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- PDB-1nu4: U1A RNA binding domain at 1.8 angstrom resolution reveals a pre-o... -

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Basic information

Entry
Database: PDB / ID: 1nu4
TitleU1A RNA binding domain at 1.8 angstrom resolution reveals a pre-organized C-terminal helix
ComponentsU1A RNA binding domain
KeywordsRNA BINDING PROTEIN / RNA recognition motif / U1 small nuclear ribonucleoprotein / RNA binding domain
Function / homology
Function and homology information


U1 snRNP binding / U1 snRNP / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / mRNA Splicing - Major Pathway / spliceosomal complex / mRNA splicing, via spliceosome / DNA binding / RNA binding / nucleoplasm ...U1 snRNP binding / U1 snRNP / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / mRNA Splicing - Major Pathway / spliceosomal complex / mRNA splicing, via spliceosome / DNA binding / RNA binding / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
U1 small nuclear ribonucleoprotein A, RNA recognition motif 2 / U1 small nuclear ribonucleoprotein A, RNA recognition motif 1 / RRM (RNA recognition motif) domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Plaits ...U1 small nuclear ribonucleoprotein A, RNA recognition motif 2 / U1 small nuclear ribonucleoprotein A, RNA recognition motif 1 / RRM (RNA recognition motif) domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
MALONIC ACID / U1 small nuclear ribonucleoprotein A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsRupert, P.B. / Xiao, H. / Ferre-D'Amare, A.R.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2003
Title: U1A RNA-binding domain at 1.8 A resolution.
Authors: Rupert, P.B. / Xiao, H. / Ferre-D'Amare, A.R.
History
DepositionJan 30, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 14, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Apr 29, 2015Group: Non-polymer description
Revision 1.5Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / 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 / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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.ptnr3_symmetry / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: U1A RNA binding domain
B: U1A RNA binding domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,78819
Polymers22,4182
Non-polymers1,37017
Water1,78399
1
A: U1A RNA binding domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,8829
Polymers11,2091
Non-polymers6738
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: U1A RNA binding domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,90610
Polymers11,2091
Non-polymers6979
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
A: U1A RNA binding domain
B: U1A RNA binding domain
hetero molecules

A: U1A RNA binding domain
B: U1A RNA binding domain
hetero molecules

A: U1A RNA binding domain
B: U1A RNA binding domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,36557
Polymers67,2556
Non-polymers4,11151
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area17900 Å2
ΔGint-214 kcal/mol
Surface area23100 Å2
MethodPISA
4
B: U1A RNA binding domain
hetero molecules

B: U1A RNA binding domain
hetero molecules

B: U1A RNA binding domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,71930
Polymers33,6273
Non-polymers2,09227
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area8170 Å2
ΔGint-129 kcal/mol
Surface area13880 Å2
MethodPISA
5
A: U1A RNA binding domain
hetero molecules

A: U1A RNA binding domain
hetero molecules

A: U1A RNA binding domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,64627
Polymers33,6273
Non-polymers2,01924
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area5960 Å2
ΔGint-78 kcal/mol
Surface area12990 Å2
MethodPISA
6
A: U1A RNA binding domain
hetero molecules

A: U1A RNA binding domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,76418
Polymers22,4182
Non-polymers1,34616
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation17_555x-y+1/3,-y+2/3,-z+2/31
Buried area4050 Å2
ΔGint-60 kcal/mol
Surface area8620 Å2
MethodPISA
7
B: U1A RNA binding domain
hetero molecules

B: U1A RNA binding domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,81320
Polymers22,4182
Non-polymers1,39518
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555-x+2/3,-x+y+1/3,-z+1/31
Buried area4700 Å2
ΔGint-88 kcal/mol
Surface area9930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.819, 91.819, 120.448
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-502-

MG

21A-504-

MG

31B-501-

MG

41B-503-

MG

51A-211-

HOH

61A-212-

HOH

71A-239-

HOH

81A-241-

HOH

91B-213-

HOH

101B-220-

HOH

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Components

#1: Protein U1A RNA binding domain / U1 snRNP A protein


Mass: 11209.120 Da / Num. of mol.: 2 / Fragment: U1A RBD1 / Mutation: Y31H,Q36R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P09012
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID / Malonic acid


Mass: 104.061 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C3H4O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 99 / 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: 2.18 Å3/Da / Density % sol: 43.56 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: Potassium Malonate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
pH: 6.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
10.15 mMRNA1drop
20.22 mMprotein1drop
35 mMpotassium cacodylate1droppH6.5
41.25 mM1dropMgCl2
50.05 mMEDTA1drop
62.0-2.4 Msodium malonate1reservoirpH5.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 15, 2002 / Details: osmics mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. all: 18308 / Num. obs: 17618 / % possible obs: 96.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 31.1 Å2 / Rmerge(I) obs: 0.031 / Rsym value: 0.031 / Net I/σ(I): 37.6
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.311 / Mean I/σ(I) obs: 2.46 / Num. unique all: 1365 / Rsym value: 0.311 / % possible all: 76.8
Reflection
*PLUS
Lowest resolution: 30 Å / Num. measured all: 70351
Reflection shell
*PLUS
% possible obs: 76.8 %

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1urn

1urn


Resolution: 1.8→29.16 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.234 1749 9.9 %RANDOM
Rwork0.203 ---
all0.203 18308 --
obs0.203 17616 96.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 57.9717 Å2 / ksol: 0.401443 e/Å3
Displacement parametersBiso mean: 40.3 Å2
Baniso -1Baniso -2Baniso -3
1-1.15 Å22.83 Å20 Å2
2--1.15 Å20 Å2
3----2.3 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 1.8→29.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1450 0 89 99 1638
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d22.8
X-RAY DIFFRACTIONc_improper_angle_d0.64
X-RAY DIFFRACTIONc_mcbond_it2.821.5
X-RAY DIFFRACTIONc_mcangle_it4.012
X-RAY DIFFRACTIONc_scbond_it4.162
X-RAY DIFFRACTIONc_scangle_it5.742.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.352 228 9.4 %
Rwork0.322 2210 -
obs--81.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3MLA.PARAMMLA.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 30 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.2344 / Rfactor Rwork: 0.2032
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0056
X-RAY DIFFRACTIONc_angle_deg1.105
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.64

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