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- PDB-6p7h: Vaccine-elicited NHP FP-targeting neutralizing antibody DF2F-b.04... -

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Basic information

Entry
Database: PDB / ID: 6p7h
TitleVaccine-elicited NHP FP-targeting neutralizing antibody DF2F-b.04 in complex with HIV fusion peptide (residue 512-519)
Components
  • Antibody DF2F-b.04 heavy chain
  • Antibody DF2F-b.04 light chain
  • HIV fusion peptide residues (512-519)
KeywordsIMMUNE SYSTEM / HIV / neutralizing / antibody / NHP / FP / Fusion Peptide / vaccine
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 / host cell endosome membrane / actin filament organization ...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 / 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 / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / apoptotic process / host cell plasma membrane / structural molecule activity / virion membrane / 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 speciesPlatyrrhini (New World monkeys)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.782 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 5, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 13, 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
B: Antibody DF2F-b.04 light chain
A: Antibody DF2F-b.04 heavy chain
C: HIV fusion peptide residues (512-519)


Theoretical massNumber of molelcules
Total (without water)48,8023
Polymers48,8023
Non-polymers00
Water6,377354
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4340 Å2
ΔGint-31 kcal/mol
Surface area19040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.164, 62.219, 136.130
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 DF2F-b.04 light chain


Mass: 23900.486 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Platyrrhini (New World monkeys) / Production host: Homo sapiens (human)
#2: Antibody Antibody DF2F-b.04 heavy chain


Mass: 24169.062 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Platyrrhini (New World monkeys) / Production host: Homo sapiens (human)
#3: Protein/peptide HIV fusion peptide residues (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.: 354 / 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: 2.59 Å3/Da / Density % sol: 52.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.2M MgCl2, 0.1M HEPES pH 7.5, 17.5% PEG 400

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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, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.78→50 Å / Num. obs: 48760 / % possible obs: 99.8 % / Redundancy: 6.5 % / Biso Wilson estimate: 28.69 Å2 / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.044 / Rrim(I) all: 0.114 / Χ2: 1.89 / Net I/σ(I): 8.9 / Num. measured all: 315917
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.78-1.813.50.79223420.6120.450.9170.60798.2
1.81-1.844.40.73123830.7240.370.8230.63898.8
1.84-1.884.80.7324130.7550.3540.8130.667100
1.88-1.925.30.67924080.8240.3150.750.792100
1.92-1.965.80.59523990.8480.2640.6520.877100
1.96-26.40.56224250.90.2390.6110.909100
2-2.056.80.50323980.9110.2070.5441.001100
2.05-2.117.10.4424090.9340.1770.4751.118100
2.11-2.177.30.36424060.9540.1440.3921.194100
2.17-2.247.30.31124350.9640.1230.3351.364100
2.24-2.327.30.25724340.970.1010.2761.548100
2.32-2.427.30.22324090.9770.0880.241.716100
2.42-2.537.30.18724380.980.0740.2021.865100
2.53-2.667.30.15824450.9850.0630.1712.004100
2.66-2.837.30.12824630.9890.0510.1382.374100
2.83-3.047.20.1124370.9910.0440.1182.757100
3.04-3.357.10.09424610.9930.0380.1013.399.9
3.35-3.836.90.07724900.9950.0320.0833.686100
3.83-4.836.80.06425200.9950.0270.0693.691100
4.83-506.30.05826450.9960.0250.0633.25599.2

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Processing

Software
NameVersionClassification
PHENIX(1.15.2_3472: ???)refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.782→36.662 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.52
RfactorNum. reflection% reflection
Rfree0.2299 2333 4.79 %
Rwork0.2005 --
obs0.2019 48691 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.782→36.662 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3310 0 0 354 3664
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043384
X-RAY DIFFRACTIONf_angle_d0.7564612
X-RAY DIFFRACTIONf_dihedral_angle_d12.4692003
X-RAY DIFFRACTIONf_chiral_restr0.052535
X-RAY DIFFRACTIONf_plane_restr0.005586
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7815-1.81790.31231360.28152554X-RAY DIFFRACTION95
1.8179-1.85740.37251320.27022680X-RAY DIFFRACTION99
1.8574-1.90060.29511510.26032683X-RAY DIFFRACTION100
1.9006-1.94810.2461380.23462698X-RAY DIFFRACTION100
1.9481-2.00080.26311570.22782685X-RAY DIFFRACTION100
2.0008-2.05970.26391510.22862678X-RAY DIFFRACTION100
2.0597-2.12610.26871160.22162742X-RAY DIFFRACTION100
2.1261-2.20210.26531230.2252725X-RAY DIFFRACTION100
2.2021-2.29030.24071370.21522701X-RAY DIFFRACTION100
2.2903-2.39450.25971410.21392736X-RAY DIFFRACTION100
2.3945-2.52070.23561370.21982716X-RAY DIFFRACTION100
2.5207-2.67860.24011180.22342761X-RAY DIFFRACTION100
2.6786-2.88530.23361540.20642713X-RAY DIFFRACTION100
2.8853-3.17560.2191480.20582755X-RAY DIFFRACTION100
3.1756-3.63470.2061280.18352771X-RAY DIFFRACTION100
3.6347-4.5780.21061290.16252821X-RAY DIFFRACTION100
4.578-36.670.19761370.18942939X-RAY DIFFRACTION100

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