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- PDB-5fvd: Human metapneumovirus N0-P complex -

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Basic information

Entry
Database: PDB / ID: 5fvd
TitleHuman metapneumovirus N0-P complex
Components
  • NUCLEOCAPSID
  • PHOSPHOPROTEIN
KeywordsVIRAL PROTEIN / NUCLEOPROTEIN / MONONEGAVIRALES / PHOSPHOPROTEIN
Function / homology
Function and homology information


helical viral capsid / virion component / viral nucleocapsid / host cell cytoplasm / ribonucleoprotein complex / RNA-directed RNA polymerase activity / RNA binding
Similarity search - Function
Phosphoprotein, pneumoviral / Pneumovirus phosphoprotein / Pneumovirus nucleocapsid protein / Pneumovirus nucleocapsid protein
Similarity search - Domain/homology
Nucleoprotein / Phosphoprotein / Phosphoprotein
Similarity search - Component
Biological speciesHUMAN METAPNEUMOVIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsRenner, M. / Bertinelli, M. / Leyrat, C. / Paesen, G.C. / Saraiva de Oliveira, L.F. / Huiskonen, J.T. / Grimes, J.M.
CitationJournal: Elife / Year: 2016
Title: Nucleocapsid assembly in pneumoviruses is regulated by conformational switching of the N protein.
Authors: Renner, M. / Bertinelli, M. / Leyrat, C. / Paesen, G.C. / Saraiva de Oliveira, L.F. / Huiskonen, J.T. / Grimes, J.M.
History
DepositionFeb 5, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 24, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 2, 2016Group: Database references
Revision 1.2Mar 22, 2017Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NUCLEOCAPSID
B: PHOSPHOPROTEIN
C: NUCLEOCAPSID
D: PHOSPHOPROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,9595
Polymers97,9234
Non-polymers351
Water10,575587
1
A: NUCLEOCAPSID
B: PHOSPHOPROTEIN


Theoretical massNumber of molelcules
Total (without water)48,9622
Polymers48,9622
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2120 Å2
ΔGint-21.3 kcal/mol
Surface area17620 Å2
MethodPISA
2
C: NUCLEOCAPSID
D: PHOSPHOPROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,9973
Polymers48,9622
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2190 Å2
ΔGint-32 kcal/mol
Surface area17420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.930, 62.780, 86.710
Angle α, β, γ (deg.)90.97, 96.38, 108.98
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
/ NCS ensembles :
ID
1
2

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Components

#1: Protein NUCLEOCAPSID / HMPV N0-P


Mass: 43576.520 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HUMAN METAPNEUMOVIRUS / Strain: NL1-00 / Variant: A1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA2 / References: UniProt: Q91F57
#2: Protein/peptide PHOSPHOPROTEIN / HMPV N0-P


Mass: 5385.217 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HUMAN METAPNEUMOVIRUS / Strain: NL1-00 / Variant: A1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA2 / References: UniProt: X4Y6K1, UniProt: Q91KZ5*PLUS
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 587 / 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: 2.13 Å3/Da / Density % sol: 52 % / Description: NONE
Crystal growpH: 7
Details: 100 MM PCB SYSTEM, PH 7, 25 % POLYETHYLENE GLYCOL 1500, 9 MM 1,2-DIAMINOCYCLOHEXANE SULFATE, 6 MM DILOXANIDE FUROATE, 17 MM FUMARIC ACID, 10 MM SPERMINE, 9 MM SULFAGUANIDINE AND 20 MM HEPES, ...Details: 100 MM PCB SYSTEM, PH 7, 25 % POLYETHYLENE GLYCOL 1500, 9 MM 1,2-DIAMINOCYCLOHEXANE SULFATE, 6 MM DILOXANIDE FUROATE, 17 MM FUMARIC ACID, 10 MM SPERMINE, 9 MM SULFAGUANIDINE AND 20 MM HEPES, PH 6.8 (SILVER BULLETS ADDITIVES)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.979
DetectorType: DECTRIS PILATUS / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.86→28.42 Å / Num. obs: 64451 / % possible obs: 94.8 % / Observed criterion σ(I): 0 / Redundancy: 1.7 % / Biso Wilson estimate: 29.37 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 9.2
Reflection shellResolution: 1.86→1.91 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 1.1 / % possible all: 75

