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- PDB-4rfo: Crystal structure of the ADCC-Potent Antibody N60-I3 Fab in compl... -

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Entry
Database: PDB / ID: 4rfo
TitleCrystal structure of the ADCC-Potent Antibody N60-I3 Fab in complex with HIV-1 Clade A/E gp120 and M48u1
Components
  • HIV-1 clade A/E gp120
  • N60-i3 Fab heavy chain
  • N60-i3 Fab light chain
  • m48u1 CD4 mimetic peptide
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM/INHIBITOR / HIV-1 GP120 / CLADE A/E 93TH057 / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM-INHIBITOR complex
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 / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / plasma membrane
Similarity search - Function
HIV Envelope Protein Gp120; Chain G / Human immunodeficiency virus 1, Gp160, envelope glycoprotein / Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Beta Complex / Immunoglobulins ...HIV Envelope Protein Gp120; Chain G / Human immunodeficiency virus 1, Gp160, envelope glycoprotein / Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / 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
CD4-MIMETIC MINIPROTEIN M48U1 / Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
Homo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsTolbert, W.D. / Gohain, N. / Pazgier, M.
CitationJournal: J.Virol. / Year: 2015
Title: Cocrystal Structures of Antibody N60-i3 and Antibody JR4 in Complex with gp120 Define More Cluster A Epitopes Involved in Effective Antibody-Dependent Effector Function against HIV-1.
Authors: Gohain, N. / Tolbert, W.D. / Acharya, P. / Yu, L. / Liu, T. / Zhao, P. / Orlandi, C. / Visciano, M.L. / Kamin-Lewis, R. / Sajadi, M.M. / Martin, L. / Robinson, J.E. / Kwong, P.D. / DeVico, A. ...Authors: Gohain, N. / Tolbert, W.D. / Acharya, P. / Yu, L. / Liu, T. / Zhao, P. / Orlandi, C. / Visciano, M.L. / Kamin-Lewis, R. / Sajadi, M.M. / Martin, L. / Robinson, J.E. / Kwong, P.D. / DeVico, A.L. / Ray, K. / Lewis, G.K. / Pazgier, M.
History
DepositionSep 26, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 19, 2015Group: Database references
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.pdbx_value_order / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Jun 2, 2021Group: Source and taxonomy / Structure summary / Category: chem_comp / entity_src_gen
Item: _chem_comp.pdbx_synonyms / _entity_src_gen.host_org_common_name ..._chem_comp.pdbx_synonyms / _entity_src_gen.host_org_common_name / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.4Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
G: HIV-1 clade A/E gp120
N: m48u1 CD4 mimetic peptide
H: N60-i3 Fab heavy chain
L: N60-i3 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,96313
Polymers89,9724
Non-polymers1,9919
Water181
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)98.305, 102.575, 108.038
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Antibody , 2 types, 2 molecules HL

#3: Antibody N60-i3 Fab heavy chain


Mass: 24412.373 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: FAB HEAVY CHAIN OF ADCC-POTENT ANTI-HIV-1 ANTIBODY N60-i3
Cell line (production host): HEK 293 / Production host: Homo sapiens (human)
#4: Antibody N60-i3 Fab light chain


Mass: 23342.707 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: FAB LIGHT CHAIN OF ADCC-POTENT ANTI-HIV-1 ANTIBODY N60-i3
Cell line (production host): HEK 293 / Production host: Homo sapiens (human)

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Protein / Protein/peptide / Sugars / Non-polymers , 4 types, 12 molecules GN

#1: Protein HIV-1 clade A/E gp120


Mass: 39160.367 Da / Num. of mol.: 1 / Mutation: H375S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: HIV-1 env / Cell line (production host): HEK 293 GnT1- / Production host: Homo sapiens (human) / References: UniProt: Q0ED31*PLUS
#2: Protein/peptide m48u1 CD4 mimetic peptide


