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- PDB-2nz4: Structural investigation of the GlmS ribozyme bound to its cataly... -

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Basic information

Entry
Database: PDB / ID: 2nz4
TitleStructural investigation of the GlmS ribozyme bound to its catalytic cofactor
Components
  • GlmS ribozyme
  • U1 Small Nuclear Ribonucleoprotein A
  • substrate strand RNA 13-mer
KeywordsSTRUCTURAL PROTEIN/RNA / 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
Chem-GLP / RNA / RNA (> 10) / RNA (> 100) / U1 small nuclear ribonucleoprotein A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.498 Å
AuthorsCochrane, J.C.
CitationJournal: Chem.Biol. / Year: 2007
Title: Structural Investigation of the GlmS Ribozyme Bound to Its Catalytic Cofactor
Authors: Cochrane, J.C. / Lipchock, S.V. / Strobel, S.A.
History
DepositionNov 22, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.conn_type_id / _struct_conn.id / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Oct 20, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Dec 27, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: substrate strand RNA 13-mer
P: GlmS ribozyme
F: substrate strand RNA 13-mer
Q: GlmS ribozyme
G: substrate strand RNA 13-mer
R: GlmS ribozyme
H: substrate strand RNA 13-mer
S: GlmS ribozyme
A: U1 Small Nuclear Ribonucleoprotein A
B: U1 Small Nuclear Ribonucleoprotein A
C: U1 Small Nuclear Ribonucleoprotein A
D: U1 Small Nuclear Ribonucleoprotein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)244,40332
Polymers242,97712
Non-polymers1,42520
Water3,711206
1
E: substrate strand RNA 13-mer
P: GlmS ribozyme
A: U1 Small Nuclear Ribonucleoprotein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,1018
Polymers60,7443
Non-polymers3565
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
F: substrate strand RNA 13-mer
Q: GlmS ribozyme
B: U1 Small Nuclear Ribonucleoprotein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,1018
Polymers60,7443
Non-polymers3565
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
G: substrate strand RNA 13-mer
R: GlmS ribozyme
C: U1 Small Nuclear Ribonucleoprotein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,1018
Polymers60,7443
Non-polymers3565
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
H: substrate strand RNA 13-mer
S: GlmS ribozyme
D: U1 Small Nuclear Ribonucleoprotein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,1018
Polymers60,7443
Non-polymers3565
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.127, 234.157, 105.003
Angle α, β, γ (deg.)90.00, 90.65, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D
12E
22H
13P
23S
14B
24C
15F
25G
16Q
26R

NCS domain segments:

Component-ID: 1 / Refine code: 4

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ARGARGILEILEAI7 - 943 - 90
21ARGARGILEILEDL7 - 943 - 90
12AAUUEA-1 - 111 - 13
22AAUUHG-1 - 111 - 13
13GTPGTPAAPB12 - 1411 - 141
23GTPGTPAASH12 - 1411 - 141
14GLUGLUILEILEBJ5 - 941 - 90
24PROPROILEILECK8 - 944 - 90
15AAUUFC-1 - 111 - 13
25AAUUGE-1 - 111 - 13
16GTPGTPAAQD12 - 1411 - 141
26GTPGTPAARF12 - 1411 - 141

NCS ensembles :
ID
1
2
3
4
5
6
DetailsThere are four biological units in the asymmetric unit, chains A, E and P, chains B, F and Q, chains C, G and R, chains D, H and S.

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Components

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RNA chain , 2 types, 8 molecules EFGHPQRS

#1: RNA chain
substrate strand RNA 13-mer


Mass: 4177.608 Da / Num. of mol.: 4 / Source method: obtained synthetically
#2: RNA chain
GlmS ribozyme


Mass: 45624.859 Da / Num. of mol.: 4 / Source method: obtained synthetically
Details: In vitro syntesis from a plasmid DNA template of natural sequence from Bacillus anthracis

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Protein / Sugars , 2 types, 8 molecules ABCD

#3: Protein
U1 Small Nuclear Ribonucleoprotein A / U1 snRNP protein A / U1A protein / U1-A


