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- PDB-4z31: Crystal structure of the RC3H2 ROQ domain in complex with stem-lo... -

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Basic information

Entry
Database: PDB / ID: 4z31
TitleCrystal structure of the RC3H2 ROQ domain in complex with stem-loop and double-stranded forms of RNA
Components
  • RNA (5'-R(*A)-D(P*UP*GP*UP*UP*CP*UP*GP*UP*GP*AP*AP*CP*AP*C)-3')
  • Roquin-2
KeywordsRNA BINDING PROTEIN/RNA / roquin2 / RNA / Structural Genomics / Structural Genomics Consortium / SGC / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


regulation of miRNA metabolic process / T follicular helper cell differentiation / negative regulation of T-helper 17 cell differentiation / RNA stem-loop binding / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / limb development / lung alveolus development / T cell homeostasis / B cell homeostasis / lymph node development ...regulation of miRNA metabolic process / T follicular helper cell differentiation / negative regulation of T-helper 17 cell differentiation / RNA stem-loop binding / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / limb development / lung alveolus development / T cell homeostasis / B cell homeostasis / lymph node development / T cell proliferation / spleen development / post-embryonic development / P-body / multicellular organism growth / RING-type E3 ubiquitin transferase / cytoplasmic stress granule / protein polyubiquitination / positive regulation of non-canonical NF-kappaB signal transduction / ubiquitin protein ligase activity / double-stranded RNA binding / T cell receptor signaling pathway / ubiquitin-dependent protein catabolic process / mRNA binding / intracellular membrane-bounded organelle / cell surface / DNA binding / RNA binding / membrane / metal ion binding
Similarity search - Function
: / Roquin 1/2-like, ROQ domain / Roquin II / Roquin II domain / zinc-RING finger domain / Zinc finger C-x8-C-x5-C-x3-H type (and similar) / Zinc finger, CCCH-type superfamily / zinc finger / Zinc finger, CCCH-type / Zinc finger C3H1-type profile. ...: / Roquin 1/2-like, ROQ domain / Roquin II / Roquin II domain / zinc-RING finger domain / Zinc finger C-x8-C-x5-C-x3-H type (and similar) / 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 / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
RNA / RNA (> 10) / Roquin-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsDONG, A. / ZHANG, Q. / TEMPEL, W. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / TONG, Y. / Structural Genomics Consortium (SGC)
CitationJournal: Sci Rep / Year: 2015
Title: New Insights into the RNA-Binding and E3 Ubiquitin Ligase Activities of Roquins.
Authors: Zhang, Q. / Fan, L. / Hou, F. / Dong, A. / Wang, Y.X. / Tong, Y.
History
DepositionMar 30, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 29, 2016Group: Database references
Revision 1.2Sep 27, 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_oper_list / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _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-2
B: Roquin-2
C: RNA (5'-R(*A)-D(P*UP*GP*UP*UP*CP*UP*GP*UP*GP*AP*AP*CP*AP*C)-3')
D: RNA (5'-R(*A)-D(P*UP*GP*UP*UP*CP*UP*GP*UP*GP*AP*AP*CP*AP*C)-3')
E: RNA (5'-R(*A)-D(P*UP*GP*UP*UP*CP*UP*GP*UP*GP*AP*AP*CP*AP*C)-3')
F: RNA (5'-R(*A)-D(P*UP*GP*UP*UP*CP*UP*GP*UP*GP*AP*AP*CP*AP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,5979
Polymers90,5626
Non-polymers353
Water72140
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7020 Å2
ΔGint-63 kcal/mol
Surface area36210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.299, 174.734, 61.290
Angle α, β, γ (deg.)90.000, 114.120, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D
13E
23F

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASNASNTYRTYRAA92 - 3957 - 310
21ASNASNTYRTYRBB92 - 3957 - 310
12UUCCCC2 - 132 - 13
22UUCCDD2 - 132 - 13
13AACCEE1 - 151 - 15
23AACCFF1 - 151 - 15

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Roquin-2 / Membrane-associated nucleic acid-binding protein / RING finger and CCCH-type zinc finger domain- ...Membrane-associated nucleic acid-binding protein / RING finger and CCCH-type zinc finger domain-containing protein 2 / RING finger protein 164


