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- PDB-5jht: Apo form of influenza strain H1N1 polymerase acidic subunit N-ter... -

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Basic information

Entry
Database: PDB / ID: 5jht
TitleApo form of influenza strain H1N1 polymerase acidic subunit N-terminal region crystallized with potassium sodium tartrate
ComponentsPolymerase acidic protein
KeywordsHYDROLASE
Function / homology
Function and homology information


cRNA Synthesis / 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 RNP Complexes in the Host Cell Nucleus / vRNA Synthesis ...cRNA Synthesis / 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 RNP Complexes in the Host Cell Nucleus / vRNA Synthesis / Transport of Ribonucleoproteins into the Host Nucleus / NEP/NS2 Interacts with the Cellular Export Machinery / vRNP Assembly / Viral Messenger RNA Synthesis / cap snatching / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / Viral mRNA Translation / endonuclease activity / host cell cytoplasm / Hydrolases; Acting on ester bonds / viral RNA genome replication / DNA-templated transcription / host cell nucleus / RNA binding / extracellular region / metal ion binding
Similarity search - Function
Influenza RNA-dependent RNA polymerase subunit PA, endonuclease domain / Restriction Endonuclease / Polymerase acidic protein / Influenza RNA-dependent RNA polymerase subunit PA / Influenza RNA-dependent RNA polymerase subunit PA, endonuclease domain / Influenza RNA-dependent RNA polymerase subunit PA / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / L(+)-TARTARIC ACID / Polymerase acidic protein
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.751 Å
Model detailsRNA binding protein
AuthorsFudo, S. / Yamamoto, N. / Nukaga, M. / Odagiri, T. / Tashiro, M. / Hoshino, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science24590548 Japan
CitationJournal: Cryst.Growth Des. / Year: 2017
Title: Influence of Precipitants on Molecular Arrangements and Space Groups of Protein Crystals
Authors: Fudo, S. / Fei, Q. / Nukaga, M. / Hoshino, T.
History
DepositionApr 21, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 11, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 1, 2017Group: Database references
Revision 1.2Feb 19, 2020Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Polymerase acidic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5604
Polymers22,3001
Non-polymers2603
Water3,549197
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.859, 66.859, 128.003
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Polymerase acidic protein / RNA-directed RNA polymerase subunit P2


Mass: 22300.494 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 1-50, 73-197
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Puerto Rico/8/1934 H1N1 / Gene: PA / Production host: Escherichia coli (E. coli) / References: UniProt: P03433
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / 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: 3.21 Å3/Da / Density % sol: 61.65 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 0.1 M MES pH 6.0, 0.8 M Potassium sodium tartrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 19, 2015
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator, direct water cooling
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 29953 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 14 % / Rmerge(I) obs: 0.059 / Rsym value: 0.059 / Net I/σ(I): 44.219
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 14.3 % / Rmerge(I) obs: 1.359 / Mean I/σ(I) obs: 2.34 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation32.35 Å2.12 Å

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
MOLREP11.0.05phasing
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZQQ

4zqq


Resolution: 1.751→32.345 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.49
RfactorNum. reflection% reflection
Rfree0.2379 1519 5.08 %
Rwork0.1943 --
obs0.1965 29878 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 93.24 Å2 / Biso mean: 35.97 Å2 / Biso min: 19 Å2
Refinement stepCycle: final / Resolution: 1.751→32.345 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1493 0 12 197 1702
Biso mean--37.69 45.84 -
Num. residues----181
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0171532
X-RAY DIFFRACTIONf_angle_d1.6342056
X-RAY DIFFRACTIONf_chiral_restr0.123220
X-RAY DIFFRACTIONf_plane_restr0.008264
X-RAY DIFFRACTIONf_dihedral_angle_d14.58584
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7513-1.80780.3131340.257225472681100
1.8078-1.87240.26881360.229225182654100
1.8724-1.94740.29481340.226625362670100
1.9474-2.0360.25621290.218725782707100
2.036-2.14330.251430.203325202663100
2.1433-2.27760.24571490.197925502699100
2.2776-2.45340.24041400.198225732713100
2.4534-2.70020.24891370.201425892726100
2.7002-3.09060.23741410.190225992740100
3.0906-3.89280.21841420.17932634277699
3.8928-32.35020.23181340.18982715284996

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