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- PDB-6x78: Vaccine-elicited mouse FP-targeting neutralizing antibody vFP48.0... -

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Basic information

Entry
Database: PDB / ID: 6x78
TitleVaccine-elicited mouse FP-targeting neutralizing antibody vFP48.03 in complex with HIV fusion peptide (residue 512-519)
Components
  • HIV fusion peptide 512-519 V2
  • antibody vFP48.03 heavy chain
  • antibody vFP48.03 light chain
KeywordsIMMUNE SYSTEM/VIRAL PROTEIN / HIV / fusion peptide / antibody / IMMUNE SYSTEM-VIRAL PROTEIN complex
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.359 Å
AuthorsXu, K. / Kwong, P.D.
CitationJournal: To Be Published
Title: Distinct Classes of HIV-1 Cross-Clade Neutralizing Antibodies Targeting Fusion Peptide Elicited in Mice by Diverse Immunization Regimens
Authors: Xu, K. / Kwong, P.D.
History
DepositionMay 29, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 2, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: antibody vFP48.03 light chain
B: antibody vFP48.03 heavy chain
H: antibody vFP48.03 heavy chain
L: antibody vFP48.03 light chain
G: HIV fusion peptide 512-519 V2
I: HIV fusion peptide 512-519 V2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,9967
Polymers99,9006
Non-polymers961
Water8,935496
1
A: antibody vFP48.03 light chain
B: antibody vFP48.03 heavy chain
I: HIV fusion peptide 512-519 V2


Theoretical massNumber of molelcules
Total (without water)49,9503
Polymers49,9503
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4120 Å2
ΔGint-24 kcal/mol
Surface area19960 Å2
MethodPISA
2
H: antibody vFP48.03 heavy chain
L: antibody vFP48.03 light chain
G: HIV fusion peptide 512-519 V2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,0464
Polymers49,9503
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4430 Å2
ΔGint-39 kcal/mol
Surface area20370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.993, 92.733, 143.424
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain L
12(chain B and (resid 1 through 158 or resid 160 through 221))
22(chain H and (resid 1 through 127 or resid 133 through 158 or resid 160 through 220))
13chain G
23chain I

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ASPASPGLUGLUchain AAA1 - 2131 - 218
211ASPASPGLUGLUchain LLD1 - 2131 - 218
112GLNGLNGLYGLY(chain B and (resid 1 through 158 or resid 160 through 221))BB1 - 1581 - 166
122LEULEUASPASP(chain B and (resid 1 through 158 or resid 160 through 221))BB160 - 221168 - 223
212GLNGLNGLYGLY(chain H and (resid 1 through 127 or resid 133 through 158 or resid 160 through 220))HC1 - 1271 - 136
222ASNASNGLYGLY(chain H and (resid 1 through 127 or resid 133 through 158 or resid 160 through 220))HC133 - 158142 - 166
232LEULEUASPASP(chain H and (resid 1 through 127 or resid 133 through 158 or resid 160 through 220))HC160 - 220168 - 223
113ALAALAGLYGLYchain GGE512 - 5161 - 5
213ALAALAGLYGLYchain IIF512 - 5161 - 5

NCS ensembles :
ID
1
2
3

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Components

#1: Antibody antibody vFP48.03 light chain


Mass: 24189.879 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#2: Antibody antibody vFP48.03 heavy chain


Mass: 25027.008 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#3: Protein/peptide HIV fusion peptide 512-519 V2


Mass: 732.868 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 496 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.83 Å3/Da / Density % sol: 56.53 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1 M Tris, pH 8.5, 25% w/v PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 20, 2019
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.359→50 Å / Num. obs: 45627 / % possible obs: 99.7 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.145 / Rpim(I) all: 0.061 / Rrim(I) all: 0.157 / Χ2: 1.016 / Net I/σ(I): 5.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.36-2.46.10.74622430.810.3270.8170.454100
2.4-2.446.20.69322620.8110.3020.7580.46799.9
2.44-2.496.30.62922490.860.2720.6870.474100
2.49-2.545.90.54622450.880.2390.5980.486100
2.54-2.66.20.52222340.8770.2230.570.49999
2.6-2.6670.45422660.9180.1840.4910.53499.8
2.66-2.727.40.42222520.9270.1670.4550.5799.8
2.72-2.87.40.35822510.9490.1420.3860.60699.9
2.8-2.887.30.322590.9530.120.3240.69899.8
2.88-2.977.10.25822510.9630.1060.2790.8299.9
2.97-3.0870.22422810.9720.0920.2430.862100
3.08-3.26.90.18922760.9750.0790.2051.051100
3.2-3.356.60.1622780.9820.0680.1741.2399.9
3.35-3.536.40.12722640.990.0550.1381.43999.8
3.53-3.755.60.10922740.9910.0490.121.57899
3.75-4.036.60.09823010.9910.0420.1081.69499.6
4.03-4.446.80.08122870.9950.0350.0881.87599.6
4.44-5.086.60.06923170.9950.030.0751.89299.8
5.08-6.46.70.06423580.9970.0260.0691.5299.8
6.4-506.10.04924790.9980.0210.0541.5699.5

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6CDO

6cdo


Resolution: 2.359→38.937 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 22.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.226 2295 5.04 %
Rwork0.1778 43247 -
obs0.1802 45542 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 106.78 Å2 / Biso mean: 36.406 Å2 / Biso min: 13.49 Å2
Refinement stepCycle: final / Resolution: 2.359→38.937 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6763 0 5 496 7264
Biso mean--69.18 39.72 -
Num. residues----887
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1314X-RAY DIFFRACTION7.005TORSIONAL
12L1314X-RAY DIFFRACTION7.005TORSIONAL
21B1294X-RAY DIFFRACTION7.005TORSIONAL
22H1294X-RAY DIFFRACTION7.005TORSIONAL
31G24X-RAY DIFFRACTION7.005TORSIONAL
32I24X-RAY DIFFRACTION7.005TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3594-2.41070.29381530.2343258998
2.4107-2.46670.30951470.22562675100
2.4667-2.52840.27191340.22242680100
2.5284-2.59680.25451380.2136264999
2.5968-2.67310.28631520.20872672100
2.6731-2.75940.27931360.20792703100
2.7594-2.8580.25921290.19592686100
2.858-2.97240.24021370.18842670100
2.9724-3.10760.23591320.18982742100
3.1076-3.27140.24691550.1882674100
3.2714-3.47620.22521430.18422701100
3.4762-3.74440.2271480.1675268699
3.7444-4.12090.21891480.1612718100
4.1209-4.71630.15471410.12832737100
4.7163-5.93860.17411440.15112776100
5.9386-38.9370.22421580.18342889100

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