Mass: 35773.043 Da / Num. of mol.: 2 / Fragment: UNP residues 87-404
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RC3H2, MNAB, RNF164 / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-V2R-pRARE2 / References: UniProt: Q9HBD1
#2: RNA chain
RNA (5'-R(*A)-D(P*UP*GP*UP*UP*CP*UP*GP*UP*GP*AP*AP*CP*AP*C)-3')


Mass: 4753.857 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 2 / Source method: obtained synthetically
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 3.25 Å3/Da / Density % sol: 62.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: The protein was diluted to 6.7 mg/ml then mixed with IER3 RNA at a ratio 1:2 before crystallized. 17% PEG10000, 0.1 M Bis-Tris pH6.5, 5% Ethylene glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97924 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 28, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97924 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 39757 / % possible obs: 99.1 % / Redundancy: 5.9 % / Biso Wilson estimate: 50.3 Å2 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.036 / Rrim(I) all: 0.09 / Χ2: 1.008 / Net I/av σ(I): 25.429 / Net I/σ(I): 8.4 / Num. measured all: 236295
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.5-2.545.40.8319550.8010.3770.9130.61397.6
2.54-2.595.60.83619250.8230.370.9160.61397.4
2.59-2.645.70.74519840.8640.3240.8140.62797.5
2.64-2.695.80.66919200.8890.2890.730.63797.8
2.69-2.755.80.57719720.9010.250.630.65497.7
2.75-2.825.90.49419680.9380.2120.5390.70499
2.82-2.895.90.37919790.9640.1640.4140.72199.1
2.89-2.965.90.28819890.9740.1250.3150.75299.7
2.96-3.055.90.2319870.9820.0990.2510.79899.1
3.05-3.155.90.19320110.9860.0840.2110.87499.4
3.15-3.265.90.14419690.9910.0620.1570.95399.6
3.26-3.3960.12320110.9940.0530.1341.04599.4
3.39-3.5560.10419950.9930.0450.1141.14999.6
3.55-3.7360.09119880.9940.040.11.36999.6
3.73-3.976.10.08419960.9950.0360.0921.51299.8
3.97-4.276.10.07820170.9950.0330.0851.612100
4.27-4.76.20.06720200.9960.0290.0731.516100
4.7-5.386.10.05819960.9970.0250.0641.19100
5.38-6.786.20.0520350.9980.0220.0551.257100
6.78-506.20.03920400.9630.0180.0431.27299.7

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Processing

Software
NameVersionClassification
HKL-3000data scaling
REFMAC5.8.0107refinement
PDB_EXTRACT3.15data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4QIK

4qik


Resolution: 2.5→50 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.928 / SU B: 9.927 / SU ML: 0.214 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.38 / ESU R Free: 0.254 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2592 822 2.1 %RANDOM
Rwork0.2451 ---
obs0.2454 38676 98.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 126.35 Å2 / Biso mean: 62.219 Å2 / Biso min: 30 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å2-0 Å20.54 Å2
2---0.84 Å2-0 Å2
3---0.33 Å2
Refinement stepCycle: final / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4534 1221 3 40 5798
Biso mean--51.44 56.47 -
Num. residues----646
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0175980
X-RAY DIFFRACTIONr_bond_other_d0.0040.025054
X-RAY DIFFRACTIONr_angle_refined_deg1.0941.7978380
X-RAY DIFFRACTIONr_angle_other_deg1.218311630
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6935586
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.0123.596203
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.39415795
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1961541
X-RAY DIFFRACTIONr_chiral_restr0.0890.2967
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0215902
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021338
X-RAY DIFFRACTIONr_mcbond_it2.0176.1642350
X-RAY DIFFRACTIONr_mcbond_other2.0176.1622349
X-RAY DIFFRACTIONr_mcangle_it3.2759.2372931
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A335660.09
12B335660.09
21C17000.18
22D17000.18
31E23560.05
32F23560.05
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.386 69 -
Rwork0.351 2733 -
all-2802 -
obs--95.24 %

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