[English] 日本語
Yorodumi
- PDB-5f5f: X-ray structure of Roquin ROQ domain in complex with a Selex-deri... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5f5f
TitleX-ray structure of Roquin ROQ domain in complex with a Selex-derived hexa-loop RNA motif
Components
  • RNA (5'-R(P*UP*GP*AP*CP*UP*GP*CP*GP*UP*UP*UP*UP*AP*GP*GP*AP*GP*UP*UP*A)-3')
  • Roquin-1
KeywordsRNA BINDING PROTEIN / ROQ domain / winged-helix domain / SELEX
Function / homology
Function and homology information


negative regulation of germinal center formation / negative regulation of T-helper cell differentiation / regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / CCR4-NOT complex binding / regulation of T cell receptor signaling pathway / regulation of miRNA metabolic process / negative regulation of T-helper 17 cell differentiation / positive regulation of mRNA catabolic process / 3'-UTR-mediated mRNA destabilization / T follicular helper cell differentiation ...negative regulation of germinal center formation / negative regulation of T-helper cell differentiation / regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / CCR4-NOT complex binding / regulation of T cell receptor signaling pathway / regulation of miRNA metabolic process / negative regulation of T-helper 17 cell differentiation / positive regulation of mRNA catabolic process / 3'-UTR-mediated mRNA destabilization / T follicular helper cell differentiation / regulation of germinal center formation / miRNA binding / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / P-body assembly / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / post-transcriptional regulation of gene expression / negative regulation of B cell proliferation / negative regulation of activated T cell proliferation / T cell homeostasis / B cell homeostasis / nuclear-transcribed mRNA catabolic process / cellular response to interleukin-1 / lymph node development / T cell proliferation / spleen development / regulation of mRNA stability / mRNA 3'-UTR binding / P-body / positive regulation of non-canonical NF-kappaB signal transduction / RING-type E3 ubiquitin transferase / RNA stem-loop binding / protein polyubiquitination / cytoplasmic stress granule / ubiquitin-protein transferase activity / T cell receptor signaling pathway / double-stranded RNA binding / regulation of gene expression / mRNA binding / zinc ion binding / cytoplasm
Similarity search - Function
Four Helix Bundle (Hemerythrin (Met), subunit A) - #1790 / Roquin II / : / : / Roquin II domain / Roquin 1/2-like, ROQ domain / zinc-RING finger domain / Zinc finger, CCCH-type superfamily / zinc finger / Zinc finger, CCCH-type ...Four Helix Bundle (Hemerythrin (Met), subunit A) - #1790 / Roquin II / : / : / Roquin II domain / Roquin 1/2-like, ROQ domain / zinc-RING finger domain / Zinc finger, CCCH-type superfamily / zinc finger / Zinc finger, CCCH-type / Zinc finger C3H1-type profile. / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Four Helix Bundle (Hemerythrin (Met), subunit A) / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
RNA / RNA (> 10) / Roquin-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsJanowski, R. / Schlundt, A. / Sattler, M. / Niessing, D.
CitationJournal: Nat Commun / Year: 2016
Title: Roquin recognizes a non-canonical hexaloop structure in the 3'-UTR of Ox40.
Authors: Janowski, R. / Heinz, G.A. / Schlundt, A. / Wommelsdorf, N. / Brenner, S. / Gruber, A.R. / Blank, M. / Buch, T. / Buhmann, R. / Zavolan, M. / Niessing, D. / Heissmeyer, V. / Sattler, M.
History
DepositionDec 4, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 6, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 21, 2018Group: Data collection / Derived calculations / Category: struct_conn / struct_conn_type
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Roquin-1
B: RNA (5'-R(P*UP*GP*AP*CP*UP*GP*CP*GP*UP*UP*UP*UP*AP*GP*GP*AP*GP*UP*UP*A)-3')
C: Roquin-1
D: RNA (5'-R(P*UP*GP*AP*CP*UP*GP*CP*GP*UP*UP*UP*UP*AP*GP*GP*AP*GP*UP*UP*A)-3')
E: Roquin-1
F: RNA (5'-R(P*UP*GP*AP*CP*UP*GP*CP*GP*UP*UP*UP*UP*AP*GP*GP*AP*GP*UP*UP*A)-3')
G: Roquin-1
H: RNA (5'-R(P*UP*GP*AP*CP*UP*GP*CP*GP*UP*UP*UP*UP*AP*GP*GP*AP*GP*UP*UP*A)-3')


