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

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Basic information

Entry
Database: PDB / ID: 6nnf
TitleCrystal Structure of HIV-1 BG505 SOSIP.664 Prefusion Env Trimer Bound to VRC01 FR3-03 scFv in Complex with Crystallization Chaperones 3H109L Fab and 35O22 scFv at 3.5 Angstrom
Components
  • (Envelope glycoprotein ...) x 2
  • (VRC01 FR3-03 ...) x 2
  • 35O22 scFv heavy chain
  • 35O22 scFv light chain
  • 3H109L Fab heavy chain
  • 3H109L Fab light chain
KeywordsIMMUNE SYSTEM / HIV-1 Envelope Prefusion Trimer / CD4-binding site antibodies / chimeric antibodies
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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.762 Å
AuthorsLai, Y.-T. / Kwong, P.D.
CitationJournal: Nat Commun / Year: 2019
Title: Improvement of antibody functionality by structure-guided paratope engraftment.
Authors: Liu, Q. / Lai, Y.T. / Zhang, P. / Louder, M.K. / Pegu, A. / Rawi, R. / Asokan, M. / Chen, X. / Shen, C.H. / Chuang, G.Y. / Yang, E.S. / Miao, H. / Wang, Y. / Fauci, A.S. / Kwong, P.D. / Mascola, J.R. / Lusso, P.
History
DepositionJan 14, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 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 11, 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
B: Envelope glycoprotein gp41
D: 35O22 scFv heavy chain
E: 35O22 scFv light chain
G: Envelope glycoprotein gp120
H: 3H109L Fab heavy chain
L: 3H109L Fab light chain
U: VRC01 FR3-03 heavy chain
V: VRC01 FR3-03 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)187,56024
Polymers179,0298
Non-polymers8,53116
Water0
1
B: Envelope glycoprotein gp41
D: 35O22 scFv heavy chain
E: 35O22 scFv light chain
G: Envelope glycoprotein gp120
H: 3H109L Fab heavy chain
L: 3H109L Fab light chain
U: VRC01 FR3-03 heavy chain
V: VRC01 FR3-03 light chain
hetero molecules

B: Envelope glycoprotein gp41
D: 35O22 scFv heavy chain
E: 35O22 scFv light chain
G: Envelope glycoprotein gp120
H: 3H109L Fab heavy chain
L: 3H109L Fab light chain
U: VRC01 FR3-03 heavy chain
V: VRC01 FR3-03 light chain
hetero molecules

B: Envelope glycoprotein gp41
D: 35O22 scFv heavy chain
E: 35O22 scFv light chain
G: Envelope glycoprotein gp120
H: 3H109L Fab heavy chain
L: 3H109L Fab light chain
U: VRC01 FR3-03 heavy chain
V: VRC01 FR3-03 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)562,67972
Polymers537,08624
Non-polymers25,59348
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Unit cell
Length a, b, c (Å)130.870, 130.870, 315.190
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 gp41


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 gp120 /


Mass: 54021.250 Da / Num. of mol.: 1 / Fragment: gp120 / Mutation: N137A, T332N, A501C
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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VRC01 FR3-03 ... , 1 types, 1 molecules V

#8: Protein VRC01 FR3-03 light chain


Mass: 11930.983 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Antibody , 5 types, 5 molecules DEHLU

#2: Antibody 35O22 scFv heavy chain


Mass: 15837.336 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


Mass: 14188.641 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)
#7: Antibody VRC01 FR3-03 heavy chain


Mass: 16232.327 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Sugars , 6 types, 16 molecules

#9: 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
#10: 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.: 7
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
#11: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-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: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 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]{}}}}}LINUCSPDB-CARE
#12: 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
#13: 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
#14: 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.: 5
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: 4.35 Å3/Da / Density % sol: 71.74 %
Crystal growTemperature: 298 K / Method: evaporation / Details: 72 mM imidazole pH 6.5, 72 mM

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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 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.76→50 Å / Num. obs: 36136 / % possible obs: 40.7 % / Redundancy: 2.2 % / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.041 / Rrim(I) all: 0.067 / Χ2: 0.643 / Net I/σ(I): 6.7 / Num. measured all: 78976
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsRpim(I) allRrim(I) allΧ2% possible allCC1/2
2.76-2.811.80.882430.7391.1580.9161
2.81-2.871.50.7781160.6791.0370.8832.60.352
2.87-2.931.40.5992220.5620.8240.73150.536
2.93-31.60.5383250.4750.720.8347.40.573
3-3.071.80.6074540.4960.7890.81410.30.678
3.07-3.151.90.4625880.3910.6090.73113.30.65
3.15-3.251.90.4527680.3770.5910.78817.40.749
3.25-3.3520.4279560.3420.550.76721.50.784
3.35-3.472.10.40612160.3260.5240.7427.40.866
3.47-3.612.10.33415630.2720.4330.71935.50.905
3.61-3.772.10.30420260.2490.3950.71745.70.918
3.77-3.972.10.28129610.2290.3640.7166.80.95
3.97-4.222.20.25541210.2030.3280.70992.80.973
4.22-4.552.20.13642110.1070.1740.68494.90.985
4.55-52.30.08341810.0630.1050.62594.10.987
5-5.732.30.05641830.0420.0710.55293.70.988
5.73-7.212.30.03941130.0290.0490.54692.60.983
7.21-502.20.02640890.0190.0330.54290.90.989

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data reduction
SCALEPACKdata scaling
PDB_EXTRACT3.24data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4TVP, 4LST

4tvp

4lst


Resolution: 2.762→42.837 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 29.92 / Stereochemistry target values: ML
Details: After data was collected and processed, UCLA anisotropy server was used to perform elliptical truncation to determine the diffraction limits along three principle directions. To account for ...Details: After data was collected and processed, UCLA anisotropy server was used to perform elliptical truncation to determine the diffraction limits along three principle directions. To account for the low completeness due to the high anisotropy, authors calculated an "effective resolution" by the following formula: Effective resolution = highest resolution / (overall completeness)^(1/3) Note: highest resolution was determined by UCLA anisotropy server.
RfactorNum. reflection% reflection
Rfree0.2976 1380 5.09 %
Rwork0.2417 25746 -
obs0.2445 27126 34.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 190.04 Å2 / Biso mean: 69.4093 Å2 / Biso min: 5.77 Å2
Refinement stepCycle: final / Resolution: 2.762→42.837 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11361 0 565 0 11926
Biso mean--83.03 --
Num. residues----1462
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 (%)
2.7615-2.86020.204620.421147491
2.8602-2.97470.359770.36451341412
2.9747-3.11010.545220.33293493715
3.1101-3.2740.4295330.32025766098
3.274-3.4790.4239530.27891002105514
3.479-3.74750.3647910.2531581167221
3.7475-4.12430.35391460.23332778292438
4.1243-4.72050.29992950.22555326562172
4.7205-5.94480.29133650.2427011737694
5.9448-42.84240.24633660.2446942730893

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