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- PDB-4w2q: Anti-Marburgvirus Nucleoprotein Single Domain Antibody C Complexe... -

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Basic information

Entry
Database: PDB / ID: 4w2q
TitleAnti-Marburgvirus Nucleoprotein Single Domain Antibody C Complexed with Nucleoprotein C-terminal domain
Components
  • Anti-Marburgvirus Nucleoprotein Single Domain Antibody C
  • 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: 2.7 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Anti-Marburgvirus Nucleoprotein Single Domain Antibody C
B: Nucleoprotein
C: Anti-Marburgvirus Nucleoprotein Single Domain Antibody C
D: Nucleoprotein
E: Anti-Marburgvirus Nucleoprotein Single Domain Antibody C
F: Nucleoprotein
G: Anti-Marburgvirus Nucleoprotein Single Domain Antibody C
H: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)87,0018
Polymers87,0018
Non-polymers00
Water1,874104
1
A: Anti-Marburgvirus Nucleoprotein Single Domain Antibody C
B: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)21,7502
Polymers21,7502
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1320 Å2
ΔGint-9 kcal/mol
Surface area9810 Å2
MethodPISA
2
C: Anti-Marburgvirus Nucleoprotein Single Domain Antibody C
D: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)21,7502
Polymers21,7502
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1320 Å2
ΔGint-9 kcal/mol
Surface area9450 Å2
MethodPISA
3
E: Anti-Marburgvirus Nucleoprotein Single Domain Antibody C
F: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)21,7502
Polymers21,7502
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1320 Å2
ΔGint-8 kcal/mol
Surface area9880 Å2
MethodPISA
4
G: Anti-Marburgvirus Nucleoprotein Single Domain Antibody C
H: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)21,7502
Polymers21,7502
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1340 Å2
ΔGint-8 kcal/mol
Surface area9450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.664, 98.461, 68.498
Angle α, β, γ (deg.)90.00, 96.23, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody
Anti-Marburgvirus Nucleoprotein Single Domain Antibody C


Mass: 12981.421 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: PECAN219 / Production host: Escherichia coli (E. coli)
#2: Protein
Nucleoprotein / Nucleocapsid protein / Protein N


Mass: 8768.806 Da / Num. of mol.: 4 / Fragment: C-terminal domain residues 632-695
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lake Victoria marburgvirus / Strain: Musoke-80 / Gene: NP / Plasmid: pE-NP632 / Production host: Escherichia coli (E. coli) / References: UniProt: P27588
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / Source method: isolated from a natural source / Formula: H2O

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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: 2.24 Å3/Da / Density % sol: 45.01 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 20% polyethylene glycol 6000, 0.2M magnesium chloride, 0.1M 1,2,3-hexanetriol, 0.1 M sodium acetate pH 5

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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: Jun 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.7→46.41 Å / Num. obs: 20770 / % possible obs: 99 % / Redundancy: 3.7 % / Biso Wilson estimate: 35.8 Å2 / Rpim(I) all: 0.092 / Rsym value: 0.154 / Net I/σ(I): 8.2
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 3013 / Rpim(I) all: 0.398 / Rsym value: 0.673 / % possible all: 98.3

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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: 2.7→41.68 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 28.88
RfactorNum. reflection% reflection
Rfree0.2739 1999 9.71 %
Rwork0.2199 --
obs0.2252 20587 98.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1 Å
Displacement parametersBiso mean: 38.7 Å2
Refinement stepCycle: LAST / Resolution: 2.7→41.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5720 0 0 104 5824
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055848
X-RAY DIFFRACTIONf_angle_d0.9717921
X-RAY DIFFRACTIONf_dihedral_angle_d13.3672175
X-RAY DIFFRACTIONf_chiral_restr0.076846
X-RAY DIFFRACTIONf_plane_restr0.0071039
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.76750.35271430.28321329X-RAY DIFFRACTION98
2.7675-2.84230.38031420.28251317X-RAY DIFFRACTION98
2.8423-2.9260.35931410.27681324X-RAY DIFFRACTION98
2.926-3.02040.31981430.24851330X-RAY DIFFRACTION99
3.0204-3.12830.33081420.26341309X-RAY DIFFRACTION98
3.1283-3.25350.32531450.2541347X-RAY DIFFRACTION99
3.2535-3.40150.34411430.25881328X-RAY DIFFRACTION99
3.4015-3.58080.28741430.23661337X-RAY DIFFRACTION99
3.5808-3.8050.40291290.31681206X-RAY DIFFRACTION89
3.805-4.09850.23551450.19591340X-RAY DIFFRACTION99
4.0985-4.51050.20321440.16541334X-RAY DIFFRACTION99
4.5105-5.16220.19061450.15331355X-RAY DIFFRACTION100
5.1622-6.49980.21371470.1781369X-RAY DIFFRACTION100
6.4998-41.68540.21321470.17641363X-RAY DIFFRACTION98

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