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- PDB-7dwh: Complex structure of SAM-dependent methyltransferase ribozyme -

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Basic information

Entry
Database: PDB / ID: 7dwh
TitleComplex structure of SAM-dependent methyltransferase ribozyme
Components
  • RNA (45-MER)
  • U1 small nuclear ribonucleoprotein A
KeywordsTRANSFERASE/RNA / Ribozyme / methyltransferase / complex / RNA / 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
COPPER (II) ION / S-ADENOSYLMETHIONINE / 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: 3.1 Å
AuthorsJiang, H.Y. / Gao, Y.Q. / Chen, D.R. / Murchie, A.
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
DepositionJan 17, 2021Deposition 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)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,81210
Polymers75,8886
Non-polymers9244
Water1086
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.923, 77.305, 101.469
Angle α, β, γ (deg.)90.000, 93.240, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain X
21chain Y
12(chain A and (resid 8 or (resid 9 and (name...
22(chain B and (resid 8 through 21 or (resid 22...
32(chain C and (resid 8 or (resid 9 and (name...
42(chain D and (resid 8 or (resid 9 and (name...

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
111GGCCchain XXE1 - 451 - 45
211GGCCchain YYF1 - 451 - 45
112PROPROPROPRO(chain A and (resid 8 or (resid 9 and (name...AA88
122ASNASNASNASN(chain A and (resid 8 or (resid 9 and (name...AA99
132THRTHRTHRTHR(chain A and (resid 8 or (resid 9 and (name...AA6 - 1006 - 100
142THRTHRTHRTHR(chain A and (resid 8 or (resid 9 and (name...AA6 - 1006 - 100
152THRTHRTHRTHR(chain A and (resid 8 or (resid 9 and (name...AA6 - 1006 - 100
162THRTHRTHRTHR(chain A and (resid 8 or (resid 9 and (name...AA6 - 1006 - 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
232PROPROASPASP(chain B and (resid 8 through 21 or (resid 22...BB8 - 928 - 92
242PROPROASPASP(chain B and (resid 8 through 21 or (resid 22...BB8 - 928 - 92
252PROPROASPASP(chain B and (resid 8 through 21 or (resid 22...BB8 - 928 - 92
262PROPROASPASP(chain B and (resid 8 through 21 or (resid 22...BB8 - 928 - 92
312PROPROPROPRO(chain C and (resid 8 or (resid 9 and (name...CC88
322ASNASNASNASN(chain C and (resid 8 or (resid 9 and (name...CC99
332THRTHRVALVAL(chain C and (resid 8 or (resid 9 and (name...CC6 - 1026 - 102
342THRTHRVALVAL(chain C and (resid 8 or (resid 9 and (name...CC6 - 1026 - 102
352THRTHRVALVAL(chain C and (resid 8 or (resid 9 and (name...CC6 - 1026 - 102
362THRTHRVALVAL(chain C and (resid 8 or (resid 9 and (name...CC6 - 1026 - 102
412PROPROPROPRO(chain D and (resid 8 or (resid 9 and (name...DD88
422ASNASNASNASN(chain D and (resid 8 or (resid 9 and (name...DD99
432GLUGLUPHEPHE(chain D and (resid 8 or (resid 9 and (name...DD5 - 1015 - 101
442GLUGLUPHEPHE(chain D and (resid 8 or (resid 9 and (name...DD5 - 1015 - 101
452GLUGLUPHEPHE(chain D and (resid 8 or (resid 9 and (name...DD5 - 1015 - 101
462GLUGLUPHEPHE(chain D and (resid 8 or (resid 9 and (name...DD5 - 1015 - 101

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)
#3: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#4: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N6O5S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.25 Å3/Da / Density % sol: 62.12 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.7
Details: sodium phosphate monobasic monohydrate, polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.97928 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 25, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97928 Å / Relative weight: 1
ReflectionResolution: 3.1→30 Å / Num. obs: 17380 / % possible obs: 97.7 % / Redundancy: 4.7 % / Biso Wilson estimate: 62.5 Å2 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.045 / Rrim(I) all: 0.108 / Χ2: 0.963 / Net I/σ(I): 8.3 / Num. measured all: 81837
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.1-3.212.90.23615950.9370.1430.2780.82290.9
3.21-3.343.40.24416960.9460.140.2830.94995.3
3.34-3.493.80.22517080.9550.1250.2590.8797
3.49-3.674.30.19817190.9730.1020.2230.92998
3.67-3.94.60.14817480.9860.0740.1670.95898.8
3.9-4.214.70.11117570.9930.0540.1240.96998.6
4.21-4.635.60.10217680.9950.0450.1121.00599.6
4.63-5.295.70.08817790.9950.0390.0970.99899.6
5.29-6.665.60.08217770.9920.0370.090.96799.3
6.66-306.30.07518330.9960.0320.0811.00899.7

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.12_2829refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7DLZ

7dlz


Resolution: 3.1→29.534 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.5 / Phase error: 27.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2584 728 4.88 %
Rwork0.2089 14197 -
obs0.2114 14925 83.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 192.19 Å2 / Biso mean: 72.2129 Å2 / Biso min: 18.82 Å2
Refinement stepCycle: final / Resolution: 3.1→29.534 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2929 1920 47 6 4902
Biso mean--90.68 27.73 -
Num. residues----464
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035176
X-RAY DIFFRACTIONf_angle_d0.6677426
X-RAY DIFFRACTIONf_chiral_restr0.04911
X-RAY DIFFRACTIONf_plane_restr0.005604
X-RAY DIFFRACTIONf_dihedral_angle_d12.3912923
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11X1074X-RAY DIFFRACTION12.191TORSIONAL
12Y1074X-RAY DIFFRACTION12.191TORSIONAL
21A1562X-RAY DIFFRACTION12.191TORSIONAL
22B1562X-RAY DIFFRACTION12.191TORSIONAL
23C1562X-RAY DIFFRACTION12.191TORSIONAL
24D1562X-RAY DIFFRACTION12.191TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.1-3.33890.3925760.2772149544
3.3389-3.67430.3291200.2582263778
3.6743-4.20470.27031890.2029325597
4.2047-5.29250.22721800.19753366100
5.2925-29.530.22811630.1916344499
Refinement TLS params.Method: refined / Origin x: -6.17 Å / Origin y: 17.4446 Å / Origin z: -23.227 Å
111213212223313233
T0.2847 Å20.0164 Å2-0.0359 Å2-0.1917 Å20.075 Å2--0.2829 Å2
L1.6295 °2-0.1302 °2-1.0839 °2-0.7566 °20.1903 °2--1.6015 °2
S0.1006 Å °-0.18 Å °0.0468 Å °0.1447 Å °-0.0204 Å °-0.0242 Å °-0.2296 Å °0.1789 Å °-0.0669 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA6 - 100
2X-RAY DIFFRACTION1allB8 - 92
3X-RAY DIFFRACTION1allC6 - 102
4X-RAY DIFFRACTION1allD5 - 101
5X-RAY DIFFRACTION1allX1 - 45
6X-RAY DIFFRACTION1allY1 - 45
7X-RAY DIFFRACTION1allE1 - 2
8X-RAY DIFFRACTION1allF1
9X-RAY DIFFRACTION1allF2
10X-RAY DIFFRACTION1allG1 - 6

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