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

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Basic information

Entry
Database: PDB / ID: 6pef
TitleVaccine-elicited NHP FP-targeting antibody DF2F-a.01 in complex with HIV fusion peptide (residue 512-519)
Components
  • HIV fusion peptide residue 512-519
  • antibody DF2F-a.01 heavy chain
  • antibody DF2F-a.01 light chain
KeywordsIMMUNE SYSTEM / HIV / neutralizing / antibody / NHP / FP / Fusion Peptide / vaccine
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 / actin filament organization / host cell endosome membrane ...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 / actin filament organization / host cell endosome membrane / Assembly Of The HIV Virion / Budding and maturation of HIV virion / clathrin-dependent endocytosis of virus by host cell / viral protein processing / receptor ligand activity / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / symbiont entry into host cell / 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: 2.004 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 1.1Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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: antibody DF2F-a.01 heavy chain
B: antibody DF2F-a.01 light chain
C: HIV fusion peptide residue 512-519
D: antibody DF2F-a.01 heavy chain
E: antibody DF2F-a.01 light chain
F: HIV fusion peptide residue 512-519


Theoretical massNumber of molelcules
Total (without water)94,3396
Polymers94,3396
Non-polymers00
Water12,538696
1
A: antibody DF2F-a.01 heavy chain
B: antibody DF2F-a.01 light chain
C: HIV fusion peptide residue 512-519


Theoretical massNumber of molelcules
Total (without water)47,1703
Polymers47,1703
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4670 Å2
ΔGint-36 kcal/mol
Surface area19310 Å2
MethodPISA
2
D: antibody DF2F-a.01 heavy chain
E: antibody DF2F-a.01 light chain
F: HIV fusion peptide residue 512-519


Theoretical massNumber of molelcules
Total (without water)47,1703
Polymers47,1703
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4660 Å2
ΔGint-36 kcal/mol
Surface area19330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.574, 52.504, 151.716
Angle α, β, γ (deg.)90.000, 90.680, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain D
12(chain B and resid 3 through 212)
22chain E
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
11VALVALILEILEchain AAA2 - 2202 - 220
21VALVALILEILEchain DDD2 - 2202 - 220
12VALVALPROPRO(chain B and resid 3 through 212)BB3 - 2123 - 212
22VALVALPROPROchain EEE3 - 2123 - 212
13ALAALAPHEPHEchain CCC512 - 5191 - 8
23ALAALAPHEPHEchain FFF512 - 5191 - 8

NCS ensembles :
ID
1
2
3

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Components

#1: Antibody antibody DF2F-a.01 heavy chain


Mass: 23785.594 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Production host: Homo sapiens (human)
#2: Antibody antibody DF2F-a.01 light chain


Mass: 22651.102 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Production host: Homo sapiens (human)
#3: Protein/peptide HIV fusion peptide residue 512-519


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


Mass: 18.015 Da / Num. of mol.: 696 / 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: 3.06 Å3/Da / Density % sol: 59.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2M NaCl, 0.1 M BIS-TRIS pH 6.5, 25% PEG 3350

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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 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 75515 / % possible obs: 97.9 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.068 / Rrim(I) all: 0.131 / Χ2: 1.274 / Net I/σ(I): 8.6 / Num. measured all: 263243
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2-2.032.60.66536620.5750.4730.820.75696.1
2.03-2.072.80.64836720.5980.4450.7890.91696.5
2.07-2.1130.60937300.6820.4050.7340.89197.1
2.11-2.153.20.51436790.7410.3320.6140.87996.8
2.15-2.23.30.46637370.8010.2950.5530.92897.3
2.2-2.253.40.46237410.8050.2880.5461.11197.4
2.25-2.313.60.42137140.8640.2590.4951.02697.4
2.31-2.373.60.34937580.8860.2130.411.08297.6
2.37-2.443.60.30537270.9160.1850.3581.15397.7
2.44-2.523.60.25337560.9530.1540.2971.18697.9
2.52-2.613.70.21838060.9540.1320.2551.37798.1
2.61-2.713.60.18937580.9650.1150.2221.49598.2
2.71-2.843.70.16237600.9690.0980.1891.698.3
2.84-2.993.70.13838070.9730.0840.1621.798.4
2.99-3.173.70.12238100.9750.0740.1421.64198.8
3.17-3.423.70.10638270.9820.0640.1241.69598.8
3.42-3.763.70.08938420.9880.0530.1041.62398.9
3.76-4.313.70.07438560.990.0450.0871.37199.1
4.31-5.433.70.05738800.9920.0340.0671.25599.4
5.43-503.60.05539930.9940.0340.0651.14898.5

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.004→43.171 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.7
RfactorNum. reflection% reflection
Rfree0.2136 3552 4.71 %
Rwork0.183 --
obs0.1845 75461 97.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 165.97 Å2 / Biso mean: 37.1861 Å2 / Biso min: 11.12 Å2
Refinement stepCycle: final / Resolution: 2.004→43.171 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6466 0 0 696 7162
Biso mean---43.54 -
Num. residues----875
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1320X-RAY DIFFRACTION2.269TORSIONAL
12D1320X-RAY DIFFRACTION2.269TORSIONAL
21B1260X-RAY DIFFRACTION2.269TORSIONAL
22E1260X-RAY DIFFRACTION2.269TORSIONAL
31C42X-RAY DIFFRACTION2.269TORSIONAL
32F42X-RAY DIFFRACTION2.269TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0036-2.0310.31781150.25132573268887
2.031-2.060.25921320.24172787291996
2.06-2.09080.27641410.23772873301497
2.0908-2.12350.29691270.23812800292797
2.1235-2.15830.33021400.22432824296497
2.1583-2.19550.26991330.21542912304597
2.1955-2.23540.27721580.21512799295797
2.2354-2.27840.24531240.21832892301697
2.2784-2.32490.23291490.21032804295397
2.3249-2.37550.27681290.21442897302698
2.3755-2.43070.22261460.21592862300898
2.4307-2.49150.24961430.20452890303398
2.4915-2.55880.30471620.20722819298198
2.5588-2.63410.26531350.20282912304798
2.6341-2.71910.25331530.20442881303498
2.7191-2.81630.24121520.18982856300898
2.8163-2.9290.20841470.19132907305498
2.929-3.06230.24941310.18892926305799
3.0623-3.22370.24911500.18612884303499
3.2237-3.42560.2121400.18312935307599
3.4256-3.690.20351220.17192963308599
3.69-4.06110.14951430.15952969311299
4.0611-4.64810.16621650.13662914307999
4.6481-5.85380.16021570.14652996315399
5.8538-43.18090.18281580.17613034319298

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