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

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Basic information

Entry
Database: PDB / ID: 4dvt
TitleCrystal structure of clade A/E 93TH057 HIV-1 gp120 core in complex with AS-II-37
Componentsclade A/E 93TH057 HIV-1 gp120 core
Keywordsviral protein/transcription inhibitor / HIV-1 gp120 / small molecule inhibitor / CD4 binding site / AS-II-37 / viral protein-transcription inhibitor complex
Function / homology
Function and homology information


membrane fusion involved in viral entry into host cell / viral envelope / symbiont entry into host cell / virion attachment to host cell / virion membrane
Similarity search - Function
HIV Envelope Protein Gp120; Chain G / Human immunodeficiency virus 1, Gp160, envelope glycoprotein / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Beta Complex / Mainly Beta
Similarity search - Domain/homology
Chem-0LZ / clade A/E 93TH057 HIV-1 gp120 core
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsKwon, Y.D. / Kwong, P.D.
CitationJournal: Plos One / Year: 2014
Title: Crystal Structures of HIV-1 gp120 Envelope Glycoprotein in Complex with NBD Analogues That Target the CD4-Binding Site.
Authors: Kwon, Y.D. / Lalonde, J.M. / Yang, Y. / Elban, M.A. / Sugawara, A. / Courter, J.R. / Jones, D.M. / Smith, A.B. / Debnath, A.K. / Kwong, P.D.
History
DepositionFeb 23, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 19, 2014Group: Database references
Revision 1.2May 31, 2017Group: Structure summary
Revision 1.3Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / 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 1.4Sep 13, 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 1.5Nov 27, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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


Theoretical massNumber of molelcules
Total (without water)84,38828
Polymers78,3212
Non-polymers6,06726
Water1,928107
1
A: clade A/E 93TH057 HIV-1 gp120 core
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,19414
Polymers39,1601
Non-polymers3,03313
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: clade A/E 93TH057 HIV-1 gp120 core
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,19414
Polymers39,1601
Non-polymers3,03313
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.809, 68.402, 93.988
Angle α, β, γ (deg.)90.00, 91.94, 90.00
Int Tables number4
Space group name H-MP1211
Detailsmonomer

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Components

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


Mass: 39160.367 Da / Num. of mol.: 2 / Mutation: S375H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: HIV-1 Env / Plasmid: pVRC8400 / Cell line (production host): 293F / Production host: Homo sapiens (human) / References: UniProt: A0A0M3KKW9
#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-0LZ / N-(4-chloro-3-fluorophenyl)-N'-[(1S)-1,2,3,4-tetrahydroisoquinolin-1-ylmethyl]ethanediamide


Mass: 361.798 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H17ClFN3O2
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CRYSTALLIZED SEQUENCE WAS CONSTRUCTED BY DELETION OF N-TERMINAL 1-43, BY REPLACING THE V1/V2 ...THE CRYSTALLIZED SEQUENCE WAS CONSTRUCTED BY DELETION OF N-TERMINAL 1-43, BY REPLACING THE V1/V2 REGIONS WITH A GG LINKER, AND REPLACING V3 REGION WITH A LINKER GGSGSG

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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: 2.66 Å3/Da / Density % sol: 53.73 %
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-BM / Wavelength: 1
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jun 6, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 29562 / Num. obs: 27759 / % possible obs: 93.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 45.16 Å2 / Rmerge(I) obs: 0.071 / Rsym value: 0.085 / Net I/σ(I): 17.6
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.432 / Mean I/σ(I) obs: 1.46 / Rsym value: 0.485 / % possible all: 60

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Processing

Software
NameVersionClassificationNB
PHENIX1.8_1069refinement
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: 2.4→28.192 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.33 / σ(F): 1.42 / Phase error: 30.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2477 1309 4.83 %
Rwork0.1964 --
obs0.199 27089 87.24 %
all-31053 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 65.4336 Å2
Baniso -1Baniso -2Baniso -3
1-7.0651 Å20 Å2-6.0723 Å2
2---2.6638 Å20 Å2
3----4.4014 Å2
Refinement stepCycle: LAST / Resolution: 2.4→28.192 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5308 0 388 107 5803
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0015846
X-RAY DIFFRACTIONf_angle_d0.4027932
X-RAY DIFFRACTIONf_dihedral_angle_d10.7732202
X-RAY DIFFRACTIONf_chiral_restr0.026922
X-RAY DIFFRACTIONf_plane_restr0.001982
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4336-2.5310.3214250.2812960X-RAY DIFFRACTION29
2.531-2.64610.36351260.26952344X-RAY DIFFRACTION73
2.6461-2.78550.30781430.25662970X-RAY DIFFRACTION91
2.7855-2.95990.30471740.24693180X-RAY DIFFRACTION97
2.9599-3.18810.30141680.23163169X-RAY DIFFRACTION98
3.1881-3.50840.29571430.21013286X-RAY DIFFRACTION99
3.5084-4.01480.22741850.18333262X-RAY DIFFRACTION100
4.0148-5.05350.21511730.1643272X-RAY DIFFRACTION99
5.0535-28.19350.21141720.17513337X-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)
13.4524-0.89951.27964.3793-1.0753.0699-0.1466-0.07610.35850.0681-0.0791-0.1123-0.2766-0.12930.21090.3245-0.01840.02470.3096-0.03060.408717.86011.613539.2879
22.8606-0.46572.0682.5242-0.45494.61340.0677-0.1799-0.1641-0.0381-0.0174-0.06720.2595-0.121-0.05620.26930.00470.04110.2671-0.04550.368214.5312-20.637140.7125
35.1944-1.1616-0.41442.8434-0.12883.36580.08880.11660.2579-0.3010.02450.2413-0.0467-0.498-0.10370.64010.0107-0.08360.36780.06790.3812-12.5524-17.28619.0779
45.456-1.456-0.76433.04810.29712.36720.0193-0.1377-0.7994-0.32430.10260.620.7186-0.3509-0.07790.9098-0.123-0.11070.4120.06930.5478-11.0922-39.568311.8538
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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