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- PDB-1jek: Visna TM CORE STRUCTURE -

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Basic information

Entry
Database: PDB / ID: 1jek
TitleVisna TM CORE STRUCTURE
Components(ENV POLYPROTEIN) x 2
KeywordsVIRAL PROTEIN / ENVELOPE GLYCOPROTEIN / RETROVIRUS / HIV / SIV / GP41
Function / homology
Function and homology information


viral envelope / symbiont entry into host cell / virion attachment to host cell / host cell plasma membrane / virion membrane / membrane
Similarity search - Function
ATP synthase delta/epsilon subunit, C-terminal domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Envelope glycoprotein gp160
Similarity search - Component
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsMalashkevich, V.N. / Singh, M. / Kim, P.S.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2001
Title: The trimer-of-hairpins motif in membrane fusion: Visna virus.
Authors: Malashkevich, V.N. / Singh, M. / Kim, P.S.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1998
Title: Crystal Structure of the Simian Immunodeficiency Virus (Siv) Gp41 Core: Conserved Helical Interactions Underlie the Broad Inhibitory Activity of Gp41 Peptides
Authors: Malashkevich, V.N. / Chan, D.C. / Chutkowski, C.T. / Kim, P.S.
#2: Journal: Cell(Cambridge,Mass.) / Year: 1997
Title: Core Structure of Gp41 from the HIV Envelope Glycoprotein
Authors: Chan, D.C. / Fass, D. / Berger, J.M. / Kim, P.S.
History
DepositionJun 18, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 25, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Aug 16, 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_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ENV POLYPROTEIN
B: ENV POLYPROTEIN


Theoretical massNumber of molelcules
Total (without water)8,4642
Polymers8,4642
Non-polymers00
Water2,558142
1
A: ENV POLYPROTEIN
B: ENV POLYPROTEIN

A: ENV POLYPROTEIN
B: ENV POLYPROTEIN

A: ENV POLYPROTEIN
B: ENV POLYPROTEIN


Theoretical massNumber of molelcules
Total (without water)25,3916
Polymers25,3916
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area13060 Å2
ΔGint-103 kcal/mol
Surface area11000 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)52.548, 52.548, 61.686
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11A-1-

HOH

21A-4-

HOH

31A-40-

HOH

41A-46-

HOH

51B-42-

HOH

DetailsTrimer is formed around the crystallographic 3-fold axis

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Components

#1: Protein/peptide ENV POLYPROTEIN / COAT POLYPROTEIN


Mass: 4336.971 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: This peptide was chemically synthesized. The sequence of the peptide is naturally found in Visna virus.
References: UniProt: P35954
#2: Protein/peptide ENV POLYPROTEIN / COAT POLYPROTEIN


Mass: 4126.549 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: This peptide was chemically synthesized. The sequence of the peptide is naturally found in Visna virus.
References: UniProt: P35954
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / 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: 2.91 Å3/Da / Density % sol: 57.67 % / Description: POLYSERINE MODEL
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 25% tert-butanol, 0.1M TRIS-HCL, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
225 %tert-butanol1reservoir
30.1 MTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 1.28
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 1, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28 Å / Relative weight: 1
ReflectionResolution: 1.5→25 Å / Num. obs: 16300 / % possible obs: 90.1 % / Observed criterion σ(I): 0 / Redundancy: 7.5 % / Biso Wilson estimate: 22.9 Å2 / Rmerge(I) obs: 0.066 / Rsym value: 0.066 / Net I/σ(I): 13.9
Reflection shellResolution: 1.5→1.52 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.138 / Mean I/σ(I) obs: 2.5 / Rsym value: 0.138 / % possible all: 64.7
Reflection
*PLUS
Num. measured all: 52353
Reflection shell
*PLUS
Highest resolution: 1.5 Å / % possible obs: 64.7 % / Rmerge(I) obs: 0.259

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2SIV

2siv


Resolution: 1.5→9.96 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 914104.1 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.265 1559 10.1 %RANDOM
Rwork0.213 ---
obs0.213 15369 94.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 94.78 Å2 / ksol: 0.451 e/Å3
Displacement parametersBiso mean: 31.1 Å2
Baniso -1Baniso -2Baniso -3
1-6.82 Å23.16 Å20 Å2
2--6.82 Å20 Å2
3----13.64 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 1.5→9.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms598 0 0 142 740
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d13.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.99
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.5→1.59 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.363 202 10.5 %
Rwork0.319 1723 -
obs--72.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAM
X-RAY DIFFRACTION3WATER_REP.PARAM
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 10.1 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 31.1 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg13.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.99
LS refinement shell
*PLUS
Rfactor Rfree: 0.363 / % reflection Rfree: 10.5 % / Rfactor Rwork: 0.319 / Rfactor obs: 0.319

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