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- PDB-3tgs: Crystal structure of HIV-1 clade C strain C1086 gp120 core in com... -

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Basic information

Entry
Database: PDB / ID: 3tgs
TitleCrystal structure of HIV-1 clade C strain C1086 gp120 core in complex with NBD-556
ComponentsHIV-1 clade C1086 gp120 core
KeywordsVIRAL PROTEIN / HIV-1 gp120 / clade C1086 / complex / NBD-556
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
Chem-03G / Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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 1.2Dec 17, 2014Group: Non-polymer description
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Revision 1.4Jul 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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HIV-1 clade C1086 gp120 core
B: HIV-1 clade C1086 gp120 core
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,06317
Polymers79,5112
Non-polymers3,55115
Water1,874104
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.960, 126.000, 191.480
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-620-

HOH

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Components

#1: Protein HIV-1 clade C1086 gp120 core


Mass: 39755.664 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Plasmid: pVRC8400 / Cell line (production host): HEK 293 / Production host: HOMO SAPIENS (human) / References: UniProt: C6G099*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.: 13
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-03G / N-(4-chlorophenyl)-N'-(2,2,6,6-tetramethylpiperidin-4-yl)ethanediamide / NBD-556


Mass: 337.844 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H24ClN3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 2.54 Å3/Da / Density % sol: 51.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 16% PEG 1500, 0.1M CaCl2, 0.1M imidazole, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 6.5

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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: Aug 7, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. all: 23729 / Num. obs: 17560 / % possible obs: 74 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Rmerge(I) obs: 0.116 / Rsym value: 0.096 / Net I/σ(I): 26.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsRsym valueDiffraction-ID% possible all
2.7-2.83.60.2220.217126.3
2.8-2.913.40.2170.172133.5
2.91-3.043.40.1950.174144.6
3.04-3.23.70.1880.172160.1
3.2-3.44.50.1920.187179.3
3.4-3.665.70.2270.246194.5
3.66-4.036.60.2040.17199.1
4.03-4.626.50.1440.122199.8
4.62-5.816.10.1110.113199.7
5.81-505.50.0660.07198.9

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Processing

Software
NameVersionClassificationNB
PHENIX1.6.4_486refinement
PDB_EXTRACT3.1data extraction
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→44.837 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.44 / σ(F): 0 / Phase error: 30.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2954 861 5.02 %
Rwork0.2394 --
obs0.2422 17156 73.52 %
all-23335 -
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 25.118 Å2 / ksol: 0.292 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--18.1429 Å2-0 Å2-0 Å2
2---15.72 Å2-0 Å2
3----16.822 Å2
Refinement stepCycle: LAST / Resolution: 2.7→44.837 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5410 0 228 104 5742
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015964
X-RAY DIFFRACTIONf_angle_d0.6998098
X-RAY DIFFRACTIONf_dihedral_angle_d16.6542240
X-RAY DIFFRACTIONf_chiral_restr0.044934
X-RAY DIFFRACTIONf_plane_restr0.0031014
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6746-2.84220.4612430.369770X-RAY DIFFRACTION21
2.8422-3.06160.3915950.32711712X-RAY DIFFRACTION47
3.0616-3.36960.41421340.27252764X-RAY DIFFRACTION75
3.3696-3.8570.26261900.21993538X-RAY DIFFRACTION97
3.857-4.85840.24742100.20223684X-RAY DIFFRACTION100
4.8584-44.84340.27781890.24143827X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.2534-0.45710.06760.8178-0.00691.8258-0.05910.322-0.41390.07880.1271-0.23730.15540.66060.18070.62520.07850.12540.4908-0.01050.3678-3.4264-21.018615.9902
20.73670.4576-0.62243.19110.35643.98610.08020.11890.1491-0.3247-0.2455-1.286-0.16860.88080.07290.19620.00890.20680.29810.10190.0158-8.8785-12.3619.3471
31.95850.42540.80962.7002-0.2872.2049-0.0397-0.29250.03860.4175-0.1763-0.0311-0.2854-0.18560.03660.238-0.01760.00030.1489-0.0014-0.0215-24.0527-9.489933.1623
40.34760.62240.5711.12271.0661.32920.1869-0.3703-0.63370.1230.3006-0.3217-0.12490.7444-0.5121-0.02160.01270.08780.6545-0.06440.4944-4.1492-10.403223.8999
50.9880.19070.45411.10920.16170.2121-0.33590.57260.2465-0.81020.01730.2423-0.5938-0.01110.34510.979-0.1067-0.35420.55940.12610.4045-26.2647-39.59092.5853
61.58060.63770.34791.4574-0.42491.49-0.21310.12520.4187-0.89680.38540.65990.3223-0.2913-0.0590.4525-0.0726-0.51790.18810.190.4126-23.6067-46.98699.973
74.80211.0237-2.3832.2641-1.38772.1443-0.1949-1.11250.532-0.20610.28120.35810.34720.38940.00120.1760.0976-0.16550.2814-0.17060.1704-13.7273-46.381728.2304
80.19050.2166-0.73541.29240.5044.5615-0.26330.49140.4418-0.53380.09430.72260.2832-0.8275-0.23690.2055-0.1404-0.49690.38690.26710.6727-29.6768-47.017213.1459
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 255:472
4X-RAY DIFFRACTION4chain A and resi 473:492
5X-RAY DIFFRACTION5chain B and resi 44:89
6X-RAY DIFFRACTION6chain B and resi 90:254
7X-RAY DIFFRACTION7chain B and resi 255:472
8X-RAY DIFFRACTION8chain B and resi 473:492

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