[English] 日本語
Yorodumi
- PDB-7tcq: Crystal structure of SARS-CoV-2 neutralizing antibody WS6 in comp... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7tcq
TitleCrystal structure of SARS-CoV-2 neutralizing antibody WS6 in complex with spike S2 peptide
Components
  • (Anti-SARS-CoV-2 antibody WS6 Fab light ...) x 2
  • Anti-SARS-CoV-2 antibody WS6 Fab heavy chain
  • Pegylated spike S2 peptide
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / SARS-CoV-2 / spike / antibody / VIRAL PROTEIN / 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 / 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 / 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
DI(HYDROXYETHYL)ETHER / Spike glycoprotein
Similarity search - Component
Biological speciesMus musculus (house mouse)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.02 Å
AuthorsZhou, T. / Kwong, P.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Structure / Year: 2022
Title: Vaccine-elicited murine antibody WS6 neutralizes diverse beta-coronaviruses by recognizing a helical stem supersite of vulnerability.
Authors: Shi, W. / Wang, L. / Zhou, T. / Sastry, M. / Yang, E.S. / Zhang, Y. / Chen, M. / Chen, X. / Choe, M. / Creanga, A. / Leung, K. / Olia, A.S. / Pegu, A. / Rawi, R. / Schon, A. / Shen, C.H. / ...Authors: Shi, W. / Wang, L. / Zhou, T. / Sastry, M. / Yang, E.S. / Zhang, Y. / Chen, M. / Chen, X. / Choe, M. / Creanga, A. / Leung, K. / Olia, A.S. / Pegu, A. / Rawi, R. / Schon, A. / Shen, C.H. / Stancofski, E.D. / Talana, C.A. / Teng, I.T. / Wang, S. / Corbett, K.S. / Tsybovsky, Y. / Mascola, J.R. / Kwong, P.D.
History
DepositionDec 28, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2022Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
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: Anti-SARS-CoV-2 antibody WS6 Fab heavy chain
L: Anti-SARS-CoV-2 antibody WS6 Fab light chain
C: Pegylated spike S2 peptide
A: Anti-SARS-CoV-2 antibody WS6 Fab heavy chain
B: Anti-SARS-CoV-2 antibody WS6 Fab light chain
D: Pegylated spike S2 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,94328
Polymers95,8096
Non-polymers2,13422
Water13,241735
1
H: Anti-SARS-CoV-2 antibody WS6 Fab heavy chain
L: Anti-SARS-CoV-2 antibody WS6 Fab light chain
C: Pegylated spike S2 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,16516
Polymers47,8963
Non-polymers1,26913
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Anti-SARS-CoV-2 antibody WS6 Fab heavy chain
B: Anti-SARS-CoV-2 antibody WS6 Fab light chain
D: Pegylated spike S2 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,77812
Polymers47,9133
Non-polymers8659
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)155.063, 64.518, 137.963
Angle α, β, γ (deg.)90.000, 117.340, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11L-569-

HOH

-
Components

-
Protein/peptide , 1 types, 2 molecules CD

#3: Protein/peptide Pegylated spike S2 peptide


Mass: 1462.708 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: N-term acetylated and C-term pegylated
Source: (synth.) Severe acute respiratory syndrome coronavirus 2
References: UniProt: P0DTC2

-
Antibody , 3 types, 4 molecules HALB

#1: Antibody Anti-SARS-CoV-2 antibody WS6 Fab heavy chain


Mass: 23120.688 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell (production host): HEK 293F / Production host: Homo sapiens (human)
#2: Antibody Anti-SARS-CoV-2 antibody WS6 Fab light chain


Mass: 23312.633 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell (production host): HEK 293F / Production host: Homo sapiens (human)
#4: Antibody Anti-SARS-CoV-2 antibody WS6 Fab light chain


Mass: 23329.662 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell (production host): HEK 293F / Production host: Homo sapiens (human)

-
Non-polymers , 3 types, 757 molecules

#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 735 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN
Sequence details(I2J) at the carboxy-terminus of the peptide (chains C and D) is a pegylation. The amino-terminal ...(I2J) at the carboxy-terminus of the peptide (chains C and D) is a pegylation. The amino-terminal glutamine of one of the light chains in the asymmetric unit (chain L) spontaneously formed pyroglutamate.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.54 Å3/Da / Density % sol: 51.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 1.5 M Ammonium sulfate and 30 % PEG400

