[English] 日本語
Yorodumi
- PDB-7yi6: bnAb 3D1 in complex with 6-mer HR1 peptide from HCoV-229E S protein -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7yi6
TitlebnAb 3D1 in complex with 6-mer HR1 peptide from HCoV-229E S protein
Components
  • Spike glycoprotein
  • heavy chain of 3D1
  • light chain of 3D1
KeywordsANTIVIRAL PROTEIN/IMMUNE SYSTEM / bnAb / HR1 / 6-mer / ANTIVIRAL PROTEIN / ANTIVIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


endocytosis involved in viral entry into host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion membrane / membrane
Similarity search - Function
Spike glycoprotein, Alphacoronavirus / Spike glycoprotein S1, coronavirus / Coronavirus spike glycoprotein S1 / 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 S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. ...Spike glycoprotein, Alphacoronavirus / Spike glycoprotein S1, coronavirus / Coronavirus spike glycoprotein S1 / 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 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
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Spike glycoprotein
Similarity search - Component
Biological speciesHuman coronavirus 229E
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å
AuthorsYan, L. / Yang, G.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Cross-reactive epitopes between HIV and Coronavirus revealed by 3D1
Authors: Yan, L. / Yang, G.
History
DepositionJul 15, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 30, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 20, 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 glycoprotein
B: light chain of 3D1
D: heavy chain of 3D1
C: Spike glycoprotein
E: light chain of 3D1
F: heavy chain of 3D1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,65713
Polymers93,2056
Non-polymers4527
Water8,251458
1
A: Spike glycoprotein
B: light chain of 3D1
D: heavy chain of 3D1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8868
Polymers46,6033
Non-polymers2845
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4910 Å2
ΔGint-29 kcal/mol
Surface area19140 Å2
MethodPISA
2
C: Spike glycoprotein
E: light chain of 3D1
F: heavy chain of 3D1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7715
Polymers46,6033
Non-polymers1682
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4600 Å2
ΔGint-22 kcal/mol
Surface area18490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.906, 72.703, 86.264
Angle α, β, γ (deg.)90.000, 109.540, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and resid 836 through 841)
21chain C
12(chain B and (resid 3 through 8 or resid 10 through 212))
22(chain E and (resid 3 through 8 or resid 10 through 212))
13(chain D and (resid 1 through 134 or resid 140 through 220))
23chain F

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
111VALVALGLYGLY(chain A and resid 836 through 841)AA836 - 8412 - 7
211VALVALGLYGLYchain CCD836 - 8412 - 7
112ALAALAPROPRO(chain B and (resid 3 through 8 or resid 10 through 212))BB3 - 81 - 6
122ALAALAPROPRO(chain B and (resid 3 through 8 or resid 10 through 212))BB10 - 2128 - 210
212ALAALAPROPRO(chain E and (resid 3 through 8 or resid 10 through 212))EE3 - 81 - 6
222ALAALAPROPRO(chain E and (resid 3 through 8 or resid 10 through 212))EE10 - 2128 - 210
113PCAPCASERSER(chain D and (resid 1 through 134 or resid 140 through 220))DC1 - 1341 - 134
123GLYGLYPROPRO(chain D and (resid 1 through 134 or resid 140 through 220))DC140 - 220140 - 220
213PCAPCAPROPROchain FFF1 - 2201 - 220

NCS ensembles :
ID
1
2
3

-
Components

-
Protein/peptide / Antibody / Protein , 3 types, 6 molecules ACBEDF

#1: Protein/peptide Spike glycoprotein / S glycoprotein / E2 / Peplomer protein


Mass: 758.777 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human coronavirus 229E / Gene: S, 2 / Production host: chemical production metagenome (others) / References: UniProt: P15423
#2: Antibody light chain of 3D1


Mass: 22473.746 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#3: Protein heavy chain of 3D1


Mass: 23370.131 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)

-
Non-polymers , 4 types, 465 molecules

#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 458 / 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: 2.35 Å3/Da / Density % sol: 47.57 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Ammonium sulfate, 0.1 M BIS-TRIS buffer at pH 5.5 and 25% (w/v) polyethylene glycol 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Jan 17, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.28→69.65 Å / Num. obs: 39040 / % possible obs: 99.2 % / Redundancy: 5.6 % / CC1/2: 1 / Net I/σ(I): 11.5
Reflection shellResolution: 2.28→2.34 Å / Num. unique obs: 3986 / CC1/2: 0.91

-
Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6KVF

6kvf


Resolution: 2.28→45.86 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2204 2000 5.13 %
Rwork0.1927 37006 -
obs0.1941 39006 98.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 85.79 Å2 / Biso mean: 32.46 Å2 / Biso min: 12.73 Å2
Refinement stepCycle: final / Resolution: 2.28→45.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6431 0 28 458 6917
Biso mean--43.57 34.5 -
Num. residues----869
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A42X-RAY DIFFRACTION10.987TORSIONAL
12C42X-RAY DIFFRACTION10.987TORSIONAL
21B1805X-RAY DIFFRACTION10.987TORSIONAL
22E1805X-RAY DIFFRACTION10.987TORSIONAL
31D1922X-RAY DIFFRACTION10.987TORSIONAL
32F1922X-RAY DIFFRACTION10.987TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.28-2.340.30511420.2444262699
2.34-2.40.25671420.2323264499
2.4-2.470.28731430.2211262199
2.47-2.550.28071400.2343261399
2.55-2.640.27771430.2222263199
2.64-2.750.26831430.22512660100
2.75-2.870.24651430.2109265799
2.87-3.030.24591430.2103263699
3.03-3.220.24341410.2185263099
3.22-3.460.19811440.1926265499
3.46-3.810.18951420.1848264399
3.81-4.360.18251450.1592266399
4.36-5.490.16211430.1427266299
5.5-60.21611460.1829266697

+
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