[English] 日本語
Yorodumi
- PDB-8dgx: Crystal structure of MERS-CoV spike stem helix peptide in complex... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8dgx
TitleCrystal structure of MERS-CoV spike stem helix peptide in complex with Fab of broadly neutralizing antibody CC68.109 isolated from a vaccinated COVID-19 convalescent
Components
  • Antibody CC68.109 Fab heavy chain
  • Antibody CC68.109 Fab light chain
  • Spike protein S2'
KeywordsIMMUNE SYSTEM / broadly neutralizing antibody / pan-betacoronavirus / S2 stem helix / spike / SARS-CoV-2 / MERS-CoV / HCoV-HKU1 / sarbecovirus / cross-reactive / cross-neutralizing
Function / homology
Function and homology information


membrane fusion / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / 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 / host cell plasma membrane / virion membrane / membrane
Similarity search - Function
Spike (S) protein S1 subunit, receptor-binding domain, MERS-CoV / Spike (S) protein S1 subunit, N-terminal domain, MERS-CoV-like / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / 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, MERS-CoV / Spike (S) protein S1 subunit, N-terminal domain, MERS-CoV-like / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / 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 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 1 (HR1) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Middle East respiratory syndrome-related coronavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.89 Å
AuthorsLiu, H. / Wilson, I.A.
Funding support United States, 1items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationINV-004923 United States
CitationJournal: Immunity / Year: 2023
Title: Broadly neutralizing anti-S2 antibodies protect against all three human betacoronaviruses that cause deadly disease.
Authors: Zhou, P. / Song, G. / Liu, H. / Yuan, M. / He, W.T. / Beutler, N. / Zhu, X. / Tse, L.V. / Martinez, D.R. / Schafer, A. / Anzanello, F. / Yong, P. / Peng, L. / Dueker, K. / Musharrafieh, R. / ...Authors: Zhou, P. / Song, G. / Liu, H. / Yuan, M. / He, W.T. / Beutler, N. / Zhu, X. / Tse, L.V. / Martinez, D.R. / Schafer, A. / Anzanello, F. / Yong, P. / Peng, L. / Dueker, K. / Musharrafieh, R. / Callaghan, S. / Capozzola, T. / Limbo, O. / Parren, M. / Garcia, E. / Rawlings, S.A. / Smith, D.M. / Nemazee, D. / Jardine, J.G. / Safonova, Y. / Briney, B. / Rogers, T.F. / Wilson, I.A. / Baric, R.S. / Gralinski, L.E. / Burton, D.R. / Andrabi, R.
History
DepositionJun 24, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 1, 2023Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_DOI
Revision 1.2Mar 22, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
H: Antibody CC68.109 Fab heavy chain
L: Antibody CC68.109 Fab light chain
A: Antibody CC68.109 Fab heavy chain
B: Antibody CC68.109 Fab light chain
C: Spike protein S2'
D: Spike protein S2'


Theoretical massNumber of molelcules
Total (without water)100,9226
Polymers100,9226
Non-polymers00
Water00
1
H: Antibody CC68.109 Fab heavy chain
L: Antibody CC68.109 Fab light chain
C: Spike protein S2'


Theoretical massNumber of molelcules
Total (without water)50,4613
Polymers50,4613
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4480 Å2
ΔGint-32 kcal/mol
Surface area19620 Å2
MethodPISA
2
A: Antibody CC68.109 Fab heavy chain
B: Antibody CC68.109 Fab light chain
D: Spike protein S2'


