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- PDB-8f9z: Crystal structure of clade A/E 93TH057 HIV-1 gp120 core in comple... -

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Basic information

Entry
Database: PDB / ID: 8f9z
TitleCrystal structure of clade A/E 93TH057 HIV-1 gp120 core in complex with NBD-14204, an HIV-1 gp120 antagonist
ComponentsHIV-1 gp120 core
KeywordsVIRAL PROTEIN/INHIBITOR / HIV-1 / NBD-14204 / small molecules / CD4-gp120 binding inhibitor / antagonist / VIRAL PROTEIN-INHIBITOR complex
Function / homologyGp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Chem-XKW / HIV-1 gp120 core
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsKwon, Y.D. / Kwong, P.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)W-31-109-Eng-38 United States
CitationJournal: Int J Mol Sci / Year: 2022
Title: Antiviral Activity and Crystal Structures of HIV-1 gp120 Antagonists.
Authors: Curreli, F. / Kwon, Y.D. / Nicolau, I. / Burgos, G. / Altieri, A. / Kurkin, A.V. / Verardi, R. / Kwong, P.D. / Debnath, A.K.
History
DepositionNov 25, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _pdbx_initial_refinement_model.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HIV-1 gp120 core
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1379
Polymers39,1601
Non-polymers1,9778
Water4,990277
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.196, 67.592, 87.907
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 gp120 core


Mass: 39160.367 Da / Num. of mol.: 1 / Mutation: V1/V2, V3 deletion, H375S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Strain: clade A/E 93TH057 / Gene: HIV-1 Env / Plasmid: pVRC8400 / Cell line (production host): 293F / Production host: Homo sapiens (human) / References: UniProt: A0A0M3KKW8
#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.: 6
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-XKW / (5M)-N-{(1S)-2-amino-1-[5-(hydroxymethyl)-1,3-thiazol-2-yl]ethyl}-5-[5-(trifluoromethyl)pyridin-2-yl]-1H-pyrrole-2-carboxamide


Mass: 411.401 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H16F3N5O2S / 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.: 277 / Source method: isolated from a natural source / Formula: H2O
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: 2.47 Å3/Da / Density % sol: 50.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4 / Details: 12-14% PEG3350, 5% isopropanol, 0.1M HEPES, 7.4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 2, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 29019 / % possible obs: 92.2 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.095 / Χ2: 0.072 / Net I/σ(I): 6.9 / Num. measured all: 123759
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.9-1.933.10.82111480.506174.1
1.93-1.973.30.71612280.549180
1.97-2.013.60.68812860.57181.9
2.01-2.0540.64813350.626185.4
2.05-2.094.20.61313640.692189
2.09-2.144.50.58214140.718191.6
2.14-2.194.70.53214690.801193.9
2.19-2.254.80.44614810.903196
2.25-2.324.80.40715100.943197
2.32-2.394.80.35114970.989197.1
2.39-2.484.80.31215241.054197.1
2.48-2.584.70.2515161.101197.1
2.58-2.74.70.20115281.168197.5
2.7-2.844.60.15515321.193196.5
2.84-3.024.50.12215361.154198.1
3.02-3.254.30.09415421.166197.2
3.25-3.584.20.07415410.987196.9
3.58-4.094.10.06315370.847196.1
4.09-5.163.80.06115460.789195.1
5.16-503.30.06314850.852185.8

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.94→36.44 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 21.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2164 1242 5.04 %
Rwork0.1826 --
obs0.1843 24631 84.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.94→36.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2654 0 127 277 3058
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008
X-RAY DIFFRACTIONf_angle_d0.767
X-RAY DIFFRACTIONf_dihedral_angle_d10.368403
X-RAY DIFFRACTIONf_chiral_restr0.053447
X-RAY DIFFRACTIONf_plane_restr0.006487
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.94-2.020.1971120.2101215X-RAY DIFFRACTION7
2.02-2.110.2433960.18941871X-RAY DIFFRACTION61
2.11-2.230.22691480.18962815X-RAY DIFFRACTION93
2.23-2.360.23271590.18072969X-RAY DIFFRACTION98
2.36-2.550.25461640.18593070X-RAY DIFFRACTION100
2.55-2.80.22121660.17883074X-RAY DIFFRACTION100
2.8-3.210.22351630.18443086X-RAY DIFFRACTION100
3.21-4.040.19681620.16833117X-RAY DIFFRACTION100
4.04-36.440.20041720.19023172X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: -15.0942 Å / Origin y: -11.0172 Å / Origin z: 14.9023 Å
111213212223313233
T0.0454 Å2-0.0204 Å20.0437 Å2-0.0999 Å20.0166 Å2--0.0881 Å2
L1.3493 °2-0.9262 °20.6637 °2-2.0308 °2-0.4449 °2--1.2137 °2
S-0.0345 Å °-0.0656 Å °-0.1986 Å °-0.0122 Å °0.1049 Å °0.2066 Å °0.0091 Å °-0.1774 Å °-0.0159 Å °
Refinement TLS groupSelection details: chain A and resi 44 through 353

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