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- PDB-1df4: INTERACTIONS BETWEEN HIV-1 GP41 CORE AND DETERGENTS AND THEIR IMP... -

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Basic information

Entry
Database: PDB / ID: 1df4
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 / actin filament organization / host cell endosome membrane ...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 / actin filament organization / host cell endosome membrane / Assembly Of The HIV Virion / Budding and maturation of HIV virion / clathrin-dependent endocytosis of virus by host cell / viral protein processing / receptor ligand activity / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host 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 / 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 / SYNCHROTRON / Resolution: 1.45 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
Water1,38777
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
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area5990 Å2
ΔGint-61 kcal/mol
Surface area8690 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)52.383, 52.383, 60.982
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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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
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: H2O
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: 39.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: SODIUM CITRATE, AMMONIUM DIHYDROGEN PHOSPHATE, BETA-OG, pH 5.6, 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 citrate1reservoir
31.0 Mammonium dihydrogen phosphate1reservoir
435 mMbeta OG1reservoir

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Data collection

DiffractionMean temperature: 130 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 0.71069
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 1, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.71069 Å / Relative weight: 1
ReflectionResolution: 1.45→16.5 Å / Num. all: 11818 / Num. obs: 11818 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 17.9 Å2 / Rmerge(I) obs: 0.028 / Net I/σ(I): 22.5
Reflection shellResolution: 1.45→1.51 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.125 / % possible all: 96.9
Reflection
*PLUS
Num. measured all: 43163
Reflection shell
*PLUS
% possible obs: 96.9 %

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Processing

Software
NameClassification
AMoREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.45→16.5 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.245 950 -RANDOM
Rwork0.2 ---
all-11818 --
obs-11818 99 %-
Refinement stepCycle: LAST / Resolution: 1.45→16.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms463 0 0 77 540
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.017
X-RAY DIFFRACTIONp_angle_d2
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_dihedral_angle_d
X-RAY DIFFRACTIONp_dihedral_angle_deg36

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