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- PDB-1i5y: HIV-1 GP41 CORE -

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Basic information

Entry
Database: PDB / ID: 1i5y
TitleHIV-1 GP41 CORE
ComponentsTRANSMEMBRANE GLYCOPROTEIN (GP41)
KeywordsVIRAL PROTEIN / GP41 / HIV-1 / MEMBRANE FUSION / HIV-1 INHIBITION
Function / homology
Function and homology information


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 / 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 / MOLECULAR REPLACEMENT / Resolution: 2.1 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)7,9902
Polymers7,8941
Non-polymers961
Water68538
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)23,9706
Polymers23,6813
Non-polymers2883
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_645-y+1,x-y-1,z1
crystal symmetry operation3_765-x+y+2,-x+1,z1
Buried area6020 Å2
ΔGint-87 kcal/mol
Surface area9340 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)52.063, 52.063, 59.740
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-101-

HOH

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Components

#1: Protein TRANSMEMBRANE GLYCOPROTEIN (GP41)


Mass: 7893.779 Da / Num. of mol.: 1 / Fragment: N34(L6)C28 / Mutation: G572A
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


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


Mass: 18.015 Da / Num. of mol.: 38 / 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: 1.97 Å3/Da / Density % sol: 37.69 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: PEG 4000, sodium acetate, ammonium sulphate, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 20, 2000 / 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. all: 23645 / Num. obs: 3507 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 30 Å2 / Rmerge(I) obs: 0.029 / Net I/σ(I): 32.2
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.142 / Mean I/σ(I) obs: 7.3 / Num. unique all: 348 / % possible all: 100

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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: 2.1→35.99 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 935711.77 / 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
Rfree0.234 356 10.2 %RANDOM
Rwork0.206 ---
obs0.206 3505 99.5 %-
all-3505 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 62.58 Å2 / ksol: 0.357 e/Å3
Displacement parametersBiso mean: 37.8 Å2
Baniso -1Baniso -2Baniso -3
1-2.77 Å23.66 Å20 Å2
2--2.77 Å20 Å2
3----5.54 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.07 Å
Refinement stepCycle: LAST / Resolution: 2.1→35.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms485 0 5 38 528
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.004
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_deg0.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d15
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.51
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.361.5
X-RAY DIFFRACTIONc_mcangle_it2.12
X-RAY DIFFRACTIONc_scbond_it2.362
X-RAY DIFFRACTIONc_scangle_it3.462.5
LS refinement shellResolution: 2.1→2.2 Å / Rfactor Rfree error: 0.035 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.256 53 12.4 %
Rwork0.227 376 -
obs-429 100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PAPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP

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