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- PDB-3tgt: Crystal structure of unliganded HIV-1 clade A/E strain 93TH057 gp... -

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Basic information

Entry
Database: PDB / ID: 3tgt
TitleCrystal structure of unliganded HIV-1 clade A/E strain 93TH057 gp120 core
ComponentsHIV-1 clade A/E 93TH057 gp120
KeywordsVIRAL PROTEIN / HIV-1 gp120 / unliganded structure / clade A/E 93TH057
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 / structural molecule activity / virion attachment to host cell / host cell plasma membrane / 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
Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsKwon, Y.D. / Kwong, P.D.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Unliganded HIV-1 gp120 core structures assume the CD4-bound conformation with regulation by quaternary interactions and variable loops.
Authors: Kwon, Y.D. / Finzi, A. / Wu, X. / Dogo-Isonagie, C. / Lee, L.K. / Moore, L.R. / Schmidt, S.D. / Stuckey, J. / Yang, Y. / Zhou, T. / Zhu, J. / Vicic, D.A. / Debnath, A.K. / Shapiro, L. / ...Authors: Kwon, Y.D. / Finzi, A. / Wu, X. / Dogo-Isonagie, C. / Lee, L.K. / Moore, L.R. / Schmidt, S.D. / Stuckey, J. / Yang, Y. / Zhou, T. / Zhu, J. / Vicic, D.A. / Debnath, A.K. / Shapiro, L. / Bewley, C.A. / Mascola, J.R. / Sodroski, J.G. / Kwong, P.D.
History
DepositionAug 17, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2012Provider: repository / Type: Initial release
Revision 1.1May 23, 2012Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
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_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HIV-1 clade A/E 93TH057 gp120
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,66212
Polymers39,2111
Non-polymers2,45011
Water2,666148
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.556, 66.944, 88.029
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 39211.434 Da / Num. of mol.: 1
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): HEK 293 / Production host: HOMO SAPIENS (human) / References: UniProt: Q0ED31*PLUS
#2: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 10
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.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 148 / 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: 2.39 Å3/Da / Density % sol: 48.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 14% PEG 1500, 12% PEG 400, 0.1M HEPES, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jul 16, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 32465 / Num. obs: 30907 / % possible obs: 95.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Rmerge(I) obs: 0.084 / Rsym value: 0.074 / Net I/σ(I): 38.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRsym valueDiffraction-ID% possible all
1.9-1.935.50.6152.10.555186.5
1.93-1.975.80.4982.70.452189.9
1.97-2.0160.4793.10.416195.2
2.01-2.056.40.4193.70.368197.8
2.05-2.096.70.3774.90.339199.5
2.09-2.146.90.3276.30.269199.8
2.14-2.197.10.2967.30.2651100
2.19-2.257.20.2579.60.2261100
2.25-2.327.30.21911.90.1971100
2.32-2.397.30.1915.50.172199.9
2.39-2.487.20.17116.50.1551100
2.48-2.587.20.14420.90.1371100
2.58-2.77.20.12924.60.1261100
2.7-2.847.10.11528.70.116199.9
2.84-3.027.10.10134.50.1031100
3.02-3.256.90.09141.90.093199.9
3.25-3.586.60.08546.20.091100
3.58-4.096.30.07551.30.081199.9
4.09-5.166.60.06757.30.075199.9
5.16-506.40.05357.90.062198.1

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Processing

Software
NameVersionClassificationNB
PHENIX1.6.1_357refinement
PDB_EXTRACT3.1data extraction
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→24.571 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.24 / σ(F): 0.11 / Phase error: 23.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2307 1437 4.91 %
Rwork0.189 --
obs0.191 29250 91.91 %
all-31824 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.441 Å2 / ksol: 0.329 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-10.722 Å2-0 Å2-0 Å2
2---4.9969 Å2-0 Å2
3----5.7251 Å2
Refinement stepCycle: LAST / Resolution: 1.9→24.571 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2677 0 155 148 2980
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072921
X-RAY DIFFRACTIONf_angle_d1.1983960
X-RAY DIFFRACTIONf_dihedral_angle_d15.9371105
X-RAY DIFFRACTIONf_chiral_restr0.069462
X-RAY DIFFRACTIONf_plane_restr0.004492
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8676-1.93430.2307830.23491817X-RAY DIFFRACTION61
1.9343-2.01170.2761520.21762475X-RAY DIFFRACTION84
2.0117-2.10320.3131660.20932717X-RAY DIFFRACTION92
2.1032-2.2140.2611440.20292814X-RAY DIFFRACTION94
2.214-2.35260.2561410.1972858X-RAY DIFFRACTION95
2.3526-2.53410.2441580.20372896X-RAY DIFFRACTION97
2.5341-2.78880.26921520.19662953X-RAY DIFFRACTION98
2.7888-3.19160.20951420.19733038X-RAY DIFFRACTION99
3.1916-4.01820.23261450.17763055X-RAY DIFFRACTION99
4.0182-24.57350.19721540.17473190X-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)
11.37190.016-0.92210.8971-0.55050.885-0.0685-0.10730.3159-0.13860.0355-0.0473-0.44790.30980.04010.4241-0.0748-0.00770.32510.00660.294815.79127.5291-18.3549
21.3780.64290.72812.40820.95752.4516-0.1086-0.16820.13670.0236-0.00190.1441-0.18410.05630.0820.2575-0.02310.02740.24360.01080.22811.6296-1.6387-13.894
31.86240.35821.20562.16980.55812.92390.05840.1011-0.29770.17760.1187-0.24880.33290.2811-0.17880.2850.05240.00710.2674-0.02560.319915.9172-21.2629-15.148
40.5689-0.42960.09951.4921-0.49370.234-0.1333-0.35780.02850.27870.1294-0.006-0.00380.12-0.00690.2943-0.0358-0.01950.3541-0.01520.259916.65890.2471-7.9503
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resi 44:89
2X-RAY DIFFRACTION2chain A and resi 90:254
3X-RAY DIFFRACTION3chain A and resi 255:474
4X-RAY DIFFRACTION4chain A and resi 475:492

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