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- PDB-1qr9: INHIBITION OF HIV-1 INFECTIVITY BY THE GP41 CORE: ROLE OF A CONSE... -

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Basic information

Entry
Database: PDB / ID: 1qr9
TitleINHIBITION OF HIV-1 INFECTIVITY BY THE GP41 CORE: ROLE OF A CONSERVED HYDROPHOBIC CAVITY IN MEMBRANE FUSION
ComponentsGP41 ENVELOPE PROTEIN
KeywordsVIRAL PROTEIN / GP41 / HIV-1 ENVELOPE PROTEIN / MEMBRANE FUSION / HIV-1 INHIBITION
Function / homology
Function and homology information


host cell plasma membrane / virion membrane / structural molecule activity / plasma membrane
Similarity search - Function
Helix Hairpins - #210 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / Resolution: 1.6 Å
AuthorsJi, H. / Shu, W. / Burling, F.T. / Jiang, S.B. / Lu, M.
CitationJournal: J.Virol. / Year: 1999
Title: Inhibition of human immunodeficiency virus type 1 infectivity by the gp41 core: role of a conserved hydrophobic cavity in membrane fusion.
Authors: Ji, H. / Shu, W. / Burling, F.T. / Jiang, S. / Lu, M.
History
DepositionJun 18, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 26, 1999Provider: 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 1.4Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GP41 ENVELOPE PROTEIN


Theoretical massNumber of molelcules
Total (without water)7,8381
Polymers7,8381
Non-polymers00
Water88349
1
A: GP41 ENVELOPE PROTEIN

A: GP41 ENVELOPE PROTEIN

A: GP41 ENVELOPE PROTEIN


Theoretical massNumber of molelcules
Total (without water)23,5133
Polymers23,5133
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 area6160 Å2
ΔGint-55 kcal/mol
Surface area10380 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)49.675, 49.675, 60.195
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Cell settingtrigonal
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-135-

HOH

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Components

#1: Protein GP41 ENVELOPE PROTEIN


Mass: 7837.673 Da / Num. of mol.: 1 / Fragment: SUBDOMAIN N34(L6)C28 / Mutation: L568A / Source method: isolated from a natural source / Source: (natural) Human immunodeficiency virus 1 / Genus: Lentivirus / References: UniProt: Q76270
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 49 / 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: 1.82 Å3/Da / Density % sol: 32.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: SODIUM ACETATE, AMMONIUM SULFATE, GLYCEROL, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlpeptide1drop
20.1 Msodium acetate1reservoir
30.2 Mammonium sulfate1reservoir
420 %(v/v)glycerol1reservoir

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 20, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→15 Å / Num. all: 7043 / Num. obs: 7043 / % possible obs: 96.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 21 Å2 / Rmerge(I) obs: 0.034 / Net I/σ(I): 33.4
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.138 / % possible all: 69.1
Reflection
*PLUS
Lowest resolution: 30 Å / Num. measured all: 29806 / Rmerge(I) obs: 0.036

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.6→15 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.261 352 5 %RANDOM
Rwork0.202 ---
obs0.202 7043 96.6 %-
all-7043 --
Displacement parametersBiso mean: 21.8 Å2
Refinement stepCycle: LAST / Resolution: 1.6→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms552 0 0 49 601
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.005
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d19.1
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.6
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 21.8 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.2
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg19.1
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.6

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