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- PDB-7sx7: Crystal structure of broadly neutralizing antibody N49P9.3-FR3-3 ... -

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Entry
Database: PDB / ID: 7sx7
TitleCrystal structure of broadly neutralizing antibody N49P9.3-FR3-3 Fab in complex with HIV-1 Clade A/E strain 93TH057 gp120 core
Components
  • (N49P9.3-FR3-3 ANTIBODY FAB ...) x 2
  • clade A/E 93TH057 HIV-1 gp120 core
KeywordsIMMUNE SYSTEM/VIRAL PROTEIN / HIV-1 / VRC01-CLASS ANTIBODY / CD4 BINDING SITE / CLADE A/E 93TH057 GP120 / VIRAL PROTEIN-IMMUNE SYSTEM COMPLEX / N49P9.3-FR3-3 / IMMUNE SYSTEM / IMMUNE SYSTEM-VIRAL PROTEIN complex
Function / homology
Function and homology information


membrane fusion involved in viral entry into host cell / viral envelope / symbiont entry into host cell / virion attachment to host cell / virion membrane
Similarity search - Function
HIV Envelope Protein Gp120; Chain G / Human immunodeficiency virus 1, Gp160, envelope glycoprotein / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Beta Complex / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
clade A/E 93TH057 HIV-1 gp120 core
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
Homo (humans)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsTolbert, W.D. / Pazgier, M.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI116274 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01 AI120756 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI129769 United States
CitationJournal: To Be Published
Title: Crystal structure of broadly neutralizing antibody N49P9.3-FR3-3 Fab in complex with HIV-1 Clade A/E strain 93TH057 gp120 core
Authors: Tolbert, W.D. / Pazgier, M.
History
DepositionNov 22, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 30, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 2.0Feb 5, 2025Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Refinement description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / pdbx_contact_author / pdbx_distant_solvent_atoms / pdbx_nonpoly_scheme / pdbx_refine_tls / pdbx_struct_assembly_prop / pdbx_struct_sheet_hbond / pdbx_validate_torsion / refine / refine_ls_restr / refine_ls_shell / software / struct_conf / struct_conn / struct_mon_prot_cis / struct_sheet_range
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_seq_id / _atom_site.label_asym_id / _atom_site.occupancy / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _pdbx_nonpoly_scheme.asym_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.ndb_seq_num / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_nonpoly_scheme.pdb_strand_id / _pdbx_refine_tls.L[1][1] / _pdbx_refine_tls.L[1][2] / _pdbx_refine_tls.L[1][3] / _pdbx_refine_tls.L[2][2] / _pdbx_refine_tls.L[2][3] / _pdbx_refine_tls.L[3][3] / _pdbx_refine_tls.S[1][1] / _pdbx_refine_tls.S[1][2] / _pdbx_refine_tls.S[1][3] / _pdbx_refine_tls.S[2][1] / _pdbx_refine_tls.S[2][2] / _pdbx_refine_tls.S[2][3] / _pdbx_refine_tls.S[3][1] / _pdbx_refine_tls.S[3][2] / _pdbx_refine_tls.S[3][3] / _pdbx_refine_tls.T[1][1] / _pdbx_refine_tls.T[1][2] / _pdbx_refine_tls.T[1][3] / _pdbx_refine_tls.T[2][2] / _pdbx_refine_tls.T[2][3] / _pdbx_refine_tls.T[3][3] / _pdbx_refine_tls.origin_x / _pdbx_refine_tls.origin_y / _pdbx_refine_tls.origin_z / _pdbx_struct_assembly_prop.value / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_number_reflns_obs / _refine.overall_SU_ML / _refine.pdbx_overall_phase_error / _refine.pdbx_solvent_vdw_probe_radii / _refine_ls_restr.dev_ideal / _refine_ls_restr.number / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _refine_ls_shell.number_reflns_R_work / _software.version / _struct_conf.beg_auth_asym_id / _struct_conf.beg_auth_comp_id / _struct_conf.beg_auth_seq_id / _struct_conf.beg_label_asym_id / _struct_conf.beg_label_comp_id / _struct_conf.beg_label_seq_id / _struct_conf.end_auth_asym_id / _struct_conf.end_auth_comp_id / _struct_conf.end_auth_seq_id / _struct_conf.end_label_asym_id / _struct_conf.end_label_comp_id / _struct_conf.end_label_seq_id / _struct_conf.pdbx_PDB_helix_class / _struct_conf.pdbx_PDB_helix_length / _struct_conn.pdbx_dist_value / _struct_mon_prot_cis.pdbx_omega_angle / _struct_sheet_range.beg_auth_comp_id / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.beg_label_comp_id / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_auth_comp_id / _struct_sheet_range.end_auth_seq_id / _struct_sheet_range.end_label_comp_id / _struct_sheet_range.end_label_seq_id / _struct_sheet_range.pdbx_end_PDB_ins_code
Description: Polymer geometry
Details: Based upon reviewer comments we have improved the Ramachandran statistics although the Rfree is now slightly higher.
Provider: author / Type: Coordinate replacement

