[English] 日本語
Yorodumi
- PDB-7dlz: Crystal Structure of Methyltransferase Ribozyme -

+
Open data


ID or keywords:

Loading...

-
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
Water00
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

-
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)

-
Experimental details

-
Experiment

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

-
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

-
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

-
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

+
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://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