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- PDB-3g9y: Crystal structure of the second zinc finger from ZRANB2/ZNF265 bo... -

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Basic information

Entry
Database: PDB / ID: 3g9y
TitleCrystal structure of the second zinc finger from ZRANB2/ZNF265 bound to 6 nt ssRNA sequence AGGUAA
Components
  • RNA (5'-R(*AP*GP*GP*UP*AP*A)-3')
  • Zinc finger Ran-binding domain-containing protein 2
KeywordsTRANSCRIPTION/RNA / zinc finger / ZRANB2 / ZNF265 / RNA / protein-RNA complex / TRANSCRIPTION-RNA COMPLEX
Function / homology
Function and homology information


RNA splicing / lipopolysaccharide binding / mRNA processing / RNA binding / nucleoplasm / metal ion binding
Similarity search - Function
Zinc finger Ran-binding domain-containing protein 2 / Zinc finger domain / Zn-finger in Ran binding protein and others / Zinc finger RanBP2 type profile. / Zinc finger RanBP2-type signature. / Zinc finger, RanBP2-type superfamily / Zinc finger, RanBP2-type
Similarity search - Domain/homology
RNA / Zinc finger Ran-binding domain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.4 Å
AuthorsLoughlin, F.E. / McGrath, A.P. / Lee, M. / Guss, J.M. / Mackay, J.P.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: The zinc fingers of the SR-like protein ZRANB2 are single-stranded RNA-binding domains that recognize 5' splice site-like sequences
Authors: Loughlin, F.E. / Mansfield, R.E. / Vaz, P.M. / McGrath, A.P. / Setiyaputra, S. / Gamsjaeger, R. / Chen, E.S. / Morris, B.J. / Guss, J.M. / Mackay, J.P.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2008
Title: Crystallization of a ZRANB2-RNA complex
Authors: Loughlin, F.E. / Lee, M. / Guss, J.M. / Mackay, J.P.
History
DepositionFeb 15, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_special_symmetry / 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 / _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_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_ref_seq_dif.details / _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: Zinc finger Ran-binding domain-containing protein 2
C: RNA (5'-R(*AP*GP*GP*UP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,7643
Polymers5,6982
Non-polymers651
Water55831
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.519, 54.519, 48.071
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11C-1-

A

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Components

#1: Protein/peptide Zinc finger Ran-binding domain-containing protein 2 / Zinc finger protein 265 / Zinc finger / splicing


Mass: 3759.196 Da / Num. of mol.: 1 / Fragment: Zinc finger domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ZRANB2 / Plasmid: pGEX-2T / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Rosetta2 / References: UniProt: O95218
#2: RNA chain RNA (5'-R(*AP*GP*GP*UP*AP*A)-3')


Mass: 1939.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Chemically synthesized 6 nt ssRNA
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 2

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Sample preparation

CrystalDensity Matthews: 1.86 Å3/Da / Density % sol: 33.75 % / Mosaicity: 0.37 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2.2M malic acid, 0.1M bis-Tris propane, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1malic acid11
2bis-Tris propane11
3HOH11
4malic acid12
5bis-Tris propane12
6HOH12

