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- PDB-4rz8: Crystal structure of HIV-1 gp120 core in complex with NBD-11021, ... -

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Basic information

Entry
Database: PDB / ID: 4rz8
TitleCrystal structure of HIV-1 gp120 core in complex with NBD-11021, a small molecule CD4-antagonist
ComponentsEnvelope glycoprotein gp120
KeywordsVIRAL PROTEIN / HIV-1 gp120 / NBD-11021 / small molecule CD4-antagonist / Phe 43 cavity
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 / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / 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 / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / apoptotic process / host cell plasma membrane / structural molecule activity / virion membrane / 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-3ZM / 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: 1.9 Å
AuthorsKwon, Y.D. / Debnath, A.K. / Kwong, P.D.
CitationJournal: J.Med.Chem. / Year: 2015
Title: Structure-Based Design of a Small Molecule CD4-Antagonist with Broad Spectrum Anti-HIV-1 Activity.
Authors: Curreli, F. / Kwon, Y.D. / Zhang, H. / Scacalossi, D. / Belov, D.S. / Tikhonov, A.A. / Andreev, I.A. / Altieri, A. / Kurkin, A.V. / Kwong, P.D. / Debnath, A.K.
History
DepositionDec 18, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 23, 2015Group: Database references
Revision 1.2Aug 2, 2017Group: Data collection / Refinement description / Source and taxonomy
Category: diffrn_detector / entity_src_gen / software / Item: _diffrn_detector.detector / _software.name
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 1.4Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Oct 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: Envelope glycoprotein gp120
B: Envelope glycoprotein gp120
C: Envelope glycoprotein gp120
D: Envelope glycoprotein gp120
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,22352
Polymers156,6414
Non-polymers11,58148
Water12,466692
1
A: Envelope glycoprotein gp120
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,83512
Polymers39,1601
Non-polymers2,67411
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Envelope glycoprotein gp120
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,83512
Polymers39,1601
Non-polymers2,67411
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Envelope glycoprotein gp120
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,27714
Polymers39,1601
Non-polymers3,11713
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Envelope glycoprotein gp120
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,27714
Polymers39,1601
Non-polymers3,11713
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)113.621, 68.842, 116.192
Angle α, β, γ (deg.)90.00, 110.59, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Envelope glycoprotein gp120


Mass: 39160.367 Da / Num. of mol.: 4 / Fragment: UNP residues 43-122, 201-303, 325-486 / 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): 293F / 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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 40
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-3ZM / 5-(4-chlorophenyl)-N-{(S)-[5-(hydroxymethyl)-4-methyl-1,3-thiazol-2-yl][(2R)-piperidin-2-yl]methyl}-1H-pyrrole-2-carboxamide


Mass: 444.978 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C22H25ClN4O2S
#4: Chemical
ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 692 / 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: 2.72 Å3/Da / Density % sol: 54.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 10% PEG 8000, 5% iso-propanol, 0.1M HEPES pH 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: Feb 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.82→50 Å / Num. all: 150137 / Num. obs: 131370 / % possible obs: 87.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 36.2 Å2 / Rmerge(I) obs: 0.067 / Rsym value: 0.063 / Net I/σ(I): 19.9
Reflection shellResolution: 1.82→1.85 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.487 / Mean I/σ(I) obs: 1.28 / Rsym value: 0.896 / % possible all: 28.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
PHENIX(phenix.refine: dev_1839)refinement
HKL-2000data reduction
PROTEUM PLUSPLUSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID: 3TGT

3tgt


Resolution: 1.9→44.027 Å / SU ML: 0.25 / σ(F): 1.34 / Phase error: 31.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2435 1896 1.52 %
Rwork0.2266 --
obs0.2269 124366 93.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 58.5 Å2
Refinement stepCycle: LAST / Resolution: 1.9→44.027 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10579 0 740 692 12011
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00111619
X-RAY DIFFRACTIONf_angle_d0.44815805
X-RAY DIFFRACTIONf_dihedral_angle_d9.044207
X-RAY DIFFRACTIONf_chiral_restr0.0211865
X-RAY DIFFRACTIONf_plane_restr0.0021997
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.94750.3333980.2995849X-RAY DIFFRACTION64
1.9475-2.00020.29961130.29157273X-RAY DIFFRACTION78
2.0002-2.0590.33951230.28558058X-RAY DIFFRACTION87
2.059-2.12550.30771330.27898721X-RAY DIFFRACTION94
2.1255-2.20150.30351430.27179128X-RAY DIFFRACTION98
2.2015-2.28960.27581500.26099252X-RAY DIFFRACTION99
2.2896-2.39380.30541370.26059231X-RAY DIFFRACTION100
2.3938-2.520.30691430.26239307X-RAY DIFFRACTION100
2.52-2.67780.28491400.25249285X-RAY DIFFRACTION100
2.6778-2.88460.26341490.25269318X-RAY DIFFRACTION100
2.8846-3.17480.24291360.24169302X-RAY DIFFRACTION100
3.1748-3.6340.25551440.21749278X-RAY DIFFRACTION99
3.634-4.57770.1711430.18659279X-RAY DIFFRACTION99
4.5777-44.03880.22151440.20199189X-RAY DIFFRACTION96
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)
13.2185-0.7865-0.11723.2191-0.4774.3948-0.1303-0.79010.12020.08070.2756-0.2910.2360.5101-0.14230.28820.05120.06990.47-0.13030.560417.5797-3.299943.1081
22.7452-0.4734-0.28452.3839-0.94232.76630.1131-0.80621.41360.30380.3424-0.3414-0.76890.1933-0.09970.5402-0.09880.23550.5118-0.46931.173814.298919.001743.2867
32.57240.48370.10532.38350.6364.1155-0.11340.5969-0.22740.08520.02240.53020.3694-0.56860.0790.2873-0.06590.10110.4276-0.0720.664319.139231.129612.6934
42.81490.1458-0.47042.43320.46083.84950.17190.54860.8077-0.05040.2120.4364-0.869-0.2103-0.23850.43160.05920.15980.36140.16910.849222.462953.066612.7677
54.41791.30480.63174.60790.86331.78390.1892-0.0695-0.44080.0492-0.0269-0.28810.22620.0161-0.17460.33990.0163-0.09280.2758-0.01080.251361.849812.325420.3875
64.07540.6850.8882.39660.55061.28750.07220.23420.2284-0.09410.0211-0.0815-0.1340.239-0.10490.299-0.0339-0.00440.2752-0.03510.196160.789934.558217.0868
73.76520.3133-0.49773.7623-0.55411.76690.0793-0.1659-0.1334-0.1245-0.12480.10960.15450.01950.05050.28190.0531-0.06750.2457-0.05060.170824.806212.3656-33.6153
84.31690.47930.12.5394-0.41710.88350.17230.12230.4578-0.0316-0.08940.1087-0.18490.0824-0.08370.31370.02520.00460.2404-0.04780.225523.928834.5027-37.1745
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 resi 253:473
3X-RAY DIFFRACTION3chain B and (resid 44:252 or resid 474:492)
4X-RAY DIFFRACTION4chain B and resi 253:473
5X-RAY DIFFRACTION5chain C and (resid 44:252 or resid 474:492)
6X-RAY DIFFRACTION6chain C and resi 253:473
7X-RAY DIFFRACTION7chain D and (resid 44:252 or resid 474:492)
8X-RAY DIFFRACTION8chain D and resi 253:473

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