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- PDB-8fa0: Crystal structure of clade A/E 93TH057 HIV-1 gp120 core in comple... -

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Basic information

Entry
Database: PDB / ID: 8fa0
TitleCrystal structure of clade A/E 93TH057 HIV-1 gp120 core in complex with NBD-14208, an HIV-1 gp120 antagonist
ComponentsHIV-1 gp120 core
KeywordsVIRAL PROTEIN / HIV-1 / NBD-14208 / small molecules / CD4-gp120 binding inhibitor / antagonist
Function / homologyHIV Envelope Protein Gp120; Chain G / Human immunodeficiency virus 1, Gp160, envelope glycoprotein / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Beta Complex / Mainly Beta / Chem-XKR / HIV-1 gp120 core
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 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
Revision 1.2Nov 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 gp120 core
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,05412
Polymers39,1601
Non-polymers2,89411
Water88349
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2530 Å2
ΔGint33 kcal/mol
Surface area17060 Å2
Unit cell
Length a, b, c (Å)61.213, 66.970, 90.351
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 (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.: 8
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-XKR / N-{(1S)-2-amino-1-[4,5-bis(hydroxymethyl)-1,3-thiazol-2-yl]ethyl}-5-(4-chloro-3,5-difluorophenyl)-1H-pyrrole-2-carboxamide / NBD-14208


Mass: 442.867 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H17ClF2N4O3S / 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.: 49 / 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: 2.36 Å3/Da / Density % sol: 47.98 %
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: Nov 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.09→50 Å / Num. obs: 39369 / % possible obs: 93.7 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.161 / Χ2: 0.102 / Net I/σ(I): 7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2.1-2.141.80.93913860.806166.4
2.14-2.181.90.84915590.864173.5
2.18-2.222.20.78117100.981181.8
2.22-2.262.50.80518010.854185.6
2.26-2.312.70.76718920.848190.9
2.31-2.373.10.79920190.881194.8
2.37-2.423.40.88820380.952198.5
2.42-2.493.80.87421020.956199.1
2.49-2.564.10.74521141.047199.5
2.56-2.654.30.70420611.219199.6
2.65-2.744.30.54221091.321199.6
2.74-2.854.40.45320631.515199.4
2.85-2.984.40.35520981.663199.4
2.98-3.144.30.27620891.683199
3.14-3.334.20.21120861.833199
3.33-3.5940.15920641.893199
3.59-3.953.70.11720781.765198.8
3.95-4.523.50.09220721.615198.5
4.52-5.73.30.08620551.458198.1
5.7-503.10.08119731.83193

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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: 2.09→36.35 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2977 1068 5 %
Rwork0.2427 --
obs0.2454 21346 94.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.09→36.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2639 0 185 49 2873
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011
X-RAY DIFFRACTIONf_angle_d0.76
X-RAY DIFFRACTIONf_dihedral_angle_d15.8631063
X-RAY DIFFRACTIONf_chiral_restr0.055456
X-RAY DIFFRACTIONf_plane_restr0.005489
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.09-2.180.36851000.34391880X-RAY DIFFRACTION71
2.18-2.30.38591260.31392408X-RAY DIFFRACTION91
2.3-2.440.34261390.3172609X-RAY DIFFRACTION98
2.44-2.630.39121360.30662636X-RAY DIFFRACTION99
2.63-2.90.37841410.27492654X-RAY DIFFRACTION99
2.9-3.320.2991400.25852670X-RAY DIFFRACTION99
3.32-4.180.28141410.23412676X-RAY DIFFRACTION99
4.18-36.350.2681450.21022745X-RAY DIFFRACTION96
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.84540.1151-0.73713.2893-0.30893.2674-0.1346-0.1205-0.162-0.4771-0.0987-0.14760.3447-0.18150.30840.47620.02320.0320.33610.01910.4156-15.3363-5.7357-17.9091
22.05560.2181-0.51852.2215-0.45241.9271-0.1907-0.226-0.0980.1325-0.0194-0.22260.2223-0.1050.16890.41990.0228-0.03010.40670.00370.3219-11.39983.453-14.3154
32.09780.1037-0.09813.1817-0.45862.58560.0362-0.15840.2841-0.0398-0.0857-0.1413-0.3211-0.16080.03310.37750.0642-0.09190.3126-0.02730.4686-14.597923.3615-17.5464
43.6740.6263-0.3256.7007-2.12833.1132-0.1558-0.69840.17410.4906-0.0598-0.4776-0.03720.1030.06770.48870.0452-0.01750.4645-0.05310.2934-14.72773.3155-7.9765
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resi 44:88
2X-RAY DIFFRACTION2chain A and resi 89:254
3X-RAY DIFFRACTION3chain A and resi 255:473
4X-RAY DIFFRACTION4chain A and resi 474:492

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