Mass: 10941.797 Da / Num. of mol.: 4 / Fragment: RNA Binding Domain / 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 (bacteria) / Strain (production host): BL21 / References: UniProt: P09012
#4: Sugar
ChemComp-GLP / 2-amino-2-deoxy-6-O-phosphono-alpha-D-glucopyranose / GLUCOSAMINE 6-PHOSPHATE / 6-O-phosphono-alpha-D-glucosamine / 2-amino-2-deoxy-6-O-phosphono-alpha-D-glucose / 2-amino-2-deoxy-6-O-phosphono-D-glucose / 2-amino-2-deoxy-6-O-phosphono-glucose


Type: D-saccharide, alpha linking / Mass: 259.151 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C6H14NO8P
IdentifierTypeProgram
a-D-GlcpN6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 2 types, 222 molecules

#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 206 / 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: 2.45 Å3/Da / Density % sol: 49.78 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.8
Details: 11% PEG 8000, 9% DMSO, 0.02M sodium cacodylate pH 6.8, 0.02M magnesium chloride, 0.15M potassium chloride, 0.002M glucosamine 6 phosphate, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 800011
2DMSODimethyl sulfoxide11
3MgCl211
4KCl11
5PEG 800012
6DMSODimethyl sulfoxide12
7MgCl212
8KCl12
9sodium cacodylate12
10glucosamine 6 phosphate12

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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, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.498→34.94 Å / Num. obs: 79785 / % possible obs: 99.8 % / Observed criterion σ(I): 1.1 / Redundancy: 6.1 % / Biso Wilson estimate: 87 Å2 / Rmerge(I) obs: 0.062 / Rsym value: 0.046 / Net I/σ(I): 23.2
Reflection shellResolution: 2.498→2.59 Å / Redundancy: 5.9 % / Mean I/σ(I) obs: 1.1 / Num. unique all: 7928 / % possible all: 100

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Processing

Software
NameVersionClassification
CBASSdata collection
SHARPphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MIR / Resolution: 2.498→34.94 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.926 / SU B: 25.698 / SU ML: 0.281 / Isotropic thermal model: TLS / Cross valid method: THROUGHOUT / σ(F): 2.2 / ESU R: 0.701 / ESU R Free: 0.318
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26897 3987 5 %RANDOM
Rwork0.22157 ---
obs0.22395 75624 99.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 50.64 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20 Å2-0.26 Å2
2---0.02 Å20 Å2
3----0.18 Å2
Refinement stepCycle: LAST / Resolution: 2.498→34.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2908 13080 80 206 16274
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.02117645
X-RAY DIFFRACTIONr_bond_other_d0.0020.027188
X-RAY DIFFRACTIONr_angle_refined_deg1.5072.84626835
X-RAY DIFFRACTIONr_angle_other_deg0.972318359
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9475360
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.1323.636132
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.81715564
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1451520
X-RAY DIFFRACTIONr_chiral_restr0.0740.23519
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.029481
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021974
X-RAY DIFFRACTIONr_nbd_refined0.1540.22937
X-RAY DIFFRACTIONr_nbd_other0.2190.28663
X-RAY DIFFRACTIONr_nbtor_refined0.2240.26809
X-RAY DIFFRACTIONr_nbtor_other0.0820.24920
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1960.2513
X-RAY DIFFRACTIONr_metal_ion_refined0.120.216
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1440.231
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1890.247
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2420.210
X-RAY DIFFRACTIONr_mcbond_it1.20141986
X-RAY DIFFRACTIONr_mcbond_other0.3264727
X-RAY DIFFRACTIONr_mcangle_it1.83762930
X-RAY DIFFRACTIONr_scbond_it0.816421946
X-RAY DIFFRACTIONr_scangle_it1.233423905
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1213medium positional0.410.5
2E367medium positional0.180.5
3P4122medium positional0.320.5
4B1217medium positional0.330.5
5F386medium positional0.470.5
6Q4147medium positional0.310.5
1A1213medium thermal0.32
2E367medium thermal0.412
3P4122medium thermal0.242
4B1217medium thermal0.392
5F386medium thermal0.382
6Q4147medium thermal0.352
LS refinement shellResolution: 2.498→2.562 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.48 254 -
Rwork0.404 5338 -
obs--94.41 %

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