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- PDB-1i5x: HIV-1 GP41 CORE -

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Basic information

Entry
Database: PDB / ID: 1i5x
TitleHIV-1 GP41 CORE
ComponentsTRANSMEMBRANE GLYCOPROTEIN (GP41)
KeywordsVIRAL PROTEIN / GP41 / HIV-1 / MEMBRANE FUSION / HIV-1 INHIBITION
Function / homology
Function and homology information


host cell plasma membrane / virion membrane / structural molecule activity / 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 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsLiu, J. / Lu, M.
CitationJournal: J.Virol. / Year: 2001
Title: Structural and functional analysis of interhelical interactions in the human immunodeficiency virus type 1 gp41 envelope glycoprotein by alanine-scanning mutagenesis.
Authors: Lu, M. / Stoller, M.O. / Wang, S. / Liu, J. / Fagan, M.B. / Nunberg, J.H.
History
DepositionMar 1, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 10, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE The sequence of this protein is not available in any sequence database.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TRANSMEMBRANE GLYCOPROTEIN (GP41)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,8902
Polymers7,7941
Non-polymers961
Water1,49583
1
A: TRANSMEMBRANE GLYCOPROTEIN (GP41)
hetero molecules

A: TRANSMEMBRANE GLYCOPROTEIN (GP41)
hetero molecules

A: TRANSMEMBRANE GLYCOPROTEIN (GP41)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6696
Polymers23,3813
Non-polymers2883
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area6340 Å2
ΔGint-86 kcal/mol
Surface area9230 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)51.252, 51.252, 59.873
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-181-

HOH

21A-182-

HOH

31A-183-

HOH

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Components

#1: Protein TRANSMEMBRANE GLYCOPROTEIN (GP41)


Mass: 7793.637 Da / Num. of mol.: 1 / Fragment: N34(L6)C28 / Mutation: R579A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Production host: Escherichia coli (E. coli) / References: UniProt: Q76270
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 1.94 Å3/Da / Density % sol: 36.66 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: PEGMME 2000, sodium acetate, ammonium sulphate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 30, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 40929 / Num. obs: 5440 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 19.1 Å2 / Rmerge(I) obs: 0.035 / Net I/σ(I): 27.5
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.104 / Mean I/σ(I) obs: 11.1 / Num. unique all: 538 / % possible all: 99.1

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SZT

1szt


Resolution: 1.8→24.82 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 972118.15 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.222 580 10.7 %RANDOM
Rwork0.179 ---
obs0.179 5439 99.7 %-
all-5439 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 113.8 Å2 / ksol: 0.477 e/Å3
Displacement parametersBiso mean: 19.8 Å2
Baniso -1Baniso -2Baniso -3
1-0.31 Å20.66 Å20 Å2
2--0.31 Å20 Å2
3----0.62 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.1 Å
Refinement stepCycle: LAST / Resolution: 1.8→24.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms489 0 5 83 577
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d14.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.65
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.231.5
X-RAY DIFFRACTIONc_mcangle_it1.722
X-RAY DIFFRACTIONc_scbond_it2.342
X-RAY DIFFRACTIONc_scangle_it3.372.5
LS refinement shellResolution: 1.8→1.86 Å / Rfactor Rfree error: 0.039 / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.273 50 10.1 %
Rwork0.221 443 -
obs-493 99.2 %

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