[English] 日本語
Yorodumi
- PDB-3wfr: tRNA processing enzyme complex 2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3wfr
TitletRNA processing enzyme complex 2
Components
  • Poly A polymerase
  • RNA (74-MER)
  • RNA (75-MER)
KeywordsTransferase/RNA / Terminal Nucleotide Transferase / Transferase-RNA complex
Function / homology
Function and homology information


CC tRNA cytidylyltransferase activity / tRNA surveillance / CCACCA tRNA nucleotidyltransferase activity / tRNA 3'-terminal CCA addition / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / tRNA binding / nucleotide binding / metal ion binding
Similarity search - Function
: / tRNA nucleotidyltransferase/poly(A) polymerase, RNA and SrmB- binding domain / Probable RNA and SrmB- binding site of polymerase A / HDIG domain / Poly A polymerase, head domain / Poly A polymerase head domain / HD domain / HD domain / Beta Polymerase, domain 2 / Metal dependent phosphohydrolases with conserved 'HD' motif. ...: / tRNA nucleotidyltransferase/poly(A) polymerase, RNA and SrmB- binding domain / Probable RNA and SrmB- binding site of polymerase A / HDIG domain / Poly A polymerase, head domain / Poly A polymerase head domain / HD domain / HD domain / Beta Polymerase, domain 2 / Metal dependent phosphohydrolases with conserved 'HD' motif. / HD/PDEase domain / Beta Polymerase; domain 2 / Nucleotidyltransferase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
CYTIDINE-5'-TRIPHOSPHATE / PYROPHOSPHATE 2- / : / RNA / RNA (> 10) / CC-adding tRNA nucleotidyltransferase
Similarity search - Component
Biological speciessynthetic construct (others)
Aquifex aeolicus (bacteria)
Thermotoga maritima MSB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.501 Å
AuthorsYamashita, S. / Takeshita, D. / Tomita, K.
CitationJournal: Structure / Year: 2014
Title: Translocation and rotation of tRNA during template-independent RNA polymerization by tRNA nucleotidyltransferase
Authors: Yamashita, S. / Takeshita, D. / Tomita, K.
History
DepositionJul 23, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 1, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 13, 2014Group: Database references
Revision 1.2Jun 28, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.3Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / 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_alt_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_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_alt_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_ptnr1_label_alt_id / _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_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_alt_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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RNA (74-MER)
B: RNA (74-MER)
C: RNA (75-MER)
D: RNA (75-MER)
E: Poly A polymerase
F: Poly A polymerase
G: Poly A polymerase
H: Poly A polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)327,33020
Polymers324,5968
Non-polymers2,73412
Water00
1
A: RNA (74-MER)
E: Poly A polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,6805
Polymers80,9962
Non-polymers6833
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RNA (74-MER)
F: Poly A polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,6805
Polymers80,9962
Non-polymers6833
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: RNA (75-MER)
G: Poly A polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,9855
Polymers81,3022
Non-polymers6833
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: RNA (75-MER)
H: Poly A polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,9855
Polymers81,3022
Non-polymers6833
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)152.810, 154.590, 174.670
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C
41chain D
12chain E
22chain F
32chain G
42chain H

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label alt-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GGCBCchain AAA1 - 741 - 74
21GGCBCchain BBB1 - 741 - 74
31GGCBCchain CCC1 - 751 - 75
41GGCBCchain DDD1 - 751 - 75
12UNKUNKUNKUNKchain EEE5 - 5055 - 505
22UNKUNKUNKUNKchain FFF5 - 5055 - 505
32UNKUNKUNKUNKchain GGG5 - 5055 - 505
42UNKUNKUNKUNKchain HHH5 - 5055 - 505

NCS ensembles :
ID
1
2

-
Components

-
RNA chain , 2 types, 4 molecules ABCD

#1: RNA chain RNA (74-MER)


Mass: 23850.168 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Thermotoga maritima MSB8 (bacteria) / References: GenBank: 498539165
#2: RNA chain RNA (75-MER)


