[English] 日本語
Yorodumi
- PDB-8dao: Crystal structure of SARS-CoV-2 spike stem fusion peptide in comp... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8dao
TitleCrystal structure of SARS-CoV-2 spike stem fusion peptide in complex with neutralizing antibody COV44-79
Components
  • COV44-79 heavy chain constant domain
  • COV44-79 heavy chain variable domain
  • COV44-79 light chain constant domain
  • COV44-79 light chain variable domain
  • Spike protein S2 fusion peptide
KeywordsIMMUNE SYSTEM / SARS-CoV-2 / coronavirus / antibody / fusion peptide / neutralizing antibody / COVID-19
Function / homology
Function and homology information


IgD immunoglobulin complex / IgM immunoglobulin complex / IgA immunoglobulin complex / IgE immunoglobulin complex / CD22 mediated BCR regulation / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / IgG immunoglobulin complex / immunoglobulin complex ...IgD immunoglobulin complex / IgM immunoglobulin complex / IgA immunoglobulin complex / IgE immunoglobulin complex / CD22 mediated BCR regulation / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / IgG immunoglobulin complex / immunoglobulin complex / immunoglobulin mediated immune response / FCGR activation / Role of phospholipids in phagocytosis / Role of LAT2/NTAL/LAB on calcium mobilization / Scavenging of heme from plasma / antigen binding / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Regulation of Complement cascade / Cell surface interactions at the vascular wall / FCGR3A-mediated phagocytosis / FCERI mediated MAPK activation / B cell receptor signaling pathway / Regulation of actin dynamics for phagocytic cup formation / FCERI mediated NF-kB activation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / blood microparticle / 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 / Potential therapeutics for SARS / 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 / adaptive immune response / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / host cell surface receptor binding / immune response / 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 / extracellular space / extracellular exosome / extracellular region / membrane / identical protein binding / plasma membrane
Similarity search - Function
Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain ...Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / 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 / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Immunoglobulin kappa constant / Immunoglobulin gamma-1 heavy chain / Spike glycoprotein
Similarity search - Component
Biological speciesHomo sapiens (human)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsLin, T.H. / Lee, C.C.D. / Yuan, M. / Wilson, I.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
Bill & Melinda Gates Foundation United States
CitationJournal: Science / Year: 2022
Title: Broadly neutralizing antibodies target the coronavirus fusion peptide.
Authors: Dacon, C. / Tucker, C. / Peng, L. / Lee, C.D. / Lin, T.H. / Yuan, M. / Cong, Y. / Wang, L. / Purser, L. / Williams, J.K. / Pyo, C.W. / Kosik, I. / Hu, Z. / Zhao, M. / Mohan, D. / Cooper, A.J. ...Authors: Dacon, C. / Tucker, C. / Peng, L. / Lee, C.D. / Lin, T.H. / Yuan, M. / Cong, Y. / Wang, L. / Purser, L. / Williams, J.K. / Pyo, C.W. / Kosik, I. / Hu, Z. / Zhao, M. / Mohan, D. / Cooper, A.J.R. / Peterson, M. / Skinner, J. / Dixit, S. / Kollins, E. / Huzella, L. / Perry, D. / Byrum, R. / Lembirik, S. / Drawbaugh, D. / Eaton, B. / Zhang, Y. / Yang, E.S. / Chen, M. / Leung, K. / Weinberg, R.S. / Pegu, A. / Geraghty, D.E. / Davidson, E. / Douagi, I. / Moir, S. / Yewdell, J.W. / Schmaljohn, C. / Crompton, P.D. / Holbrook, M.R. / Nemazee, D. / Mascola, J.R. / Wilson, I.A. / Tan, J.
History
DepositionJun 13, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 27, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 3, 2022Group: Database references / Derived calculations
Category: citation / citation_author / pdbx_struct_assembly_gen
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name / _pdbx_struct_assembly_gen.asym_id_list
Revision 1.2Aug 24, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Oct 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
C: COV44-79 heavy chain variable domain
D: COV44-79 light chain variable domain
E: COV44-79 heavy chain constant domain
F: COV44-79 light chain constant domain
I: Spike protein S2 fusion peptide
A: COV44-79 heavy chain variable domain
B: COV44-79 light chain variable domain
G: COV44-79 heavy chain constant domain
H: COV44-79 light chain constant domain
J: Spike protein S2 fusion peptide


Theoretical massNumber of molelcules
Total (without water)99,47610
Polymers99,47610
Non-polymers00
Water0
1
C: COV44-79 heavy chain variable domain
D: COV44-79 light chain variable domain
E: COV44-79 heavy chain constant domain
F: COV44-79 light chain constant domain
I: Spike protein S2 fusion peptide