Theoretical massNumber of molelcules
Total (without water)111,8268
Polymers111,8268
Non-polymers00
Water88349
1
A: Roquin-1
B: RNA (5'-R(P*UP*GP*AP*CP*UP*GP*CP*GP*UP*UP*UP*UP*AP*GP*GP*AP*GP*UP*UP*A)-3')


Theoretical massNumber of molelcules
Total (without water)27,9572
Polymers27,9572
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Roquin-1
D: RNA (5'-R(P*UP*GP*AP*CP*UP*GP*CP*GP*UP*UP*UP*UP*AP*GP*GP*AP*GP*UP*UP*A)-3')


Theoretical massNumber of molelcules
Total (without water)27,9572
Polymers27,9572
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Roquin-1
F: RNA (5'-R(P*UP*GP*AP*CP*UP*GP*CP*GP*UP*UP*UP*UP*AP*GP*GP*AP*GP*UP*UP*A)-3')


Theoretical massNumber of molelcules
Total (without water)27,9572
Polymers27,9572
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: Roquin-1
H: RNA (5'-R(P*UP*GP*AP*CP*UP*GP*CP*GP*UP*UP*UP*UP*AP*GP*GP*AP*GP*UP*UP*A)-3')


Theoretical massNumber of molelcules
Total (without water)27,9572
Polymers27,9572
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.900, 89.300, 144.700
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
11A
21C
12A
22E
13A
23G
14B
24D
15B
25F
16B
26H
17C
27E
18C
28G
19D
29F
110D
210H
111E
211G
112F
212H

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASNASNTHRTHRAA175 - 3265 - 156
21ASNASNTHRTHRCC175 - 3265 - 156
12ASNASNTHRTHRAA175 - 3265 - 156
22ASNASNTHRTHREE175 - 3265 - 156
13GLNGLNLEULEUAA178 - 3248 - 154
23GLNGLNLEULEUGG178 - 3248 - 154
14UUAABB1 - 201 - 20
24UUAADD1 - 201 - 20
15UUAABB1 - 201 - 20
25UUAAFF1 - 201 - 20
16UUAABB1 - 201 - 20
26UUAAHH1 - 201 - 20
17ASNASNTHRTHRCC175 - 3265 - 156
27ASNASNTHRTHREE175 - 3265 - 156
18GLNGLNLEULEUCC178 - 3248 - 154
28GLNGLNLEULEUGG178 - 3248 - 154
19UUAADD1 - 201 - 20
29UUAAFF1 - 201 - 20
110UUAADD1 - 201 - 20
210UUAAHH1 - 201 - 20
111GLNGLNLEULEUEE178 - 3248 - 154
211GLNGLNLEULEUGG178 - 3248 - 154
112UUAAFF1 - 201 - 20
212UUAAHH1 - 201 - 20

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12

-
Components

#1: Protein
Roquin-1 / Roquin / Protein Sanroque / RING finger and C3H zinc finger protein 1 / RING finger and CCCH-type ...Roquin / Protein Sanroque / RING finger and C3H zinc finger protein 1 / RING finger and CCCH-type zinc finger domain-containing protein 1


Mass: 21553.719 Da / Num. of mol.: 4 / Fragment: ROQ domain, UNP residues 171-360
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Rc3h1, Gm551, Kiaa2025 / Production host: Escherichia coli (E. coli) / References: UniProt: Q4VGL6
#2: RNA chain
RNA (5'-R(P*UP*GP*AP*CP*UP*GP*CP*GP*UP*UP*UP*UP*AP*GP*GP*AP*GP*UP*UP*A)-3')


Mass: 6402.792 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41.59 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, NaCl, Bis-TRIS / PH range: 5.5-6.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00003 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 18598 / % possible obs: 99.9 % / Redundancy: 13.2 % / Rmerge(I) obs: 0.148 / Net I/σ(I): 16.7
Reflection shellResolution: 3→3.08 Å / Redundancy: 12.7 % / Rmerge(I) obs: 0.938 / Mean I/σ(I) obs: 3.1 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
REFMAC5.8.0123refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4QI0

