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- PDB-6oz3: Crystal structure of broadly neutralizing antibody N49P9.1 Fab in... -

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Basic information

Entry
Database: PDB / ID: 6oz3
TitleCrystal structure of broadly neutralizing antibody N49P9.1 Fab in complex with HIV-1 Clade A/E strain 93TH057 gp120 core
Components
  • N49P9.1 antibody Fab heavy chain
  • N49P9.1 antibody Fab light chain
  • clade A/E 93TH057 HIV-1 gp120 core
KeywordsIMMUNE SYSTEM / HIV-1 / VRC01-CLASS ANTIBODY / CD4 BINDING SITE / CLADE A/E 93TH057 GP120 / VIRAL PROTEIN-IMMUNE SYSTEM COMPLEX / N49P9.1
Function / homologyGp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / viral envelope / clade A/E 93TH057 HIV-1 gp120 core
Function and homology information
Biological speciesHuman immunodeficiency virus 1
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 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 N49P9.1 Fab in complex with HIV-1 Clade A/E strain 93TH)57 gp120 core
Authors: Tolbert, W.D. / Pazgier, M.
History
DepositionMay 15, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
G: clade A/E 93TH057 HIV-1 gp120 core
H: N49P9.1 antibody Fab heavy chain
L: N49P9.1 antibody Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,67415
Polymers85,2183
Non-polymers2,45612
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8150 Å2
ΔGint10 kcal/mol
Surface area34240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.754, 110.454, 152.165
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121
Components on special symmetry positions
IDModelComponents
11H-301-

NA

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Components

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


Mass: 39356.613 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 (production host): HEK 293 GnT1- / Production host: Homo sapiens (human) / References: UniProt: A0A0M3KKW9
#2: Antibody N49P9.1 antibody Fab heavy chain


Mass: 24081.217 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell (production host): HEK 293 / Production host: Homo sapiens (human)
#3: Antibody N49P9.1 antibody Fab light chain


Mass: 21780.215 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell (production host): HEK 293 / Production host: Homo sapiens (human)
#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 / N-Acetylglucosamine


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
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
Has ligand of interestN

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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: 2.59 Å3/Da / Density % sol: 52.49 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 12% PEG 6000 0.1 M Bis-Tris pH 6.5

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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: Nov 9, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 3.15→50 Å / Num. obs: 14779 / % possible obs: 94.4 % / Redundancy: 4 % / Rmerge(I) obs: 0.138 / Rpim(I) all: 0.072 / Net I/σ(I): 12.8
Reflection shellResolution: 3.15→3.2 Å / Redundancy: 4 % / Rmerge(I) obs: 0.794 / Mean I/σ(I) obs: 1 / Num. unique obs: 746 / CC1/2: 0.65 / Rpim(I) all: 0.414 / % possible all: 96.4

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Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TGT, 3TNN

3tgt

3tnn


Resolution: 3.15→34.03 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 30.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2954 733 4.97 %
Rwork0.2428 --
obs0.2453 14754 93.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.15→34.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5662 0 155 0 5817
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065953
X-RAY DIFFRACTIONf_angle_d0.9998104
X-RAY DIFFRACTIONf_dihedral_angle_d21.111839
X-RAY DIFFRACTIONf_chiral_restr0.064940
X-RAY DIFFRACTIONf_plane_restr0.0071031
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.15-3.390.32441360.30072790X-RAY DIFFRACTION94
3.39-3.730.3711580.32794X-RAY DIFFRACTION96
3.73-4.270.29971570.26152818X-RAY DIFFRACTION96
4.27-5.370.25791270.222813X-RAY DIFFRACTION94
5.37-34.030.29021550.22772806X-RAY DIFFRACTION91
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)
13.0274-1.0862-0.98114.8436-1.44915.907-0.2784-0.4819-0.65730.7008-0.04060.72790.2197-0.43860.28430.7939-0.16830.13450.761-0.09341.1381-25.6499-30.072138.2683
22.70760.1714-0.65892.8693-2.14347.3455-0.10560.18490.1532-0.1411-0.4549-0.5982-0.37621.29880.58780.6132-0.0998-0.08271.0445-0.07850.65922.0164-7.97658.4433
33.5318-0.2486-1.66241.2194-2.03946.78870.02810.69940.1136-0.0483-0.05360.0224-0.4768-0.09250.01690.5541-0.0313-0.15680.8217-0.02970.5775-11.74811.04060.9552
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'G' and resid 47 through 491)
2X-RAY DIFFRACTION2(chain 'H' and resid 1 through 213)
3X-RAY DIFFRACTION3(chain 'L' and resid 3 through 209)

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