[English] 日本語
Yorodumi
- PDB-8u0r: The crystal structure of protein A21, a component of the conserve... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8u0r
TitleThe crystal structure of protein A21, a component of the conserved poxvirus entry-fusion complex
ComponentsVirion membrane protein A21
KeywordsVIRAL PROTEIN / Poxvirus / entry-fusion complex / poxvirus A21 protein / vaccinia virus
Function / homology
Function and homology information


membrane fusion involved in viral entry into host cell / viral envelope / symbiont entry into host cell / virion membrane / membrane
Similarity search - Function
Poxvirus A21 / Poxvirus A21 Protein
Similarity search - Domain/homology
2-AMINO-ETHANETHIOL / ETHANOL / IODIDE ION / ISOPROPYL ALCOHOL / METHANOL / 1,3-PROPANDIOL / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / R-1,2-PROPANEDIOL / N-PROPANOL / Virion membrane protein A21
Similarity search - Component
Biological speciesVaccinia virus Western Reserve
MethodX-RAY DIFFRACTION / SAD / Resolution: 2.3 Å
AuthorsDiesterbeck, U. / Gittis, A.G. / Garboczi, D.N. / Moss, B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: J.Mol.Biol. / Year: 2025
Title: The 2.3 angstrom Structure of A21, a Protein Component of the Conserved Poxvirus Entry-Fusion Complex.
Authors: Diesterbeck, U.S. / Muslinkina, L.A. / Gittis, A.G. / Singh, K. / Moss, B. / Garboczi, D.N.
History
DepositionAug 29, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 2, 2025Group: Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / pdbx_entry_details / pdbx_modification_feature
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification
Revision 1.2Apr 9, 2025Group: Database references / Category: citation / Item: _citation.journal_volume

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Virion membrane protein A21
B: Virion membrane protein A21
C: Virion membrane protein A21
D: Virion membrane protein A21
E: Virion membrane protein A21
F: Virion membrane protein A21
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,88673
Polymers66,0516
Non-polymers4,83667
Water1,51384
1
A: Virion membrane protein A21
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,76213
Polymers11,0081
Non-polymers75312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Virion membrane protein A21
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,39717
Polymers11,0081
Non-polymers1,38916
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Virion membrane protein A21
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,77612
Polymers11,0081
Non-polymers76811
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Virion membrane protein A21
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,71010
Polymers11,0081
Non-polymers7029
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Virion membrane protein A21
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,4398
Polymers11,0081
Non-polymers4317
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Virion membrane protein A21
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,80113
Polymers11,0081
Non-polymers79312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.860, 70.060, 78.950
Angle α, β, γ (deg.)90.000, 95.290, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

-
Protein , 1 types, 6 molecules ABCDEF

#1: Protein
Virion membrane protein A21


Mass: 11008.442 Da / Num. of mol.: 6 / Mutation: Residues 24-117
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vaccinia virus Western Reserve / Gene: MVA131L / Production host: Escherichia coli (E. coli) / References: UniProt: P68711

-
Non-polymers , 16 types, 151 molecules

#2: Chemical
ChemComp-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-MOH / METHANOL


Mass: 32.042 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: CH4O
#5: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: I
#6: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cl
#7: Chemical
ChemComp-PDO / 1,3-PROPANDIOL


Mass: 76.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O2
#8: Chemical ChemComp-PGR / R-1,2-PROPANEDIOL


Mass: 76.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O2
#9: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#10: Chemical ChemComp-PG0 / 2-(2-METHOXYETHOXY)ETHANOL / PEG 6000


Mass: 120.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12O3 / Comment: precipitant*YM
#11: Chemical ChemComp-DHL / 2-AMINO-ETHANETHIOL / 2,3-DESHYDROLANTHIONINE


Type: L-peptide linking / Mass: 77.149 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H7NS
#12: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#13: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#14: Chemical ChemComp-POL / N-PROPANOL / 1-PROPONOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O
#15: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#16: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O
#17: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 1.95 Å3/Da / Density % sol: 37.04 % / Description: Rod-shaped
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: One mL of protein at a concentration of 10 mg/ml in i10 mM Tris-HCl, 50 mM NaCl, pH 8.0 was mixed with 1 mL of mother liquor containing 20% PEG 4000, 0.1 M Na-citrate, 10% ethanol, and 1-5% ...Details: One mL of protein at a concentration of 10 mg/ml in i10 mM Tris-HCl, 50 mM NaCl, pH 8.0 was mixed with 1 mL of mother liquor containing 20% PEG 4000, 0.1 M Na-citrate, 10% ethanol, and 1-5% cocktail mixture of low molecular alcohols,

-
Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: RIGAKU MICROMAX-003 / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Oct 28, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.3→39.31 Å / Num. obs: 22602 / % possible obs: 99.2 % / Redundancy: 7.31 % / Biso Wilson estimate: 48.69 Å2 / Rmerge(I) obs: 0.101 / Rrim(I) all: 0.118 / Net I/σ(I): 8.2
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.333 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 1595 / Rrim(I) all: 0.399 / % possible all: 91

-
Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
CrystalCleardata reduction
CrystalCleardata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→39.31 Å / SU ML: 0.3143 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 27.0987
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2394 1810 8.01 %
Rwork0.2113 20792 -
obs0.2136 22602 99.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51 Å2
Refinement stepCycle: LAST / Resolution: 2.3→39.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3389 0 213 84 3686
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01133602
X-RAY DIFFRACTIONf_angle_d1.30134804
X-RAY DIFFRACTIONf_chiral_restr0.2326523
X-RAY DIFFRACTIONf_plane_restr0.0073628
X-RAY DIFFRACTIONf_dihedral_angle_d15.11541255
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.360.33161270.29241468X-RAY DIFFRACTION91.14
2.36-2.430.36111400.27041606X-RAY DIFFRACTION100
2.43-2.510.32231400.26711598X-RAY DIFFRACTION99.89
2.51-2.60.30341390.26051598X-RAY DIFFRACTION100
2.6-2.70.28621380.25171590X-RAY DIFFRACTION99.94
2.7-2.830.28861390.23991597X-RAY DIFFRACTION99.94
2.83-2.980.27631390.24241606X-RAY DIFFRACTION100
2.98-3.160.22711420.22681626X-RAY DIFFRACTION100
3.16-3.410.23691380.20121599X-RAY DIFFRACTION99.88
3.41-3.750.21721400.19161605X-RAY DIFFRACTION99.94
3.75-4.290.18211400.18251609X-RAY DIFFRACTION100
4.29-5.40.20841420.17051632X-RAY DIFFRACTION100
5.4-39.310.26381460.23291658X-RAY DIFFRACTION99.61

+
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