Theoretical massNumber of molelcules
Total (without water)50,4613
Polymers50,4613
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4610 Å2
ΔGint-33 kcal/mol
Surface area19000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.997, 66.499, 94.386
Angle α, β, γ (deg.)90.000, 107.760, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 4 through 18 or (resid 19...
21(chain H and (resid 4 through 12 or (resid 13...
12(chain B and (resid 2 through 17 or (resid 18...
22(chain L and (resid 2 through 126 or (resid 127...
13chain C
23(chain D and (resid 1228 through 1236 or (resid 1237...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111LEULEUVALVAL(chain A and (resid 4 through 18 or (resid 19...AC4 - 184 - 18
121LYSLYSLYSLYS(chain A and (resid 4 through 18 or (resid 19...AC1919
131LEULEULYSLYS(chain A and (resid 4 through 18 or (resid 19...AC4 - 2144 - 219
141LEULEULYSLYS(chain A and (resid 4 through 18 or (resid 19...AC4 - 2144 - 219
151LEULEULYSLYS(chain A and (resid 4 through 18 or (resid 19...AC4 - 2144 - 219
161LEULEULYSLYS(chain A and (resid 4 through 18 or (resid 19...AC4 - 2144 - 219
211LEULEULYSLYS(chain H and (resid 4 through 12 or (resid 13...HA4 - 124 - 12
221LYSLYSLYSLYS(chain H and (resid 4 through 12 or (resid 13...HA1313
231LEULEULYSLYS(chain H and (resid 4 through 12 or (resid 13...HA4 - 2144 - 219
241LEULEULYSLYS(chain H and (resid 4 through 12 or (resid 13...HA4 - 2144 - 219
251LEULEULYSLYS(chain H and (resid 4 through 12 or (resid 13...HA4 - 2144 - 219
261LEULEULYSLYS(chain H and (resid 4 through 12 or (resid 13...HA4 - 2144 - 219
112ILEILEGLUGLU(chain B and (resid 2 through 17 or (resid 18...BD2 - 172 - 17
122ARGARGALAALA(chain B and (resid 2 through 17 or (resid 18...BD18 - 1918 - 19
132ILEILEARGARG(chain B and (resid 2 through 17 or (resid 18...BD2 - 2112 - 214
142ILEILEARGARG(chain B and (resid 2 through 17 or (resid 18...BD2 - 2112 - 214
152ILEILEARGARG(chain B and (resid 2 through 17 or (resid 18...BD2 - 2112 - 214
162ILEILEARGARG(chain B and (resid 2 through 17 or (resid 18...BD2 - 2112 - 214
212ILEILELYSLYS(chain L and (resid 2 through 126 or (resid 127...LB2 - 1262 - 129
222SERSERSERSER(chain L and (resid 2 through 126 or (resid 127...LB127130
232ILEILEARGARG(chain L and (resid 2 through 126 or (resid 127...LB2 - 2112 - 214
242ILEILEARGARG(chain L and (resid 2 through 126 or (resid 127...LB2 - 2112 - 214
252ILEILEARGARG(chain L and (resid 2 through 126 or (resid 127...LB2 - 2112 - 214
262ILEILEARGARG(chain L and (resid 2 through 126 or (resid 127...LB2 - 2112 - 214
113GLYGLYVALVALchain CCE1228 - 12428 - 22
213GLYGLYASPASP(chain D and (resid 1228 through 1236 or (resid 1237...DF1228 - 12368 - 16
223GLUGLUGLUGLU(chain D and (resid 1228 through 1236 or (resid 1237...DF123717
233GLYGLYVALVAL(chain D and (resid 1228 through 1236 or (resid 1237...DF1228 - 12428 - 22
243GLYGLYVALVAL(chain D and (resid 1228 through 1236 or (resid 1237...DF1228 - 12428 - 22
253GLYGLYVALVAL(chain D and (resid 1228 through 1236 or (resid 1237...DF1228 - 12428 - 22
263GLYGLYVALVAL(chain D and (resid 1228 through 1236 or (resid 1237...DF1228 - 12428 - 22

NCS ensembles :
ID
1
2
3

-
Components

#1: Antibody Antibody CC68.109 Fab heavy chain


Mass: 23606.367 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody Antibody CC68.109 Fab light chain


Mass: 23869.520 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Protein/peptide Spike protein S2'


