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- PDB-4i53: Crystal structure of clade C1086 HIV-1 gp120 core in complex with... -

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Basic information

Entry
Database: PDB / ID: 4i53
TitleCrystal structure of clade C1086 HIV-1 gp120 core in complex with DMJ-II-121
ComponentsHIV-1 glycoprotein
KeywordsVIRAL PROTEIN/INHIBITOR / HIV / gp120 / entry inhibitor / DMJ-II-121 / CD4-mimetic / VIRAL PROTEIN-INHIBITOR COMPLEX / C1086 / Extracellular
Function / homology
Function and homology information


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 / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope ...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 / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / plasma membrane
Similarity search - Function
HIV Envelope Protein Gp120; Chain G / Human immunodeficiency virus 1, Gp160, envelope glycoprotein / Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Beta Complex / Mainly Beta
Similarity search - Domain/homology
Chem-1C1 / FORMIC ACID / Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHUMAN IMMUNODEFICIENCY VIRUS TYPE 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5002 Å
AuthorsLe-Khac, M. / Hendrickson, W.A.
CitationJournal: ACS Med Chem Lett / Year: 2013
Title: Structure-Based Design and Synthesis of an HIV-1 Entry Inhibitor Exploiting X-Ray and Thermodynamic Characterization.
Authors: Lalonde, J.M. / Le-Khac, M. / Jones, D.M. / Courter, J.R. / Park, J. / Schon, A. / Princiotto, A.M. / Wu, X. / Mascola, J.R. / Freire, E. / Sodroski, J. / Madani, N. / Hendrickson, W.A. / Smith, A.B.
History
DepositionNov 28, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2May 26, 2021Group: Source and taxonomy / Structure summary / Category: chem_comp / entity_src_gen
Item: _chem_comp.pdbx_synonyms / _entity_src_gen.host_org_common_name ..._chem_comp.pdbx_synonyms / _entity_src_gen.host_org_common_name / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HIV-1 glycoprotein
B: HIV-1 glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,24318
Polymers79,5112
Non-polymers3,73116
Water4,666259
1
A: HIV-1 glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7099
Polymers39,7561
Non-polymers1,9538
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: HIV-1 glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5349
Polymers39,7561
Non-polymers1,7788
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.450, 127.670, 192.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-602-

HOH

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Components

#1: Protein HIV-1 glycoprotein


Mass: 39755.664 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 / Strain: C1086 / Plasmid: PVRC8400 / Cell line (production host): 293F / Production host: Homo Sapiens (human) / References: UniProt: C6G099*PLUS
#2: Chemical ChemComp-1C1 / amino({[(1R,2R)-1-({[(4-chloro-3-fluorophenyl)amino](oxo)acetyl}amino)-2,3-dihydro-1H-inden-2-yl]methyl}amino)methanimi nium / [amino({[(1R,2R)-1-{[(4-chloro-3- fluorophenyl)carbamoyl]formamido}-2,3-dihydro-1H- inden-2-yl]methyl}amino)methylidene]azanium


Mass: 404.846 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H20ClFN5O2
#3: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 13
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 259 / 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: 2.61 Å3/Da / Density % sol: 52.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 18-20% (w/v) PEG 1500, 0.1 M CaCl2, 0.1 M imidazole pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.97894 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 15, 2011
RadiationMonochromator: Bent single crystal monochromator Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97894 Å / Relative weight: 1
ReflectionResolution: 2.5→38.58 Å / Num. obs: 29249 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8_1069) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5002→29.819 Å / SU ML: 0.36 / σ(F): 1.37 / Phase error: 27.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2733 1087 3.78 %
Rwork0.2539 --
obs0.2546 28780 98.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5002→29.819 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5262 0 241 259 5762
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0535637
X-RAY DIFFRACTIONf_angle_d1.3087632
X-RAY DIFFRACTIONf_dihedral_angle_d14.6212092
X-RAY DIFFRACTIONf_chiral_restr0.065877
X-RAY DIFFRACTIONf_plane_restr0.01970
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5002-2.6140.36361220.33073052X-RAY DIFFRACTION89
2.614-2.75170.34761350.32983436X-RAY DIFFRACTION100
2.7517-2.9240.3321420.30723501X-RAY DIFFRACTION100
2.924-3.14950.3251370.30083493X-RAY DIFFRACTION100
3.1495-3.4660.29131290.26983481X-RAY DIFFRACTION100
3.466-3.96650.30341440.24473518X-RAY DIFFRACTION100
3.9665-4.99360.2171350.20853540X-RAY DIFFRACTION100
4.9936-29.82140.19691430.2073672X-RAY DIFFRACTION100

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