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

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Basic information

Entry
Database: PDB / ID: 4dvw
TitleCrystal structure of clade A/E 93TH057 HIV-1 gp120 core in complex with MAE-II-167
Componentsclade A/E 93TH057 HIV-1 gp120 core
Keywordsviral protein/transcription inhibitor / HIV-1 gp120 / small molecule inhibitor / CD4 binding site / MAE-II-167 / viral protein-transcription inhibitor complex
Function / homology
Function and homology information


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-0M4 / clade A/E 93TH057 HIV-1 gp120 core
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)83,90126
Polymers78,3212
Non-polymers5,58024
Water4,161231
1
A: clade A/E 93TH057 HIV-1 gp120 core
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,95113
Polymers39,1601
Non-polymers2,79012
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)41,95113
Polymers39,1601
Non-polymers2,79012
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.591, 68.533, 94.155
Angle α, β, γ (deg.)90.00, 91.27, 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 20
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-0M4 / N-(4-chloro-3-fluorophenyl)-N'-[(3aS,6aS)-hexahydrocyclopenta[c]pyrrol-3a(1H)-ylmethyl]ethanediamide


Mass: 339.792 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H19ClFN3O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 231 / Source method: isolated from a natural source / Formula: H2O
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: 53.76 %
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
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jun 23, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 42164 / Num. obs: 40942 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 40.71 Å2 / Rmerge(I) obs: 0.05 / Rsym value: 0.062 / Net I/σ(I): 19.6
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.357 / Mean I/σ(I) obs: 2.13 / Rsym value: 0.402 / % possible all: 80.3

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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: pdb entry 3TGT

3tgt


Resolution: 2.2→27.739 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.27 / σ(F): 1.42 / Phase error: 25.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2325 2006 5.02 %
Rwork0.1845 --
obs0.187 39980 94.08 %
all-42494 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 57.4785 Å2
Baniso -1Baniso -2Baniso -3
1-6.3929 Å2-0 Å2-2.081 Å2
2--0.52 Å2-0 Å2
3----6.9129 Å2
Refinement stepCycle: LAST / Resolution: 2.2→27.739 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5308 0 355 231 5894
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025811
X-RAY DIFFRACTIONf_angle_d0.5217886
X-RAY DIFFRACTIONf_dihedral_angle_d11.9982186
X-RAY DIFFRACTIONf_chiral_restr0.034915
X-RAY DIFFRACTIONf_plane_restr0.002978
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1901-2.24490.28781070.24751924X-RAY DIFFRACTION67
2.2449-2.30560.32181200.23632359X-RAY DIFFRACTION82
2.3056-2.37340.27721490.22312542X-RAY DIFFRACTION90
2.3734-2.44990.25161350.22462677X-RAY DIFFRACTION93
2.4499-2.53740.26251370.21252786X-RAY DIFFRACTION96
2.5374-2.63890.26391610.2092783X-RAY DIFFRACTION98
2.6389-2.75890.27551500.20442815X-RAY DIFFRACTION98
2.7589-2.90430.25331400.20542833X-RAY DIFFRACTION99
2.9043-3.0860.25081540.19842854X-RAY DIFFRACTION99
3.086-3.32390.23261560.19382846X-RAY DIFFRACTION99
3.3239-3.65770.22041390.18152856X-RAY DIFFRACTION98
3.6577-4.18550.19341570.16722840X-RAY DIFFRACTION98
4.1855-5.26730.19831510.15252902X-RAY DIFFRACTION99
5.2673-27.74150.24341500.17872957X-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)
12.6453-0.47961.03333.5863-0.87513.0171-0.05430.02670.24270.0488-0.08060.0005-0.2915-0.08380.10650.1882-0.00380.02960.2198-0.02680.277118.26872.497439.3487
22.211-0.32521.98152.0541-0.40333.41330.0275-0.1834-0.13680.0332-0.03180.00440.2733-0.1041-0.00930.18690.01530.05890.237-0.02030.275814.8954-19.811240.7309
35.3767-1.3951-0.96183.4971-0.15843.32740.0930.09420.2665-0.25290.05190.2927-0.1566-0.4761-0.11130.49490.0282-0.08030.30580.07190.3286-12.4127-16.38579.228
44.0532-1.0476-0.64332.80450.41082.8538-0.0165-0.0928-0.8375-0.180.14310.5830.7396-0.4754-0.05110.7341-0.1272-0.1130.34040.08710.5401-10.985-38.642912.0497
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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