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- PDB-1pd3: Influenza A NEP M1-binding domain -

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Basic information

Entry
Database: PDB / ID: 1pd3
TitleInfluenza A NEP M1-binding domain
ComponentsNonstructural protein NS2
KeywordsUNKNOWN FUNCTION / influenza virus A / NEP/NS2
Function / homology
Function and homology information


uncoating of virus / exit of virus from host cell nucleus through nuclear pore / intracellular transport of virus / Influenza Infection / Fusion of the Influenza Virion to the Host Cell Endosome / Release / Budding / Packaging of Eight RNA Segments / Uncoating of the Influenza Virion / Entry of Influenza Virion into Host Cell via Endocytosis ...uncoating of virus / exit of virus from host cell nucleus through nuclear pore / intracellular transport of virus / Influenza Infection / Fusion of the Influenza Virion to the Host Cell Endosome / Release / Budding / Packaging of Eight RNA Segments / Uncoating of the Influenza Virion / Entry of Influenza Virion into Host Cell via Endocytosis / viral genome packaging / Viral RNP Complexes in the Host Cell Nucleus / virion component => GO:0044423 / NEP/NS2 Interacts with the Cellular Export Machinery / Viral mRNA Translation / viral budding from plasma membrane / endosome lumen / endocytic vesicle membrane / receptor-mediated endocytosis of virus by host cell / fusion of virus membrane with host plasma membrane / host cell nucleus / virion attachment to host cell / extracellular region / nucleoplasm / cytosol
Similarity search - Function
Influenza nuclear export protein NS2 / Influenza non-structural protein (NS2) / Helix Hairpins - #230 / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Nuclear export protein
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.6 Å
AuthorsBaudin, F.
CitationJournal: Embo J. / Year: 2003
Title: Crystal structure of the M1 protein-binding domain of the influenza A virus nuclear export protein (NEP/NS2).
Authors: Akarsu, H. / Burmeister, W.P. / Petosa, C. / Petit, I. / Muller, C.W. / Ruigrok, R.W. / Baudin, F.
History
DepositionMay 19, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Nonstructural protein NS2
B: Nonstructural protein NS2


Theoretical massNumber of molelcules
Total (without water)14,4822
Polymers14,4822
Non-polymers00
Water0
1
A: Nonstructural protein NS2


Theoretical massNumber of molelcules
Total (without water)7,2411
Polymers7,2411
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Nonstructural protein NS2


Theoretical massNumber of molelcules
Total (without water)7,2411
Polymers7,2411
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2540 Å2
ΔGint-25 kcal/mol
Surface area6970 Å2
MethodPISA, PQS
4
A: Nonstructural protein NS2

B: Nonstructural protein NS2


Theoretical massNumber of molelcules
Total (without water)14,4822
Polymers14,4822
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_654-y+1,x-y,z-1/31
Buried area2440 Å2
ΔGint-6 kcal/mol
Surface area7070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.691, 82.691, 61.111
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Nonstructural protein NS2


Mass: 7241.248 Da / Num. of mol.: 2 / Fragment: Residues 59-116
Source method: isolated from a genetically manipulated source
Details: M1-binding domain of NEP / Source: (gene. exp.) Influenza A virus / Genus: Influenzavirus A / Gene: NS2 / Production host: Escherichia coli (E. coli) / References: UniProt: P03508

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.62 Å3/Da / Density % sol: 73.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PROTEIN IN 20 MM TRIS-HCL PH7.5, 150 MM NACL, HANGING DROP METHOD, ROOM TEMPERATURE, vapor diffusion, hanging drop, temperature 298.0K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlprotein1drop
20.4 Mammonium di-phosphate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 30, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.6→46.6 Å / Num. obs: 7302 / % possible obs: 99.6 % / Redundancy: 3.8 % / Biso Wilson estimate: 48.47 Å2 / Rmerge(I) obs: 0.09 / Rsym value: 0.09 / Net I/σ(I): 6
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 2 / Rsym value: 0.32 / % possible all: 100
Reflection
*PLUS
Highest resolution: 2.6 Å / Rmerge(I) obs: 0.09
Reflection shell
*PLUS
% possible obs: 100 %

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
SOLVEphasing
RefinementMethod to determine structure: MIR / Resolution: 2.6→19.88 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.909 / SU B: 7.689 / SU ML: 0.162 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.269 / ESU R Free: 0.244
RfactorNum. reflection% reflectionSelection details
Rfree0.244 340 4.7 %RANDOM
Rwork0.176 ---
obs0.179 6962 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 43.46 Å2
Baniso -1Baniso -2Baniso -3
1-3.6 Å21.8 Å20 Å2
2--3.6 Å20 Å2
3----5.4 Å2
Refinement stepCycle: LAST / Resolution: 2.6→19.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms948 0 0 0 948
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0430.021964
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg3.3021.9331290
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1275106
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_chiral_restr0.1880.2138
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.02718
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2680.2424
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2630.231
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3230.238
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.6950.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.7731.5534
X-RAY DIFFRACTIONr_mcangle_it3.5342864
X-RAY DIFFRACTIONr_scbond_it5.8263430
X-RAY DIFFRACTIONr_scangle_it9.5854.5426
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.67 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.319 23
Rwork0.225 465
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0996-0.27990.04051.306-0.12020.6619-0.0383-0.0023-0.00790.00060.12240.07210.0388-0.167-0.08410.0327-0.012-0.00480.0280.01110.023636.615318.49434.9896
20.00081.0704-0.07053.29320.5890.67340.0109-0.0514-0.0220.00820.0253-0.08630.0180.057-0.03620.0421-0.01550.01850.0154-0.00530.027347.377120.64525.0394
3-0.1333-0.2254-0.35471.48240.44161.1298-0.0725-0.03590.05960.07240.1654-0.07560.06930.195-0.09290.02610.02-0.00440.0456-0.01710.01547.40820.038414.9174
4-0.4309-0.33590.42390.4878-0.00561.48570.03970.0376-0.01780.02760.04290.03230.0787-0.098-0.08260.03110.02330.00640.01760.00720.036236.508518.888814.8256
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA63 - 875 - 29
2X-RAY DIFFRACTION2AA93 - 11635 - 58
3X-RAY DIFFRACTION3BB63 - 875 - 29
4X-RAY DIFFRACTION4BB93 - 11635 - 58
Refinement
*PLUS
Highest resolution: 2.6 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.043
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg3.3

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