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- PDB-3cp1: Structure of a longer thermalstable core domain of HIV-1 gp41 con... -

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Basic information

Entry
Database: PDB / ID: 3cp1
TitleStructure of a longer thermalstable core domain of HIV-1 gp41 containing the enfuvirtide resistance mutation N43D
ComponentsTransmembrane Protein
KeywordsVIRAL PROTEIN / HIV-1 ENVELOPE GLYCOPROTEIN / 6-helix bundle / gp41 / N43D / AIDS / Apoptosis / Coiled coil / Envelope protein / Fusion protein / Host-virus interaction / Membrane / Transmembrane / Virion
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 1
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 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
DepositionMar 30, 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 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Oct 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 1.5Aug 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
Water39622
1
A: Transmembrane Protein

A: Transmembrane Protein

A: Transmembrane Protein


Theoretical massNumber of molelcules
Total (without water)29,9253
Polymers29,9253
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation5_555z,x,y1
Buried area7370 Å2
ΔGint-65.8 kcal/mol
Surface area11460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.517, 59.517, 59.517
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-87-

HOH

21A-88-

HOH

31A-96-

HOH

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Components

#1: Protein Transmembrane Protein / TM / Glycoprotein41 / gp41


Mass: 9975.124 Da / Num. of mol.: 1
Fragment: Fusion protein of UNP residues 536-579, Linker, and UNP residues 628-663
Mutation: N43D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 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.: 22 / 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: 1.76 Å3/Da / Density % sol: 30.16 %
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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 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: 1.95→19.84 Å / Num. all: 5312 / Num. obs: 4896 / % possible obs: 91.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.089 / Net I/σ(I): 8
Reflection shellResolution: 1.95→2.02 Å / Rmerge(I) obs: 0.827 / % possible all: 21.1

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Processing

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

1env


Resolution: 2→19.84 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.286 469 -RANDOM
Rwork0.249 ---
all-4955 --
obs-4548 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→19.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms606 0 0 22 628

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