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- PDB-5fvc: Structure of RNA-bound decameric HMPV nucleoprotein -

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Basic information

Entry
Database: PDB / ID: 5fvc
TitleStructure of RNA-bound decameric HMPV nucleoprotein
Components
  • HMPV NUCLEOPROTEIN
  • RNA
KeywordsVIRAL PROTEIN / NUCLEOPROTEIN / MONONEGAVIRALES / PNEUMOVIRUS
Function / homology
Function and homology information


helical viral capsid / viral nucleocapsid / host cell cytoplasm / ribonucleoprotein complex / RNA binding
Similarity search - Function
Pneumovirus nucleocapsid protein / Pneumovirus nucleocapsid protein
Similarity search - Domain/homology
RNA / RNA (> 10) / Nucleoprotein
Similarity search - Component
Biological speciesHUMAN METAPNEUMOVIRUS
ESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.17 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 24, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.4Oct 30, 2019Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Other
Category: pdbx_database_status / pdbx_validate_close_contact / struct_conn
Item: _pdbx_database_status.status_code_sf
Revision 1.5May 1, 2024Group: 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: HMPV NUCLEOPROTEIN
B: HMPV NUCLEOPROTEIN
C: HMPV NUCLEOPROTEIN
D: HMPV NUCLEOPROTEIN
E: HMPV NUCLEOPROTEIN
F: HMPV NUCLEOPROTEIN
G: HMPV NUCLEOPROTEIN
H: HMPV NUCLEOPROTEIN
I: HMPV NUCLEOPROTEIN
J: HMPV NUCLEOPROTEIN
K: RNA


Theoretical massNumber of molelcules
Total (without water)466,66311
Polymers466,66311
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area71690 Å2
ΔGint-383.7 kcal/mol
Surface area139490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)202.010, 233.210, 203.640
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
HMPV NUCLEOPROTEIN


Mass: 44534.570 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HUMAN METAPNEUMOVIRUS / Strain: NL1-00 / Variant: A1 / Plasmid: POPINE / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): ROSETTA2 / References: UniProt: Q91F57
#2: RNA chain RNA


Mass: 21317.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: E. COLI RNA / Source: (natural) ESCHERICHIA COLI (E. coli) / Variant: ROSETTA2 / Strain: BL21(DE3)

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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: 2.57 Å3/Da / Density % sol: 51 % / Description: NONE
Crystal growpH: 8.5
Details: 100 MM TRIS/BICINE, PH 8.5, 90 MM NPS (NAN03, NA2HPO4, (NH4)2SO4), 37.5 % METHYL-2 4-PENTANEDIOL, POLYETHYLENE GLYCOL 1000 AND POLYETHYLENE GLYCOL 3350 (MORPHEUS SCREEN)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.917
DetectorType: DECTRIS PILATUS / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.917 Å / Relative weight: 1
ReflectionResolution: 4.17→101.19 Å / Num. obs: 36125 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 13.5 % / Biso Wilson estimate: 161.61 Å2 / Rmerge(I) obs: 0.22 / Net I/σ(I): 9.2
Reflection shellResolution: 4.17→4.28 Å / Redundancy: 13.8 % / Mean I/σ(I) obs: 1 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: DECAMER OF MONOMERIC HMPV N0

Resolution: 4.17→101.19 Å / Cor.coef. Fo:Fc: 0.9455 / Cor.coef. Fo:Fc free: 0.9274 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.839
RfactorNum. reflection% reflectionSelection details
Rfree0.2302 1798 4.98 %RANDOM
Rwork0.1913 ---
obs0.1932 36102 99.9 %-
Displacement parametersBiso mean: 216.01 Å2
Baniso -1Baniso -2Baniso -3
1-9.9257 Å20 Å20 Å2
2---3.5113 Å20 Å2
3----6.4144 Å2
Refine analyzeLuzzati coordinate error obs: 0.516 Å
Refinement stepCycle: LAST / Resolution: 4.17→101.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms27957 1400 0 0 29357
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0129942HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1240737HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d10479SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes660HARMONIC2
X-RAY DIFFRACTIONt_gen_planes4182HARMONIC5
X-RAY DIFFRACTIONt_it29942HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.21
X-RAY DIFFRACTIONt_other_torsion20.53
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion4079SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact36542SEMIHARMONIC4
LS refinement shellResolution: 4.17→4.29 Å / Total num. of bins used: 18
RfactorNum. reflection% reflection
Rfree0.2565 148 5.11 %
Rwork0.251 2751 -
all0.2513 2899 -
obs--100 %
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)
10.8894-0.31321.46510.10570.28710.5086-0.1015-0.2706-0.11180.11810.1699-0.28080.11180.4327-0.0684-0.60950.33460.255-0.35880.16710.2498246.22416.7818255.985
21.92061.58851.51522.8162.87693.1956-0.00850.1809-0.5337-0.108-0.2475-0.16910.4140.230.256-0.22650.17160.187-0.4387-0.13180.3874225.4737.2484233.599
30.96380.85150.63281.66891.3031.66150.04720.1857-0.3269-0.3709-0.31180.04910.1704-0.2930.2646-0.0575-0.18650.1666-0.1012-0.4483-0.0433202.12515.1195212.827
41.2728-1.42590.04072.9169-0.45880.473-0.0057-0.4316-0.306-0.23610.1241-0.37790.00630.6063-0.1184-0.4153-0.51570.0810.3336-0.03660.3254261.38645.3444266.56
52.2338-1.09770.83131.0128-0.70651.11840.0761-0.40630.0598-0.12820.0796-0.5331-0.44020.4947-0.1557-0.0799-0.47830.24140.0433-0.10610.1307259.20677.3546266.929
61.40350.59381.1871.33550.53971.57740.20020.26250.51050.0105-0.0671-0.1806-0.89260.2587-0.13310.39780.02420.269-0.41340.1973-0.5165220.169109.967229.056
72.41810.80911.69470.580.78731.77020.2418-0.08050.4675-0.1977-0.1805-0.1643-0.49750.0615-0.06140.1027-0.09460.2816-0.0093-0.0418-0.2207243.375101.871249.791
80.49820.3509-0.04881.7543-0.17220.58340.04290.52030.349-0.2446-0.00740.2678-0.6736-0.1914-0.03550.41290.38070.07010.00230.1213-0.421197.56798.6872208.74
90.3868-0.91390.21944.2483-1.87631.0336-0.0510.5208-0.134-0.35830.05630.1605-0.1541-0.4744-0.00520.2490.2194-0.05510.3542-0.2083-0.3859184.2671.8763196.935
102.3877-2.10942.25742.627-2.34463.0215-0.06340.4114-0.3421-0.6168-0.04410.17470.069-0.62790.10750.07580.25330.02490.3125-0.3558-0.2364184.4639.887198.782
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C
4X-RAY DIFFRACTION4CHAIN D
5X-RAY DIFFRACTION5CHAIN E
6X-RAY DIFFRACTION6CHAIN F
7X-RAY DIFFRACTION7CHAIN G
8X-RAY DIFFRACTION8CHAIN H
9X-RAY DIFFRACTION9CHAIN I
10X-RAY DIFFRACTION10CHAIN J

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