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
G: clade A/E 93TH057 HIV-1 gp120 core
H: N49P9.3-FR3-3 ANTIBODY FAB HEAVY CHAIN
L: N49P9.3-FR3-3 ANTIBODY FAB LIGHT CHAIN
A: clade A/E 93TH057 HIV-1 gp120 core
B: N49P9.3-FR3-3 ANTIBODY FAB HEAVY CHAIN
C: N49P9.3-FR3-3 ANTIBODY FAB LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)178,14332
Polymers172,3406
Non-polymers5,80326
Water7,981443
1
G: clade A/E 93TH057 HIV-1 gp120 core
H: N49P9.3-FR3-3 ANTIBODY FAB HEAVY CHAIN
L: N49P9.3-FR3-3 ANTIBODY FAB LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,84215
Polymers86,1703
Non-polymers2,67212
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9350 Å2
ΔGint20 kcal/mol
Surface area35090 Å2
MethodPISA
2
A: clade A/E 93TH057 HIV-1 gp120 core
B: N49P9.3-FR3-3 ANTIBODY FAB HEAVY CHAIN
C: N49P9.3-FR3-3 ANTIBODY FAB LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,30117
Polymers86,1703
Non-polymers3,13114
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9020 Å2
ΔGint21 kcal/mol
Surface area35140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.367, 65.418, 112.381
Angle α, β, γ (deg.)90.02, 104.85, 90.02
Int Tables number1
Space group name H-MP1

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Components

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Antibody , 2 types, 4 molecules HBLC

#2: Antibody N49P9.3-FR3-3 ANTIBODY FAB HEAVY CHAIN


Mass: 25050.166 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo (humans) / Cell (production host): HEK 293 / Production host: Homo sapiens (human)
#3: Antibody N49P9.3-FR3-3 ANTIBODY FAB LIGHT CHAIN


Mass: 21763.316 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell (production host): HEK 293 / Production host: Homo sapiens (human)

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Protein / Sugars , 2 types, 25 molecules GA

#1: Protein clade A/E 93TH057 HIV-1 gp120 core


Mass: 39356.613 Da / Num. of mol.: 2 / Mutation: H375S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: HIV-1 Env / Cell (production host): HEK 293 GnT1- / Production host: Homo sapiens (human) / References: UniProt: A0A0M3KKW9
#4: 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.: 23
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, 446 molecules

#5: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 443 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 2.49 Å3/Da / Density % sol: 50.59 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 10% PEG 3350 0.1 M HEPES pH 7.0 0.1 M magnesium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 19, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 73767 / % possible obs: 82.7 % / Redundancy: 1.8 % / CC1/2: 0.949 / Rmerge(I) obs: 0.135 / Rpim(I) all: 0.135 / Net I/σ(I): 6.9
Reflection shellResolution: 2.15→2.19 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.645 / Mean I/σ(I) obs: 1 / Num. unique obs: 2786 / CC1/2: 0.394 / Rpim(I) all: 0.645 / % possible all: 63.6

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Processing

Software
NameVersionClassification
PHENIX(1.21.2_5419: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6OZ3

