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- PDB-6u54: Anti-Zaire ebolavirus Nucleoprotein Single Domain Antibody Zaire ... -

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Basic information

Entry
Database: PDB / ID: 6u54
TitleAnti-Zaire ebolavirus Nucleoprotein Single Domain Antibody Zaire C (ZC) Complexed with Zaire ebolavirus Nucleoprotein C-terminal Domain 634-739
Components
  • Anti-Zaire ebolavirus Nucleoprotein Single Domain Antibody Zaire C (ZC)
  • Nucleoprotein
KeywordsIMMUNE SYSTEM / Antibody / nanobody / Ebola / filovirus
Function / homologyEbola nucleoprotein / Ebola nucleoprotein / viral RNA genome packaging / helical viral capsid / viral nucleocapsid / host cell cytoplasm / ribonucleoprotein complex / RNA binding / Nucleoprotein
Function and homology information
Biological speciesLama glama (llama)
Zaire ebolavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsTaylor, A.B. / Sherwood, L.J. / Hart, P.J. / Hayhurst, A.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI112851 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R21 AI105568 United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)C06 012087 United States
CitationJournal: J.Mol.Biol. / Year: 2019
Title: Paratope Duality and Gullying are Among the Atypical Recognition Mechanisms Used by a Trio of Nanobodies to Differentiate Ebolavirus Nucleoproteins.
Authors: Sherwood, L.J. / Taylor, A.B. / Hart, P.J. / Hayhurst, A.
History
DepositionAug 26, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 11, 2019Group: Database references / Category: citation / Item: _citation.title
Revision 1.3Jan 1, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Anti-Zaire ebolavirus Nucleoprotein Single Domain Antibody Zaire C (ZC)
B: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)26,4712
Polymers26,4712
Non-polymers00
Water3,657203
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1470 Å2
ΔGint-9 kcal/mol
Surface area10890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.355, 87.355, 76.868
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-302-

HOH

21A-305-

HOH

31B-871-

HOH

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Components

#1: Antibody Anti-Zaire ebolavirus Nucleoprotein Single Domain Antibody Zaire C (ZC)


Mass: 12334.829 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Semi-synthetic single pot library Nomad 1 based upon Lama glama
Source: (gene. exp.) Lama glama (llama) / Plasmid: pecan219 / Production host: Escherichia coli (E. coli)
#2: Protein Nucleoprotein / Ebola NP / eNP / Nucleocapsid protein / Protein N


Mass: 14136.546 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: C-terminal domain (residues 634-739) / Source: (gene. exp.) Zaire ebolavirus (strain Kikwit-95) / Strain: Kikwit-95 / Gene: NP / Plasmid: pecan236/237 / Production host: Escherichia coli (E. coli) / References: UniProt: O72142
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 203 / 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: 2.77 Å3/Da / Density % sol: 55.59 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 1.1 M malonic acid, 0.15 M ammonium citrate tribasic, 0.072 M succinic acid, 0.18 M DL-malic acid, 0.24 M sodium acetate, 0.3 M sodium formate, 0.096 M ammonium tartrate dibasic
PH range: 7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 21, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.6→57.71 Å / Num. obs: 38012 / % possible obs: 96.2 % / Redundancy: 4.2 % / Biso Wilson estimate: 28.48 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.025 / Rrim(I) all: 0.054 / Net I/σ(I): 13.5
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 0.8 / Num. unique obs: 5651 / CC1/2: 0.499 / Rpim(I) all: 0.902 / Rrim(I) all: 1.886 / % possible all: 98.9

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6U51

6u51


Resolution: 1.6→57.71 Å / SU ML: 0.2169 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.5724
RfactorNum. reflection% reflection
Rfree0.2151 2000 5.27 %
Rwork0.1725 --
obs0.1747 37979 95.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 39.64 Å2
Refinement stepCycle: LAST / Resolution: 1.6→57.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1675 0 0 203 1878
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00921748
X-RAY DIFFRACTIONf_angle_d0.85882374
X-RAY DIFFRACTIONf_chiral_restr0.0737240
X-RAY DIFFRACTIONf_plane_restr0.0072312
X-RAY DIFFRACTIONf_dihedral_angle_d14.8031640
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.640.37571460.35322612X-RAY DIFFRACTION98.64
1.64-1.680.36071440.31352609X-RAY DIFFRACTION98.57
1.68-1.730.3481450.28842607X-RAY DIFFRACTION98.15
1.73-1.790.30671440.25252592X-RAY DIFFRACTION97.57
1.79-1.850.2871440.23232588X-RAY DIFFRACTION97.92
1.85-1.930.25441440.20332597X-RAY DIFFRACTION97.58
1.93-2.020.27891440.18192576X-RAY DIFFRACTION96.9
2.02-2.120.2311350.16762433X-RAY DIFFRACTION90.77
2.12-2.260.22961430.16652584X-RAY DIFFRACTION96.43
2.26-2.430.21450.16592591X-RAY DIFFRACTION96.27
2.43-2.670.20481420.17752573X-RAY DIFFRACTION95.43
2.67-3.060.21921430.19512564X-RAY DIFFRACTION94.29
3.06-3.860.20551410.15552530X-RAY DIFFRACTION91.35
3.86-57.710.17311400.13852523X-RAY DIFFRACTION86.88

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