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- PDB-6vjn: Structure of NHP D11A.B5Fab in complex with 16055 V2b peptide -

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Basic information

Entry
Database: PDB / ID: 6vjn
TitleStructure of NHP D11A.B5Fab in complex with 16055 V2b peptide
Components
  • D11A.B5 Fab Heavy chain
  • D11A.B5 Fab Light chain
  • V2b peptide
KeywordsIMMUNE SYSTEM / Fragment binding antigen and peptide complex
Function / homology
Function and homology information


symbiont-mediated perturbation of host defense response / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell ...symbiont-mediated perturbation of host defense response / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / 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
Similarity search - Domain/homology
Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSingh, S. / Liban, T.J. / Pancera, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01AI104722 United States
CitationJournal: Plos Pathog. / Year: 2021
Title: Structurally related but genetically unrelated antibody lineages converge on an immunodominant HIV-1 Env neutralizing determinant following trimer immunization.
Authors: Aljedani, S.S. / Liban, T.J. / Tran, K. / Phad, G. / Singh, S. / Dubrovskaya, V. / Pushparaj, P. / Martinez-Murillo, P. / Rodarte, J. / Mileant, A. / Mangala Prasad, V. / Kinzelman, R. / ...Authors: Aljedani, S.S. / Liban, T.J. / Tran, K. / Phad, G. / Singh, S. / Dubrovskaya, V. / Pushparaj, P. / Martinez-Murillo, P. / Rodarte, J. / Mileant, A. / Mangala Prasad, V. / Kinzelman, R. / O'Dell, S. / Mascola, J.R. / Lee, K.K. / Karlsson Hedestam, G.B. / Wyatt, R.T. / Pancera, M.
History
DepositionJan 16, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 2, 2022Group: Advisory / Database references
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 11, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: D11A.B5 Fab Heavy chain
L: D11A.B5 Fab Light chain
G: V2b peptide
F: V2b peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,49210
Polymers55,3544
Non-polymers1386
Water5,296294
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6540 Å2
ΔGint-89 kcal/mol
Surface area19810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.780, 74.780, 101.450
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Antibody D11A.B5 Fab Heavy chain


Mass: 25610.855 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody D11A.B5 Fab Light chain


Mass: 25241.766 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Protein/peptide V2b peptide


Mass: 2250.552 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: A1EAI1*PLUS
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 294 / 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: 2.22 Å3/Da / Density % sol: 44.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1 M Tris, pH 8.0, 1.32 M sodium/potasssium tartrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 17, 2017
RadiationMonochromator: Rosenbaum-Rock 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→48.96 Å / Num. obs: 33842 / % possible obs: 99.4 % / Redundancy: 6.4 % / Biso Wilson estimate: 26.93 Å2 / CC1/2: 0.993 / Net I/σ(I): 7.4
Reflection shellResolution: 2→2.05 Å / Num. unique obs: 2389 / CC1/2: 0.863

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PHENIX1.14_3260refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6RCS

6rcs


Resolution: 2→41.98 Å / SU ML: 0.2293 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.3829
RfactorNum. reflection% reflection
Rfree0.2364 1707 5.05 %
Rwork0.1801 --
obs0.1829 33780 99.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 40.14 Å2
Refinement stepCycle: LAST / Resolution: 2→41.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3359 0 6 294 3659
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113471
X-RAY DIFFRACTIONf_angle_d1.10724758
X-RAY DIFFRACTIONf_chiral_restr0.0652548
X-RAY DIFFRACTIONf_plane_restr0.0077607
X-RAY DIFFRACTIONf_dihedral_angle_d4.43993031
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.060.3291140.26122569X-RAY DIFFRACTION96.41
2.06-2.130.24031440.23452568X-RAY DIFFRACTION97.59
2.13-2.20.26781530.21462629X-RAY DIFFRACTION98.97
2.2-2.290.29351390.20372648X-RAY DIFFRACTION99.57
2.29-2.390.28721450.20352640X-RAY DIFFRACTION99.96
2.39-2.520.2731360.20722680X-RAY DIFFRACTION100
2.52-2.680.30991490.20132681X-RAY DIFFRACTION99.93
2.68-2.880.23641470.18812652X-RAY DIFFRACTION100
2.88-3.170.24181360.18252697X-RAY DIFFRACTION100
3.17-3.630.24091480.15872712X-RAY DIFFRACTION100
3.63-4.580.17791440.14942734X-RAY DIFFRACTION100
4.58-41.980.20691520.16342863X-RAY DIFFRACTION99.7
Refinement TLS params.Method: refined / Origin x: 17.639019689 Å / Origin y: -8.09372828333 Å / Origin z: -7.49368639999 Å
111213212223313233
T0.137690491581 Å2-0.0081813381749 Å2-0.00101809848743 Å2-0.327212537669 Å2-0.00139613830094 Å2--0.159093089141 Å2
L0.62498223736 °20.087259816208 °20.119232733182 °2-1.25307312636 °2-0.420890267844 °2--1.90192589418 °2
S-0.00929275056618 Å °0.0805001993077 Å °-0.00521219927897 Å °-0.000720412325753 Å °-0.00622383175866 Å °0.0146451282576 Å °-0.277219920619 Å °-0.0257054848569 Å °0.0149556746955 Å °
Refinement TLS groupSelection details: all

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