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- PDB-4w2o: Anti-Marburgvirus Nucleoprotein Single Domain Antibody B Complexe... -

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Basic information

Entry
Database: PDB / ID: 4w2o
TitleAnti-Marburgvirus Nucleoprotein Single Domain Antibody B Complexed with Nucleoprotein C-terminal domain
Components
  • Anti-Marburgvirus Nucleoprotein Single Domain Antibody B
  • 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 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 1.2Sep 27, 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 1.3Nov 6, 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 B
B: Nucleoprotein
C: Anti-Marburgvirus Nucleoprotein Single Domain Antibody B
D: Nucleoprotein
E: Anti-Marburgvirus Nucleoprotein Single Domain Antibody B
F: Nucleoprotein
G: Anti-Marburgvirus Nucleoprotein Single Domain Antibody B
H: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,75516
Polymers103,9868
Non-polymers7698
Water00
1
A: Anti-Marburgvirus Nucleoprotein Single Domain Antibody B
B: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1894
Polymers25,9972
Non-polymers1922
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1710 Å2
ΔGint-33 kcal/mol
Surface area9110 Å2
MethodPISA
2
C: Anti-Marburgvirus Nucleoprotein Single Domain Antibody B
D: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1894
Polymers25,9972
Non-polymers1922
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1760 Å2
ΔGint-36 kcal/mol
Surface area9210 Å2
MethodPISA
3
E: Anti-Marburgvirus Nucleoprotein Single Domain Antibody B
F: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1894
Polymers25,9972
Non-polymers1922
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1650 Å2
ΔGint-33 kcal/mol
Surface area9240 Å2
MethodPISA
4
G: Anti-Marburgvirus Nucleoprotein Single Domain Antibody B
H: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1894
Polymers25,9972
Non-polymers1922
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1720 Å2
ΔGint-37 kcal/mol
Surface area9230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.998, 108.657, 141.272
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 B


Mass: 13758.283 Da / Num. of mol.: 4
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.: 4 / 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: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
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: 2.14 Å3/Da / Density % sol: 42.53 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 20% polyethylene glycol 4000, 0.16M ammonium sulfate, 20% glycerol, 0.08M sodium acetate pH 4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 0.97626 Å
DetectorType: NOIR-1 / Detector: CCD / Date: May 23, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97626 Å / Relative weight: 1
ReflectionResolution: 3.2→58 Å / Num. obs: 15378 / % possible obs: 100 % / Redundancy: 7.2 % / Biso Wilson estimate: 55.1 Å2 / Rpim(I) all: 0.081 / Rsym value: 0.189 / Net I/σ(I): 10.6
Reflection shellResolution: 3.2→3.37 Å / Redundancy: 7.4 % / Mean I/σ(I) obs: 3 / Num. unique obs: 2189 / Rpim(I) all: 0.297 / Rsym value: 0.705 / % possible all: 100

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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: 6APP

6app


Resolution: 3.2→54.328 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.94 / Phase error: 30.32
RfactorNum. reflection% reflection
Rfree0.2846 1530 10.01 %
Rwork0.2267 --
obs0.2325 15287 99.67 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso mean: 51.3 Å2
Refinement stepCycle: LAST / Resolution: 3.2→54.328 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5712 0 40 0 5752
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035876
X-RAY DIFFRACTIONf_angle_d0.5647968
X-RAY DIFFRACTIONf_dihedral_angle_d17.482160
X-RAY DIFFRACTIONf_chiral_restr0.041836
X-RAY DIFFRACTIONf_plane_restr0.0031036
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2001-3.30340.37161350.30241214X-RAY DIFFRACTION100
3.3034-3.42150.35321380.26811241X-RAY DIFFRACTION100
3.4215-3.55840.33571360.25571209X-RAY DIFFRACTION100
3.5584-3.72030.35471380.25451242X-RAY DIFFRACTION100
3.7203-3.91640.31521320.24821221X-RAY DIFFRACTION100
3.9164-4.16170.27681410.2371255X-RAY DIFFRACTION100
4.1617-4.48290.23311370.20231245X-RAY DIFFRACTION100
4.4829-4.93380.26091400.18961246X-RAY DIFFRACTION100
4.9338-5.64710.24791380.20421256X-RAY DIFFRACTION100
5.6471-7.11220.27151430.23111277X-RAY DIFFRACTION100
7.1122-54.33630.24361520.19721351X-RAY DIFFRACTION99

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