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- PDB-6onh: Crystal structure of HIV-1 LM/HT Clade A/E CRF01 gp120 core in co... -

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Basic information

Entry
Database: PDB / ID: 6onh
TitleCrystal structure of HIV-1 LM/HT Clade A/E CRF01 gp120 core in complex with (S)-MCG-IV-031-A05.
ComponentsHIV-1 LM/HT Clade A/E CRF01 gp120
Keywordsviral protein/inhibitor / HIV-1 gp120 / CLADE A/E CF01 / viral protein / viral protein-inhibitor complex
Function / homology
Function and homology information


membrane fusion involved in viral entry into host cell / symbiont entry into host cell / viral envelope / virion attachment to host cell / virion membrane
Similarity search - Function
Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120
Similarity search - Domain/homology
Chem-MWD / clade A/E 93TH057 HIV-1 gp120 core
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.244 Å
AuthorsTolbert, W.D. / Sherburn, R. / Pazgier, M.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI116274 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01AI120756 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI129769 United States
CitationJournal: J.Virol. / Year: 2019
Title: A New Family of Small-Molecule CD4-Mimetic Compounds Contacts Highly Conserved Aspartic Acid 368 of HIV-1 gp120 and Mediates Antibody-Dependent Cellular Cytotoxicity.
Authors: Ding, S. / Grenier, M.C. / Tolbert, W.D. / Vezina, D. / Sherburn, R. / Richard, J. / Prevost, J. / Chapleau, J.P. / Gendron-Lepage, G. / Medjahed, H. / Abrams, C. / Sodroski, J. / Pazgier, M. ...Authors: Ding, S. / Grenier, M.C. / Tolbert, W.D. / Vezina, D. / Sherburn, R. / Richard, J. / Prevost, J. / Chapleau, J.P. / Gendron-Lepage, G. / Medjahed, H. / Abrams, C. / Sodroski, J. / Pazgier, M. / Smith 3rd, A.B. / Finzi, A.
History
DepositionApr 22, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2019Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jul 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_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HIV-1 LM/HT Clade A/E CRF01 gp120
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,25913
Polymers39,4671
Non-polymers2,79212
Water2,360131
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.100, 66.830, 85.870
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein HIV-1 LM/HT Clade A/E CRF01 gp120


Mass: 39466.750 Da / Num. of mol.: 1 / Mutation: H61Y, Q105H, V108I, H375T, N474D, I475M, K476R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: HIV-1 Env / Cell (production host): HEK GnT1- / Production host: Homo sapiens (human) / References: UniProt: A0A0M3KKW9
#2: 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.: 10
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
#3: Chemical ChemComp-MWD / (3S)-N~3~-(4-chloro-3-fluorophenyl)-N~1~-propylpiperidine-1,3-dicarboxamide


Mass: 341.808 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H21ClFN3O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.44 Å3/Da / Density % sol: 49.57 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 10% PEG 1500 5% PEG 400 0.1 M HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 9, 2018
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.24→50 Å / Num. obs: 15219 / % possible obs: 80.6 % / Redundancy: 3.1 % / CC1/2: 0.96 / Rpim(I) all: 0.107 / Rsym value: 0.165 / Net I/σ(I): 5.2
Reflection shellResolution: 2.24→2.37 Å / Mean I/σ(I) obs: 3 / Num. unique obs: 2436 / CC1/2: 0.45 / Rpim(I) all: 0.364 / Rsym value: 0.557 / % possible all: 85.5

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Processing

Software
NameVersionClassification
PHENIX(1.15.2_3472: ???)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TGT

3tgt


Resolution: 2.244→52.74 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 0.02 / Phase error: 26.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2786 1290 5.04 %
Rwork0.2202 --
obs0.223 25592 71.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.244→52.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2657 0 178 131 2966
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072893
X-RAY DIFFRACTIONf_angle_d0.9913927
X-RAY DIFFRACTIONf_dihedral_angle_d6.3161710
X-RAY DIFFRACTIONf_chiral_restr0.064467
X-RAY DIFFRACTIONf_plane_restr0.005499
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2441-2.3340.34131630.26752835X-RAY DIFFRACTION76
2.334-2.44020.32061790.27142732X-RAY DIFFRACTION74
2.4402-2.56880.29271650.25442566X-RAY DIFFRACTION68
2.5688-2.72980.30061380.24612794X-RAY DIFFRACTION74
2.7298-2.94050.3061150.24512805X-RAY DIFFRACTION73
2.9405-3.23640.24411290.21222551X-RAY DIFFRACTION68
3.2364-3.70460.23981640.21432743X-RAY DIFFRACTION73
3.7046-4.6670.27461090.18332639X-RAY DIFFRACTION69
4.667-52.75440.26331280.19522637X-RAY DIFFRACTION70

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