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- PDB-1fav: THE STRUCTURE OF AN HIV-1 SPECIFIC CELL ENTRY INHIBITOR IN COMPLE... -

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Basic information

Entry
Database: PDB / ID: 1fav
TitleTHE STRUCTURE OF AN HIV-1 SPECIFIC CELL ENTRY INHIBITOR IN COMPLEX WITH THE HIV-1 GP41 TRIMERIC CORE
Components
  • HIV-1 ENVELOPE PROTEIN CHIMERA
  • PROTEIN (TRANSMEMBRANE GLYCOPROTEIN)
KeywordsVIRAL PROTEIN / HIV-1 / gp41 / inhibitor
Function / homology
Function and homology information


Synthesis and processing of ENV and VPU / protein localization to nuclear periphery / Activation of the AP-1 family of transcription factors / response to amino acid starvation / mediator complex binding / evasion of host immune response / negative regulation of ribosomal protein gene transcription by RNA polymerase II / positive regulation of cellular response to amino acid starvation / nitrogen catabolite activation of transcription from RNA polymerase II promoter / Alpha-defensins ...Synthesis and processing of ENV and VPU / protein localization to nuclear periphery / Activation of the AP-1 family of transcription factors / response to amino acid starvation / mediator complex binding / evasion of host immune response / negative regulation of ribosomal protein gene transcription by RNA polymerase II / positive regulation of cellular response to amino acid starvation / nitrogen catabolite activation of transcription from RNA polymerase II promoter / Alpha-defensins / Dectin-2 family / TFIID-class transcription factor complex binding / amino acid biosynthetic process / positive regulation of transcription initiation by RNA polymerase II / positive regulation of RNA polymerase II transcription preinitiation complex assembly / Binding and entry of HIV virion / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / cellular response to amino acid starvation / positive regulation of establishment of T cell polarity / virus-mediated perturbation of host defense response / host cell endosome membrane / actin filament organization / Assembly Of The HIV Virion / Budding and maturation of HIV virion / RNA polymerase II transcription regulator complex / : / DNA-binding transcription activator activity, RNA polymerase II-specific / clathrin-dependent endocytosis of virus by host cell / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA binding / viral protein processing / DNA-binding transcription factor activity, RNA polymerase II-specific / intracellular signal transduction / symbiont entry into host cell / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / chromatin binding / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / membrane / identical protein binding / nucleus
Similarity search - Function
Basic region leucine zipper / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / Basic-leucine zipper (bZIP) domain signature. / Basic-leucine zipper (bZIP) domain profile. / basic region leucin zipper / Basic-leucine zipper domain superfamily / Basic-leucine zipper domain / Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like ...Basic region leucine zipper / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / Basic-leucine zipper (bZIP) domain signature. / Basic-leucine zipper (bZIP) domain profile. / basic region leucin zipper / Basic-leucine zipper domain superfamily / Basic-leucine zipper domain / Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
General control transcription factor GCN4 / Envelope glycoprotein gp160 / Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
Saccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / Resolution: 3 Å
AuthorsZhou, G. / Ferrer, M. / Chopra, R. / Strassmaier, T. / Weissenhorn, W. / Skehel, J.J. / Oprian, D. / Schreiber, S.L. / Harrison, S.C. / Wiley, D.C.
CitationJournal: Bioorg.Med.Chem. / Year: 2000
Title: The structure of an HIV-1 specific cell entry inhibitor in complex with the HIV-1 gp41 trimeric core.
Authors: Zhou, G. / Ferrer, M. / Chopra, R. / Kapoor, T.M. / Strassmaier, T. / Weissenhorn, W. / Skehel, J.J. / Oprian, D. / Schreiber, S.L. / Harrison, S.C. / Wiley, D.C.
History
DepositionJul 13, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 23, 2000Provider: 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: Advisory / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_unobs_or_zero_occ_residues / software
Revision 1.4Nov 3, 2021Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_unobs_or_zero_occ_residues ...database_2 / pdbx_unobs_or_zero_occ_residues / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr2_label_atom_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HIV-1 ENVELOPE PROTEIN CHIMERA
C: PROTEIN (TRANSMEMBRANE GLYCOPROTEIN)


Theoretical massNumber of molelcules
Total (without water)13,3182
Polymers13,3182
Non-polymers00
Water0
1
A: HIV-1 ENVELOPE PROTEIN CHIMERA
C: PROTEIN (TRANSMEMBRANE GLYCOPROTEIN)

A: HIV-1 ENVELOPE PROTEIN CHIMERA
C: PROTEIN (TRANSMEMBRANE GLYCOPROTEIN)

A: HIV-1 ENVELOPE PROTEIN CHIMERA
C: PROTEIN (TRANSMEMBRANE GLYCOPROTEIN)


Theoretical massNumber of molelcules
Total (without water)39,9546
Polymers39,9546
Non-polymers00
Water0
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 area17320 Å2
ΔGint-109 kcal/mol
Surface area16880 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)35.819, 35.819, 164.691
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 HIV-1 ENVELOPE PROTEIN CHIMERA


Mass: 9268.784 Da / Num. of mol.: 1 / Mutation: L2I, V6I, L9I, N13I, L16I, V20I, L23I, V27I
Source method: isolated from a genetically manipulated source
Details: CHIMERA CONSISTS OF A FRAGMENT OF GCN4 ZIPPER CLONED N-TERMINAL TO A FRAGMENT OF GP41
Source: (gene. exp.) Human immunodeficiency virus 1, (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Genus: Lentivirus / Plasmid: PRSET / Gene: GCN4,AAS3,ARG9,YEL009C / Production host: Escherichia coli (E. coli) / References: UniProt: P03069, UniProt: P03377
#2: Protein/peptide PROTEIN (TRANSMEMBRANE GLYCOPROTEIN)


Mass: 4049.338 Da / Num. of mol.: 1 / Fragment: OUTER PEPTIDE OF GP41 OF HIV-1 / Source method: obtained synthetically
Details: The peptide was chemically synthesized. The sequence of the peptide is naturally found in HIV-1.
References: UniProt: P03377, UniProt: P04578*PLUS

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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: 2.29 Å3/Da / Density % sol: 46.29 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.9
Details: 25mM PIPES, 0.25M MgAc, 2.5% isopropanol, 10mM Hepes, 37.5mM NaCl, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal grow
*PLUS
Details: drop consists of equal amounts of protein and reservoir solutions
pH: 8.3
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlprotein1drop
220 mMHEPES1droppH8.3
450 mMPIPES1reservoirpH6.9
65 %isopropanol1reservoir
375 mM1dropNaCl
50.5 M1reservoirMgAc2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ELLIOTT GX-13 / Wavelength: 1.54
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 14, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 3→15 Å / Num. all: 2806 / Num. obs: 2574 / % possible obs: 88 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.072

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Processing

Software
NameVersionClassification
AMoREphasing
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 3→15 Å / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
Details: Residue 125 chain C was modelled based on residues 124 and 126. The occupancy of this residue is 0.00.
RfactorNum. reflection% reflectionSelection details
Rfree0.295 398 -random
Rwork0.24 ---
all0.24 2806 --
obs0.24 2574 88 %-
Refinement stepCycle: LAST / Resolution: 3→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms888 0 0 0 888
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.6

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