[English] 日本語
Yorodumi
- PDB-2jdq: C-terminal domain of influenza A virus polymerase PB2 subunit in ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2jdq
TitleC-terminal domain of influenza A virus polymerase PB2 subunit in complex with human importin alpha5
Components
  • IMPORTIN ALPHA-1 SUBUNITImportin α
  • POLYMERASE BASIC PROTEIN 2
KeywordsPROTEIN TRANSPORT / TRANSPORT / PB2 SUBUNIT / NUCLEAR PROTEIN / ARMADILLO REPEATS / INFLUENZA A VIRUS RNA-DEPENDENT RNA POLYMERASE / BIPARTITE NUCLEAR LOCALISATION SIGNAL / NUCLEAR IMPORT ADAPTER / HUMAN IMPORTIN ALPHA5 / HOST-VIRUS INTERACTION
Function / homology
Function and homology information


satellite cell activation involved in skeletal muscle regeneration / skeletal muscle satellite cell proliferation / Inhibition of nitric oxide production / regulation of DNA recombination / Transport of Ribonucleoproteins into the Host Nucleus / NS1 Mediated Effects on Host Pathways / NLS-dependent protein nuclear import complex / Apoptosis induced DNA fragmentation / postsynapse to nucleus signaling pathway / regulation of canonical Wnt signaling pathway ...satellite cell activation involved in skeletal muscle regeneration / skeletal muscle satellite cell proliferation / Inhibition of nitric oxide production / regulation of DNA recombination / Transport of Ribonucleoproteins into the Host Nucleus / NS1 Mediated Effects on Host Pathways / NLS-dependent protein nuclear import complex / Apoptosis induced DNA fragmentation / postsynapse to nucleus signaling pathway / regulation of canonical Wnt signaling pathway / nuclear import signal receptor activity / nuclear localization sequence binding / NLS-bearing protein import into nucleus / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / cap snatching / Vpr-mediated nuclear import of PICs / 7-methylguanosine mRNA capping / Integration of provirus / host cell mitochondrion / nuclear pore / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / Assembly of the ORC complex at the origin of replication / virion component / ISG15 antiviral mechanism / protein import into nucleus / Interferon alpha/beta signaling / regulation of apoptotic process / postsynaptic density / viral RNA genome replication / RNA-dependent RNA polymerase activity / dendrite / DNA-templated transcription / glutamatergic synapse / host cell nucleus / RNA binding / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Polymerase Basic Protein 2, C-terminal domain / Influenza RNA-dependent RNA polymerase subunit PB2 / PB2, C-terminal / Importin subunit alpha / Atypical Arm repeat / Importin-alpha, importin-beta-binding domain superfamily / Importin beta binding domain / Atypical Arm repeat / Importin-alpha, importin-beta-binding domain / IBB domain profile. ...Polymerase Basic Protein 2, C-terminal domain / Influenza RNA-dependent RNA polymerase subunit PB2 / PB2, C-terminal / Importin subunit alpha / Atypical Arm repeat / Importin-alpha, importin-beta-binding domain superfamily / Importin beta binding domain / Atypical Arm repeat / Importin-alpha, importin-beta-binding domain / IBB domain profile. / : / : / : / : / : / Influenza RNA polymerase PB2 N-terminal region / Influenza RNA polymerase PB2 second domain / Influenza RNA polymerase PB2 middle domain / Influenza RNA polymerase PB2 6th domain / Influenza RNA polymerase PB2 C-terminal domain / : / : / Influenza RNA polymerase PB2 helical domain / Influenza RNA polymerase PB2 CAP binding domain / Defensin A-like / Armadillo/plakoglobin ARM repeat profile. / Armadillo/beta-catenin-like repeat / Armadillo/beta-catenin-like repeats / Armadillo / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Polymerase basic protein 2 / Importin subunit alpha-5
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
INFLUENZA A VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsTarendeau, F. / Guilligay, D. / Mas, P. / Boulo, S. / Baudin, F. / Ruigrok, R.W.H. / Hart, D.J. / Cusack, S.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2007
Title: Structure and Nuclear Import Function of the C- Terminal Domain of Influenza Virus Polymerase Pb2 Subunit
Authors: Tarendeau, F. / Boudet, J. / Guilligay, D. / Mas, P. / Bougault, C. / Boulo, S. / Baudin, F. / Ruigrok, R.W.H. / Daigle, N. / Ellenberg, J. / Cusack, S. / Simorre, J.-P. / Hart, D.J.
History
DepositionJan 11, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 27, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 9, 2019Group: Data collection / Derived calculations / Other
Category: pdbx_database_status / pdbx_struct_assembly ...pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Item: _pdbx_database_status.status_code_sf
Revision 1.3Dec 13, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: IMPORTIN ALPHA-1 SUBUNIT
B: IMPORTIN ALPHA-1 SUBUNIT
D: POLYMERASE BASIC PROTEIN 2
E: POLYMERASE BASIC PROTEIN 2


Theoretical massNumber of molelcules
Total (without water)117,3464
Polymers117,3464
Non-polymers00
Water4,774265
1
A: IMPORTIN ALPHA-1 SUBUNIT
E: POLYMERASE BASIC PROTEIN 2


Theoretical massNumber of molelcules
Total (without water)58,6732
Polymers58,6732
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3230 Å2
ΔGint4 kcal/mol
Surface area23340 Å2
MethodPISA
2
B: IMPORTIN ALPHA-1 SUBUNIT
D: POLYMERASE BASIC PROTEIN 2


