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- PDB-8u0r: The crystal structure of protein A21, a component of the conserve... -

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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 / symbiont entry into host cell / viral envelope / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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Components

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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

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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: inhibitor, 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 / Comment: alkaloid*YM
#17: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

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

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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,

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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

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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

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