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- PDB-3vgx: Structure of gp41 T21/Cp621-652 -

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Basic information

Entry
Database: PDB / ID: 3vgx
TitleStructure of gp41 T21/Cp621-652
Components(Envelope glycoprotein gp160) x 2
KeywordsMEMBRANE PROTEIN / 6-helix bundle / membrane fusion
Function / homology
Function and homology information


host cell periphery / CD4 receptor binding / Dectin-2 family / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / virus-mediated perturbation of host defense response / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / host cell perinuclear region of cytoplasm ...host cell periphery / CD4 receptor binding / Dectin-2 family / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / virus-mediated perturbation of host defense response / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / host cell perinuclear region of cytoplasm / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / protein-containing complex binding / structural molecule activity / virion attachment to host cell / host cell plasma membrane / 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
ACETIC ACID / Envelope glycoprotein gp160 / Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHuman immunodeficiency virus type 1
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsYao, X. / Waltersperger, S. / Wang, M. / Cui, S.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Discovery of critical residues for viral entry and inhibition through structural Insight of HIV-1 fusion inhibitor CP621-652.
Authors: Chong, H. / Yao, X. / Qiu, Z. / Qin, B. / Han, R. / Waltersperger, S. / Wang, M. / Cui, S. / He, Y.
History
DepositionAug 22, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 25, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2013Group: Database references
Revision 1.2Nov 8, 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 / pdbx_struct_special_symmetry / struct_conn / struct_ref_seq_dif / struct_site
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 / _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
C: Envelope glycoprotein gp160
D: Envelope glycoprotein gp160
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,6944
Polymers8,5422
Non-polymers1522
Water1,56787
1
C: Envelope glycoprotein gp160
D: Envelope glycoprotein gp160
hetero molecules

C: Envelope glycoprotein gp160
D: Envelope glycoprotein gp160
hetero molecules

C: Envelope glycoprotein gp160
D: Envelope glycoprotein gp160
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,08112
Polymers25,6256
Non-polymers4566
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area10550 Å2
ΔGint-93 kcal/mol
Surface area11000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.967, 44.967, 209.237
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
11C-601-

ACY

21C-707-

HOH

31C-746-

HOH

41C-748-

HOH

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Components

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


Mass: 4515.291 Da / Num. of mol.: 1 / Fragment: NHR (UNP RESIDIES 553-590) / Source method: obtained synthetically / Details: This sequence occurs naturally in humans. / Source: (synth.) Human immunodeficiency virus type 1 / References: UniProt: P03375, UniProt: P03377*PLUS
#2: Protein/peptide Envelope glycoprotein gp160 / Env polyprotein / Surface protein gp120 / SU / Glycoprotein 120 / gp120 / Transmembrane protein ...Env polyprotein / Surface protein gp120 / SU / Glycoprotein 120 / gp120 / Transmembrane protein gp41 / TM / Glycoprotein 41 / gp41


Mass: 4026.382 Da / Num. of mol.: 1 / Fragment: CHR (UNP RESIDIES 621-652) / Source method: obtained synthetically / Details: This sequence occurs naturally in humans. / Source: (synth.) Human immunodeficiency virus type 1 / References: UniProt: P03375, UniProt: P03377*PLUS
#3: Chemical ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 87 / 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: 2.39 Å3/Da / Density % sol: 48.53 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 8.5
Details: 0.05M Tris HCl, 0.05M Potassium, 0.01M Magnesium chloride, 15% (w/v) PEG 6000, pH 8.5, VAPOR DIFFUSION, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Jul 14, 2011
RadiationMonochromator: Osmic VariMax optic / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.739→23.711 Å / Num. all: 8804 / Num. obs: 8601 / % possible obs: 99.8 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 6.51 % / Rmerge(I) obs: 0.034 / Rsym value: 0.037 / Net I/σ(I): 33
Reflection shellResolution: 1.74→1.8 Å / Redundancy: 3.84 % / Rmerge(I) obs: 0.179 / Mean I/σ(I) obs: 5.6 / Rsym value: 0.207 / % possible all: 98.7

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.1_357)refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 3F4Y

3f4y


Resolution: 1.74→23.711 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 0.06 / Phase error: 19.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1968 411 4.78 %RANDOM
Rwork0.1921 ---
obs0.1923 8595 97.44 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.247 Å2 / ksol: 0.463 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.5435 Å2-0 Å2-0 Å2
2--1.5435 Å2-0 Å2
3----3.0869 Å2
Refinement stepCycle: LAST / Resolution: 1.74→23.711 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms562 0 10 87 659
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005605
X-RAY DIFFRACTIONf_angle_d0.832824
X-RAY DIFFRACTIONf_dihedral_angle_d14.652233
X-RAY DIFFRACTIONf_chiral_restr0.05192
X-RAY DIFFRACTIONf_plane_restr0.003107
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7393-1.99080.25371180.2063257694
1.9908-2.50780.18721510.1633273099
2.5078-23.71350.18581420.1948287899

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