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- PDB-1yvp: Ro autoantigen complexed with RNAs -

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Basic information

Entry
Database: PDB / ID: 1yvp
TitleRo autoantigen complexed with RNAs
Components
  • (Y RNA sequence, ...) x 2
  • 60-kDa SS-A/Ro ribonucleoprotein
KeywordsRNA BINDING PROTEIN/RNA / HEAT repeat / von Willebrand Factor A / Rossmann fold / MIDAS motif / RNA duplex / ssRNA / 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-binding protein RO60
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.2 Å
AuthorsStein, A.J. / Fuchs, G. / Fu, C. / Wolin, S.L. / Reinisch, K.M.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2005
Title: Structural Insights into RNA Quality Control: The Ro Autoantigen Binds Misfolded RNAs via Its Central Cavity
Authors: Stein, A.J. / Fuchs, G. / Fu, C. / Wolin, S.L. / Reinisch, K.M.
History
DepositionFeb 16, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 7, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 28, 2011Group: Advisory
Revision 1.4Feb 14, 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_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: Y RNA sequence, first strand
D: Y RNA sequence, second strand
E: Y RNA sequence, first strand
F: Y RNA sequence, second strand
G: Y RNA sequence, first strand
H: Y RNA sequence, first strand
A: 60-kDa SS-A/Ro ribonucleoprotein
B: 60-kDa SS-A/Ro ribonucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,01812
Polymers141,8518
Non-polymers1674
Water7,350408
1
C: Y RNA sequence, first strand
D: Y RNA sequence, second strand
G: Y RNA sequence, first strand
A: 60-kDa SS-A/Ro ribonucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,0096
Polymers70,9264
Non-polymers832
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Y RNA sequence, first strand
F: Y RNA sequence, second strand
H: Y RNA sequence, first strand
B: 60-kDa SS-A/Ro ribonucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,0096
Polymers70,9264
Non-polymers832
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.30, 153.65, 80.56
Angle α, β, γ (deg.)90, 92.8, 90
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211

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Components

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Y RNA sequence, ... , 2 types, 6 molecules CEGHDF

#1: RNA chain
Y RNA sequence, first strand


Mass: 3318.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: chains G and H are single strands bound by protein
#2: RNA chain Y RNA sequence, second strand


Mass: 3515.599 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 / Ro autoantigen / 60 kDa Ro protein / 60 kDa ribonucleoprotein Ro / RoRNP


Mass: 60772.383 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: protein A binds RNA chain G, B binds H / Source: (gene. exp.) Xenopus laevis (African clawed frog) / Cell line (production host): Tn5 B1-4 / Organ (production host): eggs / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P42700

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Non-polymers , 3 types, 412 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.: 408 / 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: 2.7 Å3/Da / Density % sol: 53.9 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 3.6
Details: MPD, sodium acetate, magnesium acetate, DTT, pH 3.6, VAPOR DIFFUSION, HANGING DROP, temperature 278K
Components of the solutions
IDNameCrystal-IDSol-ID
1MPD11
2sodium acetate11
3magnesium acetate11
4DTT11
5MPD12
6sodium acetate12
7magnesium acetate12
8DTT12

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1
DetectorDetector: CCD / Date: Aug 24, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. all: 72908 / Num. obs: 72908 / % possible obs: 95 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.2→2.28 Å / % possible all: 86.3

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement
SOLVEphasing
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: MIRAS / Resolution: 2.2→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.238 7098 10 %Random
Rwork0.202 ---
all0.2021 70300 --
obs0.2021 70300 --
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8378 1094 10 408 9890
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0064
X-RAY DIFFRACTIONc_angle_deg1.269

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