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- PDB-4zmj: Crystal Structure of Ligand-Free BG505 SOSIP.664 HIV-1 Env Trimer -

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Basic information

Entry
Database: PDB / ID: 4zmj
TitleCrystal Structure of Ligand-Free BG505 SOSIP.664 HIV-1 Env Trimer
Components(Envelope glycoprotein gp160) x 2
KeywordsVIRAL PROTEIN / HIV-1 / Env trimer / unliganded / BG505 SOSIP
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 / identical protein binding / plasma membrane
Similarity search - Function
Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120
Similarity search - Domain/homology
Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.31 Å
AuthorsKwon, Y.D. / Kwong, P.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2015
Title: Crystal structure, conformational fixation and entry-related interactions of mature ligand-free HIV-1 Env.
Authors: Do Kwon, Y. / Pancera, M. / Acharya, P. / Georgiev, I.S. / Crooks, E.T. / Gorman, J. / Joyce, M.G. / Guttman, M. / Ma, X. / Narpala, S. / Soto, C. / Terry, D.S. / Yang, Y. / Zhou, T. / ...Authors: Do Kwon, Y. / Pancera, M. / Acharya, P. / Georgiev, I.S. / Crooks, E.T. / Gorman, J. / Joyce, M.G. / Guttman, M. / Ma, X. / Narpala, S. / Soto, C. / Terry, D.S. / Yang, Y. / Zhou, T. / Ahlsen, G. / Bailer, R.T. / Chambers, M. / Chuang, G.Y. / Doria-Rose, N.A. / Druz, A. / Hallen, M.A. / Harned, A. / Kirys, T. / Louder, M.K. / O'Dell, S. / Ofek, G. / Osawa, K. / Prabhakaran, M. / Sastry, M. / Stewart-Jones, G.B. / Stuckey, J. / Thomas, P.V. / Tittley, T. / Williams, C. / Zhang, B. / Zhao, H. / Zhou, Z. / Donald, B.R. / Lee, L.K. / Zolla-Pazner, S. / Baxa, U. / Schon, A. / Freire, E. / Shapiro, L. / Lee, K.K. / Arthos, J. / Munro, J.B. / Blanchard, S.C. / Mothes, W. / Binley, J.M. / McDermott, A.B. / Mascola, J.R. / Kwong, P.D.
History
DepositionMay 4, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 8, 2015Group: Database references
Revision 1.2Jul 29, 2015Group: Database references
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Derived calculations / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support / pdbx_struct_oper_list
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_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 2.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
G: Envelope glycoprotein gp160
B: Envelope glycoprotein gp160
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,45120
Polymers71,2112
Non-polymers5,24018
Water0
1
G: Envelope glycoprotein gp160
B: Envelope glycoprotein gp160
hetero molecules

G: Envelope glycoprotein gp160
B: Envelope glycoprotein gp160
hetero molecules

G: Envelope glycoprotein gp160
B: Envelope glycoprotein gp160
hetero molecules


Theoretical massNumber of molelcules
Total (without water)229,35260
Polymers213,6326
Non-polymers15,72054
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_775-y+2,x-y+2,z1
crystal symmetry operation3_575-x+y,-x+2,z1
Buried area44090 Å2
ΔGint81 kcal/mol
Surface area82270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.180, 107.180, 103.060
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein Envelope glycoprotein gp160


Mass: 54064.277 Da / Num. of mol.: 1 / Mutation: T332N, A501C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: env / Plasmid: pVRC8400 / Cell (production host): HEK293 GNTI-/- / Production host: Homo sapiens (human) / References: UniProt: Q2N0S6
#2: Protein Envelope glycoprotein gp160


Mass: 17146.482 Da / Num. of mol.: 1 / Mutation: I559P, T605C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: env / Plasmid: pVRC8400 / Cell (production host): HEK293 GNTI-/- / Production host: Homo sapiens (human) / References: UniProt: Q2N0S6
#3: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1072.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3/a4-b1_b4-c1_c3-d1_c6-f1_d2-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#5: 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.: 15
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

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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: 2.43 Å3/Da / Density % sol: 49.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 26% PEG 400, 3.2% PEG 3350, and 0.1M sodium acetate pH 5.5
PH range: 5.5-7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: May 29, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.31→50 Å / Num. all: 7041 / Num. obs: 7041 / % possible obs: 68.3 % / Redundancy: 5.2 % / Biso Wilson estimate: 88.6 Å2 / Rmerge(I) obs: 0.089 / Rsym value: 0.073 / Net I/σ(I): 18.5
Reflection shellResolution: 3.3→3.36 Å / Redundancy: 2 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 1.16 / % possible all: 11.2

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data scaling
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4TVP

