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- PDB-3u91: Structural Determinants of Trimerization Specificity in HIV-1 gp4... -

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Basic information

Entry
Database: PDB / ID: 3u91
TitleStructural Determinants of Trimerization Specificity in HIV-1 gp41 Protein
ComponentsGp41
KeywordsVIRAL PROTEIN / gp41 / HIV-1 / trimerization domain / oligomeric structure
Function / homology
Function and homology information


membrane => GO:0016020 / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / plasma membrane
Similarity search - Function
Retroviral envelope protein / Retroviral envelope protein GP41-like
Similarity search - Domain/homology
Chem-JEF / Env polyprotein / Env polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsLiu, J. / Lu, M.
CitationJournal: To be Published
Title: Structural Determinants of Trimerization Specificity in HIV-1 gp41 Protein
Authors: Liu, J. / Li, Q. / Dey, A.K. / Moore, J.P. / Lu, M.
History
DepositionOct 17, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Gp41
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,5342
Polymers3,9371
Non-polymers5981
Water86548
1
A: Gp41
hetero molecules

A: Gp41
hetero molecules

A: Gp41
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6036
Polymers11,8103
Non-polymers1,7933
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area4690 Å2
ΔGint-31 kcal/mol
Surface area6750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.308, 45.308, 42.160
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11A-67-

HOH

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Components

#1: Protein/peptide Gp41 /


Mass: 3936.581 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: env / Production host: Escherichia coli (E. coli) / References: UniProt: Q9YYZ1, UniProt: Q7ZC55*PLUS
#2: Chemical ChemComp-JEF / O-(O-(2-AMINOPROPYL)-O'-(2-METHOXYETHYL)POLYPROPYLENE GLYCOL 500) / JEFFAMINE


Mass: 597.822 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H63NO10
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 3.17 Å3/Da / Density % sol: 61.24 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 20% Jeffamine M600, 0.1M MES, 25mM Cesium Chloride, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9676 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 25, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9676 Å / Relative weight: 1
ReflectionResolution: 1.45→42.14 Å / Num. obs: 9173 / % possible obs: 99.8 % / Redundancy: 8.8 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 9.1
Reflection shellResolution: 1.45→1.5 Å / Redundancy: 8.8 % / Mean I/σ(I) obs: 6.4 / Rsym value: 0.467 / % possible all: 99.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.2.0005refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AIK

1aik


Resolution: 1.45→42.14 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.928 / SU B: 1.818 / SU ML: 0.037 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.061 / ESU R Free: 0.069 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23341 917 10 %RANDOM
Rwork0.19191 ---
obs0.19585 8256 99.85 %-
all-9173 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 26.142 Å2
Baniso -1Baniso -2Baniso -3
1-0.62 Å20.31 Å20 Å2
2--0.62 Å20 Å2
3----0.93 Å2
Refinement stepCycle: LAST / Resolution: 1.45→42.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms255 0 13 48 316
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.022270
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1382.01362
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.226529
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.21324.61513
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.0351553
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.733152
X-RAY DIFFRACTIONr_chiral_restr0.0730.244
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02186
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2060.2115
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3010.2185
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.130.220
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1380.247
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1030.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7841.5152
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.422239
X-RAY DIFFRACTIONr_scbond_it2.3623131
X-RAY DIFFRACTIONr_scangle_it3.8464.5123
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.45→1.489 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.25 72 -
Rwork0.202 568 -
obs--99.69 %
Refinement TLS params.Method: refined / Origin x: -21.502 Å / Origin y: 6.958 Å / Origin z: -8.623 Å
111213212223313233
T-0.0559 Å20.0044 Å20.0076 Å2--0.1179 Å20.0043 Å2---0.1738 Å2
L1.0872 °20.2375 °2-0.549 °2-1.3105 °2-0.834 °2--6.0814 °2
S-0.0522 Å °0.1599 Å °0.0426 Å °-0.2306 Å °0.0059 Å °-0.0361 Å °0.3026 Å °0.1494 Å °0.0463 Å °

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