Mass: 2985.236 Da / Num. of mol.: 2 / Fragment: Stem helix domain, residues 1221-1247 / Source method: obtained synthetically
Source: (synth.) Middle East respiratory syndrome-related coronavirus (isolate United Kingdom/H123990006/2012)
References: UniProt: K9N5Q8
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.04 Å3/Da / Density % sol: 39.8 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.17 M Sodium acetate, 25.5% (w/v) PEG 4000, 15% (v/v) Glycerol, 0.085 M Tris pH 8.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 31, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.89→50 Å / Num. obs: 17356 / % possible obs: 94.4 % / Redundancy: 3 % / Biso Wilson estimate: 53.82 Å2 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.056 / Rrim(I) all: 0.1 / Χ2: 0.87 / Net I/σ(I): 6.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.9-2.952.60.7256310.450.5090.890.77173
2.95-32.60.6766920.4850.4740.8290.79975.5
3-3.062.60.557430.7470.3770.670.73682.1
3.06-3.122.70.527760.7660.3570.6330.79684.6
3.12-3.192.70.4138240.7930.2940.5090.84988.8
3.19-3.272.70.4468410.7920.3080.5440.80594.2
3.27-3.352.90.3488860.8910.2410.4250.86196.2
3.35-3.443.10.2958940.9240.1970.3560.89299
3.44-3.543.20.2689260.920.1780.3230.92899.4
3.54-3.653.20.229110.9550.1460.2650.92899.5
3.65-3.783.10.1669050.970.1130.2020.92599.5
3.78-3.942.90.1469280.9630.1010.1791.05399.8
3.94-4.1130.1199100.9740.0810.1450.94299.7
4.11-4.333.20.0929170.9850.0620.1110.99399.6
4.33-4.63.20.0819150.9870.0540.0981.04399
4.6-4.963.10.0689280.9910.0450.0820.96699.3
4.96-5.462.90.0639010.990.0440.0770.86898.9
5.46-6.243.20.0639300.9880.0420.0760.78199.5
6.24-7.863.10.0549410.9910.0360.0650.72799.5
7.86-5030.0439570.9940.0290.0530.57599.1

-
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: 7JMW; 7KN4

7jmw

7kn4


Resolution: 2.89→46.69 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 28.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2798 651 4.83 %
Rwork0.2327 12835 -
obs0.2351 13486 73.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 177.52 Å2 / Biso mean: 51.5285 Å2 / Biso min: 15.24 Å2
Refinement stepCycle: final / Resolution: 2.89→46.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6507 0 0 0 6507
Num. residues----888
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1298X-RAY DIFFRACTION9.667TORSIONAL
12H1298X-RAY DIFFRACTION9.667TORSIONAL
21B1288X-RAY DIFFRACTION9.667TORSIONAL
22L1288X-RAY DIFFRACTION9.667TORSIONAL
31C84X-RAY DIFFRACTION9.667TORSIONAL
32D84X-RAY DIFFRACTION9.667TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.89-3.120.3251600.3126940100028
3.12-3.430.3715930.2761975206857
3.43-3.930.30411640.25552901306583
3.93-4.950.28241730.20683462363599
4.95-46.690.23261610.22443557371899
Refinement TLS params.Method: refined / Origin x: -28.2564 Å / Origin y: -5.0219 Å / Origin z: -20.2292 Å
111213212223313233
T0.2485 Å20.0094 Å20.0971 Å2-0.1467 Å2-0.0314 Å2--0.1703 Å2
L1.3674 °20.2465 °20.5169 °2-0.841 °20.0427 °2--0.6598 °2
S0.1253 Å °0.1844 Å °0.1552 Å °-0.1707 Å °-0.1033 Å °-0.1983 Å °0.1548 Å °-0.0593 Å °-0.0072 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allH4 - 214
2X-RAY DIFFRACTION1allL2 - 211
3X-RAY DIFFRACTION1allA4 - 214
4X-RAY DIFFRACTION1allB2 - 211
5X-RAY DIFFRACTION1allC1228 - 1242
6X-RAY DIFFRACTION1allD1228 - 1242

+
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