4tvp


Resolution: 3.31→35.083 Å / SU ML: 0.51 / Cross valid method: FREE R-VALUE / σ(F): 1.42 / Phase error: 36.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2855 323 5.02 %
Rwork0.2664 --
obs0.2676 6434 63.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.31→35.083 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4518 0 338 0 4856
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044983
X-RAY DIFFRACTIONf_angle_d1.1666790
X-RAY DIFFRACTIONf_dihedral_angle_d12.8371245
X-RAY DIFFRACTIONf_chiral_restr0.047831
X-RAY DIFFRACTIONf_plane_restr0.004842
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3097-3.64240.376730.3558250X-RAY DIFFRACTION10
3.6424-4.16880.2937540.29831153X-RAY DIFFRACTION48
4.1688-5.24940.30581290.29172286X-RAY DIFFRACTION96
5.2494-35.08480.26871370.23812422X-RAY DIFFRACTION100
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)
11.7995-0.77960.34981.41881.34492.1112-0.02680.57150.9827-0.4998-0.2497-0.4866-0.71630.5125-0.07630.1412-0.75520.0536-0.61520.47120.162214.983110.979620.6844
20.2816-0.0281-0.2158-0.0110.01120.29970.13460.2029-0.0761-0.17530.1749-0.2599-0.20230.05860.1604-0.03350.59510.37310.0391-0.18270.29916.8138113.9047-23.9766
30.33320.0565-0.08450.04230.00730.0313-0.01210.5562-0.045-0.24470.0606-0.093-0.0402-0.19040.180.279-0.05180.4913-0.39070.3737-0.176916.9804109.68955.6335
40.02850.0191-0.0730.0865-0.07760.39430.0023-0.0750.09910.09860.1875-0.18930.47120.08610.5150.4405-0.10250.515-0.04580.5464-0.314627.3235101.7652.4135
50.13410.0258-0.08730.11790.18520.39590.288-0.0493-0.10740.24510.05120.0450.36460.02820.6892-0.21810.12440.4747-0.86440.0485-0.423624.85996.4834-3.5996
60.1326-0.11330.01260.5631-0.06810.174-0.0154-0.2031-0.10250.3395-0.0156-0.0748-0.06580.0270.27210.4075-0.19020.152-0.02110.14030.319710.3283104.699230.9633
70.0084-0.0041-0.02180.03330.02030.0532-0.0199-0.00080.03240.0264-0.0040.005-0.00970.0655-0.00430.72880.1185-0.08670.9668-0.26790.335518.0459108.293637.0419
80.0060.0064-0.00440.0132-0.0180.02250.023-0.00610.0531-0.03320.0322-0.03090.0053-0.01760.00340.91540.0130.1781.04990.03430.381315.6722103.2545.9796
90.0194-0.00310.01920.00220.00090.03520.0080.0063-0.0447-0.02590.0534-0.0160.05930.00870.01721.0164-0.27910.06990.7473-0.3420.632414.436114.417240.1517
100.09170.00440.0851-0.0004-0.01240.41740.09190.15470.0125-0.0795-0.0223-0.03620.01480.02310.10310.45420.47490.08250.2626-0.10960.02559.4672121.439318.0453
110.00020.0017-0.01040.0934-0.03590.05260.0958-0.08120.0228-0.142-0.16060.08820.13840.0026-0.0520.53540.07820.0510.378-0.00120.19261.6112117.159530.086
120.00120.00340.00240.0250.01830.0151-0.05130.0109-0.0733-0.0157-0.02990.0451-0.0544-0.0569-0.06650.2947-0.30430.26620.8160.01350.50091.7196114.340348.1038
130.00220.00310.00090.00350.00290.0037-0.081-0.0908-0.0630.09990.0036-0.0096-0.1119-0.073801.2164-0.43240.22671.0090.21161.0983-3.293198.962951.5357
14-0.0004-0.00020.0010.0012-0.00340.00650.06890.0286-0.0122-0.03460.0806-0.02780.0664-0.0555-01.2269-0.39750.22631.4840.56581.099710.104195.3951.9414
150.0218-0.0178-0.00650.1087-0.01810.1125-0.1065-0.0099-0.1144-0.12160.02490.11410.09340.0811-0.0561.2479-0.1743-0.05740.58360.2970.34521.1602100.030842.1991
160.0038-0.00520.00180.0056-0.00280.00160.0273-0.0118-0.037-0.0398-0.06540.002-0.00450.092800.99750.24430.06291.0748-0.13960.8833-12.5781113.80652.2712
170.00050.0006-0.0006-0.0002-0.00190.00250.01720.00980.08130.00210.0134-0.0243-0.05520.0137-00.66550.2870.36231.23440.14730.7569-16.1391122.863360.6855
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'G' and (resid 34 through 114 )
2X-RAY DIFFRACTION2chain 'G' and (resid 115 through 190 )
3X-RAY DIFFRACTION3chain 'G' and (resid 191 through 235 )
4X-RAY DIFFRACTION4chain 'G' and (resid 236 through 353 )
5X-RAY DIFFRACTION5chain 'G' and (resid 354 through 474 )
6X-RAY DIFFRACTION6chain 'G' and (resid 475 through 505 )
7X-RAY DIFFRACTION7chain 'B' and (resid 521 through 526 )
8X-RAY DIFFRACTION8chain 'B' and (resid 527 through 534 )
9X-RAY DIFFRACTION9chain 'B' and (resid 535 through 544 )
10X-RAY DIFFRACTION10chain 'B' and (resid 545 through 572 )
11X-RAY DIFFRACTION11chain 'B' and (resid 573 through 595 )
12X-RAY DIFFRACTION12chain 'B' and (resid 596 through 605 )
13X-RAY DIFFRACTION13chain 'B' and (resid 606 through 615 )
14X-RAY DIFFRACTION14chain 'B' and (resid 616 through 625 )
15X-RAY DIFFRACTION15chain 'B' and (resid 626 through 647 )
16X-RAY DIFFRACTION16chain 'B' and (resid 648 through 657 )
17X-RAY DIFFRACTION17chain 'B' and (resid 658 through 664 )

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