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- PDB-6mtn: Crystal Structure of HIV-1 BG505 SOSIP.664 Prefusion Env Trimer B... -

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Basic information

Entry
Database: PDB / ID: 6mtn
TitleCrystal Structure of HIV-1 BG505 SOSIP.664 Prefusion Env Trimer Bound to Small Molecule HIV-1 Entry Inhibitor Compound 484 in Complex with Human Antibodies 3H109L and 35O22 at 3.0 Angstrom
Components
  • (Envelope glycoprotein ...) x 2
  • 35O22 scFv heavy chain portion
  • 35O22 scFv light chain portion
  • 3H109L Fab heavy chain
  • 3H109L Fab light chain
KeywordsIMMUNE SYSTEM/INHIBITOR / HIV-1 Envelope Prefusion Trimer / Entry Inhibitors / IMMUNE SYSTEM-INHIBITOR complex
Function / homology
Function and homology information


positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / 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 / virion attachment to host cell / host cell plasma membrane ...positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / 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 / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / identical protein binding / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-JYJ / Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å
AuthorsLai, Y.-T. / Kwong, P.D.
CitationJournal: Nat Commun / Year: 2019
Title: Lattice engineering enables definition of molecular features allowing for potent small-molecule inhibition of HIV-1 entry.
Authors: Lai, Y.T. / Wang, T. / O'Dell, S. / Louder, M.K. / Schon, A. / Cheung, C.S.F. / Chuang, G.Y. / Druz, A. / Lin, B. / McKee, K. / Peng, D. / Yang, Y. / Zhang, B. / Herschhorn, A. / Sodroski, J. ...Authors: Lai, Y.T. / Wang, T. / O'Dell, S. / Louder, M.K. / Schon, A. / Cheung, C.S.F. / Chuang, G.Y. / Druz, A. / Lin, B. / McKee, K. / Peng, D. / Yang, Y. / Zhang, B. / Herschhorn, A. / Sodroski, J. / Bailer, R.T. / Doria-Rose, N.A. / Mascola, J.R. / Langley, D.R. / Kwong, P.D.
History
DepositionOct 20, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2019Provider: repository / Type: Initial release
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 / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _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_atom_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 2.1Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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
B: Envelope glycoprotein gp160
D: 35O22 scFv heavy chain portion
E: 35O22 scFv light chain portion
G: Envelope glycoprotein gp160
H: 3H109L Fab heavy chain
L: 3H109L Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,33526
Polymers147,8616
Non-polymers8,47320
Water543
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24660 Å2
ΔGint62 kcal/mol
Surface area58260 Å2
Unit cell
Length a, b, c (Å)131.500, 131.500, 315.740
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63

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Components

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Envelope glycoprotein ... , 2 types, 2 molecules BG

#1: Protein Envelope glycoprotein gp160 / Env polyprotein


Mass: 17146.482 Da / Num. of mol.: 1 / Fragment: gp41 / Mutation: I559P, A605C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: env / Production host: Homo sapiens (human) / References: UniProt: Q2N0S6
#4: Protein Envelope glycoprotein gp160 / Env polyprotein


Mass: 54021.250 Da / Num. of mol.: 1 / Fragment: gp120 / Mutation: N137A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: env / Production host: Homo sapiens (human) / References: UniProt: Q2N0S6

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Antibody , 4 types, 4 molecules DEHL

#2: Antibody 35O22 scFv heavy chain portion


Mass: 14663.281 Da / Num. of mol.: 1 / Mutation: E10T, L11T, K12T, A16S, I68N, K83T, F84S,
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody 35O22 scFv light chain portion


Mass: 12358.635 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#5: Antibody 3H109L Fab heavy chain


Mass: 26255.498 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#6: Antibody 3H109L Fab light chain


Mass: 23416.145 Da / Num. of mol.: 1 / Mutation: E184M, S188M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Sugars , 5 types, 19 molecules

