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- PDB-3cyo: Structure of a longer thermalstable core domain of HIV-1 GP41 con... -

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Basic information

Entry
Database: PDB / ID: 3cyo
TitleStructure of a longer thermalstable core domain of HIV-1 GP41 containing the enfuvirtide resistance mutation N43D and complementary mutation E137K
ComponentsTransmembrane protein
KeywordsVIRAL PROTEIN / HIV-1 ENVELOPE GLYCOPROTEIN / 6-HELIX BUNDLE / GP41 / N43D / E137K / AIDS / APOPTOSIS / COILED COIL / ENVELOPE PROTEIN / FUSION PROTEIN / HOST-VIRUS INTERACTION / MEMBRANE / TRANSMEMBRANE / VIRION / Cleavage on pair of basic residues / Lipoprotein / Palmitate / Viral immunoevasion
Function / homology
Function and homology information


Dectin-2 family / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / symbiont entry into host cell ...Dectin-2 family / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / 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
Env polyprotein / Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHuman immunodeficiency virus type 1
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsWang, Z.M. / Dwyer, J.J.
CitationJournal: Biochemistry / Year: 2008
Title: Impact of the enfuvirtide resistance mutation N43D and the associated baseline polymorphism E137K on peptide sensitivity and six-helix bundle structure.
Authors: Bai, X. / Wilson, K.L. / Seedorff, J.E. / Ahrens, D. / Green, J. / Davison, D.K. / Jin, L. / Stanfield-Oakley, S.A. / Mosier, S.M. / Melby, T.E. / Cammack, N. / Wang, Z. / Greenberg, M.L. / Dwyer, J.J.
History
DepositionApr 25, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 16, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transmembrane protein


Theoretical massNumber of molelcules
Total (without water)9,9751
Polymers9,9751
Non-polymers00
Water48627
1
A: Transmembrane protein

A: Transmembrane protein

A: Transmembrane protein


Theoretical massNumber of molelcules
Total (without water)29,9263
Polymers29,9263
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area7410 Å2
ΔGint-63.7 kcal/mol
Surface area11280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.290, 59.290, 59.290
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-101-

HOH

21A-102-

HOH

31A-103-

HOH

41A-104-

HOH

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Components

#1: Protein Transmembrane protein / TM / GLYCOPROTEIN41 / GP41


Mass: 9975.190 Da / Num. of mol.: 1
Fragment: FUSION PROTEIN OF UNP RESIDUES 536-579, LINKER, AND UNP RESIDUES 628-663
Mutation: N554D,E648K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 / Gene: env / Plasmid: PET41A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLYSS / References: UniProt: Q70626, UniProt: Q53I19*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 1.74 Å3/Da / Density % sol: 29.35 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 25-40% ETHYLENE GLYCOL, 0.2 M MGCL2 AND 0.1 M HEPES PH 7.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 295K, pH 7.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 1, 2007 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 4263 / % possible obs: 98.7 % / Observed criterion σ(I): 0 / Rsym value: 0.096 / Net I/σ(I): 9.3
Reflection shellResolution: 2.1→2.18 Å / Rmerge(I) obs: 0.879 / % possible all: 88.3

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ENV

1env


Resolution: 2.1→50 Å / Isotropic thermal model: ANISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.332 396 -RANDOM
Rwork0.242 ---
obs0.242 3876 91.8 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms605 0 0 27 632

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