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- PDB-3h00: Structure of the C-terminal Domain of a Putative HIV-1 gp41 Fusio... -

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Basic information

Entry
Database: PDB / ID: 3h00
TitleStructure of the C-terminal Domain of a Putative HIV-1 gp41 Fusion Intermediate
ComponentsEnvelope glycoprotein gp160
KeywordsVIRAL PROTEIN / viral membrane fusion / HIV-1 / gp41 / envelope protein / neutralizing antibodies / AIDS / Apoptosis / Cell membrane / Cleavage on pair of basic residues / Disulfide bond / Fusion protein / Glycoprotein / Host-virus interaction / Lipoprotein / Membrane / Palmitate / Transmembrane / Viral immunoevasion / Virion
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 / apoptotic process / 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 speciesHuman immunodeficiency virus type 1 lw12.3 isolate
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsLiu, J.
CitationJournal: J.Virol. / Year: 2010
Title: Role of a putative gp41 dimerization domain in human immunodeficiency virus type 1 membrane fusion.
Authors: Liu, J. / Deng, Y. / Li, Q. / Dey, A.K. / Moore, J.P. / Lu, M.
History
DepositionApr 8, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 15, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 19, 2013Group: Database references
Revision 1.3Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Envelope glycoprotein gp160
B: Envelope glycoprotein gp160
C: Envelope glycoprotein gp160
D: Envelope glycoprotein gp160


Theoretical massNumber of molelcules
Total (without water)19,1854
Polymers19,1854
Non-polymers00
Water1,67593
1
A: Envelope glycoprotein gp160
C: Envelope glycoprotein gp160


Theoretical massNumber of molelcules
Total (without water)9,5922
Polymers9,5922
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1590 Å2
ΔGint-9 kcal/mol
Surface area6460 Å2
MethodPISA
2
B: Envelope glycoprotein gp160
D: Envelope glycoprotein gp160


Theoretical massNumber of molelcules
Total (without water)9,5922
Polymers9,5922
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1480 Å2
ΔGint-8 kcal/mol
Surface area6100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.764, 47.499, 74.824
Angle α, β, γ (deg.)90.00, 128.32, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein/peptide
Envelope glycoprotein gp160 / Env polyprotein / Surface protein / SU / Glycoprotein 120 / gp120 / Transmembrane protein / TM / ...Env polyprotein / Surface protein / SU / Glycoprotein 120 / gp120 / Transmembrane protein / TM / Glycoprotein 41 / gp41


Mass: 4796.156 Da / Num. of mol.: 4 / Fragment: C-TERMINAL DOMAIN (UNP residues 636 to 674)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 lw12.3 isolate
Strain: HXB2 ISOLATE / Gene: env / Production host: Escherichia coli (E. coli) / References: UniProt: Q70626
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / 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: 4.39 Å3/Da / Density % sol: 71.97 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 3% PEG8000, 0.1M Tris-HCl, 0.1M cesium chloride, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 24, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.53
11H+2.000L, -K, -L20.47
ReflectionResolution: 2.2→40.1 Å / Num. all: 16151 / Num. obs: 16151 / % possible obs: 93.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 46.5 Å2 / Rmerge(I) obs: 0.044 / Net I/σ(I): 18.7
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.269 / Mean I/σ(I) obs: 3.1 / Num. unique all: 1309 / % possible all: 76.2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.5.0063refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3GWO

3gwo


Resolution: 2.2→40.1 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.938 / SU B: 9.299 / SU ML: 0.104
Isotropic thermal model: Isotropic with TLS groups assigned for each protein chain
Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.039 / ESU R Free: 0.037 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25526 807 5 %RANDOM
Rwork0.2118 ---
all0.21403 16151 --
obs0.21403 16151 93.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 37.058 Å2
Baniso -1Baniso -2Baniso -3
1-3.09 Å20 Å2-25.75 Å2
2---15.13 Å20 Å2
3---12.04 Å2
Refinement stepCycle: LAST / Resolution: 2.2→40.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1309 0 0 93 1402
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.0211338
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.4061.8981819
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3375148
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.21227.588
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.07415236
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1770.2188
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021051
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3681.5758
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.21821214
X-RAY DIFFRACTIONr_scbond_it3.8343580
X-RAY DIFFRACTIONr_scangle_it5.9334.5605
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.196→2.253 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 39 -
Rwork0.243 906 -
obs-906 74.2 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.47133.92263.606510.442510.11779.87380.04160.0567-0.10340.0596-0.09220.02540.1281-0.06980.05060.23490.0198-0.020.10570.02180.026230.67910.75611.123
29.8664-8.69291.68097.7495-1.5910.56620.1014-0.00280.3027-0.0678-0.0669-0.2295-0.0599-0.069-0.03460.03560.02130.0270.1880.02430.292616.614-12.06526.852
33.23245.00724.743610.44718.94399.2627-0.0066-0.0351-0.0313-0.0504-0.25210.2366-0.0745-0.36170.25870.1610.0253-0.0390.1991-0.01610.055122.9029.135-1.45
411.01-9.24042.02958.0454-1.92371.19180.23130.1472-0.0777-0.23-0.19320.0622-0.0474-0.0914-0.03810.0584-0.0111-0.00320.1731-0.01920.16635.23-14.14123.72
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 39
2X-RAY DIFFRACTION2B1 - 38
3X-RAY DIFFRACTION3C1 - 39
4X-RAY DIFFRACTION4D1 - 36

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