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- PDB-5cck: Crystal structure of Human anti-HIV-1 broadly neutralizing antibo... -

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Basic information

Entry
Database: PDB / ID: 5cck
TitleCrystal structure of Human anti-HIV-1 broadly neutralizing antibody 3BC315 Fab
Components
  • Antibody 3BC315 Fab heavy chain
  • Antibody 3BC315 Fab light chain
KeywordsIMMUNE SYSTEM / HIV-1 / Env / bnAb / antibody
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsLee, J.H. / Ward, A.B. / Wilson, I.A.
Funding support United States, 6items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01 AI082362 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)UM1 AI100663 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI084817 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI114401 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI098602 United States
Bill & Melinda Gates Foundation United States
CitationJournal: Nat Commun / Year: 2015
Title: Antibodies to a conformational epitope on gp41 neutralize HIV-1 by destabilizing the Env spike.
Authors: Jeong Hyun Lee / Daniel P Leaman / Arthur S Kim / Alba Torrents de la Peña / Kwinten Sliepen / Anila Yasmeen / Ronald Derking / Alejandra Ramos / Steven W de Taeye / Gabriel Ozorowski / ...Authors: Jeong Hyun Lee / Daniel P Leaman / Arthur S Kim / Alba Torrents de la Peña / Kwinten Sliepen / Anila Yasmeen / Ronald Derking / Alejandra Ramos / Steven W de Taeye / Gabriel Ozorowski / Florian Klein / Dennis R Burton / Michel C Nussenzweig / Pascal Poignard / John P Moore / Per Johan Klasse / Rogier W Sanders / Michael B Zwick / Ian A Wilson / Andrew B Ward /
Abstract: The recent identification of three broadly neutralizing antibodies (bnAbs) against gp120-gp41 interface epitopes has expanded the targetable surface on the HIV-1 envelope glycoprotein (Env) trimer. ...The recent identification of three broadly neutralizing antibodies (bnAbs) against gp120-gp41 interface epitopes has expanded the targetable surface on the HIV-1 envelope glycoprotein (Env) trimer. By using biochemical, biophysical and computational methods, we map the previously unknown trimer epitopes of two related antibodies, 3BC315 and 3BC176. A cryo-EM reconstruction of a soluble Env trimer bound to 3BC315 Fab at 9.3 Å resolution reveals that the antibody binds between two gp41 protomers, and neutralizes the virus by accelerating trimer decay. In contrast, bnAb 35O22 binding to a partially overlapping quaternary epitope at the gp120-gp41 interface does not induce decay. A conserved gp41-proximal glycan at N88 was also shown to play a role in the binding kinetics of 3BC176 and 3BC315. Finally, our data suggest that the dynamic structure of the Env trimer influences exposure of bnAb epitopes.
History
DepositionJul 2, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 30, 2015Group: Other
Revision 1.2Sep 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 1.3Nov 27, 2019Group: Database references / Category: pdbx_database_related / Item: _pdbx_database_related.content_type
Revision 1.4Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Antibody 3BC315 Fab heavy chain
L: Antibody 3BC315 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2303
Polymers48,0092
Non-polymers2211
Water6,107339
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3550 Å2
ΔGint-25 kcal/mol
Surface area19550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.075, 49.522, 159.025
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: Antibody Antibody 3BC315 Fab heavy chain


Mass: 24999.240 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293F / Production host: Homo sapiens (human)
#2: Antibody Antibody 3BC315 Fab light chain


Mass: 23009.605 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293F / Production host: Homo sapiens (human)
#3: Chemical ChemComp-CXS / 3-CYCLOHEXYL-1-PROPYLSULFONIC ACID


Mass: 221.317 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H19NO3S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 339 / Source method: isolated from a natural source / Formula: H2O

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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: 1.97 Å3/Da / Density % sol: 37.61 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 10.3 / Details: 0.1M CAPS pH 10.3, 0.25 M NaCl, 20% PEG8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 17, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.95→47.28 Å / Num. obs: 27626 / % possible obs: 96.8 % / Redundancy: 6.2 % / Net I/σ(I): 61.2

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→47.28 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2066 2002 7.25 %
Rwork0.1561 --
obs0.1597 27626 96.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.95→47.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3276 0 14 339 3629
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073427
X-RAY DIFFRACTIONf_angle_d1.1824672
X-RAY DIFFRACTIONf_dihedral_angle_d12.9081227
X-RAY DIFFRACTIONf_chiral_restr0.047524
X-RAY DIFFRACTIONf_plane_restr0.005596
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9507-1.99950.23861330.15421679X-RAY DIFFRACTION90
1.9995-2.05350.24231270.14511708X-RAY DIFFRACTION93
2.0535-2.11390.1951450.14411744X-RAY DIFFRACTION93
2.1139-2.18220.20611300.14561732X-RAY DIFFRACTION93
2.1822-2.26020.2091410.14321737X-RAY DIFFRACTION94
2.2602-2.35070.22181320.15681805X-RAY DIFFRACTION96
2.3507-2.45760.22091460.15761841X-RAY DIFFRACTION98
2.4576-2.58720.2321460.17611868X-RAY DIFFRACTION99
2.5872-2.74930.24381470.18041873X-RAY DIFFRACTION100
2.7493-2.96150.21041510.17161869X-RAY DIFFRACTION100
2.9615-3.25950.23111480.17051904X-RAY DIFFRACTION100
3.2595-3.7310.20161460.15251906X-RAY DIFFRACTION100
3.731-4.70.14961530.13191911X-RAY DIFFRACTION99
4.7-47.29630.20571570.16082047X-RAY DIFFRACTION99

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