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- PDB-6wx2: Vaccine-elicited mouse FP-targeting neutralizing antibody vFP16.0... -

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Basic information

Entry
Database: PDB / ID: 6wx2
TitleVaccine-elicited mouse FP-targeting neutralizing antibody vFP16.02 with F60P mutation on light chain in complex with HIV fusion peptide (residue 512-519)
Components
  • fusion peptide
  • vFP16.02 antibody heavy chain
  • vFP16.02 antibody 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: 2.39 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 1.0Mar 17, 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 23, 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
A: vFP16.02 antibody heavy chain
B: vFP16.02 antibody light chain
C: fusion peptide
H: vFP16.02 antibody heavy chain
L: vFP16.02 antibody light chain
F: fusion peptide


Theoretical massNumber of molelcules
Total (without water)95,7896
Polymers95,7896
Non-polymers00
Water2,486138
1
A: vFP16.02 antibody heavy chain
B: vFP16.02 antibody light chain
C: fusion peptide


Theoretical massNumber of molelcules
Total (without water)47,8943
Polymers47,8943
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4590 Å2
ΔGint-34 kcal/mol
Surface area19140 Å2
MethodPISA
2
H: vFP16.02 antibody heavy chain
L: vFP16.02 antibody light chain
F: fusion peptide


Theoretical massNumber of molelcules
Total (without water)47,8943
Polymers47,8943
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4630 Å2
ΔGint-34 kcal/mol
Surface area19440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.246, 111.697, 123.804
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
11(chain A and (resid 2 through 83 or resid 85 through 217))
21(chain H and (resid 2 through 83 or resid 85 through 217))
12(chain B and (resid 1 through 81 or resid 83 through 151 or resid 153 through 217))
22(chain L and (resid 1 or (resid 2 and (name...
13chain C
23chain F

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
111VALVALLEULEU(chain A and (resid 2 through 83 or resid 85 through 217))AA2 - 832 - 83
121SERSERPROPRO(chain A and (resid 2 through 83 or resid 85 through 217))AA85 - 21785 - 217
211VALVALLEULEU(chain H and (resid 2 through 83 or resid 85 through 217))HD2 - 832 - 83
221SERSERPROPRO(chain H and (resid 2 through 83 or resid 85 through 217))HD85 - 21785 - 217
112ASPASPSERSER(chain B and (resid 1 through 81 or resid 83 through 151 or resid 153 through 217))BB1 - 811 - 81
122VALVALVALVAL(chain B and (resid 1 through 81 or resid 83 through 151 or resid 153 through 217))BB83 - 15183 - 151
132TRPTRPASNASN(chain B and (resid 1 through 81 or resid 83 through 151 or resid 153 through 217))BB153 - 217153 - 217
212ASPASPASPASP(chain L and (resid 1 or (resid 2 and (name...LE11
222VALVALVALVAL(chain L and (resid 1 or (resid 2 and (name...LE22
232ASPASPGLUGLU(chain L and (resid 1 or (resid 2 and (name...LE1 - 2181 - 218
242ASPASPGLUGLU(chain L and (resid 1 or (resid 2 and (name...LE1 - 2181 - 218
252ASPASPGLUGLU(chain L and (resid 1 or (resid 2 and (name...LE1 - 2181 - 218
262ASPASPGLUGLU(chain L and (resid 1 or (resid 2 and (name...LE1 - 2181 - 218
272ASPASPGLUGLU(chain L and (resid 1 or (resid 2 and (name...LE1 - 2181 - 218
113ALAALAPHEPHEchain CCC512 - 5191 - 8
213ALAALAPHEPHEchain FFF512 - 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: 24087.680 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


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


Mass: 18.015 Da / Num. of mol.: 138 / 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: 2.68 Å3/Da / Density % sol: 54.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 9.9% v/v isopropanol, 0.1 M Tris-HCl, pH 8.5, 9.9% v/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: 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: 2.39→50 Å / Num. obs: 39911 / % possible obs: 99.6 % / Redundancy: 11 % / Rmerge(I) obs: 0.155 / Rpim(I) all: 0.048 / Rrim(I) all: 0.162 / Χ2: 1.954 / Net I/σ(I): 6.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.4-2.449.50.80619470.9130.2690.8520.68899.5
2.44-2.499.70.78419730.8980.2630.8290.7499.8
2.49-2.539.20.75219650.8860.2590.7980.81299.7
2.53-2.599.50.67419570.9180.2280.7140.91899.7
2.59-2.6410.80.60119700.9570.1890.6310.92199.5
2.64-2.7120.56519790.9580.1690.5911.01399.8
2.7-2.7712.20.47219770.9730.140.4931.15699.7
2.77-2.8512.30.4119470.9780.1220.4281.27799.1
2.85-2.9311.90.34119920.9850.1030.3571.48299.9
2.93-3.0211.80.30619860.9890.0930.3211.60799.4
3.02-3.1311.70.28219780.9870.0860.2951.88299.7
3.13-3.2611.50.25519800.9910.0790.2672.06299.8
3.26-3.4111.10.22519950.9920.0710.2372.38599.5
3.41-3.5810.20.19319940.9930.0640.2042.64999.6
3.58-3.819.30.15220000.9950.0530.1622.86499.3
3.81-4.111.60.13419850.9960.0410.1413.09999.8
4.1-4.5211.60.10720380.9970.0330.1123.40799.7
4.52-5.1711.50.09320320.9970.0290.0973.39999.8
5.17-6.5111.50.10420600.9970.0320.1093.02699.5
6.51-5011.20.07321560.9980.0220.0762.92298.8

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Processing

Software
NameVersionClassification
PHENIX1.18_3861refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6CDO

6cdo


Resolution: 2.39→35.65 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 30.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2502 1992 5.01 %
Rwork0.2002 37745 -
obs0.2027 39737 97.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 118.83 Å2 / Biso mean: 51.4472 Å2 / Biso min: 19.44 Å2
Refinement stepCycle: final / Resolution: 2.39→35.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6645 0 0 138 6783
Biso mean---48.69 -
Num. residues----872
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1234X-RAY DIFFRACTION4.343TORSIONAL
12H1234X-RAY DIFFRACTION4.343TORSIONAL
21B1263X-RAY DIFFRACTION4.343TORSIONAL
22L1263X-RAY DIFFRACTION4.343TORSIONAL
31C42X-RAY DIFFRACTION4.343TORSIONAL
32F42X-RAY DIFFRACTION4.343TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.39-2.450.3041010.2575181267
2.45-2.520.34991380.2805273799
2.52-2.590.33411370.2793270899
2.59-2.670.32891550.2669272399
2.67-2.770.29351700.25022684100
2.77-2.880.3011520.2355273599
2.88-3.010.31921240.2267274599
3.01-3.170.29941420.2365274799
3.17-3.370.31571350.23372754100
3.37-3.630.25421490.2136276199
3.63-3.990.26671400.1957277099
3.99-4.570.18941480.15142790100
4.57-5.750.17831490.15382832100
5.75-35.650.20821520.1759294799

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