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Sep 19, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.02→50 Å / Num. obs: 75544 / % possible obs: 95.4 % / Redundancy: 3.3 % / Biso Wilson estimate: 27.88 Å2 / Rmerge(I) obs: 0.132 / Rpim(I) all: 0.083 / Rrim(I) all: 0.157 / Χ2: 1.453 / Net I/σ(I): 6.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.03-2.072.80.79233260.4130.5130.9490.49288.8
2.07-2.12.90.70234680.5290.4580.8440.52591.4
2.1-2.1430.63434950.570.4090.760.57793.6
2.14-2.193.10.58936130.5970.380.7050.62594.6
2.19-2.233.10.56935560.5740.3710.6830.62795.3
2.23-2.293.20.50736210.6270.3310.610.6796
2.29-2.343.20.46636360.6480.3040.560.67596.1
2.34-2.413.30.4536530.6890.2930.540.7396.8
2.41-2.483.30.39636740.7470.2580.4750.80896.7
2.48-2.563.20.34734590.7830.2270.4170.90790.8
2.56-2.653.50.31636820.8220.1970.3740.97697.4
2.65-2.763.60.25937080.8630.160.3061.10798.1
2.76-2.883.60.21137060.9180.1290.2481.29198.1
2.88-3.033.60.1737300.9380.1050.2011.51898
3.03-3.223.50.13237350.9640.0820.1561.99597.9
3.22-3.473.40.10536870.9780.0660.1252.37397.2
3.47-3.823.30.08735220.9840.0550.1032.94192.2
3.82-4.373.60.0737240.990.0430.0822.91997
4.37-5.513.60.0637150.9920.0370.0712.8996.5
5.51-503.50.05837690.9930.0350.0682.92195.5

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.8 Å40.23 Å
Translation3.8 Å40.23 Å

-
Processing

Software
NameVersionClassification
PHENIX1.19refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASER2.8.3phasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7JKT

