[English] 日本語
Yorodumi
- PDB-8d6z: Crystal structure of SARS-CoV-2 spike stem fusion peptide in comp... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8d6z
TitleCrystal structure of SARS-CoV-2 spike stem fusion peptide in complex with neutralizing antibody COV91-27
Components
  • Neutralizing antibody COV91-27 heavy chain
  • Neutralizing antibody COV91-27 light chain
  • Spike protein S2 fusion peptide
KeywordsIMMUNE SYSTEM / SARS-CoV-2 / coronavirus / antibody / fusion peptide / neutralizing antibody / COVID-19
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 / 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 speciesHomo sapiens (human)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsLee, C.C.D. / Lin, T.H. / 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 6, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 27, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 3, 2022Group: Database references / Category: citation / citation_author
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
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
A: Neutralizing antibody COV91-27 heavy chain
B: Neutralizing antibody COV91-27 light chain
C: Neutralizing antibody COV91-27 heavy chain
D: Neutralizing antibody COV91-27 light chain
E: Neutralizing antibody COV91-27 heavy chain
F: Neutralizing antibody COV91-27 light chain
G: Neutralizing antibody COV91-27 heavy chain
H: Spike protein S2 fusion peptide
I: Neutralizing antibody COV91-27 light chain
J: Spike protein S2 fusion peptide
K: Spike protein S2 fusion peptide
L: Spike protein S2 fusion peptide


Theoretical massNumber of molelcules
Total (without water)195,63112
Polymers195,63112
Non-polymers00
Water3,297183
1
A: Neutralizing antibody COV91-27 heavy chain
B: Neutralizing antibody COV91-27 light chain
H: Spike protein S2 fusion peptide


Theoretical massNumber of molelcules
Total (without water)48,9083
Polymers48,9083
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4800 Å2
ΔGint-32 kcal/mol
Surface area19650 Å2
MethodPISA
2
C: Neutralizing antibody COV91-27 heavy chain
D: Neutralizing antibody COV91-27 light chain
K: Spike protein S2 fusion peptide


Theoretical massNumber of molelcules
Total (without water)48,9083
Polymers48,9083
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4800 Å2
ΔGint-31 kcal/mol
Surface area19700 Å2
MethodPISA
3
E: Neutralizing antibody COV91-27 heavy chain
F: Neutralizing antibody COV91-27 light chain
J: Spike protein S2 fusion peptide


Theoretical massNumber of molelcules
Total (without water)48,9083
Polymers48,9083
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4720 Å2
ΔGint-28 kcal/mol
Surface area19780 Å2
MethodPISA
4
G: Neutralizing antibody COV91-27 heavy chain
I: Neutralizing antibody COV91-27 light chain
L: Spike protein S2 fusion peptide


Theoretical massNumber of molelcules
Total (without water)48,9083
Polymers48,9083
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4770 Å2
ΔGint-31 kcal/mol
Surface area19970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)196.173, 60.314, 186.509
Angle α, β, γ (deg.)90.000, 109.520, 90.000
Int Tables number5
Space group name H-MC121

-
Components

#1: Antibody
Neutralizing antibody COV91-27 heavy chain


Mass: 23758.676 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Mus musculus (house mouse)
#2: Antibody
Neutralizing antibody COV91-27 light chain


Mass: 23382.014 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Mus musculus (house mouse)
#3: Protein/peptide
Spike protein S2 fusion peptide


Mass: 1767.054 Da / Num. of mol.: 4 / Source method: obtained synthetically
Source: (synth.) Severe acute respiratory syndrome coronavirus 2
References: UniProt: P0DTC2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 183 / 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: 2.66 Å3/Da / Density % sol: 53.72 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 70% 2-methyl-2,4-pentanediol and 0.1M HEPES, pH 7.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.97946 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 10, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 88859 / % possible obs: 97.2 % / Redundancy: 4.8 % / Biso Wilson estimate: 52.01 Å2 / Rmerge(I) obs: 0.128 / Rpim(I) all: 0.067 / Rrim(I) all: 0.146 / Χ2: 0.779 / Net I/σ(I): 4.2 / Num. measured all: 424101
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.3-2.345.11.43544130.4820.71.6060.32198.5
2.34-2.385.11.23445100.5520.5981.3790.32198.7
2.38-2.435.11.10944360.5640.5421.2410.34398.6
2.43-2.485.20.97844690.7110.4741.0920.33698.7
2.48-2.535.20.944610.7390.4351.0050.35998.4
2.53-2.595.10.73844580.8140.3610.8260.38798
2.59-2.6650.64344250.8240.3160.720.41997.7
2.66-2.7350.52144990.8860.2590.5850.46597.7
2.73-2.814.80.45143920.9060.2280.5080.49397.5
2.81-2.94.30.34643380.9370.1860.3950.57294.4
2.9-35.10.30645040.9550.1510.3430.66198.8
3-3.125.10.24545050.9720.1210.2750.74799.2
3.12-3.264.90.20344980.9780.1020.2280.92198.8
3.26-3.444.70.15844690.9840.0820.1791.02497.8
3.44-3.654.50.12244490.9910.0660.1391.1996.9
3.65-3.934.30.09743610.9930.0530.1111.27795
3.93-4.333.80.0741790.9960.0420.0821.41390.7
4.33-4.954.30.05843930.9970.0330.0671.58495.2
4.95-6.244.60.0645060.9960.0320.0681.64797.2
6.24-504.20.05145940.9970.030.0591.99295.7

-
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: 6W41

6w41


Resolution: 2.3→46.22 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 35.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2793 4453 5.03 %
Rwork0.2354 84062 -
obs0.2376 88515 96.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 121.13 Å2 / Biso mean: 57.49 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 2.3→46.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13591 0 0 183 13774
Biso mean---56.82 -
Num. residues----1790
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.330.38231020.37682284238678
2.33-2.350.40851590.37092746290597
2.35-2.380.37871560.35142876303298
2.38-2.410.40431530.34962834298798
2.41-2.440.36221530.352854300798
2.44-2.480.3461390.33432828296799
2.48-2.510.38261530.33232900305398
2.51-2.550.34021480.32482788293698
2.55-2.590.37831740.31092802297698
2.59-2.630.33121370.29162898303598
2.63-2.680.3681410.2872804294598
2.68-2.730.33861580.27622835299397
2.73-2.780.3431440.27462820296498
2.78-2.840.36421370.28172809294697
2.84-2.90.32751360.28162738287494
2.9-2.960.3591380.292827296598
2.96-3.040.32641710.27092898306999
3.04-3.120.32771650.26272849301499
3.12-3.210.34041540.25252902305699
3.21-3.320.25161370.25012895303298
3.32-3.440.3131560.23722791294797
3.44-3.570.26051680.22482817298597
3.57-3.730.27751260.23242805293196
3.74-3.930.27651410.21862801294295
3.93-4.180.22771510.212668281992
4.18-4.50.22611430.18132671281491
4.5-4.950.21091450.17532806295195
4.95-5.670.23991510.19552876302797
5.67-7.140.26541640.22662870303497
7.14-46.220.21181530.18412770292390

+
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