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- PDB-4qi2: X-ray structure of the ROQ domain from murine Roquin-1 in complex... -

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Basic information

Entry
Database: PDB / ID: 4qi2
TitleX-ray structure of the ROQ domain from murine Roquin-1 in complex with a 23-mer Tnf-CDE RNA
Components
  • RNA (5'-R(*AP*CP*AP*UP*GP*UP*UP*UP*UP*CP*UP*GP*UP*GP*AP*AP*AP*AP*CP*GP*GP*AP*G)-3')
  • Roquin-1
KeywordsRNA BINDING PROTEIN/RNA / ROQ domain / winged-helix domain / RNA binding / Tnf CDE RNA / RNA BINDING PROTEIN / RNA BINDING PROTEIN-RNA complex
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 / T follicular helper cell differentiation / positive regulation of mRNA catabolic process / negative regulation of T-helper 17 cell differentiation / regulation of germinal center formation ...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 / T follicular helper cell differentiation / positive regulation of mRNA catabolic process / negative regulation of T-helper 17 cell differentiation / regulation of germinal center formation / 3'-UTR-mediated mRNA destabilization / P-body assembly / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / miRNA binding / nuclear-transcribed mRNA catabolic process / post-transcriptional regulation of gene expression / negative regulation of B cell proliferation / T cell homeostasis / negative regulation of activated T cell proliferation / B cell homeostasis / cellular response to interleukin-1 / lymph node development / T cell proliferation / spleen development / regulation of mRNA stability / mRNA 3'-UTR binding / P-body / RING-type E3 ubiquitin transferase / cytoplasmic stress granule / positive regulation of non-canonical NF-kappaB signal transduction / protein polyubiquitination / RNA stem-loop binding / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / double-stranded RNA binding / T cell receptor signaling pathway / ubiquitin-dependent protein catabolic process / regulation of gene expression / mRNA binding / zinc ion binding / cytoplasm
Similarity search - Function
Four Helix Bundle (Hemerythrin (Met), subunit A) - #1790 / : / Roquin 1/2-like, ROQ domain / Roquin II / Roquin II domain / zinc-RING finger domain / Zinc finger, CCCH-type superfamily / zinc finger / Zinc finger, CCCH-type / Zinc finger C3H1-type profile. ...Four Helix Bundle (Hemerythrin (Met), subunit A) - #1790 / : / Roquin 1/2-like, ROQ domain / Roquin II / Roquin II 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.Struct.Mol.Biol. / Year: 2014
Title: Structural basis for RNA recognition in roquin-mediated post-transcriptional gene regulation.
Authors: Schlundt, A. / Heinz, G.A. / Janowski, R. / Geerlof, A. / Stehle, R. / Heissmeyer, V. / Niessing, D. / Sattler, M.
History
DepositionMay 30, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 16, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 20, 2014Group: Database references
Revision 1.2Sep 20, 2023Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Roquin-1
B: Roquin-1
C: Roquin-1
D: Roquin-1
E: RNA (5'-R(*AP*CP*AP*UP*GP*UP*UP*UP*UP*CP*UP*GP*UP*GP*AP*AP*AP*AP*CP*GP*GP*AP*G)-3')
F: RNA (5'-R(*AP*CP*AP*UP*GP*UP*UP*UP*UP*CP*UP*GP*UP*GP*AP*AP*AP*AP*CP*GP*GP*AP*G)-3')
G: RNA (5'-R(*AP*CP*AP*UP*GP*UP*UP*UP*UP*CP*UP*GP*UP*GP*AP*AP*AP*AP*CP*GP*GP*AP*G)-3')
H: RNA (5'-R(*AP*CP*AP*UP*GP*UP*UP*UP*UP*CP*UP*GP*UP*GP*AP*AP*AP*AP*CP*GP*GP*AP*G)-3')


Theoretical massNumber of molelcules
Total (without water)111,6728
Polymers111,6728
Non-polymers00
Water57632
1
A: Roquin-1
E: RNA (5'-R(*AP*CP*AP*UP*GP*UP*UP*UP*UP*CP*UP*GP*UP*GP*AP*AP*AP*AP*CP*GP*GP*AP*G)-3')


Theoretical massNumber of molelcules
Total (without water)27,9182
Polymers27,9182
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1540 Å2
ΔGint-13 kcal/mol
Surface area10380 Å2
MethodPISA
2
B: Roquin-1
F: RNA (5'-R(*AP*CP*AP*UP*GP*UP*UP*UP*UP*CP*UP*GP*UP*GP*AP*AP*AP*AP*CP*GP*GP*AP*G)-3')


Theoretical massNumber of molelcules
Total (without water)27,9182
Polymers27,9182
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1540 Å2
ΔGint-13 kcal/mol
Surface area10320 Å2
MethodPISA
3
C: Roquin-1
G: RNA (5'-R(*AP*CP*AP*UP*GP*UP*UP*UP*UP*CP*UP*GP*UP*GP*AP*AP*AP*AP*CP*GP*GP*AP*G)-3')


