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- PDB-8fm4: HIV-1 gp120 complex with CJF-IV-047 -

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Basic information

Entry
Database: PDB / ID: 8fm4
TitleHIV-1 gp120 complex with CJF-IV-047
ComponentsEnvelope glycoprotein gp120
KeywordsVIRAL PROTEIN/INHIBITOR / retrovirus / gp120 / entry inhibitor / structure-based drug design / small molecule / antiretroviral therapy / VIRAL PROTEIN-INHIBITOR complex
Function / homologyChem-Y2K
Function and homology information
Biological speciesHIV-1 06TG.HT008 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.18 Å
AuthorsGong, Z. / Hendrickson, W.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)AI150471-25 8117 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
Revision 1.1Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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
B: Envelope glycoprotein gp120
D: Envelope glycoprotein gp120
A: Envelope glycoprotein gp120
C: Envelope glycoprotein gp120
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,07034
Polymers159,0234
Non-polymers8,04730
Water3,531196
1
B: Envelope glycoprotein gp120
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6578
Polymers39,7561
Non-polymers1,9017
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Envelope glycoprotein gp120
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6578
Polymers39,7561
Non-polymers1,9017
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Envelope glycoprotein gp120
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8789
Polymers39,7561
Non-polymers2,1228
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
C: Envelope glycoprotein gp120
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8789
Polymers39,7561
Non-polymers2,1228
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.910, 121.260, 194.600
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


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-Y2K / 2,2,2-trifluoroethyl (2R,3S)-2-(carbamimidamidomethyl)-3-[2-(4-chloro-3-fluoroanilino)(oxo)acetamido]-6-[(methylamino)methyl]-2,3-dihydro-1H-indole-1-carboxylate


Mass: 573.928 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C23H24ClF4N7O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 196 / 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: 2.67 Å3/Da / Density % sol: 53.89 %
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-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Dec 17, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.18→48.65 Å / Num. obs: 65466 / % possible obs: 94.9 % / Redundancy: 19.5 % / Biso Wilson estimate: 35.84 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.216 / Rpim(I) all: 0.05 / Net I/σ(I): 12
Reflection shellResolution: 2.18→2.42 Å / Rmerge(I) obs: 2.248 / Num. unique obs: 4092 / CC1/2: 0.62 / Rpim(I) all: 0.515

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Processing

Software
NameVersionClassification
PHENIX1.20rc3_4406refinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.18→48.65 Å / SU ML: 0.2824 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.025
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2611 1998 3.05 %
Rwork0.2369 63451 -
obs0.2376 65449 73.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.4 Å2
Refinement stepCycle: LAST / Resolution: 2.18→48.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10508 0 520 196 11224
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013311256
X-RAY DIFFRACTIONf_angle_d1.789515290
X-RAY DIFFRACTIONf_chiral_restr0.09261774
X-RAY DIFFRACTIONf_plane_restr0.02851942
X-RAY DIFFRACTIONf_dihedral_angle_d17.67061592
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.18-2.240.234360.3276182X-RAY DIFFRACTION3
2.24-2.30.2355220.3256734X-RAY DIFFRACTION12.11
2.3-2.370.4305430.31831337X-RAY DIFFRACTION21.94
2.37-2.440.3265800.31752534X-RAY DIFFRACTION41.53
2.44-2.530.32841300.31024122X-RAY DIFFRACTION67.59
2.53-2.630.41061610.3065121X-RAY DIFFRACTION83.54
2.63-2.750.30461820.27965758X-RAY DIFFRACTION94
2.75-2.90.2911920.28066132X-RAY DIFFRACTION99.84
2.9-3.080.28271950.26666138X-RAY DIFFRACTION100
3.08-3.310.26841940.25676171X-RAY DIFFRACTION99.97
3.31-3.650.27561940.2416187X-RAY DIFFRACTION99.97
3.65-4.180.25561960.21496240X-RAY DIFFRACTION100
4.18-5.260.21091980.18716276X-RAY DIFFRACTION99.98
5.26-48.650.2132050.20966519X-RAY DIFFRACTION99.84
Refinement TLS params.Method: refined / Origin x: -20.3133863715 Å / Origin y: 12.2364146999 Å / Origin z: -33.2695572379 Å
111213212223313233
T0.145080404356 Å20.0478355213694 Å20.00866221970197 Å2-0.24214090237 Å2-0.027700593271 Å2--0.162125519468 Å2
L0.0996485718359 °20.0681400864666 °20.126190970796 °2-0.296614021916 °20.0558031167243 °2--0.194462634368 °2
S0.00258227887905 Å °0.0219977017143 Å °-0.016116230708 Å °0.0232826472691 Å °0.0295809431674 Å °0.0322190494312 Å °0.00924353604761 Å °0.00466498513472 Å °-0.0120946093734 Å °
Refinement TLS groupSelection details: all

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