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- PDB-8fm7: HIV-1 gp120 complex with CJF-III-192 -

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Basic information

Entry
Database: PDB / ID: 8fm7
TitleHIV-1 gp120 complex with CJF-III-192
ComponentsEnvelope glycoprotein gp120
KeywordsVIRAL PROTEIN/INHIBITOR / retrovirus / gp120 / entry inhibitor / structure-based drug design / small molecule / antiretroviral therapy / VIRAL PROTEIN-INHIBITOR complex
Function / homologyHIV Envelope Protein Gp120; Chain G / Human immunodeficiency virus 1, Gp160, envelope glycoprotein / Beta Complex / Mainly Beta / Chem-Y2O
Function and homology information
Biological speciesHIV-1 06TG.HT008 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.34 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)167,10234
Polymers159,0234
Non-polymers8,08030
Water3,531196
1
A: Envelope glycoprotein gp120
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8869
Polymers39,7561
Non-polymers2,1308
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Envelope glycoprotein gp120
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6658
Polymers39,7561
Non-polymers1,9097
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Envelope glycoprotein gp120
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8869
Polymers39,7561
Non-polymers2,1308
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Envelope glycoprotein gp120
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6658
Polymers39,7561
Non-polymers1,9097
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.360, 121.100, 195.110
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-Y2O / benzyl (2R,3S)-2-(carbamimidamidomethyl)-3-[2-(4-chloro-3-fluoroanilino)(oxo)acetamido]-6-[(methylamino)methyl]-2,3-dihydro-1H-indole-1-carboxylate


Mass: 582.026 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C28H29ClFN7O4 / 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: 2.69 Å3/Da / Density % sol: 54.24 %
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: 2.34→48.78 Å / Num. obs: 49263 / % possible obs: 94.5 % / Redundancy: 12.1 % / Biso Wilson estimate: 38.01 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.256 / Rpim(I) all: 0.077 / Net I/σ(I): 8.5
Reflection shellResolution: 2.34→2.63 Å / Rmerge(I) obs: 1.509 / Num. unique obs: 2738 / CC1/2: 0.657 / Rpim(I) all: 0.475

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Processing

Software
NameVersionClassification
PHENIX1.20rc3_4406refinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.34→48.78 Å / SU ML: 0.3259 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.6036
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2713 1999 4.06 %
Rwork0.2369 47255 -
obs0.2383 49254 67.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.78 Å2
Refinement stepCycle: LAST / Resolution: 2.34→48.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10508 0 528 196 11232
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012911268
X-RAY DIFFRACTIONf_angle_d1.700115298
X-RAY DIFFRACTIONf_chiral_restr0.09951774
X-RAY DIFFRACTIONf_plane_restr0.01351946
X-RAY DIFFRACTIONf_dihedral_angle_d16.68141596
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.34-2.40.578630.379988X-RAY DIFFRACTION1.8
2.4-2.470.4408170.4052381X-RAY DIFFRACTION7.79
2.47-2.540.3914290.3296691X-RAY DIFFRACTION14.01
2.54-2.620.3823560.31691338X-RAY DIFFRACTION27.17
2.62-2.710.3106900.30612103X-RAY DIFFRACTION42.52
2.71-2.820.38551350.30193200X-RAY DIFFRACTION64.48
2.82-2.950.35131750.30254155X-RAY DIFFRACTION83.98
2.95-3.110.30562090.29154919X-RAY DIFFRACTION98.94
3.11-3.30.30042100.27684975X-RAY DIFFRACTION100
3.3-3.560.31452100.24944976X-RAY DIFFRACTION99.98
3.56-3.910.27192130.22775012X-RAY DIFFRACTION100
3.91-4.480.24182120.20185034X-RAY DIFFRACTION99.98
4.48-5.640.22112160.18955096X-RAY DIFFRACTION100
5.64-48.780.22042240.21625287X-RAY DIFFRACTION99.86
Refinement TLS params.Method: refined / Origin x: -20.353935834 Å / Origin y: 12.2631890157 Å / Origin z: -33.3776717953 Å
111213212223313233
T0.0636904897066 Å20.0678163814498 Å20.00557893793505 Å2-0.232203109628 Å2-0.0398305532989 Å2--0.142361219109 Å2
L0.109566844398 °20.118873490314 °20.139451781614 °2-0.469673273533 °20.076316889277 °2--0.302645715723 °2
S0.00643850813087 Å °0.0357120078945 Å °-0.0329764150621 Å °0.0158338568711 Å °0.0443626493141 Å °0.0485094906882 Å °0.0223795829649 Å °0.0080326297576 Å °-0.00852036952468 Å °
Refinement TLS groupSelection details: all

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