[English] 日本語
Yorodumi
- PDB-4lj0: Nab2 Zn fingers complexed with polyadenosine -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4lj0
TitleNab2 Zn fingers complexed with polyadenosine
Components
  • Nab2
  • polyadenosine RNA
KeywordsRNA BINDING PROTEIN / Zn finger / polyadenylation / polyadenosine RNA
Function / homology
Function and homology information


: / poly(A) binding / regulation of mRNA stability / nucleus / metal ion binding
Similarity search - Function
CCCH zinc finger - #30 / CCCH zinc finger / Nuclear polyadenylated RNA-binding protein Nab2/ZC3H14 / RNA-binding, Nab2-type zinc finger / Few Secondary Structures / Irregular
Similarity search - Domain/homology
ACETATE ION / RNA / Uncharacterized protein
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.15 Å
AuthorsStewart, M. / Kuhlmann, S.I. / Valkov, E.
CitationJournal: Nucleic Acids Res. / Year: 2014
Title: Structural basis for the molecular recognition of polyadenosine RNA by Nab2 Zn fingers.
Authors: Kuhlmann, S.I. / Valkov, E. / Stewart, M.
History
DepositionJul 4, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2014Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_conn.ptnr2_label_seq_id / _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: Nab2
B: Nab2
C: polyadenosine RNA
D: polyadenosine RNA
E: polyadenosine RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,42317
Polymers22,8165
Non-polymers60812
Water45025
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.929, 90.929, 54.081
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

-
Components

-
Protein / RNA chain , 2 types, 5 molecules ABCDE

#1: Protein Nab2


Mass: 7524.717 Da / Num. of mol.: 2 / Fragment: Nab2 Zn fingers 3-5, UNP residues 401-466
Source method: isolated from a genetically manipulated source
Details: see publication / Source: (gene. exp.) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0057680, Nab2 / Production host: Escherichia coli (E. coli) / References: UniProt: G0SCL7
#2: RNA chain polyadenosine RNA


Mass: 2588.689 Da / Num. of mol.: 3 / Source method: obtained synthetically / Details: AAAAAA

-
Non-polymers , 4 types, 37 molecules

#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.83 Å3/Da / Density % sol: 56.52 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: see manuscript, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 17, 2012 / Details: mirrors
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.15→44.58 Å / Num. all: 14357 / Num. obs: 14357 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Net I/σ(I): 12.4
Reflection shellResolution: 2.15→2.27 Å / Mean I/σ(I) obs: 2.3 / % possible all: 100

-
Processing

Software
NameVersionClassification
EDNAdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8.2_1309)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.15→44.58 Å / SU ML: 0.23 / σ(F): 1.34 / Phase error: 21.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2066 701 4.89 %random
Rwork0.1946 ---
obs0.1952 14328 99.93 %-
all-14328 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.15→44.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1024 217 18 25 1284
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031310
X-RAY DIFFRACTIONf_angle_d0.8661813
X-RAY DIFFRACTIONf_dihedral_angle_d14.125523
X-RAY DIFFRACTIONf_chiral_restr0.043185
X-RAY DIFFRACTIONf_plane_restr0.004207
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.3160.29021450.2662679X-RAY DIFFRACTION100
2.316-2.54910.24161490.21682683X-RAY DIFFRACTION100
2.5491-2.91780.23051230.21452711X-RAY DIFFRACTION100
2.9178-3.67590.22611480.20192724X-RAY DIFFRACTION100
3.6759-44.58990.17221360.17482830X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
14.2059-2.1360.40455.20223.04792.6099-0.0367-0.640.16120.36320.43740.2480.3042-0.0939-0.3010.2993-0.2037-0.01650.45840.07340.4747-26.972530.8932-16.4063
23.4016-0.410.18963.95710.44132.34890.07770.0894-0.06010.1508-0.1583-0.0333-0.2473-0.07850.0690.3922-0.088-0.02890.3714-0.02480.2834-41.925124.7447-16.9515
38.2898-0.8693.17299.6501-2.13148.6044-0.096-0.04960.5766-0.0563-0.01220.3175-0.9506-1.0540.05810.4810.059-0.05360.4911-0.03450.3159-49.024732.7773-21.6716
44.6053-2.58580.26374.3991-3.0564.18150.2015-1.42530.23551.39760.3035-0.0762-0.29170.241-0.36510.5354-0.17430.03850.9195-0.0940.6388-21.431938.8893-2.7161
56.5005-0.5894-3.64133.32120.77296.09520.3228-1.42091.9984-0.01060.2019-0.4883-0.88370.6083-0.39090.4341-0.13450.12650.5939-0.14720.6115-32.73642.89420.7055
64.2532.55252.23262.22070.36142.5635-0.0897-0.24611.62830.0031-0.09630.3998-1.0669-0.01490.36481.3448-0.21310.31630.4943-0.09141.7999-31.015756.9495-4.3455
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 402:419)
2X-RAY DIFFRACTION2(chain A and resid 420:448)
3X-RAY DIFFRACTION3(chain A and resid 449:466)
4X-RAY DIFFRACTION4(chain B and resid 402:414)
5X-RAY DIFFRACTION5(chain B and resid 415:444)
6X-RAY DIFFRACTION6(chain B and resid 445:465)

+
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://pdbjlvh1.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