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- PDB-1jq0: Mutation that destabilize the gp41 core: determinants for stabili... -

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Basic information

Entry
Database: PDB / ID: 1jq0
TitleMutation that destabilize the gp41 core: determinants for stabilizing the SIV/CPmac envelope glycoprotein complex. Mutant structure.
Componentsgp41 envelope protein
KeywordsVIRAL PROTEIN / GP41 / SIV / HIV-1 / MEMBRANE FUSION / SIX-HELIX BUNDLE / TRIMER-of-HAIRPINS
Function / homology
Function and homology information


membrane fusion involved in viral entry into host cell / host cell endosome membrane / viral envelope / symbiont entry into host cell / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / membrane
Similarity search - Function
Helix Hairpins - #210 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Envelope glycoprotein gp160 / Envelope glycoprotein gp160
Similarity search - Component
Biological speciesSimian immunodeficiency virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsLiu, J. / Wang, S. / LaBranche, C.C. / Hoxie, J.A. / Lu, M.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: Mutations that destabilize the gp41 core are determinants for stabilizing the simian immunodeficiency virus-CPmac envelope glycoprotein complex.
Authors: Liu, J. / Wang, S. / Hoxie, J.A. / LaBranche, C.C. / Lu, M.
History
DepositionAug 3, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 9, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.4Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.5Oct 27, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.6Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: gp41 envelope protein


Theoretical massNumber of molelcules
Total (without water)9,8351
Polymers9,8351
Non-polymers00
Water84747
1
A: gp41 envelope protein

A: gp41 envelope protein

A: gp41 envelope protein


Theoretical massNumber of molelcules
Total (without water)29,5053
Polymers29,5053
Non-polymers00
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 area6790 Å2
ΔGint-65 kcal/mol
Surface area10630 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)48.877, 48.877, 150.987
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-101-

HOH

21A-102-

HOH

DetailsThe biological assembly is a trimer generated from the monomer by the three fold axis.

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Components

#1: Protein gp41 envelope protein / envelope glycoprotein


Mass: 9835.155 Da / Num. of mol.: 1 / Fragment: N40(L6)C38 / Mutation: L3S, V17L, K19T, T32I, E51K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Simian immunodeficiency virus / Genus: Lentivirus / Strain: mac251 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q88007, UniProt: S4WCF9*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 1.76 Å3/Da / Density % sol: 30.29 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: Sodium formate, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 mg/mlprotein1drop
23.8 Msodium formate1reservoir

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: BRANDEIS - B4 / Detector: CCD / Date: May 30, 2001
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 7973 / Num. obs: 7973 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.6 % / Biso Wilson estimate: 24 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 16.6
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 9.4 % / Rmerge(I) obs: 0.249 / Mean I/σ(I) obs: 9 / Num. unique all: 770 / % possible all: 99.5
Reflection
*PLUS
Lowest resolution: 50 Å / Num. measured all: 137718 / Rmerge(I) obs: 0.04
Reflection shell
*PLUS
Rmerge(I) obs: 0.249

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1refinement
MADNESSdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QBZ

1qbz


Resolution: 1.7→36.92 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1580800.13 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.252 847 10.6 %RANDOM
Rwork0.209 ---
all-7973 --
obs-7973 99.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 76.1332 Å2 / ksol: 0.410957 e/Å3
Displacement parametersBiso mean: 24.3 Å2
Baniso -1Baniso -2Baniso -3
1-0.54 Å2-0.94 Å20 Å2
2--0.54 Å20 Å2
3----1.08 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.05 Å
Refinement stepCycle: LAST / Resolution: 1.7→36.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms577 0 0 47 624
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg0.9
X-RAY DIFFRACTIONc_dihedral_angle_d13.6
X-RAY DIFFRACTIONc_improper_angle_d0.63
X-RAY DIFFRACTIONc_mcbond_it1.631.5
X-RAY DIFFRACTIONc_mcangle_it2.192
X-RAY DIFFRACTIONc_scbond_it3.512
X-RAY DIFFRACTIONc_scangle_it5.252.5
LS refinement shellResolution: 1.7→1.75 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.229 59 8.6 %
Rwork0.207 630 -
obs-689 99.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 50 Å / % reflection Rfree: 10 % / Rfactor obs: 0.209 / Rfactor Rfree: 0.252 / Rfactor Rwork: 0.209
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg13.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.63
LS refinement shell
*PLUS
Rfactor Rfree: 0.229 / Rfactor Rwork: 0.207 / Rfactor obs: 0.207

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