4qi0


Resolution: 3→50 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.916 / SU B: 39.817 / SU ML: 0.324 / Cross valid method: THROUGHOUT / ESU R Free: 0.424 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2338 952 4.9 %RANDOM
Rwork0.18321 ---
obs0.18572 18598 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 66.89 Å2
Baniso -1Baniso -2Baniso -3
1-6.47 Å20 Å20 Å2
2---2.72 Å20 Å2
3----3.75 Å2
Refinement stepCycle: 1 / Resolution: 3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4817 1708 0 49 6574
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0176804
X-RAY DIFFRACTIONr_bond_other_d0.0110.025604
X-RAY DIFFRACTIONr_angle_refined_deg1.7571.7589566
X-RAY DIFFRACTIONr_angle_other_deg1.87312986
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3845602
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.14123.739230
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.95915929
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8921544
X-RAY DIFFRACTIONr_chiral_restr0.1010.21064
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.026422
X-RAY DIFFRACTIONr_gen_planes_other0.0090.021526
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.574.7622414
X-RAY DIFFRACTIONr_mcbond_other2.574.7612413
X-RAY DIFFRACTIONr_mcangle_it4.1677.1323011
X-RAY DIFFRACTIONr_mcangle_other4.1677.1323012
X-RAY DIFFRACTIONr_scbond_it2.8924.7814390
X-RAY DIFFRACTIONr_scbond_other2.8924.7814391
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.6667.0896555
X-RAY DIFFRACTIONr_long_range_B_refined7.13639.4137995
X-RAY DIFFRACTIONr_long_range_B_other7.13539.4177994
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A190600.08
12C190600.08
21A187800.09
22E187800.09
31A185860.07
32G185860.07
41B33540.09
42D33540.09
51B32080.12
52F32080.12
61B33540.05
62H33540.05
71C187780.09
72E187780.09
81C185200.08
82G185200.08
91D31340.09
92F31340.09
101D31900.08
102H31900.08
111E182080.08
112G182080.08
121F31660.1
122H31660.1
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.377 52 -
Rwork0.319 1361 -
obs--99.93 %
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)
11.72771.3807-0.12443.7574-0.21041.96240.0322-0.04810.1583-0.1528-0.06910.0056-0.10910.05630.0370.0780.00170.02350.0040.00630.097529.352112.554135.5303
21.18290.18640.0833.3229-0.42762.75420.1355-0.1144-0.1039-0.0725-0.20960.1850.1137-0.30480.07410.0812-0.01180.04680.0619-0.00370.140680.1491-16.099835.3295
32.23150.52850.11281.9712-0.26586.11980.1340.1836-0.0102-0.02050.0719-0.10060.19950.2754-0.20590.06220.02520.02420.1488-0.02680.033781.0682-7.17145.1833
44.9992-0.7620.46153.0493-1.10546.0588-0.18320.0604-0.28990.0231-0.2819-0.1770.35640.77170.46510.10520.08110.03810.15530.04380.080644.58346.88275.7889
52.5227-0.2782-0.41933.30.52041.0484-0.0017-0.0546-0.0539-0.0856-0.0562-0.4930.02480.1770.05790.15150.02990.06980.08940.07420.233140.6824-1.580935.0989
62.6677-0.11420.633.5224-2.69864.9381-0.0454-0.18810.10730.2371-0.03680.5044-0.0936-0.28920.08210.18350.02090.02880.0628-0.04560.285569.2951-2.381337.1293
72.91441.0092-0.77631.1736-1.70296.27990.22670.24830.13020.20630.05110.421-0.2762-1.2152-0.27780.2545-0.00980.07820.4709-0.10490.264364.485-8.86325.9916
84.26940.6589-2.64490.7915-0.76364.14160.10650.15480.52940.0180.03560.1038-0.8322-0.4531-0.14220.3350.0726-0.02980.20210.01860.142232.186720.09636.5988
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A160 - 326
2X-RAY DIFFRACTION2C160 - 326
3X-RAY DIFFRACTION3E160 - 326
4X-RAY DIFFRACTION4G160 - 326
5X-RAY DIFFRACTION5B1 - 20
6X-RAY DIFFRACTION6D1 - 20
7X-RAY DIFFRACTION7F1 - 20
8X-RAY DIFFRACTION8H1 - 20

+
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