Mass: 24155.350 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Thermotoga maritima MSB8 (bacteria) / References: GenBank: 498539165

-
Protein , 1 types, 4 molecules EFGH

#3: Protein
Poly A polymerase


Mass: 57146.211 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others), (gene. exp.) Aquifex aeolicus (strain VF5) (bacteria)
Strain: VF5 / Gene: pcnB2 / Production host: Escherichia coli (E. coli)
References: UniProt: O67911, CCA tRNA nucleotidyltransferase

-
Non-polymers , 3 types, 12 molecules

#4: Chemical
ChemComp-CTP / CYTIDINE-5'-TRIPHOSPHATE


Mass: 483.156 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H16N3O14P3
#5: Chemical
ChemComp-POP / PYROPHOSPHATE 2-


Mass: 175.959 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: H2O7P2
#6: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg

-
Details

Sequence detailsTHE AUTHORS CRYSTALLIZED THE ENTIRE PROTEIN, RESIDUES 1-512 FOR E, F, G, H CHAINS. THE AUTHORS KNOW ...THE AUTHORS CRYSTALLIZED THE ENTIRE PROTEIN, RESIDUES 1-512 FOR E, F, G, H CHAINS. THE AUTHORS KNOW THE COMPLETE SEQUENCE. THE SEQUENCE OF RESIDUES 1-15 AND 454-512 (THE UNK PART) IS AS FOLLOWS. (1) MENIEIVSSGKHTLH (15), (454)PLLNGDEIMEILGIKPGKIVGILKKALLEAQIDGKVETKEEAIEFIKRSTKNLKPLDEG(512) THE AUTHORS COULD OBSERVE A PART OF N- and C-TERMINAL RESIDUES (1-15 and 454-512, RESPECTIVLY) OF ALL PROTEIN CHAINS BUT THEY ARE NOT SURE WHICH PART CORRESPONDS WITH THESE OBSERVED RESIDUES. SO THE RESIDUE NUMBERS OF UNK ARE MEANINGLESS.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 3.16 Å3/Da / Density % sol: 61.1 %

-
Data collection

Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1 Å
DetectorDate: Apr 19, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.5→20 Å / Num. obs: 37144 / Biso Wilson estimate: 19.43 Å2

-
Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
PHENIX(phenix.refine: dev_1389)refinement
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WFO, 3L0U

