[English] 日本語
Yorodumi
- PDB-9n55: X-ray Crystallographic Structure of Lipid-bound Orf9b Homodimer -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9n55
TitleX-ray Crystallographic Structure of Lipid-bound Orf9b Homodimer
ComponentsORF9b protein
KeywordsVIRAL PROTEIN / Lipid-binding protein / homodimer / SARS-CoV-2 / Innate immune suppressor
Function / homology
Function and homology information


Translation of Accessory Proteins / outer mitochondrial membrane protein complex / negative regulation of defense response to virus / positive regulation of autophagosome assembly / negative regulation of mitochondrial fission / host cell mitochondrion / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / protein sequestering activity / mitochondrial membrane / DDX58/IFIH1-mediated induction of interferon-alpha/beta ...Translation of Accessory Proteins / outer mitochondrial membrane protein complex / negative regulation of defense response to virus / positive regulation of autophagosome assembly / negative regulation of mitochondrial fission / host cell mitochondrion / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / protein sequestering activity / mitochondrial membrane / DDX58/IFIH1-mediated induction of interferon-alpha/beta / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / SARS-CoV-2 activates/modulates innate and adaptive immune responses / identical protein binding
Similarity search - Function
Protein 9b, Betacoronavirus / Protein 9b, SARS-CoV / Betacoronavirus lipid binding protein / Sarbecovirus 9b domain profile.
Similarity search - Domain/homology
N-OCTANE / ORF9b protein
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsSan Felipe, C.J. / Fraser, J.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U19AI171110 United States
CitationJournal: To Be Published
Title: X-ray Crystallographic Structure of Lipid-bound Orf9b Homodimer
Authors: San Felipe, C.J. / Fraser, J.S.
History
DepositionFeb 3, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 12, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ORF9b protein
B: ORF9b protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7323
Polymers21,6172
Non-polymers1141
Water90150
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3810 Å2
ΔGint-9 kcal/mol
Surface area9890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.850, 64.230, 73.570
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

#1: Protein ORF9b protein / ORF9b / Accessory protein 9b / ORF-9b / Protein 9b


Mass: 10808.636 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: 9b
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P0DTD2
#2: Chemical ChemComp-OCT / N-OCTANE


Mass: 114.229 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.96 Å3/Da / Density % sol: 37.22 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: PEG3350, PEG1K, MPD, Ethylene Glycol, Imidazole, MES

-
Data collection

DiffractionMean temperature: 193 K / Ambient temp details: Cryogenic / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.116 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 5, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.116 Å / Relative weight: 1
ReflectionResolution: 1.65→48.38 Å / Num. obs: 38516 / % possible obs: 98.06 % / Redundancy: 3.4 % / Biso Wilson estimate: 27.18 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.07945 / Rrim(I) all: 0.09461 / Net I/σ(I): 7.22
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 3.1 % / Rmerge(I) obs: 1.435 / Mean I/σ(I) obs: 0.97 / Num. unique obs: 1312 / CC1/2: 0.228 / Rrim(I) all: 1.71 / % possible all: 85.11

-
Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→48.38 Å / SU ML: 0.2309 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.0964
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.221 3693 9.59 %
Rwork0.1984 34806 -
obs0.2006 38499 98.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.45 Å2
Refinement stepCycle: LAST / Resolution: 1.65→48.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1309 0 8 50 1367
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00361368
X-RAY DIFFRACTIONf_angle_d0.68561862
X-RAY DIFFRACTIONf_chiral_restr0.0502236
X-RAY DIFFRACTIONf_plane_restr0.0058234
X-RAY DIFFRACTIONf_dihedral_angle_d18.1827537
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.680.35281250.35251173X-RAY DIFFRACTION85.11
1.68-1.70.37041420.35371361X-RAY DIFFRACTION99.87
1.7-1.720.31621460.31361344X-RAY DIFFRACTION99.53
1.72-1.750.40981510.30441360X-RAY DIFFRACTION99.41
1.75-1.780.30071480.28431371X-RAY DIFFRACTION98.7
1.78-1.80.321400.28791342X-RAY DIFFRACTION98.93
1.8-1.840.27361420.24991349X-RAY DIFFRACTION99.73
1.84-1.870.22571410.23561382X-RAY DIFFRACTION99.87
1.87-1.90.28211420.2231365X-RAY DIFFRACTION99.87
1.91-1.940.21991440.2241347X-RAY DIFFRACTION99.93
1.94-1.990.22061460.22571380X-RAY DIFFRACTION99.8
1.99-2.030.19191430.2311318X-RAY DIFFRACTION99.39
2.03-2.080.22761490.21651369X-RAY DIFFRACTION98.89
2.08-2.140.2471430.18781332X-RAY DIFFRACTION98.14
2.14-2.20.18651430.1961354X-RAY DIFFRACTION99.07
2.2-2.270.20651450.19781373X-RAY DIFFRACTION99.54
2.27-2.350.24611450.1771337X-RAY DIFFRACTION99.53
2.36-2.450.22441390.20351362X-RAY DIFFRACTION98.75
2.45-2.560.19841390.19541337X-RAY DIFFRACTION98.07
2.56-2.70.22461440.19651315X-RAY DIFFRACTION96.69
2.7-2.860.25841430.21381315X-RAY DIFFRACTION97.98
2.86-3.090.17481400.1891358X-RAY DIFFRACTION98.75
3.09-3.40.23361420.18021327X-RAY DIFFRACTION97.09
3.4-3.890.20721370.18141304X-RAY DIFFRACTION94.68
3.89-4.90.18361420.15741306X-RAY DIFFRACTION95.96
4.9-48.380.22261320.19961325X-RAY DIFFRACTION96.75
Refinement TLS params.Method: refined / Origin x: 7.4429594855 Å / Origin y: -0.71327402082 Å / Origin z: -3.80636433986 Å
111213212223313233
T0.178366800937 Å20.0090229156293 Å2-0.00526748784318 Å2-0.230232346891 Å20.0649025820844 Å2--0.190935244681 Å2
L1.14800880226 °2-0.549484220401 °2-0.331645576822 °2-4.2573241339 °21.88376196161 °2--3.43266264602 °2
S0.00760355119939 Å °-0.0279676853405 Å °-0.0546711804143 Å °0.0293129499483 Å °-0.0796811483451 Å °-0.0331222365527 Å °0.481232721502 Å °-0.00717836857299 Å °0.0479732783838 Å °
Refinement TLS groupSelection details: all

+
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