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- PDB-8fm3: HIV-1 gp120 complex with CJF-III-288 -

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Basic information

Entry
Database: PDB / ID: 8fm3
TitleHIV-1 gp120 complex with CJF-III-288
ComponentsEnvelope glycoprotein gp120
KeywordsVIRAL PROTEIN/INHIBITOR / retrovirus / gp120 / entry inhibitor / structure-based drug design / small molecule / antiretroviral therapy / VIRAL PROTEIN-INHIBITOR complex
Function / homologyChem-Y26
Function and homology information
Biological speciesHIV-1 06TG.HT008 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 Å
AuthorsGong, Z. / Hendrickson, W.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)5P01AI150471-25 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2023
Title: Indoline CD4-mimetic compounds mediate potent and broad HIV-1 inhibition and sensitization to antibody-dependent cellular cytotoxicity.
Authors: Fritschi, C.J. / Anang, S. / Gong, Z. / Mohammadi, M. / Richard, J. / Bourassa, C. / Severino, K.T. / Richter, H. / Yang, D. / Chen, H.C. / Chiu, T.J. / Seaman, M.S. / Madani, N. / Abrams, C. ...Authors: Fritschi, C.J. / Anang, S. / Gong, Z. / Mohammadi, M. / Richard, J. / Bourassa, C. / Severino, K.T. / Richter, H. / Yang, D. / Chen, H.C. / Chiu, T.J. / Seaman, M.S. / Madani, N. / Abrams, C. / Finzi, A. / Hendrickson, W.A. / Sodroski, J.G. / Smith III, A.B.
History
DepositionDec 22, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 5, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Envelope glycoprotein gp120
C: Envelope glycoprotein gp120
D: Envelope glycoprotein gp120
B: Envelope glycoprotein gp120
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,91034
Polymers159,0234
Non-polymers7,88730
Water3,531196
1
A: Envelope glycoprotein gp120
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8389
Polymers39,7561
Non-polymers2,0828
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Envelope glycoprotein gp120
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8389
Polymers39,7561
Non-polymers2,0828
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
D: Envelope glycoprotein gp120
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6178
Polymers39,7561
Non-polymers1,8617
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
B: Envelope glycoprotein gp120
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6178
Polymers39,7561
Non-polymers1,8617
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.464, 121.718, 195.183
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein
Envelope glycoprotein gp120 /


Mass: 39755.664 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HIV-1 06TG.HT008 (virus) / Production host: Homo sapiens (human)
#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.: 26 / Source method: obtained synthetically / 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-Y26 / propyl (2R,3S)-2-(carbamimidamidomethyl)-3-[2-(4-chloro-3-fluoroanilino)(oxo)acetamido]-6-[(methylamino)methyl]-2,3-dihydro-1H-indole-1-carboxylate


Mass: 533.983 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C24H29ClFN7O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 196 / 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: 2.67 Å3/Da / Density % sol: 53.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 14% to 16% (w/v) PEG 1500, 0.1 M calcium chloride, 0.1 M imidazole pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Nov 12, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.11→48.8 Å / Num. obs: 55435 / % possible obs: 99.6 % / Redundancy: 6.7 % / Biso Wilson estimate: 38.22 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.168 / Rpim(I) all: 0.07 / Net I/σ(I): 8.6
Reflection shellResolution: 2.11→2.41 Å / Rmerge(I) obs: 1.298 / Num. unique obs: 2771 / CC1/2: 0.572 / Rpim(I) all: 0.544

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Processing

Software
NameVersionClassification
PHENIX1.20rc3_4406refinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.11→48.8 Å / SU ML: 0.2738 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 36.8419
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2729 2000 3.61 %
Rwork0.2469 53334 -
obs0.2479 55334 56.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.1 Å2
Refinement stepCycle: LAST / Resolution: 2.11→48.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10508 0 512 196 11216
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008911248
X-RAY DIFFRACTIONf_angle_d1.402515270
X-RAY DIFFRACTIONf_chiral_restr0.09641774
X-RAY DIFFRACTIONf_plane_restr0.0261942
X-RAY DIFFRACTIONf_dihedral_angle_d17.5421596
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.11-2.170.538250.3255115X-RAY DIFFRACTION1.73
2.17-2.220.4488140.3477397X-RAY DIFFRACTION5.97
2.22-2.290.4239230.3598588X-RAY DIFFRACTION8.83
2.29-2.360.2993310.3676857X-RAY DIFFRACTION12.8
2.36-2.450.3513490.35491309X-RAY DIFFRACTION19.59
2.45-2.550.3986730.35721922X-RAY DIFFRACTION28.58
2.55-2.660.39531100.34022949X-RAY DIFFRACTION44.01
2.66-2.80.3141680.31824467X-RAY DIFFRACTION66.64
2.8-2.980.36612400.31746418X-RAY DIFFRACTION94.79
2.98-3.210.32462530.29496748X-RAY DIFFRACTION99.97
3.21-3.530.29932540.26156771X-RAY DIFFRACTION99.9
3.53-4.040.27442550.23066803X-RAY DIFFRACTION99.93
4.04-5.090.2182570.19756871X-RAY DIFFRACTION99.82
5.09-48.80.21862680.21087119X-RAY DIFFRACTION99.77
Refinement TLS params.Method: refined / Origin x: -20.1903401659 Å / Origin y: 12.2600376122 Å / Origin z: -33.3567843113 Å
111213212223313233
T0.102491631069 Å20.0408666374321 Å20.00413419365105 Å2-0.19325736036 Å2-0.0261378782172 Å2--0.106996279499 Å2
L0.0592377533904 °20.04417188245 °20.10614106516 °2-0.312310903001 °20.0751912947488 °2--0.226313828423 °2
S-0.00793399765374 Å °0.0271238099424 Å °-0.0170702934464 Å °0.02640599581 Å °0.0349430647191 Å °0.0372182135918 Å °0.0108041162307 Å °-0.00291931056327 Å °-0.0118624578855 Å °
Refinement TLS groupSelection details: all

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