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- PDB-4pkd: U1-70k in complex with U1 snRNA stem-loops 1 and U1-A RRM in comp... -

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Basic information

Entry
Database: PDB / ID: 4pkd
TitleU1-70k in complex with U1 snRNA stem-loops 1 and U1-A RRM in complex with stem-loop 2
Components
  • U1 small nuclear ribonucleoprotein A,U1 small nuclear ribonucleoprotein 70 kDa
  • U1 snRNA stem-loops 1 and 2 (55-MER)
KeywordsGENE REGULATION / U1-70k / U1 snRNP / Pre-mRNA splicing / Spliceosome
Function / homology
Function and homology information


negative regulation of protein refolding / regulation of ATP-dependent activity / U1 snRNP binding / mRNA Splicing - Major Pathway / positive regulation of mRNA splicing, via spliceosome / negative regulation of chaperone-mediated autophagy / U1 snRNP / U2-type prespliceosome / regulation of RNA splicing / cellular response to transforming growth factor beta stimulus ...negative regulation of protein refolding / regulation of ATP-dependent activity / U1 snRNP binding / mRNA Splicing - Major Pathway / positive regulation of mRNA splicing, via spliceosome / negative regulation of chaperone-mediated autophagy / U1 snRNP / U2-type prespliceosome / regulation of RNA splicing / cellular response to transforming growth factor beta stimulus / U1 snRNA binding / cellular response to retinoic acid / mRNA Splicing - Major Pathway / spliceosomal complex / mRNA splicing, via spliceosome / cellular response to tumor necrosis factor / nuclear speck / mRNA binding / RNA binding / nucleoplasm / nucleus
Similarity search - Function
snRNP70, RNA recognition motif / U1 small nuclear ribonucleoprotein of 70kDa N-terminal / U1 small nuclear ribonucleoprotein of 70kDa MW N terminal / : / 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. ...snRNP70, RNA recognition motif / U1 small nuclear ribonucleoprotein of 70kDa N-terminal / U1 small nuclear ribonucleoprotein of 70kDa MW N terminal / : / 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
IMIDAZOLE / RNA / RNA (> 10) / U1 small nuclear ribonucleoprotein 70 kDa / U1 small nuclear ribonucleoprotein A
Similarity search - Component
Biological speciesSus scrofa (pig)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsOubridge, C. / Kondo, Y. / van Roon, A.M. / Nagai, K.
Funding support Japan, 1items
OrganizationGrant numberCountry
Nakajima Foundation Japan
Citation
Journal: Elife / Year: 2015
Title: Crystal structure of human U1 snRNP, a small nuclear ribonucleoprotein particle, reveals the mechanism of 5' splice site recognition.
Authors: Kondo, Y. / Oubridge, C. / van Roon, A.M. / Nagai, K.
#1: Journal: Nature / Year: 2009
Title: Crystal structure of human spliceosomal U1 snRNP at 5.5 A resolution.
Authors: Pomeranz Krummel, D.A. / Oubridge, C. / Leung, A.K. / Li, J. / Nagai, K.
#2: Journal: Nature / Year: 1994
Title: Crystal structure at 1.92 A resolution of the RNA-binding domain of the U1A spliceosomal protein complexed with an RNA hairpin.
Authors: Oubridge, C. / Ito, N. / Evans, P.R. / Teo, C.H. / Nagai, K.
#3: Journal: EMBO J. / Year: 2010
Title: Functional organization of the Sm core in the crystal structure of human U1 snRNP.
Authors: Weber, G. / Trowitzsch, S. / Kastner, B. / Luhrmann, R. / Wahl, M.C.
History
DepositionMay 14, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 31, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 14, 2015Group: Database references
Revision 1.2Dec 20, 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
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_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _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_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_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
V: U1 snRNA stem-loops 1 and 2 (55-MER)
B: U1 small nuclear ribonucleoprotein A,U1 small nuclear ribonucleoprotein 70 kDa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,1126
Polymers49,9702
Non-polymers1424
Water2,036113
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6920 Å2
ΔGint-37 kcal/mol
Surface area21550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.220, 66.600, 93.730
Angle α, β, γ (deg.)90.00, 110.95, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: RNA chain U1 snRNA stem-loops 1 and 2 (55-MER)


