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- PDB-6pec: Vaccine-elicited NHP FP-targeting antibody DF2F-e.01 in complex w... -

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Basic information

Entry
Database: PDB / ID: 6pec
TitleVaccine-elicited NHP FP-targeting antibody DF2F-e.01 in complex with HIV fusion peptide (residue 512-519)
Components
  • HIV-1 fusion peptide residue 512-519
  • antibody heavy chain
  • antibody light chain
KeywordsIMMUNE SYSTEM / HIV / neutralizing / antibody / NHP / FP / Fusion Peptide / vaccine / mouse
Function / homology
Function and homology information


Synthesis and processing of ENV and VPU / symbiont-mediated evasion of host immune response / positive regulation of establishment of T cell polarity / Alpha-defensins / Dectin-2 family / Binding and entry of HIV virion / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / host cell endosome membrane / actin filament organization ...Synthesis and processing of ENV and VPU / symbiont-mediated evasion of host immune response / positive regulation of establishment of T cell polarity / Alpha-defensins / Dectin-2 family / Binding and entry of HIV virion / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Envelope glycoprotein gp160
Similarity search - Component
Biological speciesMacaca mulatta (Rhesus monkey)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.746 Å
AuthorsXu, K. / Liu, K. / Wang, Y. / Kwong, P.D.
CitationJournal: To Be Published
Title: Modular recognition of antigens provides a mechanism that improves vaccine-elicited antibody-class frequencies
Authors: Xu, K. / Liu, K. / Wang, Y. / Kwong, P.D.
History
DepositionJun 20, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: antibody light chain
H: antibody heavy chain
A: HIV-1 fusion peptide residue 512-519


Theoretical massNumber of molelcules
Total (without water)46,2113
Polymers46,2113
Non-polymers00
Water7,981443
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4460 Å2
ΔGint-33 kcal/mol
Surface area19470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.763, 88.378, 121.276
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody antibody light chain


Mass: 22658.131 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Production host: Homo sapiens (human)
#2: Antibody antibody heavy chain


Mass: 22820.488 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Production host: Homo sapiens (human)
#3: Protein/peptide HIV-1 fusion peptide residue 512-519


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


Mass: 18.015 Da / Num. of mol.: 443 / 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: 3.18 Å3/Da / Density % sol: 61.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2M calcium acetate, 0.1M Cacodylate pH 6.5, 18% PEG 8000

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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: Jun 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.74→50 Å / Num. obs: 59700 / % possible obs: 98.8 % / Redundancy: 7.1 % / Biso Wilson estimate: 26.65 Å2 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.034 / Rrim(I) all: 0.091 / Χ2: 1.289 / Net I/σ(I): 9.6 / Num. measured all: 424862
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.74-1.775.70.81629240.850.3630.8960.67597.3
1.77-1.86.20.78929280.890.3370.860.71198.5
1.8-1.846.60.71729120.9040.2970.7770.75597.9
1.84-1.876.80.59929310.9330.2430.6470.82798
1.87-1.9270.49229550.9610.1980.5310.89398.9
1.92-1.967.20.41329020.9630.1650.4460.96197.6
1.96-2.017.30.35129630.9710.1390.3781.04899.1
2.01-2.067.40.29929450.9760.1180.3221.15798.8
2.06-2.127.40.2529280.9810.0990.271.28698.4
2.12-2.197.40.21529810.9820.0850.2311.43398.6
2.19-2.277.40.18629520.9850.0740.21.51199.2
2.27-2.367.40.16829920.9860.0660.1811.55899.4
2.36-2.477.50.14429840.9870.0570.1551.67399.2
2.47-2.67.50.12529950.9910.0490.1351.67699
2.6-2.767.50.10630020.9930.0420.1141.59399.5
2.76-2.987.40.09330150.9940.0370.1011.5199.7
2.98-3.277.40.07930450.9950.0310.0851.53599.6
3.27-3.757.30.06930580.9950.0280.0751.55299.8
3.75-4.727.20.05331030.9970.0210.0571.45199.7
4.72-506.70.04731850.9970.0190.0511.47697.2

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.746→35.712 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.76
RfactorNum. reflection% reflection
Rfree0.2147 2985 5.01 %
Rwork0.1938 --
obs0.1948 59599 98.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 86.5 Å2 / Biso mean: 37.49 Å2 / Biso min: 16.73 Å2
Refinement stepCycle: final / Resolution: 1.746→35.712 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3250 0 0 443 3693
Biso mean---43.11 -
Num. residues----432
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083329
X-RAY DIFFRACTIONf_angle_d1.2534527
X-RAY DIFFRACTIONf_chiral_restr0.061518
X-RAY DIFFRACTIONf_plane_restr0.006573
X-RAY DIFFRACTIONf_dihedral_angle_d13.771179
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7455-1.77420.26951310.27342400253189
1.7742-1.80470.3031300.25822662279299
1.8047-1.83760.2761410.24782648278997
1.8376-1.87290.32171450.23072646279198
1.8729-1.91110.23441350.21232648278398
1.9111-1.95270.19751730.21222642281598
1.9527-1.99810.22351270.20152688281599
1.9981-2.04810.22421400.2062656279698
2.0481-2.10340.22791480.20612683283198
2.1034-2.16530.23361550.198126882843100
2.1653-2.23520.2341470.20552657280499
2.2352-2.31510.23651400.21022705284599
2.3151-2.40770.24621350.21492706284199
2.4077-2.51730.22911380.20892721285999
2.5173-2.650.22531470.20412727287499
2.65-2.81590.23071510.20927282879100
2.8159-3.03330.18791470.198227492896100
3.0333-3.33830.18151290.187527692898100
3.3383-3.82090.20641440.179327852929100
3.8209-4.81210.1771350.161928212956100
4.8121-35.71990.23081470.18872885303297

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