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- PDB-4jpr: Structure of the ASLV fusion subunit core -

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Basic information

Entry
Database: PDB / ID: 4jpr
TitleStructure of the ASLV fusion subunit core
ComponentsASLV fusion TM
KeywordsVIRAL PROTEIN / alpha-helix six-helix bundle / membrane fusion
Function / homology
Function and homology information


symbiont entry into host cell / fusion of virus membrane with host plasma membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / membrane
Similarity search - Function
Rous sarcoma virus, Gp95, envelope protein / Avian retrovirus envelope protein, gp85 / ENV polyprotein (coat polyprotein) / TLV/ENV coat polyprotein / Helix Hairpins - #210 / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Envelope glycoprotein gp95
Similarity search - Component
Biological speciesRous sarcoma virus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.001 Å
AuthorsAydin, H. / Smrke, B.M. / Lee, J.E.
CitationJournal: Faseb J. / Year: 2013
Title: Structural characterization of a fusion glycoprotein from a retrovirus that undergoes a hybrid 2-step entry mechanism.
Authors: Aydin, H. / Smrke, B.M. / Lee, J.E.
History
DepositionMar 19, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2013Group: Database references
Revision 1.2Apr 9, 2014Group: Source and taxonomy
Revision 1.3Sep 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: ASLV fusion TM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,7462
Polymers10,7111
Non-polymers351
Water1267
1
A: ASLV fusion TM
hetero molecules

A: ASLV fusion TM
hetero molecules

A: ASLV fusion TM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2396
Polymers32,1333
Non-polymers1063
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-y+2,x-y+1,z1
crystal symmetry operation3_675-x+y+1,-x+2,z1
Buried area6820 Å2
ΔGint-76 kcal/mol
Surface area10430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.544, 42.544, 119.982
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-601-

CL

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Components

#1: Protein ASLV fusion TM / Transmembrane protein / TM / Glycoprotein 37 / gp37


Mass: 10710.980 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rous sarcoma virus (strain Schmidt-Ruppin A)
Strain: Schmidt-Ruppin A / Gene: env / Plasmid: pET46-Ek/LIC / Production host: Escherichia coli (E. coli) / Strain (production host): SHuffle(DE3) / References: UniProt: P03397
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 1.95 Å3/Da / Density % sol: 36.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20% (w/v) MPD, 5% (w/v) PEG 8000, 0.1 M sodium cacodylate pH 6.5, 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: 1.54 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: May 16, 2012
RadiationMonochromator: VariMax / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2→35.22 Å / Num. all: 5486 / Num. obs: 5371 / % possible obs: 97.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.28 % / Rmerge(I) obs: 0.026 / Χ2: 0.96 / Net I/σ(I): 28.6 / Scaling rejects: 580
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
2-2.072.540.3082.711304441.2481.8
2.07-2.153.010.2763.816525441.1197.3
2.15-2.254.550.2135.225445541.08100
2.25-2.375.890.1498.832665460.9999.8
2.37-2.526.020.1071232975380.97100
2.52-2.716.10.0791634065520.89100
2.71-2.996.170.05723.333885420.88100
2.99-3.426.060.03339.133925450.8699.8
3.42-4.316.140.02556.634845550.82100
4.31-35.225.830.01983.134015511.11100

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Processing

Software
NameVersionClassificationNB
d*TREK9.9.9.1Ddata reduction
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
CrystalCleardata collection
d*TREKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MOF

1mof


Resolution: 2.001→35.22 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7412 / SU ML: 0.23 / σ(F): 0.08 / Phase error: 32.47 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.237 531 10.03 %Random
Rwork0.2069 ---
all0.2103 5486 --
obs0.2103 5371 97.9 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 106.11 Å2 / Biso mean: 40.9966 Å2 / Biso min: 12.32 Å2
Refinement stepCycle: LAST / Resolution: 2.001→35.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms556 0 1 7 564
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014564
X-RAY DIFFRACTIONf_angle_d1.363762
X-RAY DIFFRACTIONf_chiral_restr0.07692
X-RAY DIFFRACTIONf_plane_restr0.00599
X-RAY DIFFRACTIONf_dihedral_angle_d15.135191
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0014-2.20280.31931190.23941091121088
2.2028-2.52150.27031350.22291222135799
2.5215-3.17650.24461400.231612211361100
3.1765-35.22610.22081370.19271228136599
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.59290.2170.48380.7091-1.21074.37060.11440.2457-0.1809-0.067-0.1644-0.05630.73110.3065-0.0260.23960.0398-0.02270.1273-0.0250.183123.242531.866256.4089
25.2618-0.1716-5.03055.10831.99118.42510.42260.62550.6999-0.24620.06620.4480.2765-2.0137-0.41320.2661-0.15240.00420.41850.04360.440511.035732.430671.5928
34.88961.0589-1.4963.8889-1.10066.88850.2789-0.6835-0.9336-0.3176-0.0822-0.09570.80830.4399-0.04940.33970.0384-0.15490.40640.07410.545719.87925.499841.1308
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 450 through 490 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 491 through 508 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 509 through 525 )A0

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