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- PDB-1dlb: HELICAL INTERACTIONS IN THE HIV-1 GP41 CORE REVEALS STRUCTURAL BA... -

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Entry
Database: PDB / ID: 1dlb
TitleHELICAL INTERACTIONS IN THE HIV-1 GP41 CORE REVEALS STRUCTURAL BASIS FOR THE INHIBITORY ACTIVITY OF GP41 PEPTIDES
ComponentsHIV-1 ENVELOPE GLYCOPROTEIN GP41
KeywordsVIRAL PROTEIN / GP41 / HIV-1 / MEMBRANE FUSION / HIV-1 INHIBITION / VIRUS/VIRAL PROTEIN
Function / homology
Function and homology information


Synthesis and processing of ENV and VPU / symbiont-mediated evasion of host immune response / positive regulation of establishment of T cell polarity / Alpha-defensins / Dectin-2 family / Binding and entry of HIV virion / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / actin filament organization / host cell endosome membrane ...Synthesis and processing of ENV and VPU / symbiont-mediated evasion of host immune response / positive regulation of establishment of T cell polarity / Alpha-defensins / Dectin-2 family / Binding and entry of HIV virion / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / actin filament organization / host cell endosome membrane / Assembly Of The HIV Virion / Budding and maturation of HIV virion / clathrin-dependent endocytosis of virus by host cell / viral protein processing / receptor ligand activity / 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
Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsShu, W. / Liu, J. / Ji, H. / Rading, L. / Jiang, S. / Lu, M.
CitationJournal: Biochemistry / Year: 2000
Title: Helical interactions in the HIV-1 gp41 core reveal structural basis for the inhibitory activity of gp41 peptides.
Authors: Shu, W. / Liu, J. / Ji, H. / Radigen, L. / Jiang, S. / Lu, M.
History
DepositionDec 9, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 15, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 9, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.4Nov 3, 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 1.5Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HIV-1 ENVELOPE GLYCOPROTEIN GP41


Theoretical massNumber of molelcules
Total (without water)7,8651
Polymers7,8651
Non-polymers00
Water1,38777
1
A: HIV-1 ENVELOPE GLYCOPROTEIN GP41

A: HIV-1 ENVELOPE GLYCOPROTEIN GP41

A: HIV-1 ENVELOPE GLYCOPROTEIN GP41


Theoretical massNumber of molelcules
Total (without water)23,5943
Polymers23,5943
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 area6420 Å2
ΔGint-61 kcal/mol
Surface area9390 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)52.382, 52.382, 60.482
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-100-

HOH

21A-102-

HOH

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Components

#1: Protein HIV-1 ENVELOPE GLYCOPROTEIN GP41


Mass: 7864.782 Da / Num. of mol.: 1
Fragment: RESIDUES 1 - 34 AND 41 - 68 CONNECTED BY A SIX-RESIDUE LINKER (SER-GLY-GLY-ARG- GLY-GLY)
Mutation: Q65L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus
Description: RECOMBINANT GP41 WITH LINKER (SER-GLY-GLY- ARG-GLY-GLY) BETWEEN TWO FRAGMENTS
Production host: Escherichia coli (E. coli) / References: UniProt: P04578
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: H2O
Compound detailsIN THE STRUCTURE, SEQUENCE 1 - 34 IS FROM GP41 RESIDUES 546 - 579 (IN GP160 NUMBERING SYSTEM), 35 - ...IN THE STRUCTURE, SEQUENCE 1 - 34 IS FROM GP41 RESIDUES 546 - 579 (IN GP160 NUMBERING SYSTEM), 35 - 40 IS AN ARTIFICIAL LINKER SGGRGG AND 41 - 68 IS GP41 RESIDUES 628 - 655.

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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: 2.03 Å3/Da / Density % sol: 39.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: PEG 4000, AMMONIUM SULPHATE, SODIUM ACETATE, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlpeptide1drop
20.2 Mammonium sulfate1reservoir
30.1 Msodium acetate1reservoirpH4.6
411 %PEG40001reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 11, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 4167 / Num. obs: 4167 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 29.4 Å2 / Rmerge(I) obs: 0.04
Reflection
*PLUS
Num. measured all: 23565 / Rmerge(I) obs: 0.04

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Processing

Software
NameVersionClassification
AMoREphasing
CNS0.5refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2→15 Å / Rfactor Rfree error: 0.011 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.243 499 12 %RANDOM
Rwork0.206 ---
obs0.206 4167 99.7 %-
all-4167 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 109.5 Å2 / ksol: 0.376 e/Å3
Displacement parametersBiso mean: 38.5 Å2
Baniso -1Baniso -2Baniso -3
1--0.88 Å21.15 Å20 Å2
2---0.88 Å20 Å2
3---1.77 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.29 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms509 0 0 77 586
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
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_deg0.8
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_d0.56
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.141.5
X-RAY DIFFRACTIONc_mcangle_it1.952
X-RAY DIFFRACTIONc_scbond_it1.492
X-RAY DIFFRACTIONc_scangle_it2.442.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.341 90 13.1 %
Rwork0.264 596 -
obs--99.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 12 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 38.5 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg0.8
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg14.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.56
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.341 / % reflection Rfree: 13.1 % / Rfactor Rwork: 0.264

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