3wfo

3l0u


Resolution: 3.501→19.975 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8229 / SU ML: 0.45 / σ(F): 2 / Phase error: 24.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2691 1839 4.99 %RANDOM
Rwork0.2244 ---
obs0.2267 36827 70.2 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 441.49 Å2 / Biso mean: 128.5234 Å2 / Biso min: 33.62 Å2
Refinement stepCycle: LAST / Resolution: 3.501→19.975 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14291 6300 156 0 20747
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00621843
X-RAY DIFFRACTIONf_angle_d0.73330981
X-RAY DIFFRACTIONf_chiral_restr0.0463703
X-RAY DIFFRACTIONf_plane_restr0.0032829
X-RAY DIFFRACTIONf_dihedral_angle_d12.5879031
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3544X-RAY DIFFRACTION10.526TORSIONAL
12B3544X-RAY DIFFRACTION10.526TORSIONAL
13C3544X-RAY DIFFRACTION10.526TORSIONAL
14D3544X-RAY DIFFRACTION10.526TORSIONAL
21E8069X-RAY DIFFRACTION10.526TORSIONAL
22F8069X-RAY DIFFRACTION10.526TORSIONAL
23G8069X-RAY DIFFRACTION10.526TORSIONAL
24H8069X-RAY DIFFRACTION10.526TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.501-3.59520.3254390.314159062916
3.5952-3.70030.3066550.27391094114929
3.7003-3.8190.3194610.24961481154239
3.819-3.95440.2707910.22971803189447
3.9544-4.11140.27251030.23122126222956
4.1114-4.29680.27021370.2242466260365
4.2968-4.52090.26071470.22432836298375
4.5209-4.80040.25941720.21523272344486
4.8004-5.16510.29372250.20583703392897
5.1651-5.67410.27072030.221538264029100
5.6741-6.47060.30061870.237138914078100
6.4706-8.06210.25342020.22539034105100
8.0621-19.97560.2162170.202639974214100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.1645-1.1265-1.90261.94590.12391.2452-0.3645-1.7669-0.22371.7590.02210.9113-0.3388-0.88290.36091.71770.01710.4292.2779-0.04241.27349.316148.4383-13.055
23.59-0.0467-1.11891.96430.65830.9042-0.4876-2.1861-0.21531.25180.0433-0.59951.09851.05910.40042.01980.1099-0.2852.37540.02451.114887.392937.6002-17.1843
35.2128-1.4916-2.50170.67170.2831.85610.1241-2.28960.98281.56-0.31860.4648-0.5212-0.18640.16132.2183-0.29580.57292.0951-0.48281.4471-7.2239-14.3024-8.2646
45.6038-0.06032.09182.10531.45781.8437-0.0763-2.80250.1172.0099-0.0438-1.359-0.81871.25420.1572.4151-0.5901-0.74062.73790.07281.740364.1754-14.4353-8.0889
52.5287-0.47990.18665.39451.21221.3845-0.0293-0.110.4319-0.26-0.2487-0.0508-0.3626-0.09710.3170.4255-0.0397-0.0130.6110.03420.354630.625151.4349-42.8607
64.97380.49290.80171.4684-0.16810.1722-0.31040.0120.7755-0.3419-0.51650.0864-0.8802-0.74220.81193.2409-0.3633-0.28562.1424-0.8561.711333.683570.61442.9566
73.1629-1.1273-0.36434.81441.09581.29050.16540.08910.6524-0.1613-0.1248-0.6134-0.28690.1553-0.01160.453-0.12970.02120.66380.10440.575565.363550.9889-43.6341
81.4010.2409-1.12811.0332-0.14852.26040.09670.7122-0.2197-0.9281-0.4277-0.13960.15130.32220.33712.68-0.4253-0.07961.29110.07141.166763.81239.556-15.7521
93.64411.06030.10795.5148-0.07911.2173-0.04190.2252-0.00670.1139-0.12840.54570.0286-0.11610.16070.3656-0.14610.08950.7236-0.04520.525210.7753-25.1416-42.1367
102.3628-1.5165-0.36124.66042.55291.5186-0.8043-1.0158-0.03582.2258-0.32540.29690.1924-0.66111.11662.4615-0.08220.21761.1447-0.4811.555314.083815.8954-13.7988
112.69270.1943-0.43873.8509-1.66481.74280.0419-0.0349-0.1628-0.28290.03020.02430.30790.001-0.07920.3548-0.0649-0.13640.5298-0.09580.431645.7902-24.2004-41.7717
120.13610.06430.29790.04240.13480.649-0.0226-0.1558-0.06840.2660.02320.07690.1014-0.01180.00372.0882-0.04570.11761.76950.58520.855242.2559-40.86734.4969
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 1:74)
2X-RAY DIFFRACTION2CHAIN B AND (RESSEQ 1:74)
3X-RAY DIFFRACTION3CHAIN C AND (RESSEQ 1:75)
4X-RAY DIFFRACTION4CHAIN D AND (RESSEQ 1:75)
5X-RAY DIFFRACTION5CHAIN E AND (RESSEQ 5:448)
6X-RAY DIFFRACTION6CHAIN E AND (RESSEQ 473:505)
7X-RAY DIFFRACTION7CHAIN F AND (RESSEQ 5:448)
8X-RAY DIFFRACTION8CHAIN F AND (RESSEQ 473:505)
9X-RAY DIFFRACTION9CHAIN G AND (RESSEQ 5:450)
10X-RAY DIFFRACTION10CHAIN G AND (RESSEQ 461:505)
11X-RAY DIFFRACTION11CHAIN H AND (RESSEQ 5:453)
12X-RAY DIFFRACTION12CHAIN H AND (RESSEQ 461:505)

+
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