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- PDB-1aik: HIV GP41 CORE STRUCTURE -

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Basic information

Entry
Database: PDB / ID: 1aik
TitleHIV GP41 CORE STRUCTURE
Components(HIV-1 GP41 GLYCOPROTEIN) x 2
KeywordsVIRAL PROTEIN / HIV / GP41 / ENVELOPE GLYCOPROTEIN / RETROVIRUS
Function / homology
Function and homology information


Synthesis and processing of ENV and VPU / evasion of host immune response / Alpha-defensins / Dectin-2 family / Binding and entry of HIV virion / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / actin filament organization ...Synthesis and processing of ENV and VPU / evasion of host immune response / Alpha-defensins / Dectin-2 family / Binding and entry of HIV virion / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / actin filament organization / Assembly Of The HIV Virion / Budding and maturation of HIV virion / clathrin-dependent endocytosis of virus by host cell / viral protein processing / symbiont entry into host cell / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / structural molecule activity / virion membrane / membrane
Similarity search - Function
Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120
Similarity search - Domain/homology
Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHIV-1 M:B_HXB2R (virus)
MethodX-RAY DIFFRACTION / MAD / Resolution: 2 Å
AuthorsChan, D.C. / Fass, D. / Berger, J.M. / Kim, P.S.
CitationJournal: Cell(Cambridge,Mass.) / Year: 1997
Title: Core structure of gp41 from the HIV envelope glycoprotein.
Authors: Chan, D.C. / Fass, D. / Berger, J.M. / Kim, P.S.
History
DepositionApr 20, 1997Processing site: BNL
Revision 1.0Jun 16, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
N: HIV-1 GP41 GLYCOPROTEIN
C: HIV-1 GP41 GLYCOPROTEIN


Theoretical massNumber of molelcules
Total (without water)8,4302
Polymers8,4302
Non-polymers00
Water77543
1
N: HIV-1 GP41 GLYCOPROTEIN
C: HIV-1 GP41 GLYCOPROTEIN

N: HIV-1 GP41 GLYCOPROTEIN
C: HIV-1 GP41 GLYCOPROTEIN

N: HIV-1 GP41 GLYCOPROTEIN
C: HIV-1 GP41 GLYCOPROTEIN


Theoretical massNumber of molelcules
Total (without water)25,2916
Polymers25,2916
Non-polymers00
Water1086
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 area12190 Å2
ΔGint-98 kcal/mol
Surface area10400 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)49.500, 49.500, 55.300
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321

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Components

#1: Protein/peptide HIV-1 GP41 GLYCOPROTEIN


Mass: 4152.843 Da / Num. of mol.: 1 / Fragment: PROTEASE-RESISTANT CORE
Source method: isolated from a genetically manipulated source
Details: N36 AND C34 ARE SYNTHETIC PEPTIDES / Source: (gene. exp.) HIV-1 M:B_HXB2R (virus) / Genus: Lentivirus / Species: Human immunodeficiency virus 1 / Strain: HXB2 / Cellular location: VIRAL MEMBRANE / Gene: GP41 / Gene (production host): GP41 / Production host: Escherichia coli (E. coli) / References: UniProt: P04578
#2: Protein/peptide HIV-1 GP41 GLYCOPROTEIN


Mass: 4277.615 Da / Num. of mol.: 1 / Fragment: PROTEASE-RESISTANT CORE
Source method: isolated from a genetically manipulated source
Details: N36 AND C34 ARE SYNTHETIC PEPTIDES / Source: (gene. exp.) HIV-1 M:B_HXB2R (virus) / Genus: Lentivirus / Species: Human immunodeficiency virus 1 / Strain: HXB2 / Cellular location: VIRAL MEMBRANE / Gene: GP41 / Gene (production host): GP41 / Production host: Escherichia coli (E. coli) / References: UniProt: P04578
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / 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: 2.32 Å3/Da / Density % sol: 46 %
Description: DATA AT NSLS USED MAD METHODS. DATA COLLECTED ON AN OSMIUM-SOAK CRYSTAL AT WAVELENGTHS 1.1398, 1.1396, 1.1344, AND 1.1406 ANGSTROMS.
Crystal growMethod: vapor diffusion, sitting drop / pH: 6
Details: A 10 MG/ML STOCK WAS DILUTED 1:1 IN A SITTING DROP WITH 80 MM NH4CL, 20% PEG200, AND 50% ISOPROPANOL, AND THEN ALLOWED TO EQUILIBRATE AGAINST 80 MM NH4CL, 20% PEG200, AND 30% ISOPROPANOL., ...Details: A 10 MG/ML STOCK WAS DILUTED 1:1 IN A SITTING DROP WITH 80 MM NH4CL, 20% PEG200, AND 50% ISOPROPANOL, AND THEN ALLOWED TO EQUILIBRATE AGAINST 80 MM NH4CL, 20% PEG200, AND 30% ISOPROPANOL., pH 6.0, vapor diffusion - sitting drop
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 mg/mlcomplex1drop
240 mM1dropNH4Cl
310 %PEG2001drop
425 %isopropanol1drop
580 mM1reservoirNH4Cl
620 %PEG2001reservoir
730 %isopropanol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Mar 1, 1997 / Details: MIRRORS
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 5287 / % possible obs: 96.5 % / Observed criterion σ(I): 1.5 / Rsym value: 0.054 / Net I/σ(I): 18.4
Reflection shellResolution: 2→2.07 Å / Mean I/σ(I) obs: 5.4 / Rsym value: 0.263 / % possible all: 98.9
Reflection
*PLUS
Rmerge(I) obs: 0.055

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Processing

Software
NameVersionClassification
X-PLOR3.851model building
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: MAD / Resolution: 2→12 Å / Data cutoff high absF: 100000000 / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.266 371 7.12 %RANDOM
Rwork0.238 ---
obs0.238 5683 96.5 %-
Refinement stepCycle: LAST / Resolution: 2→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms594 0 0 43 637
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.742
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it

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