Theoretical massNumber of molelcules
Total (without water)58,6732
Polymers58,6732
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3430 Å2
ΔGint7 kcal/mol
Surface area23720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.970, 100.550, 151.840
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.012908, 0.998917, 0.044708), (-0.998464, 0.010467, 0.054411), (0.053884, -0.045341, 0.997517)
Vector: 21.1432, 120.6953, 36.3854)

-
Components

#1: Protein IMPORTIN ALPHA-1 SUBUNIT / Importin α / KARYOPHERIN ALPHA-1 SUBUNIT / SRP1-BETA / RAG COHORT PROTEIN 2 / NUCLEOPROTEIN INTERACTOR 1 / NPI-1 ...KARYOPHERIN ALPHA-1 SUBUNIT / SRP1-BETA / RAG COHORT PROTEIN 2 / NUCLEOPROTEIN INTERACTOR 1 / NPI-1 / IMPORTIN ALPHA 5


Mass: 49687.676 Da / Num. of mol.: 2 / Fragment: RESIDUES 66-512
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P52294
#2: Protein POLYMERASE BASIC PROTEIN 2 / RNA-DIRECTED RNA POLYMERASE SUBUNIT P3 / INFLUENZA A VIRUS POLYMERASE PB2 SUBUNIT


Mass: 8985.251 Da / Num. of mol.: 2 / Fragment: C-TERMINAL DOMAIN, RESIDUES 678-759
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) INFLUENZA A VIRUS / Strain: A/VICTORIA/3/75 (H3N2) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P31345
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 265 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsADDITIONAL GLYCINE AT N-TERMINUS DUE TO CLONING (CHAINS DE) ADDITIONAL GLYCINE-ALANINE-METHIONINE ...ADDITIONAL GLYCINE AT N-TERMINUS DUE TO CLONING (CHAINS DE) ADDITIONAL GLYCINE-ALANINE-METHIONINE AT N-TERMINUS DUE TO CLONING (CHAINS AB)

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.1 Å3/Da / Density % sol: 60.3 %
Crystal growpH: 4.6
Details: 1 MICROLITRE OF PROTEIN SOLUTION, AT 20 MG/ML IN 30 MM TRIS-HCL, PH 7.5, 150 MM NACL, 3 MM BETA-MERCAPTOETHANOL WAS MIXED WITH AN EQUAL VOLUME OF RESERVOIR SOLUTION (0.1 M NAAC, PH 4.6, 5 MM CACL2, 15% MPD)

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.07225
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 15, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07225 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 74104 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 9.4
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 4.06 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 2.4 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1Q1S

1q1s


Resolution: 2.2→30 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.929 / SU B: 13.255 / SU ML: 0.166 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.205 / ESU R Free: 0.183 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.247 2969 4 %RANDOM
Rwork0.206 ---
obs0.208 71120 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.77 Å2
Baniso -1Baniso -2Baniso -3
1-2.72 Å20 Å20 Å2
2--0.08 Å20 Å2
3----2.8 Å2
Refinement stepCycle: LAST / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7597 0 0 265 7862
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0227715
X-RAY DIFFRACTIONr_bond_other_d0.0010.025213
X-RAY DIFFRACTIONr_angle_refined_deg1.2731.97210454
X-RAY DIFFRACTIONr_angle_other_deg0.928312806
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5235972
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.58825.06332
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.576151398
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3911546
X-RAY DIFFRACTIONr_chiral_restr0.0730.21233
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.028484
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021436
X-RAY DIFFRACTIONr_nbd_refined0.2020.21841
X-RAY DIFFRACTIONr_nbd_other0.1760.25350
X-RAY DIFFRACTIONr_nbtor_refined0.1740.23828
X-RAY DIFFRACTIONr_nbtor_other0.0870.23928
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1760.2273
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1890.229
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1870.264
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1850.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7971.56353
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.92127872
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.48333264
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.2134.52582
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.26 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.34 221
Rwork0.284 5187
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)
12.2868-0.80610.63592.1945-1.60613.3045-0.04370.4770.5576-0.3652-0.00730.1454-0.9949-0.28630.05110.42280.1289-0.12140.1760.11030.034450.16675.5332.349
21.1563-0.17-0.42811.09321.20241.374-0.1119-0.0762-0.04030.3140.06940.005-0.29070.01730.04250.23310.0024-0.02020.18120.02870.057761.31665.72143.729
31.35110.19470.61741.40691.38484.1821-0.07530.2427-0.1873-0.3137-0.29930.42830.0141-0.98610.37460.2033-0.0353-0.04030.3393-0.15310.028247.0633.137-28.839
41.53571.1879-0.70763.151-0.29311.2696-0.0358-0.0832-0.11870.22910.0118-0.13780.31430.05830.0240.2111-0.01420.01470.223-0.00720.062253.76836.27814.208
55.12793.7247-4.561512.9164-2.010516.3221-0.5201-0.318-1.03650.5292-0.0624-0.68881.76640.28310.58260.4305-0.01320.16130.03190.02250.109158.8821.7781.668
610.3317-2.2681-3.2044.28893.313416.2995-0.038-0.3449-0.5210.4099-0.40230.88030.406-1.36460.44030.14860.07970.04940.2049-0.0740.151343.77162.26740.154
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A47 - 281
2X-RAY DIFFRACTION1E749 - 757
3X-RAY DIFFRACTION2A282 - 470
4X-RAY DIFFRACTION3B47 - 356
5X-RAY DIFFRACTION3D748 - 756
6X-RAY DIFFRACTION4B357 - 472
7X-RAY DIFFRACTION5D688 - 741
8X-RAY DIFFRACTION6E686 - 741

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more