[English] 日本語
Yorodumi
- PDB-8x5o: Crystal structure of the post-fusion core of MjHKUr-CoV spike protein. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8x5o
TitleCrystal structure of the post-fusion core of MjHKUr-CoV spike protein.
Componentsspike protein S2
KeywordsVIRAL PROTEIN / MjHKUr-CoV / spike protein / postfusion / VIRUS
Function / homology
Function and homology information


host cell endoplasmic reticulum-Golgi intermediate compartment membrane / 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, HKU4-like / 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, HKU4-like / 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
Similarity search - Domain/homology
Spike glycoprotein / Spike glycoprotein
Similarity search - Component
Biological speciesCoronavirus HKU15
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.67 Å
AuthorsZhu, Y. / Yang, X. / Sun, F.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Fusion mechanism of MjHKUr-CoV spike and its entry inhibitor
Authors: Zhu, Y. / Sun, F. / Lu, L.
History
DepositionNov 17, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 21, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: spike protein S2
B: spike protein S2
C: spike protein S2


Theoretical massNumber of molelcules
Total (without water)40,2183
Polymers40,2183
Non-polymers00
Water2,252125
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9690 Å2
ΔGint-87 kcal/mol
Surface area17870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)198.736, 198.736, 64.130
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-1212-

HOH

-
Components

#1: Protein spike protein S2


Mass: 13405.909 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coronavirus HKU15 / Gene: S / Production host: Escherichia coli (E. coli) / References: UniProt: A3EX94, UniProt: S4WYD6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.55 Å3/Da / Density % sol: 72.94 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: 2.8M Sodium Acetate, HCl pH 7.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU / Detector: CCD / Date: Nov 9, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.47→34.42 Å / Num. obs: 26093 / % possible obs: 96.8 % / Redundancy: 27.1 % / CC1/2: 0.982 / Net I/σ(I): 9.5
Reflection shellResolution: 2.47→2.57 Å / Num. unique obs: 2602 / CC1/2: 0.226

-
Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.67→34.42 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2915 1096 5.07 %
Rwork0.2407 --
obs0.2433 21610 99.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.67→34.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2489 0 0 125 2614
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003
X-RAY DIFFRACTIONf_angle_d0.489
X-RAY DIFFRACTIONf_dihedral_angle_d3.94331
X-RAY DIFFRACTIONf_chiral_restr0.033425
X-RAY DIFFRACTIONf_plane_restr0.002436
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.67-2.790.36181320.30282437X-RAY DIFFRACTION97
2.79-2.930.34351170.27522517X-RAY DIFFRACTION99
2.93-3.120.33341310.27872533X-RAY DIFFRACTION99
3.12-3.360.27021360.26522533X-RAY DIFFRACTION100
3.36-3.70.31141290.22662560X-RAY DIFFRACTION99
3.7-4.230.22161490.20562573X-RAY DIFFRACTION100
4.23-5.330.24851440.2022604X-RAY DIFFRACTION100
5.33-34.420.33841580.24912757X-RAY DIFFRACTION100
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)
10.03980.01190.05410.02320.00210.1740.134-0.04740.03770.0995-0.13770.0596-0.14170.03230.0330.2521-0.2207-0.10370.128-0.07470.150359.0063-59.25215.4747
20.16010.12220.02890.1010.05290.0538-0.05030.09370.00960.1385-0.02680.026-0.15770.008-0.00120.3774-0.0790.00520.2613-0.03370.266154.323-56.235611.6526
30.04780.048-0.02530.1032-0.01930.04720.0066-0.02080.00180.1524-0.06210.0116-0.0380.0065-0.01330.1684-0.203-0.05410.1695-0.05010.070355.9418-65.81349.2683
40.0032-0.00390.00070.0034-0.00050.001-0.00440.0036-0.0159-0.01860.02050.00320.0243-0.024400.4629-0.0190.00830.4047-0.03150.456350.7762-85.2575-28.2525
50.02650.0299-0.00590.0266-0.00650.01320.0008-0.0574-0.00430.0767-0.0579-0.0474-0.01770.0188-0.04860.1163-0.22270.01040.22550.0240.135961.0349-69.586221.0695
60.03440.02730.02320.09160.01170.02550.02990.0347-0.05750.0935-0.0284-0.0608-0.0240.0136-0.0430.2155-0.189-0.10050.1865-0.01780.147563.0241-66.28824.8259
70.00050.00320.00180.00580.00030.00070.00310.00920.0218-0.0266-0.03330.0399-0.0314-0.0125-0.00010.412-0.13820.04750.31790.07450.32354.9977-60.5607-22.8663
80.0076-0.0076-0.00730.01510.01090.00870.002-0.03710.00490.03910.02-0.07780.00630.03240.00950.21-0.2131-0.09840.25780.0460.245275.905-59.906718.2763
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 989 through 1060 )
2X-RAY DIFFRACTION2chain 'A' and (resid 1061 through 1111 )
3X-RAY DIFFRACTION3chain 'B' and (resid 989 through 1059 )
4X-RAY DIFFRACTION4chain 'B' and (resid 1060 through 1081 )
5X-RAY DIFFRACTION5chain 'B' and (resid 1082 through 1110 )
6X-RAY DIFFRACTION6chain 'C' and (resid 990 through 1060 )
7X-RAY DIFFRACTION7chain 'C' and (resid 1061 through 1087 )
8X-RAY DIFFRACTION8chain 'C' and (resid 1088 through 1110 )

+
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