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

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Basic information

Entry
Database: PDB / ID: 4dku
TitleCrystal structure of clade A/E 93TH057 HIV-1 gp120 core in complex with NBD-09027
ComponentsHIV-1 gp120 core
KeywordsHYDROLASE / HIV-1 gp120 / clade A/E / CD4 mimic / NBD-09027
Function / homology
Function and homology information


positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / virus-mediated perturbation of host defense response / 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 ...positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / virus-mediated perturbation of host defense response / 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 / plasma 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-0KU / clade A/E 93TH057 HIV-1 gp120 core / Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4902 Å
AuthorsKwon, Y.D. / Debnath, A.K. / Kwong, P.D.
CitationJournal: Antimicrob. Agents Chemother. / Year: 2014
Title: Binding mode characterization of NBD series CD4-mimetic HIV-1 entry inhibitors by X-ray structure and resistance study.
Authors: Curreli, F. / Kwon, Y.D. / Zhang, H. / Yang, Y. / Scacalossi, D. / Kwong, P.D. / Debnath, A.K.
History
DepositionFeb 4, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2017Group: Database references / Source and taxonomy / Category: citation / citation_author / entity_src_gen
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / 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 / _struct_ref_seq_dif.details
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HIV-1 gp120 core
B: HIV-1 gp120 core
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,84625
Polymers78,3212
Non-polymers5,52523
Water1,820101
1
A: HIV-1 gp120 core
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,03413
Polymers39,1601
Non-polymers2,87312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: HIV-1 gp120 core
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,81212
Polymers39,1601
Non-polymers2,65211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.232, 68.436, 93.967
Angle α, β, γ (deg.)90.00, 91.81, 90.00
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 / Fragment: Chimera residue 44-492 / Mutation: V1V2 and V3 deletion, H375S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Strain: clade A/E 93TH057 / Gene: env / Plasmid: pVRC8400 / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: Q0ED31, UniProt: A0A0M3KKW9*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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 19
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 / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Chemical ChemComp-0KU / N-(4-chlorophenyl)-N'-{(S)-[5-(hydroxymethyl)-4-methyl-1,3-thiazol-2-yl][(2S)-piperidin-2-yl]methyl}ethanediamide


Mass: 422.929 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H23ClN4O3S
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 101 / Source method: isolated from a natural source / Formula: H2O

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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: 2.64 Å3/Da / Density % sol: 53.33 %
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-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 23, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.49→50 Å / Num. all: 28539 / Num. obs: 26599 / % possible obs: 93.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Rmerge(I) obs: 0.067 / Rsym value: 0.088 / Net I/σ(I): 12.1
Reflection shellResolution: 2.49→2.54 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.309 / Mean I/σ(I) obs: 2.43 / Rsym value: 0.329 / % possible all: 56.6

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Processing

Software
NameVersionClassificationNB
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3TGT

3tgt


Resolution: 2.4902→28.496 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.35 / σ(F): 1.34 / Phase error: 28.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2486 1283 4.83 %
Rwork0.2003 --
obs0.2027 26571 92.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.4312 Å2-0 Å2-3.6929 Å2
2--6.9785 Å2-0 Å2
3----10.4097 Å2
Refinement stepCycle: LAST / Resolution: 2.4902→28.496 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5308 0 352 101 5761
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075807
X-RAY DIFFRACTIONf_angle_d0.8717877
X-RAY DIFFRACTIONf_dihedral_angle_d14.2142180
X-RAY DIFFRACTIONf_chiral_restr0.046912
X-RAY DIFFRACTIONf_plane_restr0.003979
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4902-2.58990.3317890.261745X-RAY DIFFRACTION58
2.5899-2.70760.34591300.24922450X-RAY DIFFRACTION81
2.7076-2.85030.31791650.25092917X-RAY DIFFRACTION96
2.8503-3.02870.27091300.23633001X-RAY DIFFRACTION99
3.0287-3.26220.30211480.2243006X-RAY DIFFRACTION99
3.2622-3.58990.25511520.20843036X-RAY DIFFRACTION99
3.5899-4.10810.24351680.18832991X-RAY DIFFRACTION100
4.1081-5.17070.21511520.17173036X-RAY DIFFRACTION99
5.1707-28.49790.21441490.18673106X-RAY DIFFRACTION99
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)
13.9283-0.72471.40224.8133-0.93895.1063-0.10090.01340.3406-0.0226-0.11260.039-0.2938-0.09290.26180.2114-0.03880.01040.2514-0.02350.244517.70022.397939.2006
23.7232-0.0283.86812.5703-0.16256.58680.1361-0.2435-0.1884-0.03830.01150.02270.407-0.1806-0.19440.2676-0.010.04690.2213-0.02620.27214.5156-19.833840.6486
37.5015-1.7294-1.61922.8773-0.26073.69640.1250.17860.1309-0.24110.03550.19140.0094-0.5775-0.20230.571-0.0205-0.11210.31690.0820.2911-12.5108-16.5629.1368
46.4666-0.9692-1.1472.4353-0.00592.46490.17310.0958-0.866-0.38010.10890.46930.8254-0.4576-0.330.8724-0.1368-0.21550.41930.09090.4655-11.0285-38.860111.8636
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and (resid 1:252 or resid 474:492)
2X-RAY DIFFRACTION2chain A and resid 253:473
3X-RAY DIFFRACTION3chain B and (resid 1:252 or resid 474:492)
4X-RAY DIFFRACTION4chain B and resid 253:473

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