-0.01130.0065-0.2319-0.16680.14230.02970.17630.23820.04741.1309-0.05330.3015-20.303315.057234.6341
72.40472.0762-1.60182.9193-0.39751.9281-0.2886-1.1020.9080.52910.11180.3266-0.3257-0.28760.07370.35720.0618-0.02721.4107-0.29930.6729-20.555223.30249.7947
83.9872-0.2154-0.34951.23860.7362.910.0173-0.7103-0.11570.10970.1246-0.1703-0.1146-0.1716-0.01230.21210.11770.04030.92510.15730.4003-12.62116.918632.3115
93.8402-0.5603-3.0284.69770.57855.36740.47261.33880.0868-2.2668-0.2320.6835-0.6187-0.7567-0.21581.3550.08410.02321.3680.1640.523-22.148513.32834.1376
102.1789-1.0464-0.04052.7059-0.79781.351-0.1338-0.0840.0287-0.0817-0.2018-0.1602-0.00160.21520.12270.3060.09940.0322-0.09250.09720.2201-49.35845.438811.3482
112.44810.786-0.26550.67580.60771.481-0.07310.0313-0.146-0.07040.0984-0.06350.15890.228-0.0710.24330.05640.04870.05140.0440.1816-45.44864.051710.5512
121.765-1.4567-0.2412.11580.09220.97150.0119-0.08280.37820.0132-0.13110.1009-0.34850.13620.06160.3518-0.01310.00770.1102-0.01740.2932-67.332523.668618.8345
131.35590.09510.22250.1798-0.13211.2097-0.1159-0.9895-0.36030.3373-0.0154-0.09480.47820.3035-0.0230.31720.29-0.07590.61780.23380.0689-45.24750.496232.6259
141.9556-0.76960.95681.3905-0.28270.4922-0.016-0.7260.26640.0294-0.05610.02540.09750.24840.0670.21090.08480.00830.659-0.0360.1871-74.745921.224632.7957
151.9635-1.41591.14124.41420.06023.93540.1694-0.5921-0.22380.1905-0.29840.26680.0936-0.00810.08820.2189-0.02720.01220.5449-0.01120.2135-80.963720.912733.2167
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 333 through 353 )A333 - 353
2X-RAY DIFFRACTION2chain 'A' and (resid 354 through 364 )A354 - 364
3X-RAY DIFFRACTION3chain 'A' and (resid 365 through 375 )A365 - 375
4X-RAY DIFFRACTION4chain 'A' and (resid 376 through 393 )A376 - 393
5X-RAY DIFFRACTION5chain 'A' and (resid 394 through 409 )A394 - 409
6X-RAY DIFFRACTION6chain 'A' and (resid 410 through 479 )A410 - 479
7X-RAY DIFFRACTION7chain 'A' and (resid 480 through 494 )A480 - 494
8X-RAY DIFFRACTION8chain 'A' and (resid 495 through 516 )A495 - 516
9X-RAY DIFFRACTION9chain 'A' and (resid 517 through 530 )A517 - 530
10X-RAY DIFFRACTION10chain 'H' and (resid 1 through 66 )H1 - 66
11X-RAY DIFFRACTION11chain 'H' and (resid 67 through 100F)H67 - 100
12X-RAY DIFFRACTION12chain 'H' and (resid 100G through 213 )H100
13X-RAY DIFFRACTION13chain 'L' and (resid 2 through 104 )L2 - 104
14X-RAY DIFFRACTION14chain 'L' and (resid 105 through 153 )L105 - 153
15X-RAY DIFFRACTION15chain 'L' and (resid 154 through 211 )L154 - 211

+
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://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