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- PDB-3wfv: HIV-1 CRF07 gp41 -

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Basic information

Entry
Database: PDB / ID: 3wfv
TitleHIV-1 CRF07 gp41
ComponentsEnvelope glycoprotein gp160
KeywordsVIRAL PROTEIN / DOUBLE HELIX / alpha-helix / virus fusion / glycoprotein / membrane
Function / homology
Function and homology information


virus-mediated perturbation of host defense response => GO:0019049 / : / 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 / membrane => GO:0016020 / viral protein processing / fusion of virus membrane with host plasma membrane ...virus-mediated perturbation of host defense response => GO:0019049 / : / 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 / membrane => GO:0016020 / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / structural molecule activity / virion attachment to host cell / host cell plasma membrane / virion membrane / plasma 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsDu, J. / Xue, H. / Ma, J. / Liu, F. / Zhou, J. / Shao, Y. / Qiao, W. / Liu, X.
CitationJournal: Virology / Year: 2013
Title: The crystal structure of HIV CRF07 B'/C gp41 reveals a hyper-mutant site in the middle of HR2 heptad repeat
Authors: Du, J. / Xue, H. / Ma, J. / Liu, F. / Zhou, J. / Shao, Y. / Qiao, W. / Liu, X.
History
DepositionJul 24, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 16, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.2Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Envelope glycoprotein gp160


Theoretical massNumber of molelcules
Total (without water)9,7461
Polymers9,7461
Non-polymers00
Water54030
1
A: Envelope glycoprotein gp160

A: Envelope glycoprotein gp160

A: Envelope glycoprotein gp160


Theoretical massNumber of molelcules
Total (without water)29,2373
Polymers29,2373
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area8110 Å2
ΔGint-67 kcal/mol
Surface area12740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.920, 46.920, 185.051
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-701-

HOH

21A-702-

HOH

31A-730-

HOH

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Components

#1: Protein Envelope glycoprotein gp160


Mass: 9745.812 Da / Num. of mol.: 1 / Fragment: UNP residues 542-577 and 624-660
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: env / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / References: UniProt: Q994K2
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 2.01 Å3/Da / Density % sol: 38.84 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 8% PEG6000, 0.1M Tris, 40% MPD, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: ENRAF-NONIUS / Detector: CCD / Date: Sep 16, 2012
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.8→20.102 Å / Num. obs: 7326 / % possible obs: 95.76 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellHighest resolution: 1.8 Å / Redundancy: 11.4 % / Rmerge(I) obs: 0.125 / Mean I/σ(I) obs: 17.5 / Num. unique all: 7326 / Rsym value: 0.053 / % possible all: 95.76

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→20.102 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7533 / SU ML: 0.21 / σ(F): 1.38 / Phase error: 29.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2582 336 4.59 %RANDOM
Rwork0.2201 ---
obs0.2219 7326 95.76 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 87.432 Å2 / ksol: 0.478 e/Å3
Displacement parametersBiso max: 91.06 Å2 / Biso mean: 32.1715 Å2 / Biso min: 13.76 Å2
Baniso -1Baniso -2Baniso -3
1--2.806 Å20 Å20 Å2
2---2.806 Å20 Å2
3---5.612 Å2
Refinement stepCycle: LAST / Resolution: 1.8→20.102 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms685 0 0 30 715
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008693
X-RAY DIFFRACTIONf_angle_d1.226935
X-RAY DIFFRACTIONf_chiral_restr0.084102
X-RAY DIFFRACTIONf_plane_restr0.004124
X-RAY DIFFRACTIONf_dihedral_angle_d19.14259
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 2 / % reflection obs: 96 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.8-2.26740.2961750.223334173592
2.2674-20.10360.24731610.219235733734

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