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- PDB-3tgr: Crystal structure of unliganded HIV-1 clade C strain C1086 gp120 core -

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Basic information

Entry
Database: PDB / ID: 3tgr
TitleCrystal structure of unliganded HIV-1 clade C strain C1086 gp120 core
ComponentsHIV-1 clade C1086 gp120
KeywordsVIRAL PROTEIN / HIV-1 gp120 / unliganded / clade C1086
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: 2.8 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 9, 2012Group: Other
Revision 1.2May 23, 2012Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)82,60816
Polymers79,5112
Non-polymers3,09714
Water1,60389
1
A: HIV-1 clade C1086 gp120
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5259
Polymers39,7561
Non-polymers1,7708
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: HIV-1 clade C1086 gp120
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0837
Polymers39,7561
Non-polymers1,3276
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.860, 127.510, 193.040
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-42-

HOH

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Components

#1: Protein HIV-1 clade C1086 gp120


Mass: 39755.664 Da / Num. of mol.: 2
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: 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.: 14
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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 2.63 Å3/Da / Density % sol: 53.16 %
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: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 4, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 21323 / Num. obs: 20001 / % possible obs: 93.8 % / Observed criterion σ(F): 0 / Redundancy: 4.2 % / Rmerge(I) obs: 0.079 / Rsym value: 0.068 / Net I/σ(I): 16.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.8-2.92.50.294182.4
2.9-3.023.20.257194.8
3.02-3.1540.237196.8
3.15-3.324.60.183198
3.32-3.534.70.138197.9
3.53-3.84.70.106197.7
3.8-4.184.70.088196.7
4.18-4.794.60.067194.9
4.79-6.034.50.06193
6.03-504.20.048185.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.6.4_486refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→45.289 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.41 / σ(F): 0 / Phase error: 28.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2819 936 4.77 %
Rwork0.223 --
obs0.2259 19639 93.25 %
all-21060 -
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 31.23 Å2 / ksol: 0.272 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--18.8646 Å2-0 Å2-0 Å2
2---3.7417 Å2-0 Å2
3----10.6074 Å2
Refinement stepCycle: LAST / Resolution: 2.8→45.289 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5428 0 196 89 5713
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025916
X-RAY DIFFRACTIONf_angle_d0.6078026
X-RAY DIFFRACTIONf_dihedral_angle_d11.022200
X-RAY DIFFRACTIONf_chiral_restr0.04932
X-RAY DIFFRACTIONf_plane_restr0.0021010
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.94760.40351100.32662196X-RAY DIFFRACTION78
2.9476-3.13230.33461310.27572580X-RAY DIFFRACTION92
3.1323-3.3740.31671360.24282705X-RAY DIFFRACTION96
3.374-3.71340.28981280.21542802X-RAY DIFFRACTION98
3.7134-4.25040.24781360.19542835X-RAY DIFFRACTION98
4.2504-5.35370.22171490.17832786X-RAY DIFFRACTION98
5.3537-45.29520.29971460.23182799X-RAY DIFFRACTION93
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)
11.63790.15050.69823.3291-0.60074.31970.25250.3451-0.2788-0.3866-0.2602-0.8755-0.18461.07930.23370.1027-0.06060.15370.25660.07670.3366-9.4157-12.484819.3903
20.7625-0.18910.52922.7849-0.60462.8897-0.0612-0.15450.10360.3648-0.0461-0.1038-0.3483-0.09290.07050.3041-0.01740.03470.10390.02490.0087-24.436-9.535433.3441
36.48386.1015-4.45445.8978-4.6347.5003-0.27390.0251-2.06450.2609-0.4633-1.5441-0.47951.84240.7010.1123-0.11120.01550.6582-0.12690.5094-3.616-11.166523.9796
40.4965-0.34660.43391.1631-0.46343.71630.18660.6286-0.1692-0.2888-0.2606-0.650.46931.03260.22470.1586-0.00240.19960.3567-0.00540.4757-3.8357-21.234115.9473
52.2124-0.08221.80862.2615-0.57161.40320.1505-0.6382-0.28091.010.0883-0.19860.1175-0.1595-0.19940.6327-0.08240.01170.3158-0.02330.2143-17.7368-12.677937.5814
61.97720.8437-0.36751.77980.06011.4707-0.50470.15940.792-0.91250.34750.79960.2109-0.24920.0490.45410.0099-0.51180.10390.10260.6371-24.0528-47.660310.0031
73.1510.2897-2.41982.3125-0.05531.7688-0.0762-0.84330.7133-0.01440.240.28020.1340.3995-0.12710.20640.0711-0.16930.4194-0.21520.3881-14.1367-46.902328.2165
85.6789-0.64213.29810.7733-0.55512.3454-0.21020.03380.9727-0.1296-0.0291.07260.6549-0.25990.36710.3866-0.0485-0.38770.40480.0160.8793-30.9945-47.065712.7253
91.4242-0.62410.15591.0877-0.13110.9031-0.3746-0.0917-0.2198-0.647-0.01130.337-0.1724-0.38880.26240.58120.0532-0.44740.3913-0.01650.5242-26.9592-40.25862.484
103.80151.40920.26330.40140.15461.99510.48860.32210.38640.62420.2536-0.3612-0.106-0.0494-0.66330.6452-0.1213-0.00730.26530.03480.3308-21.2232-42.044728.9408
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 90:255 )A90 - 255
2X-RAY DIFFRACTION2( CHAIN A AND RESID 256:474 )A256 - 474
3X-RAY DIFFRACTION3( CHAIN A AND RESID 475:492 )A475 - 492
4X-RAY DIFFRACTION4( CHAIN A AND RESID 44:89 )A44 - 89
5X-RAY DIFFRACTION5( CHAIN A AND RESID 762:948 )A762 - 948
6X-RAY DIFFRACTION6( CHAIN B AND RESID 90:255 )B90 - 255
7X-RAY DIFFRACTION7( CHAIN B AND RESID 256:474 )B256 - 474
8X-RAY DIFFRACTION8( CHAIN B AND RESID 475:492 )B475 - 492
9X-RAY DIFFRACTION9( CHAIN B AND RESID 44:89 )B44 - 89
10X-RAY DIFFRACTION10( CHAIN B AND RESID 734:892 )B734 - 892

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