Type: Peptide-like / Class: Inhibitor / Mass: 3056.804 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: M48U1 is an engineered CD4 mimetic / Source: (synth.) synthetic construct (others) / References: CD4-MIMETIC MINIPROTEIN M48U1
#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.: 9
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
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsTHE CD4-MIMETIC MINIPROTEINS INHIBIT HIV-1 ENTRY AND ARE DERIVED FROM SCYLLATOXIN (A SCORPION TOXIN) ...THE CD4-MIMETIC MINIPROTEINS INHIBIT HIV-1 ENTRY AND ARE DERIVED FROM SCYLLATOXIN (A SCORPION TOXIN) BY TRANSPLANTING THE GP120-INTERACTIVE REGION OF CD4 ONTO THE SCYLLATOXIN SCAFFOLD, FOLLOWED BY MANY ROUNDS OF ITERATIVE OPTIMIZATION

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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: 3.03 Å3/Da / Density % sol: 59.37 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 10-16% PEG 8000, 0.1 M Tris-HCl pH 8.5, 65 mM NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.12709 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 31, 2013 / Details: RH coated flat mirror
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12709 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. all: 18694 / Num. obs: 17516 / % possible obs: 93.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rmerge(I) obs: 0.126 / Net I/σ(I): 10.7
Reflection shellResolution: 3.2→3.26 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.899 / Mean I/σ(I) obs: 1.3 / % possible all: 96

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.8.0073/Phenix 1.9refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3TNN FOR N60-I3, PDB ENTRY 4H8W FOR GP120, PDB ENTRY 4JZW FOR M48U1

3tnn

4h8w

4jzw


Resolution: 3.2→36.013 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.892 / SU B: 73.662 / SU ML: 0.543 / Cross valid method: THROUGHOUT / ESU R Free: 0.562 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27702 876 5 %RANDOM
Rwork0.21981 ---
obs0.2226 16589 93.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 116.914 Å2
Baniso -1Baniso -2Baniso -3
1-0.98 Å20 Å2-0 Å2
2---8.03 Å2-0 Å2
3---7.05 Å2
Refinement stepCycle: LAST / Resolution: 3.2→36.013 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6042 0 126 1 6169
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.026328
X-RAY DIFFRACTIONr_bond_other_d0.0020.025859
X-RAY DIFFRACTIONr_angle_refined_deg1.4111.9698547
X-RAY DIFFRACTIONr_angle_other_deg0.836313494
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8345762
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.93625.143245
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.34151005
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5571518
X-RAY DIFFRACTIONr_chiral_restr0.080.2994
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216899
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021361
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.8136.3943147
X-RAY DIFFRACTIONr_mcbond_other1.8136.3943146
X-RAY DIFFRACTIONr_mcangle_it3.1019.6013863
X-RAY DIFFRACTIONr_mcangle_other3.0729.5153912
X-RAY DIFFRACTIONr_scbond_it2.2266.6243181
X-RAY DIFFRACTIONr_scbond_other1.9716.5763190
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.3049.8194716
X-RAY DIFFRACTIONr_long_range_B_refined7.91660.47625361
X-RAY DIFFRACTIONr_long_range_B_other7.91660.47925362
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.2→3.283 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 65 -
Rwork0.35 1214 -
obs--95.38 %
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)
13.31470.33020.14064.64681.59854.89510.1678-0.36990.44810.6416-0.29610.4217-0.3286-0.41490.12820.2384-0.04130.11910.236-0.00740.156112.7138113.3152112.9531
25.45596.46124.15987.87534.74133.32890.2419-0.198-0.5120.3036-0.1058-0.89810.165-0.2308-0.13610.4404-0.06760.01270.213-0.10990.453626.1465130.5376116.8838
31.8028-1.0647-2.50412.64112.62985.2389-0.31560.5931-0.5191-0.28460.02280.11630.6361-0.00040.29290.39930.0084-0.0310.7158-0.32340.287722.767289.735266.1348
40.9053-0.941-1.69732.8392.82655.35370.34650.52910.0039-1.2192-0.0888-0.5278-1.06680.339-0.25770.8009-0.01330.09831.1627-0.0640.229532.6221103.073758.8227
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1G44 - 492
2X-RAY DIFFRACTION2N2 - 27
3X-RAY DIFFRACTION3H1 - 212
4X-RAY DIFFRACTION4L1 - 208

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