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- PDB-3wmj: Crystal structure of EIAV vaccine gp45 -

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Basic information

Entry
Database: PDB / ID: 3wmj
TitleCrystal structure of EIAV vaccine gp45
Components(EIAV vaccine gp45) x 2
KeywordsVIRAL PROTEIN / alpha-helix / virus fusion / envelope
Function / homology
Function and homology information


viral envelope / host cell plasma membrane / virion membrane / structural molecule activity / plasma membrane
Similarity search - Function
Gp90 envelope polyprotein of equine infectious anemia virus (EIAV) / EIAV coat protein, gp90 / Retroviral envelope protein / Retroviral envelope protein GP41-like
Similarity search - Domain/homology
Envelope glycoprotein
Similarity search - Component
Biological speciesEquine (horse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.998 Å
AuthorsLiu, X. / Du, J. / Qiao, W.
CitationJournal: To be Published
Title: A mutation associated with EIAV vaccine strain within heptad repeat of EIAV gp45 provides insight into vaccine development for HIV
Authors: Liu, X. / Du, J. / Qiao, W.
History
DepositionNov 19, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 19, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: EIAV vaccine gp45
B: EIAV vaccine gp45


Theoretical massNumber of molelcules
Total (without water)11,0312
Polymers11,0312
Non-polymers00
Water1,15364
1
A: EIAV vaccine gp45
B: EIAV vaccine gp45

A: EIAV vaccine gp45
B: EIAV vaccine gp45

A: EIAV vaccine gp45
B: EIAV vaccine gp45


Theoretical massNumber of molelcules
Total (without water)33,0936
Polymers33,0936
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area13220 Å2
ΔGint-120 kcal/mol
Surface area14370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.947, 46.947, 101.605
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11A-601-

HOH

21A-604-

HOH

31A-615-

HOH

41A-634-

HOH

51A-635-

HOH

61A-636-

HOH

71A-639-

HOH

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Components

#1: Protein EIAV vaccine gp45


Mass: 6580.127 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Equine (horse) / Production host: Escherichia coli (E. coli) / References: UniProt: E2E2L9*PLUS
#2: Protein/peptide EIAV vaccine gp45


Mass: 4450.874 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Equine (horse) / Production host: Escherichia coli (E. coli) / References: UniProt: E2E2L9*PLUS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 64 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT ...THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT THE TIME OF DEPOSITION. THE MUTATION OF THE GP45 IN POSITION 505, IN WILD TYPE IS 505VAL AND IN VACCINE IS 505THR.

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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: 2.93 Å3/Da / Density % sol: 58.03 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 4.6
Details: 0.2M NaCl, 0.1M sodium acetate trihydrate, 30%(v/v) (+/-)-2-methyl-2,4-pentanediol, pH 4.6, EVAPORATION, temperature 293K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9794 Å
DetectorType: ENRAF-NONIUS / Detector: CCD / Date: May 9, 2011
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.998→26.022 Å / Num. obs: 8643 / % possible obs: 11 % / Observed criterion σ(F): 2.2 / Observed criterion σ(I): 2
Reflection shellResolution: 1.998→2.02 Å / % possible all: 95

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.2_1309) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.998→26.022 Å / SU ML: 0.18 / σ(F): 1.36 / Phase error: 23.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2247 409 4.75 %RANDOM
Rwork0.187 ---
obs0.1886 8604 99.64 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.998→26.022 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms772 0 0 64 836
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007784
X-RAY DIFFRACTIONf_angle_d0.8671067
X-RAY DIFFRACTIONf_dihedral_angle_d18.22278
X-RAY DIFFRACTIONf_chiral_restr0.062125
X-RAY DIFFRACTIONf_plane_restr0.003140
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.998-2.28660.24281530.18132702100
2.2866-2.88030.2611220.19992736100
2.8803-26.02460.2081340.183275799

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