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- PDB-6ooo: 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: 6ooo
TitleCrystal structure of HIV-1 LM/HT Clade A/E CRF01 gp120 core in complex with (S)-MCG-IV-226.
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 / homologyGp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / viral envelope / Chem-MXJ / clade A/E 93TH057 HIV-1 gp120 core
Function and homology information
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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: Acs Med.Chem.Lett. / Year: 2020
Title: Optimization of Small Molecules That Sensitize HIV-1 Infected Cells to Antibody-Dependent Cellular Cytotoxicity.
Authors: Grenier, M.C. / Ding, S. / Vezina, D. / Chapleau, J.P. / Tolbert, W.D. / Sherburn, R. / Schon, A. / Somisetti, S. / Abrams, C.F. / Pazgier, M. / Finzi, A. / Smith 3rd, A.B.
History
DepositionApr 23, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Jul 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 / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Oct 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 1.4Nov 13, 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)42,27413
Polymers39,4671
Non-polymers2,80712
Water1,44180
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)66.370, 66.850, 85.390
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: Y20H, H61Y, Q105H, V108I, S375T, 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-MXJ / (3S,5R)-5-amino-N~3~-(4-chloro-3-fluorophenyl)-N~1~-propylpiperidine-1,3-dicarboxamide


Mass: 356.823 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H22ClFN4O2 / 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.: 80 / 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: 2.4 Å3/Da / Density % sol: 48.75 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 10% PEG 1500 5% PEG 400 0.1M 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: 1.03317 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 13, 2019
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03317 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 12065 / % possible obs: 79.1 % / Redundancy: 2.9 % / CC1/2: 0.98 / Rpim(I) all: 0.102 / Rsym value: 0.164 / Net I/σ(I): 3.4
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 0.8 / Num. unique obs: 1799 / CC1/2: 0.63 / Rpim(I) all: 0.469 / Rsym value: 0.749 / % possible all: 82.3

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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: 2.4→42.695 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 0.01 / Phase error: 26.32
RfactorNum. reflection% reflection
Rfree0.2754 964 4.86 %
Rwork0.2159 --
obs0.2186 19848 69.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.4→42.695 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2667 0 179 80 2926
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062904
X-RAY DIFFRACTIONf_angle_d1.0053943
X-RAY DIFFRACTIONf_dihedral_angle_d6.0881715
X-RAY DIFFRACTIONf_chiral_restr0.057469
X-RAY DIFFRACTIONf_plane_restr0.005502
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4001-2.52660.37031640.28872715X-RAY DIFFRACTION70
2.5266-2.68490.28911420.27152547X-RAY DIFFRACTION66
2.6849-2.89210.29451170.25922833X-RAY DIFFRACTION72
2.8921-3.18310.30511250.23392768X-RAY DIFFRACTION70
3.1831-3.64350.28291640.20692639X-RAY DIFFRACTION69
3.6435-4.58960.22971230.18182759X-RAY DIFFRACTION71
4.5896-42.70170.24681290.18942623X-RAY DIFFRACTION67

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