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- PDB-1zzn: Crystal structure of a group I intron/two exon complex that inclu... -

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Basic information

Entry
Database: PDB / ID: 1zzn
TitleCrystal structure of a group I intron/two exon complex that includes all catalytic metal ion ligands.
Components
  • 197-MER
  • 5'-R(*AP*AP*GP*CP*CP*AP*CP*AP*CP*AP*AP*AP*CP*CP*AP*GP*AP*CP*GP*GP*CP*C)-3'
  • 5'-R(*CP*AP*(5MU))-3'
  • U1 SMALL NUCLEAR RIBONUCLEOPROTEIN A RNA BINDING DOMAIN
KeywordsSTRUCTURAL PROTEIN/RNA / RNA structure / ribozyme / self-splicing intron / Azoarcus / two-metal-ion mechanism / STRUCTURAL PROTEIN-RNA COMPLEX
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
: / RNA / RNA (> 10) / RNA (> 100) / U1 small nuclear ribonucleoprotein A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 3.37 Å
AuthorsStahley, M.R. / Strobel, S.A.
Citation
Journal: Science / Year: 2005
Title: Structural evidence for a two-metal-ion mechanism of group I intron splicing.
Authors: Stahley, M.R. / Strobel, S.A.
#1: Journal: Nature / Year: 2004
Title: Crystal Structure of a Self-Splicing Group I Intron with Both Exons
Authors: Adams, P.L. / Stahley, M.R. / Kosek, A.B. / Wang, J. / Strobel, S.A.
#2: Journal: RNA / Year: 2004
Title: Crystal Structure of a group I intron splicing intermediate
Authors: Adams, P.L. / Stahley, M.R. / Gill, M.L. / Kosek, A.B. / Wang, J. / Strobel, S.A.
#3: Journal: Cell(Cambridge,Mass.) / Year: 1981
Title: In vitro splicing of the ribosomal RNA precursor of tetrahymena: involvement of a guanosine nucleotide in the excision of intervening sequence
Authors: Cech, T.R. / Zaug, A.J. / Grabowaski, P.J.
#4: Journal: Nature / Year: 1992
Title: Self-splicing intron in tRNA genes of widely divergent bacteria
Authors: Reinhold-Hurek, B. / Shub, D.A.
History
DepositionJun 14, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 30, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Oct 20, 2021Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / 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_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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _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_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.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_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
Revision 1.5Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 999SEQUENCE NUCLEOTIDES 1001B TO 1014B BELONG TO AN ENGINEERED U1A LOOP AND ARE INSERTED BETWEEN GUA- ...SEQUENCE NUCLEOTIDES 1001B TO 1014B BELONG TO AN ENGINEERED U1A LOOP AND ARE INSERTED BETWEEN GUA-107B AND CYT-112B. THERE ARE NO NUCLEOTIDES BETWEEN GUA-1B AND GUA-5B DUE TO A CLONING DESIGN. CHAINS B AND C ARE TWO PARTS OF THE ORIGINAL ONE INTRON SEQUENCE BECAUSE OF AN EXPERIMENTAL DESIGN. THE FIRST THREE RESIDUES IN U1A PROTEIN WERE MISSING IN THE STRUCTURE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: 197-MER
C: 5'-R(*AP*AP*GP*CP*CP*AP*CP*AP*CP*AP*AP*AP*CP*CP*AP*GP*AP*CP*GP*GP*CP*C)-3'
D: 5'-R(*CP*AP*(5MU))-3'
A: U1 SMALL NUCLEAR RIBONUCLEOPROTEIN A RNA BINDING DOMAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,51310
Polymers83,3524
Non-polymers1616
Water97354
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)108.466, 108.466, 246.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122

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Components

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RNA chain , 3 types, 3 molecules BCD

#1: RNA chain 197-MER


Mass: 64057.023 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: RNA WAS IS TRANSCRIBED BY T7 RNA POLYMERASE. SEQUENCE FROM AZOARCUS GROUP I INTRON
#2: RNA chain 5'-R(*AP*AP*GP*CP*CP*AP*CP*AP*CP*AP*AP*AP*CP*CP*AP*GP*AP*CP*GP*GP*CP*C)-3'


Mass: 7045.354 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: solid phase sythesis. Sequence from Azoarcus intron and exon sequence.
#3: RNA chain 5'-R(*CP*AP*(5MU))-3'


Mass: 909.623 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Solid phase synthesis. Sequence from Azoarcus group I intron 5'-exon sequence.

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Protein , 1 types, 1 molecules A

#4: Protein U1 SMALL NUCLEAR RIBONUCLEOPROTEIN A RNA BINDING DOMAIN / U1 snRNP protein A / U1A protein / U1-A


Mass: 11340.315 Da / Num. of mol.: 1 / Fragment: RRM 1 / Mutation: Y31H, Q36R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNRPA / Plasmid: pet11 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P09012

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Non-polymers , 3 types, 60 molecules

#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 4.6 Å3/Da / Density % sol: 69.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: MPD, sodium cacodylate, magnesium acetate, potassium chloride, cobalt heximine, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 29, 2004
RadiationMonochromator: crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 3.37→50 Å / Num. all: 20658 / Num. obs: 20658 / % possible obs: 95.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.5 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 18.2
Reflection shellResolution: 3.37→3.49 Å / Redundancy: 5.6 % / Mean I/σ(I) obs: 1.1 / % possible all: 71.1

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNS1refinement
PDB_EXTRACT1.601data extraction
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 1U6B

1u6b


Resolution: 3.37→33.04 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 198973.33 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: CNS
Details: Experimental phases from 1U6B structure were used followed by maximum likelihood refinement. Octahedral parameters for Mg2+ coordination were used to refine M1 and M2 in the final round of refinement only
RfactorNum. reflection% reflectionSelection details
Rfree0.307 801 4.4 %RANDOM
Rwork0.269 ---
obs0.269 18224 84.8 %-
all-18224 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 10 Å2 / ksol: 0.0527796 e/Å3
Displacement parametersBiso mean: 100.7 Å2
Baniso -1Baniso -2Baniso -3
1-5.88 Å20 Å20 Å2
2--5.88 Å20 Å2
3----11.76 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.6 Å0.51 Å
Luzzati d res low-5 Å
Luzzati sigma a0.69 Å0.69 Å
Refinement stepCycle: LAST / Resolution: 3.37→33.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms775 4768 6 54 5603
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d15.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.71
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.461.5
X-RAY DIFFRACTIONc_mcangle_it4.612
X-RAY DIFFRACTIONc_scbond_it42
X-RAY DIFFRACTIONc_scangle_it6.182.5
LS refinement shellResolution: 3.37→3.58 Å / Rfactor Rfree error: 0.039 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.411 109 4.4 %
Rwork0.381 2379 -
obs--71.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2rna_dna_modified.paramdna-rna_modified.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top

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