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- PDB-6wwc: Vaccine-elicited mouse FP-targeting neutralizing antibody vFP16.0... -

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Basic information

Entry
Database: PDB / ID: 6wwc
TitleVaccine-elicited mouse FP-targeting neutralizing antibody vFP16.02 with S48K mutation in light chain in complex with HIV fusion peptide (residue 512-519)
Components
  • fusion peptideMembrane fusion protein
  • vFP16.02 antibody heavy chain
  • vFP16.02 antibody light chain
KeywordsIMMUNE SYSTEM/VIRAL PROTEIN / HIV / fusion peptide / antibody / IMMUNE SYSTEM-VIRAL PROTEIN complex
Function / homology
Function and homology information


Synthesis and processing of ENV and VPU / evasion of host immune response / Alpha-defensins / Dectin-2 family / Binding and entry of HIV virion / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / virus-mediated perturbation of host defense response / host cell endosome membrane ...Synthesis and processing of ENV and VPU / evasion of host immune response / Alpha-defensins / Dectin-2 family / Binding and entry of HIV virion / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / virus-mediated perturbation of host defense response / host cell endosome membrane / actin filament organization / Assembly Of The HIV Virion / Budding and maturation of HIV virion / clathrin-dependent endocytosis of virus by host cell / viral protein processing / symbiont entry into host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / membrane
Similarity search - Function
Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120
Similarity search - Domain/homology
Envelope glycoprotein gp160
Similarity search - Component
Biological speciesMus musculus (house mouse)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.563 Å
AuthorsXu, K. / Wang, Y. / Kwong, P.D.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2021
Title: Mutational fitness landscapes reveal genetic and structural improvement pathways for a vaccine-elicited HIV-1 broadly neutralizing antibody.
Authors: Madan, B. / Zhang, B. / Xu, K. / Chao, C.W. / O'Dell, S. / Wolfe, J.R. / Chuang, G.Y. / Fahad, A.S. / Geng, H. / Kong, R. / Louder, M.K. / Nguyen, T.D. / Rawi, R. / Schon, A. / Sheng, Z. / ...Authors: Madan, B. / Zhang, B. / Xu, K. / Chao, C.W. / O'Dell, S. / Wolfe, J.R. / Chuang, G.Y. / Fahad, A.S. / Geng, H. / Kong, R. / Louder, M.K. / Nguyen, T.D. / Rawi, R. / Schon, A. / Sheng, Z. / Nimrania, R. / Wang, Y. / Zhou, T. / Lin, B.C. / Doria-Rose, N.A. / Shapiro, L. / Kwong, P.D. / DeKosky, B.J.
History
DepositionMay 9, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 24, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 17, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: vFP16.02 antibody heavy chain
B: vFP16.02 antibody light chain
C: fusion peptide
D: vFP16.02 antibody heavy chain
F: fusion peptide
H: vFP16.02 antibody light chain


Theoretical massNumber of molelcules
Total (without water)95,9736
Polymers95,9736
Non-polymers00
Water1,946108
1
A: vFP16.02 antibody heavy chain
B: vFP16.02 antibody light chain
C: fusion peptide


Theoretical massNumber of molelcules
Total (without water)47,9873
Polymers47,9873
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4550 Å2
ΔGint-38 kcal/mol
Surface area19480 Å2
MethodPISA
2
D: vFP16.02 antibody heavy chain
F: fusion peptide
H: vFP16.02 antibody light chain


Theoretical massNumber of molelcules
Total (without water)47,9873
Polymers47,9873
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4640 Å2
ΔGint-37 kcal/mol
Surface area19150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.628, 70.526, 93.292
Angle α, β, γ (deg.)90.000, 94.790, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain D
12chain B
22chain H
13chain C
23chain F

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNGLNPROPROchain AAA1 - 2171 - 217
21GLNGLNPROPROchain DDD1 - 2171 - 217
12ASPASPGLUGLUchain BBB1 - 2181 - 218
22ASPASPGLUGLUchain HHF1 - 2181 - 218
13ALAALAPHEPHEchain CCC512 - 5191 - 8
23ALAALAPHEPHEchain FFE512 - 5191 - 8

NCS ensembles :
ID
1
2
3

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Components

#1: Antibody vFP16.02 antibody heavy chain


Mass: 23073.844 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 vFP16.02 antibody light chain


Mass: 24179.842 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 fusion peptide / Membrane fusion protein


Mass: 732.868 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: P04578*PLUS
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 108 / 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: 2.36 Å3/Da / Density % sol: 47.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Tris-HCl, pH 8.5, 30% v/v PEG400

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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: Oct 2, 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: 2.5→50 Å / Num. obs: 23890 / % possible obs: 97.5 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.124 / Rpim(I) all: 0.083 / Rrim(I) all: 0.15 / Χ2: 0.749 / Net I/σ(I): 5.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.6-2.642.90.43811520.8570.2890.5270.47194.2
2.64-2.6930.37611890.8960.2450.450.49898.2
2.69-2.7430.37411910.8870.2450.4480.48598.8
2.74-2.83.10.30712260.910.2010.3680.51699.2
2.8-2.863.10.29711870.9320.1950.3570.55498.8
2.86-2.933.20.26512040.940.1720.3170.5499.1
2.93-33.10.23511980.9510.1540.2820.55999
3-3.083.10.20512070.9660.1360.2470.58198.6
3.08-3.1730.18712020.9520.1250.2260.61998.6
3.17-3.282.90.16412190.9630.1130.2010.6698.6
3.28-3.392.90.15111960.9730.1030.1840.65598.8
3.39-3.5330.13511770.9670.0910.1630.8197
3.53-3.693.10.11711850.9770.0760.140.81897.4
3.69-3.883.20.10111980.9820.0660.1220.89497.2
3.88-4.133.30.09312000.9870.060.1120.97598.5
4.13-4.453.20.08311810.9870.0550.11.01896.6
4.45-4.8930.0811780.9770.0570.0991.07594.5
4.89-5.630.07311830.9870.0510.090.97895.3
5.6-7.052.70.06811900.9910.0490.0840.93895.9
7.05-503.10.04512270.9960.0290.0541.26995.2

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.16_3549refinement
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6CDO

6cdo


Resolution: 2.563→35.263 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2665 1108 4.64 %
Rwork0.2092 22766 -
obs0.2117 23874 83.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 101.71 Å2 / Biso mean: 42.9783 Å2 / Biso min: 22.1 Å2
Refinement stepCycle: final / Resolution: 2.563→35.263 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6706 0 0 108 6814
Biso mean---38.8 -
Num. residues----878
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1278X-RAY DIFFRACTION4.804TORSIONAL
12D1278X-RAY DIFFRACTION4.804TORSIONAL
21B1314X-RAY DIFFRACTION4.804TORSIONAL
22H1314X-RAY DIFFRACTION4.804TORSIONAL
31C42X-RAY DIFFRACTION4.804TORSIONAL
32F42X-RAY DIFFRACTION4.804TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.5634-2.68010.4294440.308887126
2.6801-2.82130.32291030.2814211762
2.8213-2.9980.28851600.2616303089
2.998-3.22930.3181710.2429334199
3.2293-3.5540.29091560.2215335698
3.554-4.06770.25021630.2001335398
4.0677-5.12230.23331550.1706330896
5.1223-35.260.2361560.1919339096

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