Theoretical massNumber of molelcules
Total (without water)27,9182
Polymers27,9182
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1830 Å2
ΔGint-16 kcal/mol
Surface area10430 Å2
MethodPISA
4
D: Roquin-1
H: RNA (5'-R(*AP*CP*AP*UP*GP*UP*UP*UP*UP*CP*UP*GP*UP*GP*AP*AP*AP*AP*CP*GP*GP*AP*G)-3')


Theoretical massNumber of molelcules
Total (without water)27,9182
Polymers27,9182
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1840 Å2
ΔGint-16 kcal/mol
Surface area10430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.560, 60.410, 84.370
Angle α, β, γ (deg.)105.68, 101.36, 95.72
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D
17E
27F
18E
28G
19E
29H
110F
210G
111F
211H
112G
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
11HISHISGLNGLNAA173 - 32527 - 179
21HISHISGLNGLNBB173 - 32527 - 179
12GLNGLNLEULEUAA174 - 32428 - 178
22GLNGLNLEULEUCC174 - 32428 - 178
13HISHISLEULEUAA173 - 32427 - 178
23HISHISLEULEUDD173 - 32427 - 178
14GLNGLNLEULEUBB174 - 32428 - 178
24GLNGLNLEULEUCC174 - 32428 - 178
15HISHISLEULEUBB173 - 32427 - 178
25HISHISLEULEUDD173 - 32427 - 178
16GLNGLNLEULEUCC174 - 32428 - 178
26GLNGLNLEULEUDD174 - 32428 - 178
17UUGGEE4 - 204 - 20
27UUGGFF4 - 204 - 20
18UUGGEE4 - 204 - 20
28UUGGGG4 - 204 - 20
19UUGGEE4 - 204 - 20
29UUGGHH4 - 204 - 20
110UUGGFF4 - 204 - 20
210UUGGGG4 - 204 - 20
111UUGGFF4 - 214 - 21
211UUGGHH4 - 214 - 21
112UUGGGG4 - 204 - 20
212UUGGHH4 - 204 - 20

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

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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: 20528.561 Da / Num. of mol.: 4 / Fragment: ROQ domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Gm551, Kiaa2025, Rc3h1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: Q4VGL6
#2: RNA chain
RNA (5'-R(*AP*CP*AP*UP*GP*UP*UP*UP*UP*CP*UP*GP*UP*GP*AP*AP*AP*AP*CP*GP*GP*AP*G)-3')


Mass: 7389.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: RNA oligomer was chemically synthesized
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H2O

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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: 2.4 Å3/Da / Density % sol: 48.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 200 mM NaCl, 100 mM Bis-Tris, 25% PEG3350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.03321 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 27, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03321 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. all: 19951 / Num. obs: 19951 / % possible obs: 95.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.07 / Net I/σ(I): 13.9
Reflection shellResolution: 3→3.08 Å / Rmerge(I) obs: 0.513 / Mean I/σ(I) obs: 3 / % possible all: 96.9

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Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
REFMAC5.8.0049refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 4QI0

4qi0


Resolution: 3→50 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.931 / SU B: 22.868 / SU ML: 0.399 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.449 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24679 1020 5.1 %RANDOM
Rwork0.20316 ---
obs0.20549 18931 95.82 %-
all-18931 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 77.711 Å2
Baniso -1Baniso -2Baniso -3
1-6.29 Å26.88 Å2-1.27 Å2
2---5.25 Å20.73 Å2
3----1.69 Å2
Refinement stepCycle: LAST / Resolution: 3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4895 1576 0 32 6503
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0176784
X-RAY DIFFRACTIONr_bond_other_d0.0050.025631
X-RAY DIFFRACTIONr_angle_refined_deg1.5131.7639510
X-RAY DIFFRACTIONr_angle_other_deg1.166313035
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5895608
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.79823.875240
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.24315941
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6191544
X-RAY DIFFRACTIONr_chiral_restr0.0750.21052
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026489
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021543
X-RAY DIFFRACTIONr_mcbond_it5.9217.6482444
X-RAY DIFFRACTIONr_mcbond_other5.9087.6482443
X-RAY DIFFRACTIONr_mcangle_it8.8811.4653048
X-RAY DIFFRACTIONr_mcangle_other8.87911.4663049
X-RAY DIFFRACTIONr_scbond_it6.6378.1754340
X-RAY DIFFRACTIONr_scbond_other6.6338.1744339
X-RAY DIFFRACTIONr_scangle_other9.99212.2126463
X-RAY DIFFRACTIONr_long_range_B_refined13.41666.8628364
X-RAY DIFFRACTIONr_long_range_B_other13.41766.8728364
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A96520.06
12B96520.06
21A94670.06
22C94670.06
31A95250.06
32D95250.06
41B94600.07
42C94600.07
51B94830.08
52D94830.08
61C93130.06
62D93130.06
71E13730.1
72F13730.1
81E13420.09
82G13420.09
91E13440.09
92H13440.09
101F13750.08
102G13750.08
111F14200.11
112H14200.11
121G13940.03
122H13940.03
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.429 68 -
Rwork0.384 1390 -
obs--96.36 %

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