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- PDB-6oz2: Crystal structure of the broadly neutralizing antibody N49P6 Fab ... -

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Basic information

Entry
Database: PDB / ID: 6oz2
TitleCrystal structure of the broadly neutralizing antibody N49P6 Fab in complex with HIV-1 Clade A/E strain 93TH057 gp120 core.
Components
  • N49P6 antibody Fab heavy chain
  • N49P6 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 / N49P6
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 sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 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: Mbio / Year: 2021
Title: Near-Pan-neutralizing, Plasma Deconvoluted Antibody N49P6 Mimics Host Receptor CD4 in Its Quaternary Interactions with the HIV-1 Envelope Trimer.
Authors: Tolbert, W.D. / Nguyen, D.N. / Tehrani, Z.R. / Sajadi, M.M. / Pazgier, M.
History
DepositionMay 15, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 4, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 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
Revision 1.3Jan 10, 2024Group: Advisory / Derived calculations / Category: pdbx_validate_close_contact / struct_conn
Revision 1.4Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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: N49P6 antibody Fab heavy chain
L: N49P6 antibody Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,48614
Polymers86,0533
Non-polymers2,43311
Water70339
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8260 Å2
ΔGint18 kcal/mol
Surface area34670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.436, 80.815, 195.214
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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 N49P6 antibody Fab heavy chain


Mass: 24885.863 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 N49P6 antibody Fab light chain


Mass: 21810.117 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


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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / Source method: isolated from a natural source / Formula: H2O
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: 3 Å3/Da / Density % sol: 58.99 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 15% PEG 3350 0.1 M Tris-HCl pH 8.0

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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 16, 2017
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. obs: 31853 / % possible obs: 92 % / Redundancy: 3.1 % / Biso Wilson estimate: 40.8 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.276 / Rpim(I) all: 0.166 / Net I/σ(I): 6.4
Reflection shellResolution: 2.55→2.59 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.727 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 1524 / CC1/2: 0.56 / Rpim(I) all: 0.556 / % possible all: 89.3

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Processing

Software
NameVersionClassification
PHENIX(1.15.2_3472: ???)refinement
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6BCK

6bck


Resolution: 2.55→34.327 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 32.91
RfactorNum. reflection% reflection
Rfree0.2733 1599 5.03 %
Rwork0.2185 --
obs0.2212 31820 91.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.55→34.327 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5864 0 154 39 6057
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0116164
X-RAY DIFFRACTIONf_angle_d1.2918387
X-RAY DIFFRACTIONf_dihedral_angle_d9.354018
X-RAY DIFFRACTIONf_chiral_restr0.07971
X-RAY DIFFRACTIONf_plane_restr0.0071078
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5475-2.62970.3821390.31472477X-RAY DIFFRACTION84
2.6297-2.72360.40721420.31472704X-RAY DIFFRACTION91
2.7236-2.83260.39191520.29742668X-RAY DIFFRACTION91
2.8326-2.96150.35031360.3012730X-RAY DIFFRACTION92
2.9615-3.11750.39351550.27852851X-RAY DIFFRACTION96
3.1175-3.31270.28421330.23932828X-RAY DIFFRACTION95
3.3127-3.56820.31741400.22972759X-RAY DIFFRACTION92
3.5682-3.92680.26751460.21392803X-RAY DIFFRACTION94
3.9268-4.4940.20971430.18112830X-RAY DIFFRACTION93
4.494-5.65780.24151520.17292747X-RAY DIFFRACTION91
5.6578-34.33060.22331610.19472824X-RAY DIFFRACTION89
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)
11.75280.23290.28351.26640.47951.1684-0.0719-0.13650.03310.0609-0.04960.0148-0.1642-0.04840.10370.4626-0.0084-0.01330.5639-0.0170.343910.7881-9.3021-12.0161
22.11711.67381.13772.47011.28180.93360.0338-0.0639-0.03110.0779-0.00320.0610.1672-0.08860.00280.462-0.02660.03850.4460.04390.3104-13.0096-42.9653-30.7775
31.28010.75330.29090.76110.41610.9723-0.0650.16840.0346-0.09840.0773-0.0008-0.03-0.0088-0.00050.41430.005-0.00740.41820.0430.3679-10.1015-38.9102-46.7878
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'G' and resid 43 through 511)
2X-RAY DIFFRACTION2(chain 'H' and resid 2 through 214)
3X-RAY DIFFRACTION3(chain 'L' and resid 3 through 209)

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