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- PDB-8dcq: 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: 8dcq
TitleCRYSTAL STRUCTURE OF HIV-1 LM/HT CLADE A/E CRF01 GP120 CORE IN COMPLEX WITH YIR-821
ComponentsHIV-1 LM/HT Clade A/E CRF01 gp120 core
KeywordsVIRAL PROTEIN / HIV-1 GP120 / CLADE A/E CF01 / VIRAL PROTEIN-INHIBITOR COMPLEX
Function / homologyGp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / viral envelope / Chem-R5K / clade A/E 93TH057 HIV-1 gp120 core
Function and homology information
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsTolbert, W.D. / Pazgier, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI129769 United States
CitationJournal: J.Virol. / Year: 2023
Title: Characterization of a Novel CD4 Mimetic Compound YIR-821 against HIV-1 Clinical Isolates.
Authors: Matsumoto, K. / Kuwata, T. / Tolbert, W.D. / Richard, J. / Ding, S. / Prevost, J. / Takahama, S. / Judicate, G.P. / Ueno, T. / Nakata, H. / Kobayakawa, T. / Tsuji, K. / Tamamura, H. / Smith ...Authors: Matsumoto, K. / Kuwata, T. / Tolbert, W.D. / Richard, J. / Ding, S. / Prevost, J. / Takahama, S. / Judicate, G.P. / Ueno, T. / Nakata, H. / Kobayakawa, T. / Tsuji, K. / Tamamura, H. / Smith 3rd, A.B. / Pazgier, M. / Finzi, A. / Matsushita, S.
History
DepositionJun 17, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2023Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.year
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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 core
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,45113
Polymers39,4671
Non-polymers2,98412
Water0
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)65.660, 67.280, 87.380
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 core


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 293 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 / N-Acetylglucosamine


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-R5K / N~1~-{(3R)-1-[2-(5-carbamimidamidopentanamido)ethyl]-1-azaspiro[5.5]undecan-3-yl}-N~2~-(4-chlorophenyl)ethanediamide


Mass: 534.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H40ClN7O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
Has ligand of interestY

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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: 2.45 Å3/Da / Density % sol: 49.7 %
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: 3.2→50 Å / Num. obs: 8078 / % possible obs: 72.3 % / Redundancy: 3.3 % / CC1/2: 0.94 / Rpim(I) all: 0.169 / Rsym value: 0.276 / Net I/σ(I): 2.1
Reflection shellResolution: 3.2→3.37 Å / Mean I/σ(I) obs: 0.5 / Num. unique obs: 722 / CC1/2: 0.464 / Rpim(I) all: 0.745 / % possible all: 75.3

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ONF

6onf


Resolution: 3.2→43.69 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 0.08 / Phase error: 24.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.273 398 4.93 %
Rwork0.218 --
obs0.2206 8078 65.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.2→43.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2646 0 192 0 2838
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072935
X-RAY DIFFRACTIONf_angle_d1.0943981
X-RAY DIFFRACTIONf_dihedral_angle_d21.031456
X-RAY DIFFRACTIONf_chiral_restr0.105465
X-RAY DIFFRACTIONf_plane_restr0.008492
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.660.31311630.27132612X-RAY DIFFRACTION67
3.66-4.610.28841240.21132575X-RAY DIFFRACTION66
4.62-43.690.23121110.19772493X-RAY DIFFRACTION63

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