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- PDB-4dkq: Crystal structure of clade A/E 93TH057 HIV-1 gp120 core in comple... -

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Basic information

Entry
Database: PDB / ID: 4dkq
TitleCrystal structure of clade A/E 93TH057 HIV-1 gp120 core in complex with DMJ-I-228
Componentsclade A/E 93TH057 HIV-1 gp120 core
KeywordsVIRAL PROTEIN/INHIBITOR / HIV-1 gp120 / clade A/E / CD4 mimic / DMJ-I-228 / VIRAL PROTEIN-INHIBITOR complex
Function / homology
Function and homology information


positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane ...positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / membrane
Similarity search - Function
HIV Envelope Protein Gp120; Chain G / Human immunodeficiency virus 1, Gp160, envelope glycoprotein / Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Beta Complex / Mainly Beta
Similarity search - Domain/homology
Chem-0LK / Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHUMAN IMMUNODEFICIENCY VIRUS TYPE 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.888 Å
AuthorsKwon, Y.D. / LaLonde, J.M. / Jones, D.M. / Sun, A.W. / Courter, J.R. / Soeta, T. / Kobayashi, T. / Princiotto, A.M. / Wu, X. / Mascola, J. ...Kwon, Y.D. / LaLonde, J.M. / Jones, D.M. / Sun, A.W. / Courter, J.R. / Soeta, T. / Kobayashi, T. / Princiotto, A.M. / Wu, X. / Mascola, J. / Schon, A. / Freire, E. / Sodroski, J. / Madani, N. / Smith III, A.B. / Kwong, P.D.
CitationJournal: J.Med.Chem. / Year: 2012
Title: Structure-Based Design, Synthesis, and Characterization of Dual Hotspot Small-Molecule HIV-1 Entry Inhibitors.
Authors: Lalonde, J.M. / Kwon, Y.D. / Jones, D.M. / Sun, A.W. / Courter, J.R. / Soeta, T. / Kobayashi, T. / Princiotto, A.M. / Wu, X. / Schon, A. / Freire, E. / Kwong, P.D. / Mascola, J.R. / ...Authors: Lalonde, J.M. / Kwon, Y.D. / Jones, D.M. / Sun, A.W. / Courter, J.R. / Soeta, T. / Kobayashi, T. / Princiotto, A.M. / Wu, X. / Schon, A. / Freire, E. / Kwong, P.D. / Mascola, J.R. / Sodroski, J. / Madani, N. / Smith, A.B.
History
DepositionFeb 3, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 2, 2012Provider: repository / Type: Initial release
Revision 1.1May 9, 2012Group: Source and taxonomy
Revision 1.2Jun 20, 2012Group: Database references
Revision 1.3Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.contact_author / _software.contact_author_email ..._software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5May 19, 2021Group: Source and taxonomy / Structure summary / Category: chem_comp / entity_src_gen
Item: _chem_comp.pdbx_synonyms / _entity_src_gen.host_org_common_name ..._chem_comp.pdbx_synonyms / _entity_src_gen.host_org_common_name / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain
Revision 1.6Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.7Dec 27, 2023Group: Advisory / Derived calculations / Category: pdbx_validate_close_contact / struct_conn
Revision 1.8Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: clade A/E 93TH057 HIV-1 gp120 core
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,22214
Polymers39,1601
Non-polymers3,06113
Water3,567198
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.741, 67.523, 89.255
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 clade A/E 93TH057 HIV-1 gp120 core


Mass: 39160.367 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 / Strain: clade A/E 93TH057 / Gene: HIV-1 Env / Plasmid: pVRC8400 / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: Q0ED31*PLUS
#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.: 11
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-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
#4: Chemical ChemComp-0LK / N-[(1S,2S)-2-carbamimidamido-2,3-dihydro-1H-inden-1-yl]-N'-(4-chloro-3-fluorophenyl)ethanediamide


Mass: 389.811 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H17ClFN5O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 198 / Source method: isolated from a natural source / Formula: H2O
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: 2.45 Å3/Da / Density % sol: 49.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 10% PEG 8000, 5% iso-propanol, 0.1M HEPES 7.5 , VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jan 1, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.888→50 Å / Num. all: 31547 / Num. obs: 30727 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Biso Wilson estimate: 28.1 Å2 / Rmerge(I) obs: 0.08 / Rsym value: 0.09 / Net I/σ(I): 34.7
Reflection shellResolution: 1.89→1.92 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.368 / Mean I/σ(I) obs: 2.5 / Num. unique all: 1107 / Rsym value: 0.379 / % possible all: 72.1

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Processing

Software
NameVersionClassificationNB
PHENIX1.6.4_486refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASESphasing
REFMACrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TGT

3tgt


Resolution: 1.888→46.351 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.22 / σ(F): 0 / Phase error: 20.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.233 1485 4.98 %Random
Rwork0.1916 ---
all0.1937 ---
obs0.1937 29830 94.39 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 29.679 Å2 / ksol: 0.343 e/Å3
Displacement parametersBiso max: 94.93 Å2 / Biso mean: 34.0177 Å2 / Biso min: 13.77 Å2
Baniso -1Baniso -2Baniso -3
1-5.7261 Å2-0 Å2-0 Å2
2---4.5338 Å2-0 Å2
3----1.1923 Å2
Refinement stepCycle: LAST / Resolution: 1.888→46.351 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2654 0 196 198 3048
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.007
X-RAY DIFFRACTIONf_angle_d0.869
X-RAY DIFFRACTIONf_chiral_restr0.054
X-RAY DIFFRACTIONf_plane_restr0.012
X-RAY DIFFRACTIONf_dihedral_angle_d12.849
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDNum. reflection obs% reflection obs (%)
1.8882-1.94920.26221080.2379X-RAY DIFFRACTION182972.1
1.9492-2.01880.211814700.1964X-RAY DIFFRACTION243890.7
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)
10.9575-0.2036-0.11771.16020.39330.3802-0.1121-0.01070.21930.20760.02150.0804-0.4875-0.33090.08060.28430.0722-0.02030.2329-0.01310.1787-16.06447.551818.7108
21.036-0.45880.54591.6109-0.33811.4444-0.07850.08230.03790.0450.0425-0.12-0.1537-0.02920.03860.15250.00460.00810.1551-0.01560.1469-11.6447-1.629514.0142
30.7842-0.46030.73291.1933-0.0691.22090.0118-0.0596-0.23070.02920.07460.22670.2208-0.1408-0.070.1486-0.01860.01660.14210.01330.2197-15.7889-21.25315.1461
40.9118-0.46220.32430.81160.16621.06210.03330.2883-0.0209-0.0541-0.13820.1287-0.2077-0.07410.09840.18930.03050.00330.1927-0.0170.1526-16.53350.37298.1739
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and resi 44:89A44 - 948
2X-RAY DIFFRACTION2chain A and resi 90:254A44 - 948
3X-RAY DIFFRACTION3chain A and resi 255:474A44 - 948
4X-RAY DIFFRACTION4chain A and resi 475:492A44 - 948

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