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- PDB-6pds: Vaccine-elicited NHP FP-targeting antibody 0PV-a.04 in complex wi... -

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Basic information

Entry
Database: PDB / ID: 6pds
TitleVaccine-elicited NHP FP-targeting antibody 0PV-a.04 in complex with HIV fusion peptide (residue 512-519)
Components
  • HIV-1 fusion peptide residue 512-519
  • antibody 0PV-a.04 heavy chain
  • antibody 0PV-a.04 light chain
KeywordsIMMUNE SYSTEM / HIV / neutralizing / antibody / murine / 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 / 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: 1.893 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 19, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 20, 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 / _pdbx_entry_details.has_protein_modification / _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 0PV-a.04 light chain
B: antibody 0PV-a.04 heavy chain
H: antibody 0PV-a.04 heavy chain
L: antibody 0PV-a.04 light chain
G: HIV-1 fusion peptide residue 512-519
C: HIV-1 fusion peptide residue 512-519
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,60610
Polymers95,2226
Non-polymers3844
Water13,115728
1
A: antibody 0PV-a.04 light chain
B: antibody 0PV-a.04 heavy chain
C: HIV-1 fusion peptide residue 512-519
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8035
Polymers47,6113
Non-polymers1922
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
H: antibody 0PV-a.04 heavy chain
L: antibody 0PV-a.04 light chain
G: HIV-1 fusion peptide residue 512-519
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8035
Polymers47,6113
Non-polymers1922
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.857, 74.381, 187.198
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
11chain A
21chain L
12(chain B and (resid 1 through 125 or resid 132 through 213))
22chain H
13(chain C and resid 11 through 17)
23chain G

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
111ASPASPGLYGLYchain AAA1 - 2121 - 212
211ASPASPGLYGLYchain LLD1 - 2121 - 212
112GLNGLNALAALA(chain B and (resid 1 through 125 or resid 132 through 213))BB1 - 1251 - 136
122SERSERILEILE(chain B and (resid 1 through 125 or resid 132 through 213))BB132 - 213139 - 220
212GLNGLNILEILEchain HHC1 - 2131 - 220
113ALAALAVALVAL(chain C and resid 11 through 17)CF11 - 171 - 7
213ALAALAVALVALchain GGE512 - 5181 - 7

NCS ensembles :
ID
1
2
3

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Components

#1: Antibody antibody 0PV-a.04 light chain


Mass: 23060.486 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 0PV-a.04 heavy chain


Mass: 23817.586 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-1 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: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 728 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.55 Å3/Da / Density % sol: 51.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.17M (NH4)2SO4, 25.5% PEG 4000, 15% Glycerol

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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 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 75448 / % possible obs: 96.3 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.121 / Rpim(I) all: 0.061 / Rrim(I) all: 0.136 / Χ2: 1.256 / Net I/σ(I): 8.2 / Num. measured all: 316884
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.9-1.934.10.63537620.7610.3410.7240.55797.3
1.93-1.9740.53738150.8180.2890.6130.60198.4
1.97-2.0140.45937600.8640.2480.5250.66297.3
2.01-2.0540.40637520.8750.220.4640.70397.6
2.05-2.093.90.35837810.8890.1950.410.77397.6
2.09-2.143.90.31837850.8960.1760.3660.91997.6
2.14-2.193.70.28334540.9090.1570.3261.03789.3
2.19-2.2540.25935200.9240.1380.2961.11790.4
2.25-2.324.40.23338500.9570.1170.2621.15398.9
2.32-2.394.50.21138180.9580.1050.2371.26699
2.39-2.484.40.19138430.9640.0960.2151.35199
2.48-2.584.40.17138590.9670.0870.1931.50698.4
2.58-2.74.30.15738540.970.0810.1781.43398.5
2.7-2.844.20.14538660.9720.0750.1641.62199.4
2.84-3.0240.12738900.9750.0680.1461.52599.2
3.02-3.2540.11733430.9790.060.1321.66685.1
3.25-3.584.70.10638930.9870.0510.1181.68298.5
3.58-4.094.60.09639870.9860.0460.1071.76199.7
4.09-5.164.40.08739230.9890.0420.0971.90298.1
5.16-504.40.06836930.9930.0320.0751.40787.2

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.14_3228refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.893→39.452 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 22.73
RfactorNum. reflection% reflection
Rfree0.2201 3794 5.03 %
Rwork0.1928 --
obs0.1943 75401 96.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 257.94 Å2 / Biso mean: 29.7808 Å2 / Biso min: 8.97 Å2
Refinement stepCycle: final / Resolution: 1.893→39.452 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6670 0 20 728 7418
Biso mean--45.28 37.23 -
Num. residues----877
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1280X-RAY DIFFRACTION6.01TORSIONAL
12L1280X-RAY DIFFRACTION6.01TORSIONAL
21B1312X-RAY DIFFRACTION6.01TORSIONAL
22H1312X-RAY DIFFRACTION6.01TORSIONAL
31C36X-RAY DIFFRACTION6.01TORSIONAL
32G36X-RAY DIFFRACTION6.01TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8933-1.91730.2541160.24652452256890
1.9173-1.94250.27911210.23572648276997
1.9425-1.96910.26181550.24122689284499
1.9691-1.99720.28821610.23182641280297
1.9972-2.02710.29571260.22392659278599
2.0271-2.05870.26311420.2272648279096
2.0587-2.09250.23951290.2192673280298
2.0925-2.12860.26981220.21392723284597
2.1286-2.16730.25681430.21452566270995
2.1673-2.20890.28381180.20812254237283
2.2089-2.2540.25191340.19992617275194
2.254-2.3030.22671440.206726742818100
2.303-2.35660.24781600.20662685284598
2.3566-2.41550.24961370.21382732286999
2.4155-2.48080.261390.205427502889100
2.4808-2.55380.22621340.20182718285299
2.5538-2.63620.25271280.2072694282298
2.6362-2.73040.24311470.20342728287599
2.7304-2.83970.22271570.19742744290199
2.8397-2.96890.21991330.20022740287399
2.9689-3.12540.21161190.1942513263291
3.1254-3.32110.20781350.18062453258888
3.3211-3.57740.19391570.182927522909100
3.5774-3.93710.20051700.167427912961100
3.9371-4.50610.16671560.15792772292899
4.5061-5.67450.18941600.1652734289496
5.6745-39.46020.21731510.19632557270886

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