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

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Basic information

Entry
Database: PDB / ID: 1jpx
TitleMutation that destabilize the gp41 core: determinants for stabilizing the SIV/CPmac envelope glycoprotein complex. Wild type.
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
Env polyprotein / Envelope glycoprotein gp160
Similarity search - Component
Biological speciesSimian immunodeficiency virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 1.4Aug 16, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: gp41 envelope protein
D: gp41 envelope protein
G: gp41 envelope protein


Theoretical massNumber of molelcules
Total (without water)29,5893
Polymers29,5893
Non-polymers00
Water1,17165
1
A: gp41 envelope protein

A: gp41 envelope protein

A: gp41 envelope protein


Theoretical massNumber of molelcules
Total (without water)29,5893
Polymers29,5893
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 area5720 Å2
ΔGint-51 kcal/mol
Surface area9420 Å2
MethodPISA
2
D: gp41 envelope protein

D: gp41 envelope protein

D: gp41 envelope protein


Theoretical massNumber of molelcules
Total (without water)29,5893
Polymers29,5893
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area5660 Å2
ΔGint-51 kcal/mol
Surface area9020 Å2
MethodPISA
3
G: gp41 envelope protein

G: gp41 envelope protein

G: gp41 envelope protein


Theoretical massNumber of molelcules
Total (without water)29,5893
Polymers29,5893
Non-polymers00
Water543
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 area5640 Å2
ΔGint-51 kcal/mol
Surface area8360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.993, 54.993, 131.140
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
DetailsThe biological assembly is a trimer generated from each of the three monomers by the three fold axis.

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Components

#1: Protein gp41 envelope protein / envelope glycoprotein


Mass: 9863.165 Da / Num. of mol.: 3 / Fragment: N40(L6)C38
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: Q87972, UniProt: S4WCF9*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / 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: 1.93 Å3/Da / Density % sol: 36.42 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: Sodium chloride, CTAB, barium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlprotein1drop
20.6 M1reservoirNaCl
30.04 M1reservoirBaCl2
40.01 Mhexadecyltrimethylammonium bromide1reservoir

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.948 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 15, 2001
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.948 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 9729 / Num. obs: 9729 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Biso Wilson estimate: 26.8 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 11.7
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.209 / Mean I/σ(I) obs: 8.1 / Num. unique all: 1003 / % possible all: 94
Reflection
*PLUS
Lowest resolution: 50 Å / Num. measured all: 129420 / Rmerge(I) obs: 0.057
Reflection shell
*PLUS
Rmerge(I) obs: 0.209

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Processing

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

1qbz


Resolution: 2.3→44.77 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 469445.28 / 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
Rfree0.283 926 9.5 %RANDOM
Rwork0.237 ---
all-9729 --
obs-9729 97.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 112.528 Å2 / ksol: 0.354022 e/Å3
Displacement parametersBiso mean: 40.3 Å2
Baniso -1Baniso -2Baniso -3
1-14.977 Å27.717 Å20 Å2
2--14.977 Å20 Å2
3----29.954 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.4 Å0.33 Å
Refinement stepCycle: LAST / Resolution: 2.3→44.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1404 0 0 65 1469
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d17.7
X-RAY DIFFRACTIONc_improper_angle_d0.51
X-RAY DIFFRACTIONc_mcbond_it1.281.5
X-RAY DIFFRACTIONc_mcangle_it2.292
X-RAY DIFFRACTIONc_scbond_it1.742
X-RAY DIFFRACTIONc_scangle_it2.962.5
LS refinement shellResolution: 2.3→2.4 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.357 147 12.6 %
Rwork0.301 1020 -
obs-1167 94.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 50 Å / % reflection Rfree: 10 % / Rfactor obs: 0.237 / Rfactor Rfree: 0.283 / Rfactor Rwork: 0.237
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg17.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.51
LS refinement shell
*PLUS
Rfactor Rfree: 0.357 / Rfactor Rwork: 0.301

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