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- PDB-5h9c: Crystal structure of the ASLV fusion protein core -

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Basic information

Entry
Database: PDB / ID: 5h9c
TitleCrystal structure of the ASLV fusion protein core
ComponentsEnvelope glycoprotein gp95
KeywordsVIRAL PROTEIN / fusion / ASLV / glycoprotein / entry / virus
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 speciesAvian leukosis virus RSA
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.783 Å
AuthorsAydin, H. / Lee, J.E.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)MOP-115066 Canada
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
DepositionDec 28, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 6, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Envelope glycoprotein gp95
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,6152
Polymers10,5801
Non-polymers351
Water41423
1
A: Envelope glycoprotein gp95
hetero molecules

A: Envelope glycoprotein gp95
hetero molecules

A: Envelope glycoprotein gp95
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8466
Polymers31,7393
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 area7340 Å2
ΔGint-76 kcal/mol
Surface area11050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.800, 42.800, 119.428
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-601-

CL

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Components

#1: Protein Envelope glycoprotein gp95 / Env polyprotein


Mass: 10579.786 Da / Num. of mol.: 1 / Mutation: C499S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Avian leukosis virus RSA / Gene: env / Production host: Escherichia coli (E. coli) / 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.: 23 / Source method: isolated from a natural source / Formula: H2O
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: 1.99 Å3/Da / Density % sol: 38.18 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20% (w/v) 2-methyl-2,4-pentanediol, 5% (w/v) PEG 8000, and 0.1 M sodium cacodylate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Feb 22, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.78→39.81 Å / Num. obs: 7712 / % possible obs: 98.9 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 17.38
Reflection shellResolution: 1.78→1.82 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.708 / Mean I/σ(I) obs: 1.7 / % possible all: 80.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
Aimlessdata scaling
PHASERphasing
PDB_EXTRACT3.15data extraction
XDSdata reduction
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JPR

4jpr


Resolution: 1.783→39.809 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 27.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1993 352 4.57 %
Rwork0.1575 --
obs0.1595 7701 98.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.783→39.809 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms588 0 1 23 612
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009599
X-RAY DIFFRACTIONf_angle_d0.987807
X-RAY DIFFRACTIONf_dihedral_angle_d12.566212
X-RAY DIFFRACTIONf_chiral_restr0.03596
X-RAY DIFFRACTIONf_plane_restr0.003105
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7832-2.04120.22761120.19122402X-RAY DIFFRACTION97
2.0412-2.57170.20281290.17512468X-RAY DIFFRACTION100
2.5717-39.81920.19361110.1462479X-RAY DIFFRACTION100
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)
11.70040.0047-1.35340.7979-0.24142.20610.04730.17610.001-0.07860.014-0.0540.2238-0.06230.00340.22420.00830.01940.1818-0.01370.19523.484932.3764.4763
21.7466-1.0959-0.4291.17710.45535.36240.14720.22890.07060.05440.07310.22510.5963-1.04240.10430.2625-0.10560.01020.3446-0.0070.295511.111332.540179.0592
34.3212-0.9443-2.66552.86012.31422.90740.03840.0406-0.75070.0714-0.0998-0.06110.09840.2696-0.00750.2591-0.0082-0.03540.35950.01280.458319.769925.218549.9416
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -6 through 490 )
2X-RAY DIFFRACTION2chain 'A' and (resid 491 through 508 )
3X-RAY DIFFRACTION3chain 'A' and (resid 509 through 526 )

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