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
ROTATING ANODERIGAKU RU20011.54178
SYNCHROTRONAPS 23-ID-D20.97942
Detector
TypeIDDetectorDateDetails
MAR scanner 345 mm plate1IMAGE PLATEApr 23, 2008OSMIC MIRRORS
MARRESEARCH2CCDAug 12, 2008
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Ni FILTERSINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.541781
20.979421
ReflectionRedundancy: 16 % / Av σ(I) over netI: 32.12 / Number: 93867 / Rmerge(I) obs: 0.039 / Χ2: 1 / D res high: 1.61 Å / D res low: 40 Å / Num. obs: 5860 / % possible obs: 99.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.37409810.0361.00514.3
3.474.3710010.0291.00815.9
3.033.4799.710.0290.99316.2
2.753.0310010.0350.98416.2
2.562.7510010.0391.01816.5
2.42.5610010.0411.02616.5
2.282.410010.0431.01816.4
2.192.2810010.0471.0116.5
2.12.1910010.0531.01216.5
2.032.110010.0630.99816.3
1.972.0310010.0721.02116.4
1.911.9710010.079116.2
1.861.9110010.0840.98116.3
1.811.8610010.0941.01716.2
1.771.8110010.1070.99416.1
1.731.7710010.1270.99716.2
1.71.7310010.1380.98416
1.671.710010.1751.03115.9
1.641.6710010.160.99315.8
1.611.6410010.2010.98414.3
ReflectionResolution: 1.4→50 Å / Num. obs: 8565 / % possible obs: 98.6 % / Redundancy: 23.6 % / Rmerge(I) obs: 0.077 / Χ2: 1.009 / Net I/σ(I): 32.12
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.4-1.4220.90.6534161.0181,297.7
1.42-1.4521.50.5564030.9951,296.9
1.45-1.4821.10.4784091.0151,298.6
1.48-1.5121.10.384191.0161,296.8
1.51-1.5421.40.2934091.0071,298.1
1.54-1.5821.10.2464171.0011,298.6
1.58-1.6221.20.2064041.0091,297.3
1.62-1.6621.20.1764080.9951,297.8
1.66-1.71210.1564250.9991,299.1
1.71-1.76210.1414291.0121,299.1
1.76-1.8321.10.1164171.0111,298.6
1.83-1.921.20.1114211.0061,298.6
1.9-1.9920.80.1044241.0031,299.1
1.99-2.0921.60.1034311.0071,298.2
2.09-2.2230.30.134271.0431,299.5
2.22-2.3930.70.1064420.9971,299.5
2.39-2.6330.50.0974370.9881,299.5
2.63-3.0230.10.0844551.0071,299.3
3.02-3.828.40.0644521.0131,2100
3.8-5023.80.0575201.0231,299.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefmac_5.5.0063refinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SHELXEmodel building
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.4→33.69 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.942 / WRfactor Rfree: 0.268 / WRfactor Rwork: 0.229 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 1.948 / SU ML: 0.05 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.074 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.235 387 4.5 %RANDOM
Rwork0.201 ---
obs0.203 8548 98.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 44.99 Å2 / Biso mean: 27.367 Å2 / Biso min: 17.32 Å2
Baniso -1Baniso -2Baniso -3
1-1.25 Å20.62 Å20 Å2
2--1.25 Å20 Å2
3----1.87 Å2
Refinement stepCycle: LAST / Resolution: 1.4→33.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms234 129 1 31 395
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.021423
X-RAY DIFFRACTIONr_bond_other_d0.0010.02228
X-RAY DIFFRACTIONr_angle_refined_deg1.5472.388608
X-RAY DIFFRACTIONr_angle_other_deg1.0273.014556
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.921530
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.08224.61513
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.5051542
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.616152
X-RAY DIFFRACTIONr_chiral_restr0.0660.268
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02355
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0265
X-RAY DIFFRACTIONr_mcbond_it0.5891.5149
X-RAY DIFFRACTIONr_mcbond_other0.1671.557
X-RAY DIFFRACTIONr_mcangle_it1.0142241
X-RAY DIFFRACTIONr_scbond_it1.6273274
X-RAY DIFFRACTIONr_scangle_it2.3244.5366
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.403-1.440.238290.22953361890.939
1.44-1.4790.271260.22757561198.363
1.479-1.5220.225280.22255059297.635
1.522-1.5690.197200.19353656997.715
1.569-1.620.203230.18652956398.046
1.62-1.6770.18200.17551153998.516
1.677-1.740.226190.1849852498.664
1.74-1.8110.198140.1849050999.018
1.811-1.8910.266340.18444948898.975
1.891-1.9830.14260.17344147099.362
1.983-2.090.183270.20641945398.455
2.09-2.2160.224130.17340542099.524
2.216-2.3680.179190.17638440699.261
2.368-2.5570.17580.198361369100
2.557-2.7990.293200.21833835999.721
2.799-3.1270.197130.215308321100
3.127-3.6060.14390.191281290100
3.606-4.4040.207150.16523725399.605
4.404-6.1750.246110.206193204100
6.175-33.6910.508130.348123136100
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)
12.186-2.6915-1.75797.56973.550516.6561-0.07760.14030.2129-0.450.2851-0.6029-0.31860.7048-0.2074-0.1065-0.02480.0579-0.0360.0130.0001-5.4248.58614.026
24.26850.5110.55475.70730.39211.6573-0.15210.1901-0.2163-0.37310.12390.2630.1201-0.8570.0282-0.1019-0.01020.0076-0.04550.0343-0.0255-12.55846.76514.859
35.8621-7.56431.524415.1251-4.71545.0625-0.05360.41440.2344-0.2795-0.3098-0.68850.07290.36650.3634-0.02270.0462-0.0004-0.0730.0465-0.052-11.47555.84714.528
414.4206-0.79158.066613.4111-2.683415.05870.23430.2302-0.922-1.20480.077-0.29341.3934-0.2636-0.31140.1379-0.02030.1081-0.0349-0.01520.0109-9.16836.87112.121
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A67 - 81
2X-RAY DIFFRACTION2A82 - 90
3X-RAY DIFFRACTION3A91 - 95
4X-RAY DIFFRACTION4C1 - 4

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