[English] 日本語
Yorodumi
- PDB-1zzn: Crystal structure of a group I intron/two exon complex that inclu... -

+
Open data


ID or keywords:

Loading...

-
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.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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.

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more