6oz3


Resolution: 2.15→46.66 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.94 / Phase error: 30.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.268 3643 4.94 %
Rwork0.2289 --
obs0.2308 73749 82.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.15→46.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11909 0 367 443 12719
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00412578
X-RAY DIFFRACTIONf_angle_d0.72717121
X-RAY DIFFRACTIONf_dihedral_angle_d16.5674964
X-RAY DIFFRACTIONf_chiral_restr0.0491961
X-RAY DIFFRACTIONf_plane_restr0.0072180
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.180.3256900.30311720X-RAY DIFFRACTION53
2.18-2.210.33891270.31932127X-RAY DIFFRACTION65
2.21-2.240.35251290.31292177X-RAY DIFFRACTION66
2.24-2.280.34371100.3182134X-RAY DIFFRACTION66
2.28-2.310.37531240.30612112X-RAY DIFFRACTION65
2.31-2.350.33421080.29342518X-RAY DIFFRACTION76
2.35-2.390.31551410.28462657X-RAY DIFFRACTION81
2.39-2.440.29721500.28992725X-RAY DIFFRACTION83
2.44-2.480.31961430.29852735X-RAY DIFFRACTION84
2.48-2.530.36381520.30512841X-RAY DIFFRACTION86
2.53-2.590.37991300.30442813X-RAY DIFFRACTION87
2.59-2.650.37071700.29882900X-RAY DIFFRACTION88
2.65-2.710.34691470.28282864X-RAY DIFFRACTION86
2.71-2.790.33851520.27782707X-RAY DIFFRACTION82
2.79-2.870.31341410.27262756X-RAY DIFFRACTION83
2.87-2.960.30251600.26282964X-RAY DIFFRACTION91
2.96-3.070.32581260.26683043X-RAY DIFFRACTION91
3.07-3.190.30961300.25882994X-RAY DIFFRACTION90
3.19-3.340.25971760.24312927X-RAY DIFFRACTION90
3.34-3.510.26541700.22842884X-RAY DIFFRACTION89
3.51-3.730.24541810.21922636X-RAY DIFFRACTION82
3.73-4.020.26011410.20513099X-RAY DIFFRACTION93
4.02-4.420.22621610.1742984X-RAY DIFFRACTION92
4.42-5.060.19011380.16162957X-RAY DIFFRACTION89
5.06-6.380.23651080.19062867X-RAY DIFFRACTION86
6.38-46.660.18661380.18522965X-RAY DIFFRACTION90
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)
10.3318-0.1419-0.19210.9785-0.2850.7701-0.0520.0493-0.0051-0.01650.030.0470.01220.034100.2189-0.0178-0.02360.1303-0.01520.229714.0334-29.9941.3621
20.2584-0.07810.02250.6579-0.28740.05280.02130.12390.02520.08130.00880.04820.0246-0.038200.22470.00280.01210.31070.03070.225-7.9158-2.215113.5425
30.509-0.177-0.23160.31250.10670.20390.06410.22980.0392-0.0514-0.1089-0.0288-0.00370.0202-00.2442-0.0278-0.00760.56260.00690.22184.4914-2.74990.4628
40.43950.0862-0.23051.0010.17730.856-0.0616-0.03810.00580.08290.0388-0.02530.03890.0054-00.23620.0075-0.02040.15060.0170.2674-15.11962.746154.9731
50.38840.3650.13270.62090.20860.1630.0015-0.13960.0269-0.08140.0183-0.01210.03560.0673-00.23480.01790.00980.3242-0.02490.23616.753630.495682.9652
60.49450.1594-0.17150.5321-0.01090.25620.0292-0.24380.0660.0316-0.05030.0289-0.0027-0.1033-00.24370.0439-0.01610.5747-0.03110.2367-5.637429.877495.9254
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'G' and resid 43 through 492)
2X-RAY DIFFRACTION2(chain 'H' and resid 1 through 216)
3X-RAY DIFFRACTION3(chain 'L' and resid 3 through 211)
4X-RAY DIFFRACTION4(chain 'A' and resid 44 through 492)
5X-RAY DIFFRACTION5(chain 'B' and resid 1 through 216)
6X-RAY DIFFRACTION6(chain 'C' and resid 3 through 211)

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