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- PDB-4lj0: Nab2 Zn fingers complexed with polyadenosine -

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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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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Components

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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

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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

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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: 2.83 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

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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

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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

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)
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)

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