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- PDB-2ot5: Crystal structure of the HIV gp41 core with the enfuvirtide resis... -

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Basic information

Entry
Database: PDB / ID: 2ot5
TitleCrystal structure of the HIV gp41 core with the enfuvirtide resistance mutation N43D
ComponentsHIV-1 gp41 glycoprotein
KeywordsVIRAL PROTEIN / gp41 / coiled-coil
Function / homology
Function and homology information


viral envelope / host cell plasma membrane / structural molecule activity / virion membrane / plasma 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 type 1
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsBai, X. / Seedorff, J.E. / Green, J. / 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
DepositionFeb 7, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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 gp41 glycoprotein


Theoretical massNumber of molelcules
Total (without water)7,8811
Polymers7,8811
Non-polymers00
Water45025
1
A: HIV-1 gp41 glycoprotein

A: HIV-1 gp41 glycoprotein

A: HIV-1 gp41 glycoprotein


Theoretical massNumber of molelcules
Total (without water)23,6423
Polymers23,6423
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 area6530 Å2
ΔGint-58 kcal/mol
Surface area10210 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)51.025, 51.025, 59.668
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

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Components

#1: Protein HIV-1 gp41 glycoprotein


Mass: 7880.738 Da / Num. of mol.: 1 / Fragment: Subdomain N34(L6)C28 / Mutation: N43D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) human immunodeficiency virus type 1 / Strain: hxb2 / Plasmid: pET4a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q53I19
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 1.9 Å3/Da / Density % sol: 35.15 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.3
Details: 0.05M sodium acetate, 0.2M ammonium sulfate, 23% PEG 4000, 10% glycerol, pH 4.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 5, 2005
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.56→17.76 Å / Num. all: 8182 / Num. obs: 6929 / % possible obs: 84.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.95 % / Rmerge(I) obs: 0.035 / Χ2: 0.94 / Net I/σ(I): 30.9 / Scaling rejects: 261
Reflection shellResolution: 1.56→1.62 Å / Redundancy: 1.52 % / Rmerge(I) obs: 0.502 / Mean I/σ(I) obs: 2 / Num. measured all: 219 / Num. unique all: 144 / Χ2: 0.47 / % possible all: 17.2

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Processing

Software
NameVersionClassificationNB
d*TREK8.0SSIdata scaling
CNSrefinement
PDB_EXTRACT2data extraction
CrystalCleardata collection
d*TREKdata reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1STZ

1stz


Resolution: 1.8→17.76 Å / Isotropic thermal model: anisotropic / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.258 583 10.8 %random
Rwork0.234 ---
obs0.234 5347 99.4 %-
all-5378 --
Solvent computationBsol: 53.988 Å2
Displacement parametersBiso mean: 34.141 Å2
Baniso -1Baniso -2Baniso -3
1-0.218 Å2-1.643 Å20 Å2
2--0.218 Å20 Å2
3----0.436 Å2
Refinement stepCycle: LAST / Resolution: 1.8→17.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms545 0 0 25 570
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_d0.867
LS refinement shellResolution: 2→2.09 Å / Rfactor Rfree error: 0.024
RfactorNum. reflection% reflection
Rfree0.237 60 -
Rwork0.213 --
obs-427 100 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION3CNS_TOPPAR:carbohydrate.param

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