[English] 日本語
Yorodumi
- PDB-4e5f: Crystal structure of avian influenza virus PAn bound to compound 1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4e5f
TitleCrystal structure of avian influenza virus PAn bound to compound 1
ComponentsPolymerase protein PA
KeywordsVIRAL PROTEIN / TRANSCRIPTION / endonuclease domain / H5N1 subtype
Function / homology
Function and homology information


cap snatching / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / endonuclease activity / host cell cytoplasm / Hydrolases; Acting on ester bonds / viral translational frameshifting / viral RNA genome replication / DNA-templated transcription / host cell nucleus / RNA binding / 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
2-hydroxyisoquinoline-1,3(2H,4H)-dione / : / Polymerase acidic protein
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.392 Å
AuthorsDuBois, R.M. / Slavish, P.J. / Webb, T.R. / White, S.W.
CitationJournal: Plos Pathog. / Year: 2012
Title: Structural and Biochemical Basis for Development of Influenza Virus Inhibitors Targeting the PA Endonuclease.
Authors: Dubois, R.M. / Slavish, P.J. / Baughman, B.M. / Yun, M.K. / Bao, J. / Webby, R.J. / Webb, T.R. / White, S.W.
History
DepositionMar 14, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 22, 2012Group: Database references
Revision 1.2Jul 26, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Sep 13, 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 / struct_ref_seq_dif / struct_site
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_asym_id / _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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Polymerase protein PA
B: Polymerase protein PA
C: Polymerase protein PA
D: Polymerase protein PA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,58024
Polymers87,6644
Non-polymers1,91720
Water1,18966
1
A: Polymerase protein PA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3956
Polymers21,9161
Non-polymers4795
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Polymerase protein PA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3956
Polymers21,9161
Non-polymers4795
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Polymerase protein PA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3956
Polymers21,9161
Non-polymers4795
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Polymerase protein PA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3956
Polymers21,9161
Non-polymers4795
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)126.568, 134.321, 126.712
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein
Polymerase protein PA / polymerase acidic protein


Mass: 21915.959 Da / Num. of mol.: 4 / Fragment: SEE REMARK 999
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Viet Nam/1203/2004 / Gene: PA / Plasmid: pET52b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5EP34
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mn
#4: Chemical
ChemComp-0N7 / 2-hydroxyisoquinoline-1,3(2H,4H)-dione


Mass: 177.157 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H7NO3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsPROTEIN COMPRISES UNP RESIDUES 1-50 AND 73-196 SEPARATED BY A GLY-GLY-SER LINKER.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.07 Å3/Da / Density % sol: 59.96 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1.5 M ammonium sulfate, 2% PEG1500, 1 mM manganese chloride, 0.1 M Tris-Cl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 17, 2011
RadiationMonochromator: double crystal Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.392→46.086 Å / Num. all: 42688 / Num. obs: 42645 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 10.3 % / Biso Wilson estimate: 59.4 Å2 / Rmerge(I) obs: 0.072 / Χ2: 1.119 / Net I/σ(I): 10.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.392-2.499.50.48842210.9271100
2.49-2.5910.30.39942000.9251100
2.59-2.710.50.30442250.9431100
2.7-2.8510.50.22442140.9631100
2.85-3.0210.50.14242381.0541100
3.02-3.2610.50.10442591.1631100
3.26-3.5810.50.06842561.381100
3.58-4.110.40.05942681.3931100
4.1-5.1710.40.06143131.4051100
5.17-46.086100.03944511.007199.5

-
Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4E5E

4e5e


Resolution: 2.392→46.086 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.895 / WRfactor Rfree: 0.2818 / WRfactor Rwork: 0.242 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7787 / SU B: 8.282 / SU ML: 0.197 / SU R Cruickshank DPI: 0.3661 / SU Rfree: 0.2732 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.366 / ESU R Free: 0.273 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2877 2154 5.1 %RANDOM
Rwork0.242 ---
obs0.2442 42613 99.31 %-
all-42909 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 92.11 Å2 / Biso mean: 47.496 Å2 / Biso min: 26.25 Å2
Baniso -1Baniso -2Baniso -3
1-0.81 Å20 Å2-0 Å2
2---1.76 Å20 Å2
3---0.95 Å2
Refinement stepCycle: LAST / Resolution: 2.392→46.086 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5959 0 100 66 6125
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0226163
X-RAY DIFFRACTIONr_angle_refined_deg1.1481.9588281
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0865717
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.6323.333318
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.987151136
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0891556
X-RAY DIFFRACTIONr_chiral_restr0.0810.2867
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024644
X-RAY DIFFRACTIONr_mcbond_it0.7251.53601
X-RAY DIFFRACTIONr_mcangle_it1.39325815
X-RAY DIFFRACTIONr_scbond_it1.68132562
X-RAY DIFFRACTIONr_scangle_it2.8684.52466
LS refinement shellResolution: 2.392→2.454 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 151 -
Rwork0.278 2734 -
all-2885 -
obs--91.82 %

+
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