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- PDB-1env: ATOMIC STRUCTURE OF THE ECTODOMAIN FROM HIV-1 GP41 -

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Entry
Database: PDB / ID: 1env
TitleATOMIC STRUCTURE OF THE ECTODOMAIN FROM HIV-1 GP41
ComponentsHIV-1 ENVELOPE PROTEIN CHIMERA CONSISTING OF A FRAGMENT OF GCN4 ZIPPER CLONED N-TERMINAL TO TWO FRAGMENTS OF GP41
KeywordsVIRAL PROTEIN / VIRAL FUSION / COAT PROTEIN
Function / homology
Function and homology information


Dectin-2 family / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane ...Dectin-2 family / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / 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
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 speciesSaccharomyces cerevisiae (brewer's yeast)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.6 Å
AuthorsWeissenhorn, W. / Dessen, A. / Harrison, S.C. / Skehel, J.J. / Wiley, D.C.
CitationJournal: Nature / Year: 1997
Title: Atomic structure of the ectodomain from HIV-1 gp41.
Authors: Weissenhorn, W. / Dessen, A. / Harrison, S.C. / Skehel, J.J. / Wiley, D.C.
History
DepositionJun 27, 1997Processing site: BNL
Revision 1.0Nov 19, 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 28, 2017Group: Database references / Other ...Database references / Other / Source and taxonomy / Structure summary
Category: entity_name_com / entity_src_gen ...entity_name_com / entity_src_gen / pdbx_database_status / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _pdbx_database_status.process_site / _struct_ref.db_code ..._pdbx_database_status.process_site / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

Deposited unit
A: HIV-1 ENVELOPE PROTEIN CHIMERA CONSISTING OF A FRAGMENT OF GCN4 ZIPPER CLONED N-TERMINAL TO TWO FRAGMENTS OF GP41


Theoretical massNumber of molelcules
Total (without water)14,7101
Polymers14,7101
Non-polymers00
Water21612
1
A: HIV-1 ENVELOPE PROTEIN CHIMERA CONSISTING OF A FRAGMENT OF GCN4 ZIPPER CLONED N-TERMINAL TO TWO FRAGMENTS OF GP41

A: HIV-1 ENVELOPE PROTEIN CHIMERA CONSISTING OF A FRAGMENT OF GCN4 ZIPPER CLONED N-TERMINAL TO TWO FRAGMENTS OF GP41

A: HIV-1 ENVELOPE PROTEIN CHIMERA CONSISTING OF A FRAGMENT OF GCN4 ZIPPER CLONED N-TERMINAL TO TWO FRAGMENTS OF GP41


Theoretical massNumber of molelcules
Total (without water)44,1293
Polymers44,1293
Non-polymers00
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 area12370 Å2
ΔGint-124 kcal/mol
Surface area18890 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)52.350, 52.350, 414.600
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein HIV-1 ENVELOPE PROTEIN CHIMERA CONSISTING OF A FRAGMENT OF GCN4 ZIPPER CLONED N-TERMINAL TO TWO FRAGMENTS OF GP41 / Env polyprotein


Mass: 14709.765 Da / Num. of mol.: 1
Fragment: GCN4 IS RESIDUES 1 - 29, GP41 IS RESIDUES 30 - 154
Mutation: L2I, V61, L9I, N13I, L16I, V20I, L23I, V27I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast), (gene. exp.) Human immunodeficiency virus 1
Fragment: 30 - 154 / Gene: GCN4, AAS3, ARG9, YEL009C, env / Genus: Saccharomyces / Gene (production host): GP41 / Production host: Escherichia coli (E. coli) / References: UniProt: P03377
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHIS STRUCTURE IS A CHIMERA. IT STARTS AT THE N-TERMINUS WITH 31 RESIDUES FROM YEAST GCN4 FOLLOWED ...THIS STRUCTURE IS A CHIMERA. IT STARTS AT THE N-TERMINUS WITH 31 RESIDUES FROM YEAST GCN4 FOLLOWED BY 50 RESIDUES FROM GP41 AND 42 ADDITIONAL RESIDUES FROM GP41, FOR A A TOTAL OF 123 RESIDUES AS SHOWN ON SEQRES. 115 OF THESE RESIDUES WERE LOCATED AND ARE PRESENTED IN THIS ENTRY. DBREF RECORDS BELOW CAN BE USED TO ASSOCIATE THE RESIDUES PRESENT IN THIS ENTRY WITH THE CORRESPONDING SWISSPROT ENTRY.

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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: 4.4 Å3/Da / Density % sol: 72 %
Crystal growpH: 8
Details: 20 MM HEPES PH 8.0 1.1 M AMMONIUM SULFATE 12% ETHYLENE GLYCOL SPACE GROUP R32 IN HEXAGONAL SETTING
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115-20 mg/mlprotein1drop
220 mg/mlHEPES1drop
375 mM1dropNaCl
4100 mMHEPES1reservoir
51.1 Mammonium sulfate1reservoir
612 %ethylene glycol1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: ELLIOTT GX-13 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 1, 1997 / Details: MIRRORS
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→25 Å / Num. obs: 8130 / % possible obs: 90.5 % / Observed criterion σ(I): 2 / Redundancy: 7.45 % / Biso Wilson estimate: 59.41 Å2 / Rmerge(I) obs: 0.071 / Rsym value: 0.071 / Net I/σ(I): 10.2
Reflection shellResolution: 2.59→2.69 Å / Redundancy: 5 % / Rmerge(I) obs: 0.179 / Mean I/σ(I) obs: 4.5 / Rsym value: 0.179 / % possible all: 91.4

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MIR / Resolution: 2.6→25 Å / Rfactor Rfree error: 0 / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.277 674 10 %RANDOM
Rwork0.244 ---
obs0.244 6432 90.5 %-
Displacement parametersBiso mean: 52.9 Å2
Refinement stepCycle: LAST / Resolution: 2.6→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms935 0 0 12 947
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
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_deg1.2
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
LS refinement shellResolution: 2.6→2.72 Å / Rfactor Rfree error: 0.004 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.277 88 10 %
Rwork0.244 695 -
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19M.SOL

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