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- PDB-4jgs: Crystal structure of the xmrv tm retroviral fusion core -

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Basic information

Entry
Database: PDB / ID: 4jgs
TitleCrystal structure of the xmrv tm retroviral fusion core
ComponentsMLV-related proviral Env polyprotein
KeywordsVIRAL PROTEIN / six helix bundle / viral-host membrane fusion / XMRV TM / viral surface
Function / homology
Function and homology information


membrane => GO:0016020 / fusion of virus membrane with host plasma membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / metal ion binding / plasma membrane
Similarity search - Function
F-MuLV receptor-binding / ENV polyprotein (coat polyprotein) / TLV/ENV coat polyprotein / Helix Hairpins - #210 / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Putative envelope glycoprotein / MLV-related proviral Env polyprotein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsCook, J.D. / Aydin, H. / Lee, J.E.
CitationJournal: J.Virol. / Year: 2014
Title: Crystal structures of Beta- and gammaretrovirus fusion proteins reveal a role for electrostatic stapling in viral entry.
Authors: Aydin, H. / Cook, J.D. / Lee, J.E.
History
DepositionMar 2, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2014Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MLV-related proviral Env polyprotein
B: MLV-related proviral Env polyprotein
C: MLV-related proviral Env polyprotein
D: MLV-related proviral Env polyprotein
E: MLV-related proviral Env polyprotein
F: MLV-related proviral Env polyprotein
G: MLV-related proviral Env polyprotein
H: MLV-related proviral Env polyprotein
I: MLV-related proviral Env polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,79612
Polymers102,6909
Non-polymers1063
Water5,423301
1
A: MLV-related proviral Env polyprotein
E: MLV-related proviral Env polyprotein
G: MLV-related proviral Env polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2654
Polymers34,2303
Non-polymers351
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7970 Å2
ΔGint-76 kcal/mol
Surface area12990 Å2
MethodPISA
2
B: MLV-related proviral Env polyprotein
F: MLV-related proviral Env polyprotein
I: MLV-related proviral Env polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2654
Polymers34,2303
Non-polymers351
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7890 Å2
ΔGint-78 kcal/mol
Surface area12040 Å2
MethodPISA
3
C: MLV-related proviral Env polyprotein
D: MLV-related proviral Env polyprotein
H: MLV-related proviral Env polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2654
Polymers34,2303
Non-polymers351
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8110 Å2
ΔGint-80 kcal/mol
Surface area12910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.973, 148.420, 58.098
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
MLV-related proviral Env polyprotein / Transmembrane protein / TM


Mass: 11409.979 Da / Num. of mol.: 9 / Fragment: fusion core, UNP residues 469-564
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pJexpress414 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P10404, UniProt: D0UFA8*PLUS
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 301 / Source method: isolated from a natural source / Formula: H2O

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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: 2.1 Å3/Da / Density % sol: 41.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 23% (w/v) PEG 3350, 0.1 M Bis-Tris pH 5.5, 0.2 M NaCl and 4% (v/v) 2,2,2-trifluoroethanol, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: Jan 10, 2011
RadiationMonochromator: VariMax HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→47.58 Å / Num. all: 44752 / Num. obs: 44752 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.6 % / Rmerge(I) obs: 0.088 / Χ2: 0.88 / Net I/σ(I): 9 / Scaling rejects: 15554
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
2.2-2.285.730.5542.12696643981.1499.6
2.28-2.376.660.4652.83097144041.09100
2.37-2.486.690.3923.33125544231.04100
2.48-2.616.70.32243132544281100
2.61-2.776.760.2714.63160344500.95100
2.77-2.996.790.2065.73150544140.9100
2.99-3.296.820.13783196544670.8100
3.29-3.766.80.07913.43197344830.69100
3.76-4.746.790.05419.13217145560.62100
4.74-47.586.30.04124.83134447290.6499.3

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Processing

Software
NameVersionClassificationNB
d*TREK9.9.8.9Ddata reduction
PHENIXrefinement
PDB_EXTRACT3.11data extraction
CrystalCleardata collection
d*TREKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MOF

1mof


Resolution: 2.2→47.58 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 2 / Stereochemistry target values: ML
RfactorNum. reflectionSelection details
Rfree0.266 1764 random
Rwork0.214 --
all0.214 44752 -
obs0.214 44752 -
Displacement parametersBiso max: 91.71 Å2 / Biso mean: 31.4206 Å2 / Biso min: 11.54 Å2
Refinement stepCycle: LAST / Resolution: 2.2→47.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5748 0 3 301 6052
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.013
X-RAY DIFFRACTIONf_angle_d1.31

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