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- PDB-6app: Anti-Marburgvirus Nucleoprotein Single Domain Antibody A Complexe... -

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Basic information

Entry
Database: PDB / ID: 6app
TitleAnti-Marburgvirus Nucleoprotein Single Domain Antibody A Complexed with Nucleoprotein C-terminal domain
Components
  • Anti-Marburgvirus Nucleoprotein Single Domain Antibody A
  • Nucleoprotein
KeywordsIMMUNE SYSTEM
Function / homology
Function and homology information


viral RNA genome packaging / helical viral capsid / viral budding via host ESCRT complex / viral nucleocapsid / host cell cytoplasm / ribonucleoprotein complex / RNA binding
Similarity search - Function
Ebola nucleoprotein / Ebola nucleoprotein
Similarity search - Domain/homology
Biological speciesLama glama (llama)
Lake Victoria marburgvirus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsTaylor, A.B. / Garza, J.A.
CitationJournal: Front Immunol / Year: 2017
Title: Unveiling a Drift Resistant Cryptotope withinMarburgvirusNucleoprotein Recognized by Llama Single-Domain Antibodies.
Authors: Garza, J.A. / Taylor, A.B. / Sherwood, L.J. / Hart, P.J. / Hayhurst, A.
History
DepositionAug 17, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 11, 2017Provider: repository / Type: Initial release
Revision 1.1May 16, 2018Group: Data collection / Database references / Category: citation
Item: _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 4, 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 1.3Oct 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-Marburgvirus Nucleoprotein Single Domain Antibody A
B: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)26,4542
Polymers26,4542
Non-polymers00
Water5,711317
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1370 Å2
ΔGint-7 kcal/mol
Surface area9300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.552, 46.150, 102.821
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 Anti-Marburgvirus Nucleoprotein Single Domain Antibody A


Mass: 14215.889 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama)
Description: Semi-synthetic single pot library Nomad 1 based upon Lama glama
Plasmid: PECAN73 / Production host: Escherichia coli (E. coli)
#2: Protein Nucleoprotein / Nucleocapsid protein / Protein N


Mass: 12238.336 Da / Num. of mol.: 1 / Fragment: C-terminal domain residues 601-695
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lake Victoria marburgvirus (strain Musoke-80)
Strain: Musoke-80 / Gene: NP / Plasmid: pE-NP600 / Production host: Escherichia coli (E. coli) / References: UniProt: P27588
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 317 / 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: 1.86 Å3/Da / Density % sol: 33.99 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 15% polyethylene glycol 6000, 5% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Mar 1, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.75→46.15 Å / Num. obs: 20487 / % possible obs: 99.2 % / Redundancy: 6.9 % / Biso Wilson estimate: 19 Å2 / Rpim(I) all: 0.039 / Rsym value: 0.089 / Net I/σ(I): 14.1
Reflection shellResolution: 1.75→1.84 Å / Redundancy: 6.9 % / Mean I/σ(I) obs: 2.6 / Num. unique obs: 2902 / Rpim(I) all: 0.281 / Rsym value: 0.64 / % possible all: 98.1

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6APO

6apo


Resolution: 1.75→34.343 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.4 / Phase error: 20.68
RfactorNum. reflection% reflection
Rfree0.2191 1998 9.78 %
Rwork0.1716 --
obs0.1762 20434 98.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 21.1 Å2
Refinement stepCycle: LAST / Resolution: 1.75→34.343 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1437 0 0 321 1758
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071490
X-RAY DIFFRACTIONf_angle_d1.092036
X-RAY DIFFRACTIONf_dihedral_angle_d12.667562
X-RAY DIFFRACTIONf_chiral_restr0.052221
X-RAY DIFFRACTIONf_plane_restr0.005264
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7501-1.79390.34951400.25921284X-RAY DIFFRACTION97
1.7939-1.84240.28521380.23541276X-RAY DIFFRACTION98
1.8424-1.89660.26671370.23681265X-RAY DIFFRACTION97
1.8966-1.95780.30281390.22121281X-RAY DIFFRACTION99
1.9578-2.02770.25661410.19191308X-RAY DIFFRACTION98
2.0277-2.10890.23871390.19091283X-RAY DIFFRACTION98
2.1089-2.20490.27211420.17861311X-RAY DIFFRACTION99
2.2049-2.32110.22421410.19211301X-RAY DIFFRACTION99
2.3211-2.46650.22571440.17661325X-RAY DIFFRACTION100
2.4665-2.65690.22141430.18141318X-RAY DIFFRACTION100
2.6569-2.92410.22721450.17521335X-RAY DIFFRACTION100
2.9241-3.34690.21521450.16351340X-RAY DIFFRACTION100
3.3469-4.21550.17951490.13571377X-RAY DIFFRACTION100
4.2155-34.34930.16771550.1421432X-RAY DIFFRACTION99

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