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- PDB-7sx6: Crystal structure of broadly neutralizing antibody N49P9.3 Fab in... -

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Basic information

Entry
Database: PDB / ID: 7sx6
TitleCrystal structure of broadly neutralizing antibody N49P9.3 Fab in complex with HIV-1 Clade A/E strain 93TH057 gp120 core
Components
  • (N49P9.3 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 / IMMUNE SYSTEM / IMMUNE SYSTEM-VIRAL PROTEIN complex
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: 3.4 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 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

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


Theoretical massNumber of molelcules
Total (without water)175,45131
Polymers170,8836
Non-polymers4,56825
Water0
1
G: clade A/E 93TH057 HIV-1 gp120 core
H: N49P9.3 ANTIBODY FAB HEAVY CHAIN
L: N49P9.3 ANTIBODY FAB LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,71315
Polymers85,4413
Non-polymers2,27212
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8150 Å2
ΔGint-9 kcal/mol
Surface area35070 Å2
MethodPISA
2
A: clade A/E 93TH057 HIV-1 gp120 core
B: N49P9.3 ANTIBODY FAB HEAVY CHAIN
C: N49P9.3 ANTIBODY FAB LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,73816
Polymers85,4413
Non-polymers2,29613
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8330 Å2
ΔGint-11 kcal/mol
Surface area35250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.209, 68.211, 115.055
Angle α, β, γ (deg.)90.26, 102.35, 90.38
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 ANTIBODY FAB HEAVY CHAIN


Mass: 24321.479 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)
#3: Antibody N49P9.3 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, 22 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 20
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, 5 molecules

#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg

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Details

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: 2.79 Å3/Da / Density % sol: 55.93 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 10% PEG 4000 0.1 M HEPES pH 7.5 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: BL9-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 20, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 3.4→50 Å / Num. obs: 25011 / % possible obs: 97.6 % / Redundancy: 3.4 % / CC1/2: 0.988 / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.074 / Net I/σ(I): 15.4
Reflection shellResolution: 3.4→3.46 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1163 / CC1/2: 0.513 / Rpim(I) all: 0.725 / % possible all: 92.6

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6OZ3

6oz3


Resolution: 3.4→35.46 Å / SU ML: 0.64 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 35.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2868 1273 5.1 %
Rwork0.2342 --
obs0.2367 24978 94.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.4→35.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11710 0 285 0 11995
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00412280
X-RAY DIFFRACTIONf_angle_d0.92316715
X-RAY DIFFRACTIONf_dihedral_angle_d6.6511726
X-RAY DIFFRACTIONf_chiral_restr0.0551921
X-RAY DIFFRACTIONf_plane_restr0.0072133
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4-3.490.3138980.34692029X-RAY DIFFRACTION72
3.5-3.650.45571550.31882733X-RAY DIFFRACTION99
3.65-3.850.37331690.29432754X-RAY DIFFRACTION99
3.85-4.090.33181440.2792672X-RAY DIFFRACTION98
4.09-4.40.31661540.25022700X-RAY DIFFRACTION97
4.4-4.840.27351210.22162628X-RAY DIFFRACTION94
4.84-5.540.25971720.21232710X-RAY DIFFRACTION100
5.54-6.970.27721420.25452774X-RAY DIFFRACTION99
6.98-35.460.23761180.19532705X-RAY DIFFRACTION96
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)
12.24641.58510.295.598-0.12.77-0.16990.1451-0.1467-0.06390.2266-0.85190.04670.3653-0.10160.78420.10560.26260.7873-0.03970.854417.8675-35.0605-40.4651
22.52190.7247-0.10583.8749-0.42650.06970.2221-0.3767-0.54671.5989-0.1020.16350.0157-0.047-0.0641.7881-0.06460.10141.1694-0.03110.7217-0.8075-64.2252-10.3828
33.0931.1297-0.75833.3382-1.52024.76560.1858-1.2536-0.6721.0306-0.7037-0.67360.5034-0.03240.49931.8833-0.0962-0.18871.88570.15261.078811.2328-60.62122.6019
42.3779-1.182-0.1265.56110.36623.5845-0.09340.101-0.05610.24560.24630.9808-0.1939-0.5585-0.22670.7762-0.07550.2780.84910.07270.9186-11.5265-0.9909-54.0623
52.4014-0.645-0.00383.69241.15441.71450.07590.3312-0.4816-1.38750.2118-0.20020.20330.4008-0.31461.6291-0.00940.08661.0816-0.0350.6757.1666-30.2162-84.1946
61.5219-1.770.36814.01320.40643.10590.30190.4292-0.608-0.9286-0.44740.9690.11210.44480.10561.6751-0.0336-0.47651.82-0.12621.293-4.8753-26.6116-97.052
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'G' and resid 44 through 492)
2X-RAY DIFFRACTION2(chain 'H' and resid 1 through 213)
3X-RAY DIFFRACTION3(chain 'L' and resid 3 through 208)
4X-RAY DIFFRACTION4(chain 'A' and resid 44 through 492)
5X-RAY DIFFRACTION5(chain 'B' and resid 1 through 213)
6X-RAY DIFFRACTION6(chain 'C' and resid 3 through 208)

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