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- PDB-6muf: Crystal Structure of HIV-1 B41 SOSIP.664 Prefusion Env Trimer in ... -

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Entry
Database: PDB / ID: 6muf
TitleCrystal Structure of HIV-1 B41 SOSIP.664 Prefusion Env Trimer in Complex with Human Antibodies 3H109L and 35O22 at 3.4 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


symbiont-mediated perturbation of host defense response / 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 ...symbiont-mediated perturbation of host defense response / 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 / 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
Envelope glycoprotein gp160 / Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.91 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 23, 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 2.1Oct 23, 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)155,44321
Polymers149,0426
Non-polymers6,40115
Water00
1
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

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

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)466,32863
Polymers447,12518
Non-polymers19,20345
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_875-y+3,x-y+2,z1
crystal symmetry operation3_685-x+y+1,-x+3,z1
Unit cell
Length a, b, c (Å)131.970, 131.970, 314.690
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: 17357.824 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: B3UEZ6
#4: Protein Envelope glycoprotein gp160 / Env polyprotein


Mass: 54991.215 Da / Num. of mol.: 1 / Fragment: gp120
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: env / Production host: Homo sapiens (human) / References: UniProt: B3UES2

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Antibody , 4 types, 4 molecules DEHL

#2: Antibody 35O22 scFv heavy chain portion


Mass: 14662.336 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, 15 molecules

#7: 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
#8: Polysaccharide alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...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: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c6-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#9: 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.: 1
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
#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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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: 5.31 Å3/Da / Density % sol: 76.83 %
Crystal growTemperature: 298 K / Method: evaporation
Details: 90mM Na Acetate pH5.5 6% PEG8,000 3% PEG400 450mM NaCl

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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: Aug 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 29704 / % possible obs: 43.9 % / Redundancy: 3.3 % / Biso Wilson estimate: 28.22 Å2 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.041 / Rrim(I) all: 0.087 / Χ2: 0.777 / Net I/σ(I): 6.9 / Num. measured all: 96862
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.9-2.955.81.0791470.5370.4831.1840.8194.4
2.95-35.81.3731860.5720.6151.5070.8235.5
3-3.0661.1332440.7640.51.240.8557.2
3.06-3.125.80.7943120.7790.3550.8710.8059.1
3.12-3.195.50.8223750.7720.380.9070.83811.2
3.19-3.275.40.7394520.8150.3490.8190.83413.4
3.27-3.355.10.5685450.8820.2740.6330.80216.1
3.35-3.444.90.4966490.9180.2440.5540.85819.2
3.44-3.544.80.3737590.9430.1880.4190.86422.5
3.54-3.654.40.329300.9510.1660.3620.87327.6
3.65-3.784.10.32311240.9370.1730.3680.93433.1
3.78-3.943.70.23513550.9580.130.270.92340.5
3.94-4.113.40.17316870.9770.0990.2010.88549.8
4.11-4.3330.12622960.9890.0720.1470.87968.2
4.33-4.62.70.11131200.990.0640.1290.85292.4
4.6-4.962.80.08630930.9940.0480.0990.81491.4
4.96-5.462.80.07531300.9940.0410.0860.75292.1
5.46-6.242.80.06330990.9930.0340.0720.63591.2
6.24-7.862.80.04531270.9960.0240.0510.52292.3
7.86-502.70.03730740.9920.0210.0430.49589.2

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
SCALEPACKdata scaling
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHASERphasing
RefinementResolution: 2.91→41.836 Å / SU ML: 0.46 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 29.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.297 1350 5.02 %
Rwork0.2526 25540 -
obs0.2549 26890 39.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 168.69 Å2 / Biso mean: 51.1955 Å2 / Biso min: 1.38 Å2
Refinement stepCycle: final / Resolution: 2.91→41.836 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9461 0 420 0 9881
Biso mean--72.75 --
Num. residues----1220
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.91-3.0140.593460.32861271332
3.014-3.13460.2252170.33053603776
3.1346-3.27720.3484310.34225856169
3.2772-3.44990.3354450.298688292714
3.4499-3.6660.4103780.26041344142221
3.666-3.94880.3229870.25721880196729
3.9488-4.34580.33131610.23883026318747
4.3458-4.97380.31212920.2395405569784
4.9738-6.26310.28363170.26346039635693
6.2631-41.83990.24523160.24725892620891

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