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- PDB-5kjr: Crystal structure of the ADCC-potent antibody N60-i3 Fab in compl... -

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Basic information

Entry
Database: PDB / ID: 5kjr
TitleCrystal structure of the ADCC-potent antibody N60-i3 Fab in complex with HIV-1 Clade A/E gp120 W69A/S115W mutant and M48U1.
Components
  • M48U1 CD4 MIMETIC PEPTIDE
  • N60-I3 FAB HEAVY CHAIN
  • N60-I3 FAB LIGHT CHAIN
  • clade A/E 93TH057 HIV-1 gp120 core
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


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
CD4-MIMETIC MINIPROTEIN M48U1 / clade A/E 93TH057 HIV-1 gp120 core
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
Homo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.98 Å
AuthorsTolbert, W.D. / Pazgier, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI116274 United States
CitationJournal: J.Virol. / Year: 2016
Title: A Highly Conserved gp120 Inner Domain Residue Modulates Env Conformation and Trimer Stability.
Authors: Ding, S. / Tolbert, W.D. / Prevost, J. / Pacheco, B. / Coutu, M. / Debbeche, O. / Xiang, S.H. / Pazgier, M. / Finzi, A.
History
DepositionJun 20, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 21, 2016Group: Database references
Revision 1.2Oct 26, 2016Group: Structure summary
Revision 1.3Sep 13, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Jul 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_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.6Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.7Nov 15, 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

Downloads & links

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Assembly

Deposited unit
G: clade A/E 93TH057 HIV-1 gp120 core
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)92,28715
Polymers89,9564
Non-polymers2,33011
Water1629
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.191, 101.944, 108.747
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 CELLS / 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 CELLS / Production host: Homo sapiens (human)

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Protein / Protein/peptide / Sugars , 3 types, 12 molecules GN

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


Mass: 39144.367 Da / Num. of mol.: 1 / Mutation: W69A, S115W, 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- CELLS / Production host: Homo sapiens (human) / References: UniProt: A0A0M3KKW9
#2: Protein/peptide M48U1 CD4 MIMETIC PEPTIDE


Type: Peptide-like / Class: Inhibitor / Mass: 3056.804 Da / Num. of mol.: 1 / Source method: obtained synthetically / 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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 10
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, 10 molecules

#6: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 2.93 Å3/Da / Density % sol: 58.06 %
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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 0.97946 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 6, 2016 / Details: RH Coated Flat mirror
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.98→50 Å / Num. obs: 19540 / % possible obs: 87.6 % / Observed criterion σ(F): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.22 / Net I/σ(I): 5.1
Reflection shellResolution: 2.98→3.05 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.676 / Mean I/σ(I) obs: 1.2 / % possible all: 67.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RFO

4rfo


Resolution: 2.98→50 Å / Cor.coef. Fo:Fc: 0.885 / Cor.coef. Fo:Fc free: 0.807 / SU B: 72.387 / SU ML: 0.586 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.562 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30602 1007 5.2 %RANDOM
Rwork0.2488 ---
obs0.2518 18481 87.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 51.54 Å2
Baniso -1Baniso -2Baniso -3
1--2.03 Å2-0 Å2-0 Å2
2---0.63 Å20 Å2
3---2.66 Å2
Refinement stepCycle: 1 / Resolution: 2.98→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6036 0 148 9 6193
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0196358
X-RAY DIFFRACTIONr_bond_other_d0.0030.025877
X-RAY DIFFRACTIONr_angle_refined_deg1.9811.9768654
X-RAY DIFFRACTIONr_angle_other_deg1.219313605
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2325778
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.65325.102245
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.349151002
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0181518
X-RAY DIFFRACTIONr_chiral_restr0.0990.2999
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0217060
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021368
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_it1.2493.0963152
X-RAY DIFFRACTIONr_mcbond_other1.2493.0963151
X-RAY DIFFRACTIONr_mcangle_it2.2114.6293913
X-RAY DIFFRACTIONr_mcangle_other2.2114.633914
X-RAY DIFFRACTIONr_scbond_it1.3443.3093206
X-RAY DIFFRACTIONr_scbond_other1.3443.313207
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.2574.924742
X-RAY DIFFRACTIONr_long_range_B_refined6.50329.74225707
X-RAY DIFFRACTIONr_long_range_B_other6.50229.74325708
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.98→3.058 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 56 -
Rwork0.348 1157 -
obs--75.53 %
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)
12.1344-0.1353-0.0691.38640.7821.7893-0.0213-0.03080.29780.17910.00530.1919-0.1419-0.13380.01590.3465-0.02070.03830.04430.00230.115511.53411.657458.9339
20.9545-0.2836-1.01160.59440.75051.4691-0.16470.0908-0.14740.09860.03530.00950.2081-0.04350.12930.44560.0012-0.01750.016-0.01920.02923.0802-12.294812.2629
30.2812-0.1649-0.350.73650.48951.1480.05070.09390.0238-0.1546-0.0061-0.1214-0.1760.0044-0.04460.3939-0.0269-0.03620.05390.0120.069131.82721.43964.5244
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1G44 - 492
2X-RAY DIFFRACTION2H1 - 214
3X-RAY DIFFRACTION3L1 - 208

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