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- PDB-4i54: Crystal structure of clade A/E 93TH057 HIV-1 gp120 H375S core in ... -

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Basic information

Entry
Database: PDB / ID: 4i54
TitleCrystal structure of clade A/E 93TH057 HIV-1 gp120 H375S core in complex with DMJ-II-121
ComponentsHIV-1 glycoprotein
KeywordsVIRAL PROTEIN/INHIBITOR / HIV / gp120 / entry inhibitor / structure-based drug design / thermodynamics / viral inhibition / DMJ-II-121 / CD4-mimetic / VIRAL PROTEIN-INHIBITOR COMPLEX / Clade A/E / CD4 / 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 / 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 ...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 / 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 / Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHUMAN IMMUNODEFICIENCY VIRUS TYPE 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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
Revision 1.3Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)83,14622
Polymers78,3212
Non-polymers4,82620
Water45025
1
A: HIV-1 glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,57311
Polymers39,1601
Non-polymers2,41310
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: HIV-1 glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,57311
Polymers39,1601
Non-polymers2,41310
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.324, 68.775, 94.443
Angle α, β, γ (deg.)90.00, 90.89, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein HIV-1 glycoprotein


Mass: 39160.367 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 / Strain: A/E 93TH057 / Plasmid: PVRC8400 / Cell line (production host): 293F / Production host: Homo Sapiens (human) / References: UniProt: Q0ED31*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: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: 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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 16
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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.71 Å3/Da / Density % sol: 54.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 12% PEG 8000, 5% ISO-PROPANOL, 0.1M HEPES 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 3, 2012
RadiationMonochromator: Cryogenically-cooled single crystal Si(111) side bounce monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.205→94.432 Å / Num. obs: 40186 / % possible obs: 94.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.205-2.31174.5
2.32-2.46199
2.47-2.63199.6
2.64-2.84199.5
2.85-3.11199.6
2.48-3.12199.4
3.49-4.02190.7
4.03-4.92199.3
4.93-6.96199.3
6.97-94.43197.7

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8_1069) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→33.628 Å / SU ML: 0.38 / σ(F): 1.34 / Phase error: 29.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2614 1457 5.11 %
Rwork0.1957 --
obs0.1992 28519 97.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→33.628 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5308 0 310 25 5643
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095778
X-RAY DIFFRACTIONf_angle_d1.2227827
X-RAY DIFFRACTIONf_dihedral_angle_d17.3362163
X-RAY DIFFRACTIONf_chiral_restr0.075904
X-RAY DIFFRACTIONf_plane_restr0.005984
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.58940.36571420.2882736X-RAY DIFFRACTION99
2.5894-2.6930.31621550.26592702X-RAY DIFFRACTION99
2.693-2.81550.32961470.24522722X-RAY DIFFRACTION99
2.8155-2.96390.29271350.23022787X-RAY DIFFRACTION100
2.9639-3.14940.36321370.21992751X-RAY DIFFRACTION100
3.1494-3.39240.32021510.2162748X-RAY DIFFRACTION100
3.3924-3.73340.27921520.20322458X-RAY DIFFRACTION90
3.7334-4.27270.22291380.18312590X-RAY DIFFRACTION93
4.2727-5.37960.20851490.15682754X-RAY DIFFRACTION99
5.3796-33.63080.22231510.16692814X-RAY DIFFRACTION98

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