Theoretical massNumber of molelcules
Total (without water)49,7385
Polymers49,7385
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: COV44-79 heavy chain variable domain
B: COV44-79 light chain variable domain
G: COV44-79 heavy chain constant domain
H: COV44-79 light chain constant domain
J: Spike protein S2 fusion peptide


Theoretical massNumber of molelcules
Total (without water)49,7385
Polymers49,7385
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.368, 100.368, 229.939
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number91
Space group name H-MP4122

-
Components

#1: Antibody COV44-79 heavy chain variable domain


Mass: 13673.513 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Mus musculus (house mouse)
#2: Antibody COV44-79 light chain variable domain


Mass: 11933.278 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Mus musculus (house mouse)
#3: Protein COV44-79 heavy chain constant domain / Immunoglobulin gamma-1 heavy chain / Immunoglobulin gamma-1 heavy chain NIE


Mass: 10585.920 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Mus musculus (house mouse) / References: UniProt: P0DOX5
#4: Protein COV44-79 light chain constant domain / Immunoglobulin kappa constant / Ig kappa chain C region / Ig kappa chain C region AG / Ig kappa ...Immunoglobulin kappa constant / Ig kappa chain C region / Ig kappa chain C region AG / Ig kappa chain C region CUM / Ig kappa chain C region EU / Ig kappa chain C region OU / Ig kappa chain C region ROY / Ig kappa chain C region TI


Mass: 11778.010 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGKC / Production host: Mus musculus (house mouse) / References: UniProt: P01834
#5: Protein/peptide Spike protein S2 fusion peptide


Mass: 1767.054 Da / Num. of mol.: 2 / Source method: obtained synthetically
Source: (synth.) Severe acute respiratory syndrome coronavirus 2
References: UniProt: P0DTC2

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.91 Å3/Da / Density % sol: 57.74 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Tris, pH 8.5, 0.01 M nickel (II) chloride, and 20% PEG monomethyl ether 2000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 22, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 29592 / % possible obs: 98.9 % / Redundancy: 10.5 % / Biso Wilson estimate: 63.87 Å2 / Rmerge(I) obs: 0.179 / Rpim(I) all: 0.056 / Rrim(I) all: 0.188 / Χ2: 0.421 / Net I/σ(I): 2.9 / Num. measured all: 309440
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.8-2.859.91.4113840.4060.4391.4820.21495.9
2.85-2.910.11.2814020.520.3971.3450.21796
2.9-2.96101.17814210.5480.3661.2380.2395.1
2.96-3.02100.94713840.6810.2940.9950.23397.5
3.02-3.089.80.8114500.7740.2560.8530.24197.8
3.08-3.159.90.67514490.8210.2140.7110.25497.8
3.15-3.239.90.58814460.8560.1880.620.27699.1
3.23-3.32100.48414610.9030.1550.510.28999.4
3.32-3.429.90.39714640.9670.1290.4190.31599.8
3.42-3.539.80.31814750.9550.1040.3360.34799.9
3.53-3.659.60.26314930.9720.0870.2780.3699.8
3.65-3.88.70.23414680.9760.0830.2490.39899.8
3.8-3.979.10.19414900.9820.0670.2060.40999.5
3.97-4.1811.50.15515050.9930.0470.1620.443100
4.18-4.44120.12814820.9940.0390.1340.516100
4.44-4.7912.10.11415220.9960.0340.1190.546100
4.79-5.2712.10.10615160.9960.0310.1110.549100
5.27-6.0311.80.1115240.9950.0330.1150.5299.8
6.03-7.5910.30.09615550.9960.0310.1010.56299.6
7.59-5012.10.06417010.9990.0190.0671.036100

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8D6Z

8d6z


Resolution: 2.8→49.88 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2837 1457 4.94 %
Rwork0.2306 28040 -
obs0.2332 29497 98.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 153.5 Å2 / Biso mean: 65.5669 Å2 / Biso min: 4.9 Å2
Refinement stepCycle: final / Resolution: 2.8→49.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6914 0 0 0 6914
Num. residues----912
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8-2.90.35711310.30042596272793
2.9-3.010.3341250.29852664278996
3.01-3.150.42841610.31152741290298
3.15-3.310.35031490.29512754290399
3.32-3.520.32481520.25427932945100
3.52-3.790.38861290.251528342963100
3.79-4.180.25811440.215328502994100
4.18-4.780.20331410.178828673008100
4.78-6.020.25521610.188528753036100
6.02-49.880.23721640.227630663230100

+
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