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- PDB-1df5: INTERACTIONS BETWEEN HIV-1 GP41 CORE AND DETERGENTS AND THEIR IMP... -

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Basic information

Entry
Database: PDB / ID: 1df5
TitleINTERACTIONS BETWEEN HIV-1 GP41 CORE AND DETERGENTS AND THEIR IMPLICATIONS FOR MEMBRANE FUSION
ComponentsHIV-1 ENVELOPE GLYCOPROTEIN GP41
KeywordsVIRAL PROTEIN / HIV-1 / GP41 / MEMBRANE FUSION / PROTEIN-DETERGENT INTERACTION
Function / homology
Function and homology information


Synthesis and processing of ENV and VPU / symbiont-mediated evasion of host immune response / positive regulation of establishment of T cell polarity / Alpha-defensins / Dectin-2 family / Binding and entry of HIV virion / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / host cell endosome membrane / actin filament organization ...Synthesis and processing of ENV and VPU / symbiont-mediated evasion of host immune response / positive regulation of establishment of T cell polarity / Alpha-defensins / Dectin-2 family / Binding and entry of HIV virion / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / host cell endosome membrane / actin filament organization / Assembly Of The HIV Virion / Budding and maturation of HIV virion / clathrin-dependent endocytosis of virus by host cell / viral protein processing / symbiont entry into host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / membrane
Similarity search - Function
Helix Hairpins - #210 / Envelope glycoprotein Gp160 / 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
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / Resolution: 2.7 Å
AuthorsShu, W. / Ji, H. / Lu, M.
CitationJournal: J.Biol.Chem. / Year: 2000
Title: Interactions between HIV-1 gp41 core and detergents and their implications for membrane fusion.
Authors: Shu, W. / Ji, H. / Lu, M.
History
DepositionNov 17, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 24, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 9, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.4Feb 7, 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: HIV-1 ENVELOPE GLYCOPROTEIN GP41


Theoretical massNumber of molelcules
Total (without water)7,8801
Polymers7,8801
Non-polymers00
Water00
1
A: HIV-1 ENVELOPE GLYCOPROTEIN GP41

A: HIV-1 ENVELOPE GLYCOPROTEIN GP41

A: HIV-1 ENVELOPE GLYCOPROTEIN GP41


Theoretical massNumber of molelcules
Total (without water)23,6393
Polymers23,6393
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_546z,x-1,y+11
crystal symmetry operation9_645y+1,z-1,x1
Buried area6610 Å2
ΔGint-63 kcal/mol
Surface area10780 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)72.77, 72.77, 72.77
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213
DetailsThe biological assembly is a homotrimer.

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Components

#1: Protein HIV-1 ENVELOPE GLYCOPROTEIN GP41


Mass: 7879.753 Da / Num. of mol.: 1
Fragment: RESIDUES 1 - 34 AND 41 - 68 CONNECTED BY A SIX-RESIDUE LINKER (SER-GLY-GLY-ARG-GLY-GLY)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus
Description: RECOMBINANT GP41 WITH LINKER (SER-GLY-GLY- ARG-GLY-GLY) BETWEEN TWO FRAGMENTS
Production host: Escherichia coli (E. coli) / References: UniProt: P04578
Compound detailsIN THE STRUCTURE, SEQUENCE 1 - 34 IS FROM GP41 RESIDUES 546 - 579 (IN GP160 NUMBERING SYSTEM), 35 - ...IN THE STRUCTURE, SEQUENCE 1 - 34 IS FROM GP41 RESIDUES 546 - 579 (IN GP160 NUMBERING SYSTEM), 35 - 40 IS AN ARTIFICIAL LINKER SGGRGG AND 41 - 68 IS GP41 RESIDUES 628 - 655.

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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: 2.04 Å3/Da / Density % sol: 39.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Potassium sodium tartrate, SDS, sodium hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
20.1 Msodium HEPES1reservoir
30.8 Mpotassium sodium tartrate1reservoir
410 mMSDS1reservoir

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Data collection

DiffractionMean temperature: 130 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 19, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. all: 1859 / Num. obs: 1859 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Rmerge(I) obs: 0.046 / Net I/σ(I): 21
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.102 / Num. unique all: 186 / % possible all: 100
Reflection
*PLUS
Num. measured all: 10354
Reflection shell
*PLUS
% possible obs: 100 %

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.7→8 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.315 86 -RANDOM
Rwork0.183 ---
all-1726 --
obs-1726 99.9 %-
Refinement stepCycle: LAST / Resolution: 2.7→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms555 0 0 0 555
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.004
X-RAY DIFFRACTIONx_angle_deg0.8
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.7

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