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- PDB-2i91: 60kDa Ro autoantigen in complex with a fragment of misfolded RNA -

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Basic information

Entry
Database: PDB / ID: 2i91
Title60kDa Ro autoantigen in complex with a fragment of misfolded RNA
Components
  • 5'-R(*C*GP*GP*UP*AP*GP*GP*CP*UP*UP*UP*UP*CP*AP*A)-3'
  • 5'-R(*GP*CP*CP*UP*AP*CP*CP*C)-3'
  • 60 kDa SS-A/Ro ribonucleoprotein
KeywordsRNA Binding Protein/RNA / von Willebrand factor A / Rossmann-fold / HEAT repeat / MIDAS motif / RNA Binding Protein-RNA COMPLEX
Function / homology
Function and homology information


cell projection organization / misfolded RNA binding / ribonucleoprotein complex / metal ion binding / cytoplasm
Similarity search - Function
TROVE domain / TROVE domain superfamily / RNA-binding protein RO60 / TROVE domain / TROVE domain profile. / von Willebrand factor, type A domain / von Willebrand factor A-like domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / RNA / RNA (> 10) / RNA-binding protein RO60
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsReinisch, K.M. / Stein, A.J.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2006
Title: Structural and biochemical basis for misfolded RNA recognition by the Ro autoantigen.
Authors: Fuchs, G. / Stein, A.J. / Fu, C. / Reinisch, K.M. / Wolin, S.L.
History
DepositionSep 4, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 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_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_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.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_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_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
C: 5'-R(*GP*CP*CP*UP*AP*CP*CP*C)-3'
D: 5'-R(*C*GP*GP*UP*AP*GP*GP*CP*UP*UP*UP*UP*CP*AP*A)-3'
E: 5'-R(*GP*CP*CP*UP*AP*CP*CP*C)-3'
F: 5'-R(*C*GP*GP*UP*AP*GP*GP*CP*UP*UP*UP*UP*CP*AP*A)-3'
A: 60 kDa SS-A/Ro ribonucleoprotein
B: 60 kDa SS-A/Ro ribonucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,17410
Polymers136,0086
Non-polymers1674
Water10,106561
1
C: 5'-R(*GP*CP*CP*UP*AP*CP*CP*C)-3'
D: 5'-R(*C*GP*GP*UP*AP*GP*GP*CP*UP*UP*UP*UP*CP*AP*A)-3'
A: 60 kDa SS-A/Ro ribonucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,0875
Polymers68,0043
Non-polymers832
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: 5'-R(*GP*CP*CP*UP*AP*CP*CP*C)-3'
F: 5'-R(*C*GP*GP*UP*AP*GP*GP*CP*UP*UP*UP*UP*CP*AP*A)-3'
B: 60 kDa SS-A/Ro ribonucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,0875
Polymers68,0043
Non-polymers832
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.680, 119.980, 73.540
Angle α, β, γ (deg.)90.00, 98.91, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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RNA chain , 2 types, 4 molecules CEDF

#1: RNA chain 5'-R(*GP*CP*CP*UP*AP*CP*CP*C)-3'


Mass: 2461.529 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: RNA chain 5'-R(*C*GP*GP*UP*AP*GP*GP*CP*UP*UP*UP*UP*CP*AP*A)-3'


Mass: 4769.857 Da / Num. of mol.: 2 / Source method: obtained synthetically

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Protein , 1 types, 2 molecules AB

#3: Protein 60 kDa SS-A/Ro ribonucleoprotein / 60 kDa Ro protein / 60 kDa ribonucleoprotein Ro / RoRNP / TROVE domain family member 2


Mass: 60772.383 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: trove2 / Production host: Escherichia coli (E. coli) / References: UniProt: P42700

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Non-polymers , 3 types, 565 molecules

#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.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 561 / 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: 2.33 Å3/Da / Density % sol: 47.17 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 18-20% PEG 6000, 250 mM magnesium acetate, 100 mM sodium acetate Protein was mixed with RNA approximately 1:1., pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 600011
2magnesium acetate11
3sodium acetate11
4H2O11
5PEG 600012
6magnesium acetate12
7sodium acetate12

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 25, 2005
RadiationMonochromator: Pt-coated toroidal Si mirror for horizontal and vertical focussing followed by double flat Si crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.65→50 Å / Num. all: 35662 / Num. obs: 34410 / % possible obs: 96.5 % / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Rmerge(I) obs: 0.13 / Rsym value: 0.13 / Net I/σ(I): 12
Reflection shellResolution: 2.65→2.74 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.398 / Mean I/σ(I) obs: 3.9 / Num. unique all: 3555 / % possible all: 99.8

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Processing

Software
NameClassification
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1YVP

1yvp


Resolution: 2.65→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.285 3467 -random
Rwork0.241 ---
all0.245 35662 --
obs0.245 34410 96.5 %-
Refinement stepCycle: LAST / Resolution: 2.65→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8269 934 10 561 9774
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009158
X-RAY DIFFRACTIONc_angle_deg1.626
X-RAY DIFFRACTIONc_dihedral_angle_d23.3
X-RAY DIFFRACTIONc_improper_angle_d0.85
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDNum. reflection obs
2.65-2.670.474580.375X-RAY DIFFRACTION669
2.67-2.690.474590.375X-RAY DIFFRACTION647

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