7jkt


Resolution: 2.02→40.23 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2128 1989 2.63 %
Rwork0.1715 73555 -
obs0.1725 75544 94.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 94.1 Å2 / Biso mean: 32.9514 Å2 / Biso min: 12.88 Å2
Refinement stepCycle: final / Resolution: 2.02→40.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6720 0 148 735 7603
Biso mean--53.7 38.92 -
Num. residues----873
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087005
X-RAY DIFFRACTIONf_angle_d0.9289553
X-RAY DIFFRACTIONf_dihedral_angle_d7.011967
X-RAY DIFFRACTIONf_chiral_restr0.0571052
X-RAY DIFFRACTIONf_plane_restr0.0071193
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.02-2.070.27631130.24674152426575
2.07-2.130.25921340.22645066520092
2.13-2.190.24791400.20415167530794
2.19-2.260.26141450.1975328547396
2.26-2.340.24921440.19745370551497
2.34-2.430.24171440.19665320546497
2.43-2.540.22941450.19665349549496
2.54-2.680.27041400.19075171531194
2.68-2.850.21711470.18325429557698
2.85-3.070.20691490.16965477562698
3.07-3.370.2091480.16145461560998
3.37-3.860.18391420.14745245538794
3.86-4.860.1751480.13635483563198
4.86-40.230.20181500.16875537568796
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)
11.6988-0.80430.14244.96530.37712.21350.0013-0.06030.06880.1063-0.01950.0550.170.03530.02130.1101-0.0011-0.01520.1569-0.01930.134542.19312.692221.1952
24.20110.64021.20011.91340.76552.1307-0.0565-0.05890.0426-0.0338-0.01440.11850.011-0.24330.05470.1120.01370.01360.14080.01760.168112.989619.42318.2319
33.4159-0.35160.3481.62690.38471.7502-0.00670.143-0.0212-0.0818-0.06390.25330.0469-0.24710.05590.13710.0045-0.01750.152-0.03730.199735.0931-7.31481.021
41.7619-1.4588-0.29931.2101-0.0906-0.0219-0.02040.1785-0.22540.0596-0.01330.22220.0238-0.02280.01330.12040.0012-0.01250.1975-0.03040.202423.02058.84384.9945
51.28520.4054-0.23026.55291.15031.9488-0.13050.18020.0691-0.4060.3077-0.3753-0.22820.1049-0.15250.16740.0134-0.01510.25720.03340.242116.601925.3308-2.7412
61.7845-0.37270.6316.00492.49863.0919-0.0580.15970.06880.0098-0.05780.3023-0.2439-0.13670.11480.1013-0.01070.040.22450.05510.174512.389123.87892.569
77.38742.954-0.50877.1376-2.43181.90820.1713-0.234-0.7890.1925-0.0327-0.65581.32360.6854-0.13820.3720.1646-0.05930.295-0.03570.264351.1296-11.793615.8213
88.08843.9884-5.472.6473-3.01075.09320.132-0.0803-0.32380.0739-0.1795-0.18020.23470.19280.05670.37090.0866-0.08620.2559-0.06510.1947-15.800230.316338.5199
95.04262.18150.20124.12411.25493.8140.15520.19380.3646-0.2241-0.08460.04650.04310.0491-0.08240.20370.0917-0.00820.1750.01030.1494-20.299238.987939.1867
104.0870.5101-2.25861.2738-0.39953.25120.07430.05920.3216-0.01320.02530.07710.11780.1356-0.09950.25790.0719-0.03750.2502-0.03690.2043-12.60638.067741.6947
111.8126-0.0325-1.06761.8217-0.47872.8993-0.15470.0440.35870.1444-0.1218-0.3266-0.1480.48390.22670.20710.02430.00750.1911-0.0140.220918.630132.935135.7864
124.7857-1.53982.59581.9294-1.23725.2308-0.0135-0.1652-0.11640.2137-0.01010.0904-0.0684-0.13340.03170.18670.02060.03490.16960.03720.162215.569428.485540.1431
134.10890.59880.91362.52240.51863.28890.0925-0.55020.07910.1568-0.12290.08510.3230.16530.08940.2882-0.00880.0160.3608-0.10130.1778-10.973541.620362.0241
143.5768-0.3402-0.35690.23670.09330.5749-0.1947-0.46930.33810.05060.0832-0.0167-0.03420.110.05190.33180.0055-0.03040.1863-0.02430.234713.306242.17749.0085
154.71640.2056-2.28181.43020.00564.51970.0049-0.25190.5522-0.00680.0325-0.1291-0.76690.2549-0.0460.4148-0.0136-0.09470.20810.00520.300524.094642.320646.0365
168.6112-1.76293.00663.2977-4.78877.03090.459-0.6381-0.22530.20710.06070.78960.194-0.9822-0.48950.3533-0.010.01710.3605-0.05770.2618-30.850139.569150.5126
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-IDBeg PDB ins code
1X-RAY DIFFRACTION1chain 'H' and (resid 1 through 111 )H1 - 111
2X-RAY DIFFRACTION2chain 'H' and (resid 112 through 213 )H112 - 213
3X-RAY DIFFRACTION3chain 'L' and (resid 2 through 75 )L2 - 75
4X-RAY DIFFRACTION4chain 'L' and (resid 76 through 139 )L76 - 139
5X-RAY DIFFRACTION5chain 'L' and (resid 140 through 158 )L140 - 158
6X-RAY DIFFRACTION6chain 'L' and (resid 159 through 213 )L159 - 213
7X-RAY DIFFRACTION7chain 'C' and (resid 1149 through 1157 )C1149 - 1157
8X-RAY DIFFRACTION8chain 'A' and (resid 1 through 32 )A1 - 32
9X-RAY DIFFRACTION9chain 'A' and (resid 33 through 82 )A33 - 82
10X-RAY DIFFRACTION10chain 'A' and (resid 82A through 111 )A82 - 111A
11X-RAY DIFFRACTION11chain 'A' and (resid 112 through 134 )A112 - 134
12X-RAY DIFFRACTION12chain 'A' and (resid 135 through 213 )A135 - 213
13X-RAY DIFFRACTION13chain 'B' and (resid 1 through 89 )B1 - 89
14X-RAY DIFFRACTION14chain 'B' and (resid 90 through 155 )B90 - 155
15X-RAY DIFFRACTION15chain 'B' and (resid 156 through 213 )B156 - 213
16X-RAY DIFFRACTION16chain 'D' and (resid 1149 through 1157 )D1149 - 1157

+
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