Mass: 17786.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: See compound details. / Source: (synth.) Homo sapiens (human)
#2: Protein U1 small nuclear ribonucleoprotein A,U1 small nuclear ribonucleoprotein 70 kDa / U1A / snRNP70


Mass: 32183.576 Da / Num. of mol.: 1 / Mutation: A2G
Source method: isolated from a genetically manipulated source
Details: Both this protein and U1-70k are expressed together as a fusion protein. The C-terminus of U1-A and the linker peptide are disordered in the structure. The two proteins have been given ...Details: Both this protein and U1-70k are expressed together as a fusion protein. The C-terminus of U1-A and the linker peptide are disordered in the structure. The two proteins have been given separate chain identifiers so that their normal numbering is preserved., U1-A and this protein are expressed together as a fusion protein. The C-terminus of U1-A and the linker peptide are disordered in the structure. The two proteins have been given separate chain identifiers so that their normal numbering is preserved.
Source: (gene. exp.) Sus scrofa (pig), (gene. exp.) Homo sapiens (human)
Gene: SNRPA, SNRNP70, RNPU1Z, RPU1, SNRP70, U1AP1 / Plasmid: pET13
Details (production host): Expresses U1-A/U1-70k fusion protein
Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): pLysS / References: UniProt: Q06AA4, UniProt: P08621
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 53 % / Description: Six-sided plates
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 40% MPD, 0.15 M sodium chloride, 0.1 M sodium acetate, pH 4.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1.0332 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 22, 2011
RadiationMonochromator: Double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.5→87.54 Å / Num. all: 16115 / Num. obs: 15967 / % possible obs: 99.1 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.076 / Rsym value: 0.047 / Net I/σ(I): 11
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 3.2 / % possible all: 99.4

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Processing

SoftwareName: REFMAC / Version: 5.8.0071 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1URN

1urn


Resolution: 2.5→87 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.893 / SU B: 10.404 / SU ML: 0.232 / Cross valid method: THROUGHOUT / ESU R: 0.618 / ESU R Free: 0.305 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25791 812 5.1 %RANDOM
Rwork0.19675 ---
obs0.19992 15156 99.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.252 Å2
Baniso -1Baniso -2Baniso -3
1-3.18 Å2-0 Å2-0.12 Å2
2--0.23 Å2-0 Å2
3----2.56 Å2
Refinement stepCycle: 1 / Resolution: 2.5→87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1954 1177 8 113 3252
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0163309
X-RAY DIFFRACTIONr_bond_other_d0.0130.022465
X-RAY DIFFRACTIONr_angle_refined_deg1.911.6884715
X-RAY DIFFRACTIONr_angle_other_deg3.14235722
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.875238
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.27722.059102
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.72315377
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8221526
X-RAY DIFFRACTIONr_chiral_restr0.120.2494
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.022886
X-RAY DIFFRACTIONr_gen_planes_other0.0080.02788
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.7354.543958
X-RAY DIFFRACTIONr_mcbond_other2.7354.543957
X-RAY DIFFRACTIONr_mcangle_it4.1686.81194
X-RAY DIFFRACTIONr_mcangle_other4.1666.81195
X-RAY DIFFRACTIONr_scbond_it3.6365.5262351
X-RAY DIFFRACTIONr_scbond_other3.6355.5262352
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.6088.2383522
X-RAY DIFFRACTIONr_long_range_B_refined8.96450.30414367
X-RAY DIFFRACTIONr_long_range_B_other8.96350.30614368
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.443 65 -
Rwork0.281 1097 -
obs--98.89 %

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