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

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Basic information

Entry
Database: PDB / ID: 4dko
TitleCrystal structure of clade A/E 93TH057 HIV-1 gp120 core in complex with TS-II-224
ComponentsHIV-1 gp120 core
KeywordsVIRAL PROTEIN/INHIBITOR / HIV-1 gp120 / clade A/E / CD4 mimic / TS-II-224 / 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-0LM / Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHUMAN IMMUNODEFICIENCY VIRUS TYPE 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.981 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 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_leaving_atom_flag / _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 1.4May 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 1.5Sep 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 1.6Nov 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: HIV-1 gp120 core
C: HIV-1 gp120 core
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,40428
Polymers78,3212
Non-polymers6,08326
Water7,098394
1
A: HIV-1 gp120 core
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,20214
Polymers39,1601
Non-polymers3,04113
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
C: HIV-1 gp120 core
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,20214
Polymers39,1601
Non-polymers3,04113
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.723, 68.902, 94.515
Angle α, β, γ (deg.)90.000, 91.230, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein 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-0LM / N-(4-chloro-3-fluorophenyl)-N'-(1,2,2,6,6-pentamethylpiperidin-4-yl)ethanediamide


Mass: 369.861 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H25ClFN3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 394 / 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: 2.69 Å3/Da / Density % sol: 54.28 %
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: 1.981→50 Å / Num. all: 57477 / Num. obs: 54086 / % possible obs: 94.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 30.3 Å2 / Rmerge(I) obs: 0.078 / Rsym value: 0.099 / Net I/σ(I): 11.5
Reflection shellResolution: 2→2.03 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 1.54 / Num. unique all: 2120 / Rsym value: 0.493 / % possible all: 74

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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
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TGT

3tgt


Resolution: 1.981→41.941 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.28 / σ(F): 1.34 / Phase error: 25.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2389 2692 4.99 %Random
Rwork0.2035 ---
obs0.2053 53979 93.08 %-
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 33.655 Å2 / ksol: 0.354 e/Å3
Displacement parametersBiso max: 151.63 Å2 / Biso mean: 43.1748 Å2 / Biso min: 11.72 Å2
Baniso -1Baniso -2Baniso -3
1-9.1064 Å20 Å2-4.0478 Å2
2---3.9388 Å20 Å2
3----5.1675 Å2
Refinement stepCycle: LAST / Resolution: 1.981→41.941 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5308 0 388 394 6090
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025844
X-RAY DIFFRACTIONf_angle_d0.6637938
X-RAY DIFFRACTIONf_chiral_restr0.042922
X-RAY DIFFRACTIONf_plane_restr0.003980
X-RAY DIFFRACTIONf_dihedral_angle_d16.1682224
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9806-2.01670.3287600.30991744180459
2.0167-2.05540.3131950.26762310240580
2.0554-2.09740.30481290.26652453258285
2.0974-2.1430.31181300.24952568269888
2.143-2.19280.28321230.24212541266489
2.1928-2.24770.26321540.22022636279092
2.2477-2.30850.26571720.22632682285494
2.3085-2.37640.25631730.22652748292197
2.3764-2.45310.30381560.23632873302999
2.4531-2.54070.24231560.22328723028100
2.5407-2.64240.25321520.21128683020100
2.6424-2.76270.24621450.21332900304599
2.7627-2.90830.28041460.211728593005100
2.9083-3.09050.26171510.19652902305399
3.0905-3.3290.21891520.19762885303799
3.329-3.66380.23751660.18742864303099
3.6638-4.19360.1981240.17192875299998
4.1936-5.28180.17981710.16022838300997
5.2818-41.95070.24741370.22272869300695
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)
11.6394-0.30530.64772.1795-0.62012.2754-0.05490.09060.10460.0162-0.0196-0.032-0.1577-0.06440.05690.08590.00250.01680.1342-0.02550.200118.58322.345139.4091
21.0526-0.11341.33621.31180.09841.96130.0378-0.0438-0.0441-0.0064-0.0305-0.00210.1828-0.1193-0.02020.0927-0.00190.0480.1778-0.00910.16715.0151-19.798540.7922
32.8745-0.7995-0.17312.1834-0.66362.54150.0092-0.04610.12690.00030.21190.3085-0.1159-0.5116-0.1750.3132-0.00160.00350.23370.08050.2005-12.1769-16.35649.278
41.4503-0.4432-0.41171.7159-0.08411.69540.09830.0041-0.5521-0.2470.21080.4610.726-0.4413-0.0070.5087-0.1814-0.1190.28070.13150.3129-11.0631-38.449812.698
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 44:252 OR RESID 474:492 ) )A44 - 252
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 44:252 OR RESID 474:492 ) )A474 - 492
3X-RAY DIFFRACTION2( CHAIN A AND RESID 253:473 )A253 - 473
4X-RAY DIFFRACTION3( CHAIN C AND ( RESID 44:252 OR RESID 474:492 ) )C44 - 252
5X-RAY DIFFRACTION3( CHAIN C AND ( RESID 44:252 OR RESID 474:492 ) )C474 - 492
6X-RAY DIFFRACTION4( CHAIN C AND RESID 253:473 )C253 - 473

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