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WJ8

2wj8


Resolution: 1.86→28.421 Å / SU ML: 0.24 / σ(F): 1.96 / Phase error: 22.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2053 3203 5 %
Rwork0.1712 --
obs0.1729 64443 94.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.86→28.421 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5707 0 1 587 6295
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075797
X-RAY DIFFRACTIONf_angle_d0.9517818
X-RAY DIFFRACTIONf_dihedral_angle_d10.3433534
X-RAY DIFFRACTIONf_chiral_restr0.047897
X-RAY DIFFRACTIONf_plane_restr0.0051000
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.86-1.88780.39511080.35241924X-RAY DIFFRACTION71
1.8878-1.91730.30761500.30022333X-RAY DIFFRACTION84
1.9173-1.94870.28361220.27032678X-RAY DIFFRACTION93
1.9487-1.98230.3071410.25562566X-RAY DIFFRACTION93
1.9823-2.01830.29391440.24562693X-RAY DIFFRACTION95
2.0183-2.05710.27031180.22792668X-RAY DIFFRACTION95
2.0571-2.09910.26161450.21382729X-RAY DIFFRACTION96
2.0991-2.14470.23931570.19022689X-RAY DIFFRACTION96
2.1447-2.19460.18831500.17992666X-RAY DIFFRACTION96
2.1946-2.24950.23171420.16992774X-RAY DIFFRACTION97
2.2495-2.31030.24761440.16962674X-RAY DIFFRACTION97
2.3103-2.37820.20121240.16792752X-RAY DIFFRACTION97
2.3782-2.45490.22451220.17082726X-RAY DIFFRACTION97
2.4549-2.54260.23021320.17752778X-RAY DIFFRACTION97
2.5426-2.64440.23471450.16922703X-RAY DIFFRACTION97
2.6444-2.76460.19891370.16792764X-RAY DIFFRACTION97
2.7646-2.91020.21921300.16962729X-RAY DIFFRACTION97
2.9102-3.09240.18571280.16292750X-RAY DIFFRACTION97
3.0924-3.33080.20461800.16352695X-RAY DIFFRACTION97
3.3308-3.66540.2211410.15622772X-RAY DIFFRACTION98
3.6654-4.19430.15811580.14282732X-RAY DIFFRACTION98
4.1943-5.27880.15451430.14322717X-RAY DIFFRACTION97
5.2788-28.42430.18551420.16942728X-RAY DIFFRACTION97
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)
15.53110.81021.33381.36830.15651.5051-0.015-0.1459-0.0511-0.01440.0012-0.21260.09620.02820.00260.24360.03760.02790.19010.00740.224344.263-45.7776-60.9483
21.54551.44490.66242.22541.26781.605-0.0095-0.05260.2416-0.0214-0.04930.1685-0.1161-0.010.06680.23990.05610.00380.2205-0.02130.249638.2225-31.0574-60.2515
32.6456-1.4448-0.12663.57490.10962.10570.03870.16130.10240.02980.0037-0.1749-0.07220.0336-0.05180.2265-0.0366-0.00640.19980.0010.212641.7051-6.9136-45.2941
45.1316-3.7226-4.65087.78465.58297.6210.08530.120.4411-0.3380.2334-0.3978-0.50360.8042-0.22420.3036-0.0813-0.01740.29620.06290.426750.48350.4836-47.3842
55.24612.14132.44136.3129-0.01451.34840.1156-1.10021.20470.8305-0.328-0.2117-0.6042-0.09840.01290.8709-0.0788-0.0410.3457-0.12280.425938.40518.7247-32.7026
60.9411-0.6898-0.37891.52250.22650.89740.00860.1129-0.0224-0.0173-0.0427-0.03480.0011-0.01950.04090.2443-0.024-0.02450.2568-0.00410.249131.44629.6647-6.6749
73.00911.9898-0.09093.631-0.2161.6702-0.033-0.2063-0.0797-0.06120.02020.01640.0915-0.044-0.0040.24460.03840.01310.21640.00940.228932.1299-21.3947-22.1623
85.57140.4454.9327.8022-0.86784.569-0.6138-1.2763-1.09422.12870.33051.08541.0822-0.35050.48260.4635-0.01720.07640.4680.16710.427841.1462-23.9844-13.6331
96.7907-0.2561.98984.08741.13223.9763-0.15460.5837-0.9986-0.68460.0019-0.43590.9642-0.0351-0.11560.5824-0.0310.10120.1969-0.00230.432133.7354-35.2728-30.431
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 30 THROUGH 141 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 142 THROUGH 255 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 256 THROUGH 383 )
4X-RAY DIFFRACTION4CHAIN 'B' AND (RESID 1 THROUGH 13 )
5X-RAY DIFFRACTION5CHAIN 'B' AND (RESID 14 THROUGH 28 )
6X-RAY DIFFRACTION6CHAIN 'C' AND (RESID 30 THROUGH 255 )
7X-RAY DIFFRACTION7CHAIN 'C' AND (RESID 256 THROUGH 382 )
8X-RAY DIFFRACTION8CHAIN 'D' AND (RESID 1 THROUGH 5 )
9X-RAY DIFFRACTION9CHAIN 'D' AND (RESID 6 THROUGH 27 )

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