#7: 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.: 4
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
#8: Polysaccharide alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D- ...alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]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
DManpa1-3DManpa1-6[DManpa1-3]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-e1_e3-f1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#9: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#10: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[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: 1721.527 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-2DManpa1-3[DManpa1-2DManpa1-6[DManpa1-3]DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,10,9/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-g1_d2-e1_e2-f1_g3-h1_g6-i1_i2-j1WURCSPDB2Glycan 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]{[(2+1)][a-D-Manp]{}}}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}}}}LINUCSPDB-CARE
#11: 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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 11
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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Non-polymers , 2 types, 4 molecules

#12: Chemical ChemComp-JYJ / {4-[1-(3-chlorophenyl)cyclopropane-1-carbonyl]piperazin-1-yl}(thiophen-3-yl)methanone


Mass: 374.884 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H19ClN2O2S / Feature type: SUBJECT OF INVESTIGATION
#13: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 5.33 Å3/Da / Density % sol: 76.92 %
Crystal growTemperature: 298 K / Method: evaporation
Details: 60mM Imidazole pH6.5 3% MPD 5% PEG3,350 120mM LiSO$

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Jun 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 54831 / % possible obs: 50.9 % / Redundancy: 4.4 % / Biso Wilson estimate: 39.54 Å2 / Rmerge(I) obs: 0.13 / Rpim(I) all: 0.069 / Rrim(I) all: 0.148 / Χ2: 0.735 / Net I/σ(I): 6.1 / Num. measured all: 241947
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.5-2.5431.141170.3620.7421.3690.522.2
2.54-2.593.21.2382090.3870.7921.480.6423.9
2.59-2.643.21.1073260.4320.7121.3260.5916
2.64-2.693.41.54380.3330.9341.7760.6228.1
2.69-2.753.61.2155950.4490.7341.4250.61111.2
2.75-2.823.71.0917520.6190.6491.2740.61214
2.82-2.893.80.9039360.6230.5351.0530.62517.4
2.89-2.963.90.81511840.7550.4740.9450.6622
2.96-3.0540.81314460.8220.4610.9370.66426.9
3.05-3.154.10.67917870.8570.3790.780.68832.9
3.15-3.264.20.59222310.9010.3260.6780.67841.8
3.26-3.394.20.51529030.9150.2810.5880.72953.4
3.39-3.554.20.50441490.940.2740.5750.72877.6
3.55-3.734.50.43253740.9570.2290.4890.74599.8
3.73-3.974.60.33353950.9660.1750.3770.80599.9
3.97-4.274.60.21854170.9790.1140.2470.806100
4.27-4.74.60.15353790.9810.0810.1730.935100
4.7-5.384.60.12853920.980.0670.1440.801100
5.38-6.784.60.1154210.9710.0570.1240.66100
6.78-504.50.08953800.9750.0470.1010.50798.1

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
SCALEPACKdata scaling
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHASERphasing
RefinementResolution: 2.5→43.043 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 29.7
RfactorNum. reflection% reflection
Rfree0.2626 2075 4.99 %
Rwork0.223 --
obs0.225 41555 39.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 158.84 Å2 / Biso mean: 49.3273 Å2 / Biso min: 0.54 Å2
Refinement stepCycle: final / Resolution: 2.5→43.043 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9597 0 557 3 10157
Biso mean--68.1 36.69 -
Num. residues----1237
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5004-2.55860.563830.297843461
2.5586-2.62260.560670.40621041112
2.6226-2.69350.327360.37221551612
2.6935-2.77270.3093130.33172622754
2.7727-2.86220.3581280.35145025308
2.8622-2.96450.3668360.30677681212
2.9645-3.08310.3297560.34371057111316
3.0831-3.22340.3689750.31521397147221
3.2234-3.39330.2916910.26871840193127
3.3933-3.60580.30171370.24582588272539
3.6058-3.8840.29932110.22814073428461
3.884-4.27460.28663460.21936540688697
4.2746-4.89230.22633530.192767347087100
4.8923-6.1610.24643610.21967357096100
6.161-43.04980.23613520.21416674702698

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