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- PDB-7dlz: Crystal Structure of Methyltransferase Ribozyme -

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Basic information

Entry
Database: PDB / ID: 7dlz
TitleCrystal Structure of Methyltransferase Ribozyme
Components
  • RNA (45-MER)
  • U1 small nuclear ribonucleoprotein A
KeywordsTRANSFERASE/RNA / RNA / Methyltransferase / TRANSFERASE-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 / 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
Similarity search - Domain/homology
RNA / RNA (> 10) / U1 small nuclear ribonucleoprotein A
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.002 Å
AuthorsGan, J.H. / Gao, Y.Q. / Jiang, H.Y. / Chen, D.R. / Murchie, A.I.H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)2016YFA0500604 China
CitationJournal: Nat Catal / Year: 2021
Title: The identification and characterization of a selected SAM-dependent methyltransferase ribozyme that is present in natural sequences
Authors: Jiang, H.Y. / Gao, Y.Q. / Zhang, L. / Chen, D.R. / Gan, J.H. / Murchie, A.I.H.
History
DepositionNov 30, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 27, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: U1 small nuclear ribonucleoprotein A
B: U1 small nuclear ribonucleoprotein A
C: U1 small nuclear ribonucleoprotein A
D: U1 small nuclear ribonucleoprotein A
X: RNA (45-MER)
Y: RNA (45-MER)


Theoretical massNumber of molelcules
Total (without water)75,8886
Polymers75,8886
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.784, 80.176, 103.296
Angle α, β, γ (deg.)90.000, 91.710, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain X and ((resid 1 and (name O5 or name...
21chain Y
12(chain A and (resid 8 or (resid 9 through 10...
22(chain B and (resid 8 through 21 or (resid 22...
32(chain C and (resid 8 or (resid 9 through 10...
42(chain D and (resid 8 or (resid 9 through 10...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111GGGG(chain X and ((resid 1 and (name O5 or name...XE11
121GGCC(chain X and ((resid 1 and (name O5 or name...XE1 - 451 - 45
131GGCC(chain X and ((resid 1 and (name O5 or name...XE1 - 451 - 45
141GGCC(chain X and ((resid 1 and (name O5 or name...XE1 - 451 - 45
151GGCC(chain X and ((resid 1 and (name O5 or name...XE1 - 451 - 45
161GGCC(chain X and ((resid 1 and (name O5 or name...XE1 - 451 - 45
171GGCC(chain X and ((resid 1 and (name O5 or name...XE1 - 451 - 45
181GGCC(chain X and ((resid 1 and (name O5 or name...XE1 - 451 - 45
191GGCC(chain X and ((resid 1 and (name O5 or name...XE1 - 451 - 45
1101GGCC(chain X and ((resid 1 and (name O5 or name...XE1 - 451 - 45
1111GGCC(chain X and ((resid 1 and (name O5 or name...XE1 - 451 - 45
1121GGCC(chain X and ((resid 1 and (name O5 or name...XE1 - 451 - 45
1131GGCC(chain X and ((resid 1 and (name O5 or name...XE1 - 451 - 45
1141GGCC(chain X and ((resid 1 and (name O5 or name...XE1 - 451 - 45
1151GGCC(chain X and ((resid 1 and (name O5 or name...XE1 - 451 - 45
1161GGCC(chain X and ((resid 1 and (name O5 or name...XE1 - 451 - 45
1171GGCC(chain X and ((resid 1 and (name O5 or name...XE1 - 451 - 45
1181GGCC(chain X and ((resid 1 and (name O5 or name...XE1 - 451 - 45
1191GGCC(chain X and ((resid 1 and (name O5 or name...XE1 - 451 - 45
1201GGCC(chain X and ((resid 1 and (name O5 or name...XE1 - 451 - 45
211GGCCchain YYF1 - 451 - 45
112PROPROPROPRO(chain A and (resid 8 or (resid 9 through 10...AA88
122ASNASNHISHIS(chain A and (resid 8 or (resid 9 through 10...AA9 - 109 - 10
132GLUGLUTHRTHR(chain A and (resid 8 or (resid 9 through 10...AA5 - 1005 - 100
142GLUGLUTHRTHR(chain A and (resid 8 or (resid 9 through 10...AA5 - 1005 - 100
152GLUGLUTHRTHR(chain A and (resid 8 or (resid 9 through 10...AA5 - 1005 - 100
162GLUGLUTHRTHR(chain A and (resid 8 or (resid 9 through 10...AA5 - 1005 - 100
212PROPROILEILE(chain B and (resid 8 through 21 or (resid 22...BB8 - 218 - 21
222LYSLYSLYSLYS(chain B and (resid 8 through 21 or (resid 22...BB22 - 2322 - 23
232PROPROILEILE(chain B and (resid 8 through 21 or (resid 22...BB8 - 948 - 94
242PROPROILEILE(chain B and (resid 8 through 21 or (resid 22...BB8 - 948 - 94
252PROPROILEILE(chain B and (resid 8 through 21 or (resid 22...BB8 - 948 - 94
262PROPROILEILE(chain B and (resid 8 through 21 or (resid 22...BB8 - 948 - 94
312PROPROPROPRO(chain C and (resid 8 or (resid 9 through 10...CC88
322ASNASNHISHIS(chain C and (resid 8 or (resid 9 through 10...CC9 - 109 - 10
332THRTHRVALVAL(chain C and (resid 8 or (resid 9 through 10...CC6 - 1026 - 102
342THRTHRVALVAL(chain C and (resid 8 or (resid 9 through 10...CC6 - 1026 - 102
352THRTHRVALVAL(chain C and (resid 8 or (resid 9 through 10...CC6 - 1026 - 102
362THRTHRVALVAL(chain C and (resid 8 or (resid 9 through 10...CC6 - 1026 - 102
412PROPROPROPRO(chain D and (resid 8 or (resid 9 through 10...DD88
422ASNASNHISHIS(chain D and (resid 8 or (resid 9 through 10...DD9 - 109 - 10
432GLUGLUVALVAL(chain D and (resid 8 or (resid 9 through 10...DD5 - 1025 - 102
442GLUGLUVALVAL(chain D and (resid 8 or (resid 9 through 10...DD5 - 1025 - 102
452GLUGLUVALVAL(chain D and (resid 8 or (resid 9 through 10...DD5 - 1025 - 102
462GLUGLUVALVAL(chain D and (resid 8 or (resid 9 through 10...DD5 - 1025 - 102

