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- PDB-1qr8: INHIBITION OF HIV-1 INFECTIVITY BY THE GP41 CORE: ROLE OF A CONSE... -

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Basic information

Entry
Database: PDB / ID: 1qr8
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 / MEMBRANE FUSION / HIV-1 INHIBITION
Function / homology
Function and homology information


membrane fusion involved in viral entry into host cell / host cell endosome / 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 / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / Resolution: 2.1 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

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Assembly

Deposited unit
A: GP41 ENVELOPE PROTEIN


Theoretical massNumber of molelcules
Total (without water)7,8511
Polymers7,8511
Non-polymers00
Water30617
1
A: GP41 ENVELOPE PROTEIN

A: GP41 ENVELOPE PROTEIN

A: GP41 ENVELOPE PROTEIN


Theoretical massNumber of molelcules
Total (without water)23,5523
Polymers23,5523
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area6110 Å2
ΔGint-50 kcal/mol
Surface area10870 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)53.587, 53.587, 59.558
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-100-

HOH

DetailsThe biological assembly is a trimer constructed from the ectodomain of the HIV- 1 gp41 envelope protein.

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Components

#1: Protein GP41 ENVELOPE PROTEIN


Mass: 7850.737 Da / Num. of mol.: 1 / Fragment: SUBDOMAIN N34(L6)C28 / Mutation: W571R / Source method: isolated from a natural source / Source: (natural) Human immunodeficiency virus 1 / Genus: Lentivirus / References: UniProt: Q76270
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 2.1 Å3/Da / Density % sol: 41.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: sodium acetate, ammonium sulfate, PEG 4000, 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
417 %PEG40001reservoir
520 %(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 10, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→15 Å / Num. all: 3505 / Num. obs: 3505 / % possible obs: 94 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.1 % / Biso Wilson estimate: 34 Å2 / Rmerge(I) obs: 0.031 / Net I/σ(I): 25.7
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.205 / Num. unique all: 369 / % possible all: 96.6
Reflection
*PLUS
Lowest resolution: 30 Å / Num. measured all: 7391 / Rmerge(I) obs: 0.06

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.1→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
Rfree0.262 175 5 %RANDOM
Rwork0.212 ---
all-3505 --
obs-3505 94 %-
Displacement parametersBiso mean: 48.9 Å2
Refinement stepCycle: LAST / Resolution: 2.1→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms552 0 0 17 569
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.004
X-RAY DIFFRACTIONx_angle_deg0.9
X-RAY DIFFRACTIONx_dihedral_angle_d23.4
X-RAY DIFFRACTIONx_improper_angle_d0.45
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.212
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 48.9 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg0.9
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.4
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.45

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