[English] 日本語
Yorodumi
- PDB-8w3l: Crystal structure of prefusion-stabilized RSV F protein UFCR2-iSS... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8w3l
TitleCrystal structure of prefusion-stabilized RSV F protein UFCR2-iSS-P2-NQ
Componentsprefusion-stabilized RSV F protein UFCR2-iSS-P2-NQ
KeywordsVIRAL PROTEIN / Respiratory syncytial virus / glycoprotein / prefusion vaccine / stabilized
Biological speciesHuman respiratory syncytial virus A2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsLee, Y.Z. / Stanfield, R.L. / Wilson, I.A. / Zhu, J.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: Nat Commun / Year: 2024
Title: Rational design of uncleaved prefusion-closed trimer vaccines for human respiratory syncytial virus and metapneumovirus.
Authors: Lee, Y.Z. / Han, J. / Zhang, Y.N. / Ward, G. / Braz Gomes, K. / Auclair, S. / Stanfield, R.L. / He, L. / Wilson, I.A. / Zhu, J.
History
DepositionFeb 22, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
F: prefusion-stabilized RSV F protein UFCR2-iSS-P2-NQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,0575
Polymers55,6501
Non-polymers4074
Water1,42379
1
F: prefusion-stabilized RSV F protein UFCR2-iSS-P2-NQ
hetero molecules

F: prefusion-stabilized RSV F protein UFCR2-iSS-P2-NQ
hetero molecules

F: prefusion-stabilized RSV F protein UFCR2-iSS-P2-NQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,17115
Polymers166,9493
Non-polymers1,22212
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_663z+1,x+1,y-21
crystal symmetry operation9_474y-1,z+2,x-11
Buried area10940 Å2
ΔGint-5 kcal/mol
Surface area56480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)168.482, 168.482, 168.482
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number213
Space group name H-MP4132
Space group name HallP4bd2ab3
Symmetry operation#1: x,y,z
#2: x+1/4,-z+1/4,y+3/4
#3: x+3/4,z+1/4,-y+1/4
#4: z+3/4,y+1/4,-x+1/4
#5: -z+1/4,y+3/4,x+1/4
#6: -y+1/4,x+3/4,z+1/4
#7: y+1/4,-x+1/4,z+3/4
#8: z,x,y
#9: y,z,x
#10: -y+1/2,-z,x+1/2
#11: z+1/2,-x+1/2,-y
#12: -y,z+1/2,-x+1/2
#13: -z+1/2,-x,y+1/2
#14: -z,x+1/2,-y+1/2
#15: y+1/2,-z+1/2,-x
#16: x+1/2,-y+1/2,-z
#17: -x,y+1/2,-z+1/2
#18: -x+1/2,-y,z+1/2
#19: y+3/4,x+1/4,-z+1/4
#20: -y+3/4,-x+3/4,-z+3/4
#21: z+1/4,-y+1/4,x+3/4
#22: -z+3/4,-y+3/4,-x+3/4
#23: -x+1/4,z+3/4,y+1/4
#24: -x+3/4,-z+3/4,-y+3/4

-
Components

#1: Protein prefusion-stabilized RSV F protein UFCR2-iSS-P2-NQ


Mass: 55649.660 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human respiratory syncytial virus A2 / Production host: Cricetulus griseus (Chinese hamster)
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.58 Å3/Da / Density % sol: 65.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M tri-Potassium citrate, 20% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.97 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 21, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.3→48.64 Å / Num. obs: 36757 / % possible obs: 99.77 % / Redundancy: 69.4 % / Biso Wilson estimate: 52.84 Å2 / CC1/2: 1 / Net I/σ(I): 29.43
Reflection shellResolution: 2.3→2.383 Å / Num. unique obs: 3545 / CC1/2: 1

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→48.64 Å / SU ML: 0.3217 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.0614
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2565 1799 4.9 %
Rwork0.2272 34941 -
obs0.2286 36740 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 66.78 Å2
Refinement stepCycle: LAST / Resolution: 2.3→48.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3443 0 26 79 3548
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00973522
X-RAY DIFFRACTIONf_angle_d1.41794772
X-RAY DIFFRACTIONf_chiral_restr0.0744577
X-RAY DIFFRACTIONf_plane_restr0.0143604
X-RAY DIFFRACTIONf_dihedral_angle_d4.2548482
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.360.38841540.33682544X-RAY DIFFRACTION98.07
2.36-2.430.33921250.32042663X-RAY DIFFRACTION99.68
2.43-2.510.3341300.30432640X-RAY DIFFRACTION100
2.51-2.60.32871330.2882648X-RAY DIFFRACTION100
2.6-2.70.32431100.26772683X-RAY DIFFRACTION100
2.7-2.830.29611310.27542648X-RAY DIFFRACTION99.96
2.83-2.980.33411470.2732668X-RAY DIFFRACTION100
2.98-3.160.28311350.25942658X-RAY DIFFRACTION100
3.16-3.410.2791440.26372685X-RAY DIFFRACTION100
3.41-3.750.291320.23022720X-RAY DIFFRACTION100
3.75-4.290.24461520.20982703X-RAY DIFFRACTION100
4.29-5.40.20831460.1792755X-RAY DIFFRACTION100
5.41-48.640.20461600.19292926X-RAY DIFFRACTION99.68

+
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