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

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Basic information

Entry
Database: PDB / ID: 4dkp
TitleCrystal structure of clade A/E 93TH057 HIV-1 gp120 core in complex with AWS-I-50
Componentsclade A/E 93TH057 HIV-1 gp120 core
KeywordsVIRAL PROTEIN/INHIBITOR / HIV-1 gp120 / clade A/E / CD4 mimic / AWS-I-50 / VIRAL PROTEIN-INHIBITOR complex
Function / homology
Function and homology information


symbiont-mediated perturbation of host defense response / 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 ...symbiont-mediated perturbation of host defense response / 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-0LL / Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHUMAN IMMUNODEFICIENCY VIRUS TYPE 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7978 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_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_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 1.7Oct 16, 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
C: clade A/E 93TH057 HIV-1 gp120 core
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,35928
Polymers78,3212
Non-polymers6,03926
Water8,629479
1
A: clade A/E 93TH057 HIV-1 gp120 core
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,18014
Polymers39,1601
Non-polymers3,01913
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
C: clade A/E 93TH057 HIV-1 gp120 core
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,18014
Polymers39,1601
Non-polymers3,01913
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.666, 68.483, 94.747
Angle α, β, γ (deg.)90.00, 91.60, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein clade A/E 93TH057 HIV-1 gp120 core


Mass: 39160.367 Da / Num. of mol.: 2
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.: 22
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.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Chemical ChemComp-0LL / N-[(1S,2S)-2-amino-2,3-dihydro-1H-inden-1-yl]-N'-(4-chloro-3-fluorophenyl)ethanediamide


Mass: 347.771 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H15ClFN3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 479 / 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: 2.68 Å3/Da / Density % sol: 54.06 %
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

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: 1.7978→50 Å / Num. all: 76573 / Num. obs: 74276 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rmerge(I) obs: 0.049 / Rsym value: 0.063 / Net I/σ(I): 17.44
Reflection shellResolution: 1.7978→1.83 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.509 / Mean I/σ(I) obs: 1.18 / Rsym value: 0.598 / % possible all: 72.9

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Processing

Software
NameVersionClassificationNB
PHENIX1.7.3_928refinement
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: 1.7978→33.705 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.25 / σ(F): 1.34 / Phase error: 24.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2247 3782 5.1 %Random
Rwork0.1988 ---
obs0.2002 74205 96.32 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.315 Å2 / ksol: 0.387 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-5.1907 Å2-0 Å2-4.7065 Å2
2---1.0821 Å2-0 Å2
3----4.1086 Å2
Refinement stepCycle: LAST / Resolution: 1.7978→33.705 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5308 0 384 479 6171
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025842
X-RAY DIFFRACTIONf_angle_d0.6997927
X-RAY DIFFRACTIONf_dihedral_angle_d13.6052195
X-RAY DIFFRACTIONf_chiral_restr0.085922
X-RAY DIFFRACTIONf_plane_restr0.003982
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7978-1.82060.3197790.37041597X-RAY DIFFRACTION60
1.8206-1.84460.38141000.35862106X-RAY DIFFRACTION78
1.8446-1.86980.37641190.32012302X-RAY DIFFRACTION85
1.8698-1.89650.30411250.29062465X-RAY DIFFRACTION91
1.8965-1.92480.2691390.2662543X-RAY DIFFRACTION95
1.9248-1.95490.29731730.25882643X-RAY DIFFRACTION98
1.9549-1.9870.29781380.23382618X-RAY DIFFRACTION99
1.987-2.02120.2851390.2242738X-RAY DIFFRACTION100
2.0212-2.0580.2481590.20952673X-RAY DIFFRACTION100
2.058-2.09750.25921400.21382695X-RAY DIFFRACTION100
2.0975-2.14040.26851730.20582680X-RAY DIFFRACTION100
2.1404-2.18690.25211330.21722654X-RAY DIFFRACTION100
2.1869-2.23770.26071220.20412739X-RAY DIFFRACTION100
2.2377-2.29370.2421360.2042731X-RAY DIFFRACTION100
2.2937-2.35570.2411400.2062682X-RAY DIFFRACTION100
2.3557-2.4250.28571420.21412704X-RAY DIFFRACTION100
2.425-2.50320.2671580.21472688X-RAY DIFFRACTION100
2.5032-2.59270.24741500.20382709X-RAY DIFFRACTION100
2.5927-2.69640.24381490.20182728X-RAY DIFFRACTION100
2.6964-2.81910.23851330.20392701X-RAY DIFFRACTION100
2.8191-2.96770.23221310.19622721X-RAY DIFFRACTION100
2.9677-3.15350.22071250.18732736X-RAY DIFFRACTION100
3.1535-3.39670.19591440.18712714X-RAY DIFFRACTION100
3.3967-3.73820.19641460.17512696X-RAY DIFFRACTION100
3.7382-4.27820.19641580.16522725X-RAY DIFFRACTION99
4.2782-5.38650.17371720.16642699X-RAY DIFFRACTION99
5.3865-33.71140.20841590.21052736X-RAY DIFFRACTION98
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)
11.7277-0.09980.65262.2957-0.42022.2205-0.04210.060.1113-0.0331-0.0293-0.0253-0.1624-0.10870.04580.09250.00670.02430.1244-0.02160.1718.16542.448339.4528
21.3864-0.12831.19451.4449-0.07321.690.0188-0.0985-0.042-0.0124-0.00920.00090.1953-0.1822-0.02630.1286-0.00830.03950.1818-0.01640.166414.7032-19.739840.9047
32.9001-0.90430.02042.5583-0.70172.3061-0.0203-0.13410.08090.06040.25750.3208-0.2458-0.4338-0.16650.32330.018-0.00440.22650.08460.2047-12.3147-16.16869.3841
41.6379-0.7457-0.28012.4852-0.01952.36350.0165-0.1421-0.5717-0.09380.25170.56720.5248-0.4632-0.07440.4484-0.1314-0.09720.26410.13750.3544-11.3052-38.300112.7953
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and (resid 44:252 or resid 474:492)
2X-RAY DIFFRACTION2chain A and resid 253:473
3X-RAY DIFFRACTION3chain C and (resid 44:252 or resid 474:492)
4X-RAY DIFFRACTION4chain C and resid 253:473

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