NCS ensembles :
ID
1
2

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Components

#1: Protein
U1 small nuclear ribonucleoprotein A / U1A


Mass: 11740.739 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNRPA / Production host: Escherichia coli (E. coli) / References: UniProt: P09012
#2: RNA chain RNA (45-MER)


Mass: 14462.654 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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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: 3.45 Å3/Da / Density % sol: 64.33 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9793 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3→30 Å / Num. obs: 19768 / % possible obs: 96 % / Redundancy: 4.3 % / Biso Wilson estimate: 51.68 Å2 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.034 / Rrim(I) all: 0.079 / Χ2: 0.946 / Net I/σ(I): 8 / Num. measured all: 84155
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3-3.112.60.34318340.640.2230.4130.78689.2
3.11-3.232.70.27218230.9120.1770.3270.78990.1
3.23-3.383.20.23819150.9340.1390.2780.85893.9
3.38-3.563.50.22819320.9520.1270.2630.92694.7
3.56-3.784.20.18919790.9670.0950.2131.05197.2
3.78-4.074.40.1220320.9920.0590.1341.01498
4.07-4.484.80.09520260.9950.0460.1061.10598.7
4.48-5.124.90.07220440.9960.0340.081.03399
5.12-6.445.80.06220610.9960.0270.0680.93799.5
6.44-3060.04521220.9980.0190.0490.80399.9

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1URN

1urn


Resolution: 3.002→29.776 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.52 / Phase error: 29.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2663 757 4.73 %
Rwork0.2121 15250 -
obs0.2147 16007 77.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 160.94 Å2 / Biso mean: 66.7836 Å2 / Biso min: 17.52 Å2
Refinement stepCycle: final / Resolution: 3.002→29.776 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2908 1915 0 0 4823
Num. residues----468
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065097
X-RAY DIFFRACTIONf_angle_d0.9377325
X-RAY DIFFRACTIONf_chiral_restr0.056907
X-RAY DIFFRACTIONf_plane_restr0.007602
X-RAY DIFFRACTIONf_dihedral_angle_d11.8682869
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11X1072X-RAY DIFFRACTION12.679TORSIONAL
12Y1072X-RAY DIFFRACTION12.679TORSIONAL
21A1464X-RAY DIFFRACTION12.679TORSIONAL
22B1464X-RAY DIFFRACTION12.679TORSIONAL
23C1464X-RAY DIFFRACTION12.679TORSIONAL
24D1464X-RAY DIFFRACTION12.679TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.0023-3.23380.3618480.2659117530
3.2338-3.55880.31411300.244252265
3.5588-4.07270.27192060.2201364894
4.0727-5.12690.25361680.1958392499
5.1269-29.7760.24582050.20243981100
Refinement TLS params.Method: refined / Origin x: 7.0398 Å / Origin y: -21.7038 Å / Origin z: 23.8363 Å
111213212223313233
T0.3277 Å2-0.0847 Å2-0.0073 Å2-0.1964 Å2-0.0988 Å2--0.2942 Å2
L1.2608 °20.0858 °2-0.7366 °2-0.7211 °2-0.1084 °2--1.0775 °2
S0.106 Å °0.1091 Å °0.1465 Å °-0.319 Å °-0.0516 Å °0.1077 Å °-0.1325 Å °-0.2953 Å °-0.0489 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA5 - 100
2X-RAY DIFFRACTION1allB8 - 94
3X-RAY DIFFRACTION1allC6 - 102
4X-RAY DIFFRACTION1allD5 - 102
5X-RAY DIFFRACTION1allX1 - 45
6X-RAY DIFFRACTION1allY1 - 45

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