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- PDB-5b16: X-ray structure of DROSHA in complex with the C-terminal tail of ... -

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Basic information

Entry
Database: PDB / ID: 5b16
TitleX-ray structure of DROSHA in complex with the C-terminal tail of DGCR8.
Components
  • Microprocessor complex subunit DGCR8
  • Ribonuclease 3,DROSHA,Ribonuclease 3,DROSHA,Ribonuclease 3
KeywordsHYDROLASE / Endonuclease / RNase III / Trimeric complex / Zinc finger
Function / homology
Function and homology information


positive regulation of pre-miRNA processing / regulation of miRNA metabolic process / protein-RNA adaptor activity / primary miRNA binding / DEAD/H-box RNA helicase binding / regulation of regulatory T cell differentiation / U4 snRNA 3'-end processing / Transcriptional Regulation by MECP2 / ribonuclease III / miRNA metabolic process ...positive regulation of pre-miRNA processing / regulation of miRNA metabolic process / protein-RNA adaptor activity / primary miRNA binding / DEAD/H-box RNA helicase binding / regulation of regulatory T cell differentiation / U4 snRNA 3'-end processing / Transcriptional Regulation by MECP2 / ribonuclease III / miRNA metabolic process / primary miRNA processing / regulation of stem cell proliferation / ribonuclease III activity / microprocessor complex / pre-miRNA processing / MicroRNA (miRNA) biogenesis / termination of RNA polymerase II transcription / SMAD binding / R-SMAD binding / lipopolysaccharide binding / rRNA processing / double-stranded RNA binding / protein-macromolecule adaptor activity / site of double-strand break / regulation of inflammatory response / defense response to Gram-negative bacterium / postsynaptic density / nuclear body / defense response to Gram-positive bacterium / glutamatergic synapse / DNA damage response / heme binding / positive regulation of gene expression / nucleolus / protein homodimerization activity / RNA binding / nucleoplasm / identical protein binding / nucleus / metal ion binding / cytoplasm / cytosol
Similarity search - Function
RNase III, double-stranded RNA binding domain, animal / Microprocessor complex subunit DGCR8 / Ribonuclease-III-like / Ribonuclease III / Ribonuclease III family signature. / Ribonuclease III domain / Ribonuclease III family domain profile. / Ribonuclease III family / Ribonuclease III domain / Double-stranded RNA binding motif ...RNase III, double-stranded RNA binding domain, animal / Microprocessor complex subunit DGCR8 / Ribonuclease-III-like / Ribonuclease III / Ribonuclease III family signature. / Ribonuclease III domain / Ribonuclease III family domain profile. / Ribonuclease III family / Ribonuclease III domain / Double-stranded RNA binding motif / Double-stranded RNA binding motif / Ribonuclease III, endonuclease domain superfamily / Double stranded RNA-binding domain (dsRBD) profile. / Double-stranded RNA-binding domain / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain
Similarity search - Domain/homology
Microprocessor complex subunit DGCR8 / Ribonuclease 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsKwon, S.C. / Nguyen, T.A. / Choi, Y.G. / Jo, M.H. / Hohng, S. / Kim, V.N. / Woo, J.S.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
Institute for Basic ScienceIBS-R008-D1 Korea, Republic Of
CitationJournal: Cell / Year: 2016
Title: Structure of Human DROSHA
Authors: Kwon, S.C. / Nguyen, T.A. / Choi, Y.G. / Jo, M.H. / Hohng, S. / Kim, V.N. / Woo, J.S.
History
DepositionNov 23, 2015Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 3, 2016Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribonuclease 3,DROSHA,Ribonuclease 3,DROSHA,Ribonuclease 3
B: Microprocessor complex subunit DGCR8
C: Microprocessor complex subunit DGCR8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,0015
Polymers117,8703
Non-polymers1312
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2940 Å2
ΔGint-62 kcal/mol
Surface area38950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.254, 118.136, 122.296
Angle α, β, γ (deg.)90.00, 102.07, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Ribonuclease 3,DROSHA,Ribonuclease 3,DROSHA,Ribonuclease 3 / Protein Drosha / Ribonuclease III / RNase III / p241


Mass: 108687.359 Da / Num. of mol.: 1
Fragment: UNP residues 411-458,UNP residues 522-711,UNP residues 850-1365
Mutation: E1045Q, E1222Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DROSHA, RN3, RNASE3L, RNASEN / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q9NRR4, ribonuclease III
#2: Protein/peptide Microprocessor complex subunit DGCR8 / DiGeorge syndrome critical region 8


Mass: 4591.254 Da / Num. of mol.: 2 / Fragment: UNP residues 728-750
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DGCR8, C22orf12, DGCRK6, LP4941 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q8WYQ5
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
Sequence detailsTHE AUTHORS CRYSTALLIZED THE FRAGMENT PROTEIN, RESIDUES 390-1365 FOR CHAIN A. THE SEQUENCES OF ...THE AUTHORS CRYSTALLIZED THE FRAGMENT PROTEIN, RESIDUES 390-1365 FOR CHAIN A. THE SEQUENCES OF RESIDUES 505-521 AND 712-849 (THE UNK PARTS) ARE AS FOLLOWS. (505)AKAARPPWEPPKTKLDEDLESSSESECESDEDSTCSSSSDSEVFDVIAEIKRKKAHPDRLHDE(521) AND (735)ALVPEEEIANMLQWEELEWQKYAEECKGMIVTNPGTKPSSVRIDQLDREQFNPDVITFPIIVHFGIRPAQLSYAGDPQYQKLWKSYVKLRHLLANSPKVKQTDKQKLAQREEALQKIRQKNTMRREVTVELSSQGFWK(849) THE AUTHORS COULD OBSERVE THREE PARTS (505-520,735-745,749-756). BUT THEY ARE NOT SURE WHICH PART CORRESPONDS TO THESE OBSERVED RESIDUES. SO THE RESIDUE NUMBERS OF UNK ARE MEANINGLESS.

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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: 3.34 Å3/Da / Density % sol: 63.17 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 100mM Citrate Bis-Tris Propane (pH 7.84), 3%(v/v) polyethylene glycol (PEG) 400, 3%(w/v) PEG 20,000, 1%(v/v) ethanol.

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Data collection

DiffractionMean temperature: 193 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 13, 2015
RadiationMonochromator: DCM Si (111) Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionRedundancy: 7.5 % / Number: 183042 / Rmerge(I) obs: 0.061 / Χ2: 0.93 / D res high: 3.3 Å / D res low: 20 Å / Num. obs: 24319 / % possible obs: 99.6
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)IDRmerge(I) obsChi squaredRedundancy
8.722010.0290.717.2
7.028.7210.0310.7197.6
6.167.0210.0380.7337.2
5.616.1610.0440.7517.3
5.225.6110.0510.8227.4
4.915.2210.0580.9587.5
4.674.9110.0661.1317.5
4.474.6710.071.0977.6
4.34.4710.081.0047.6
4.154.310.0920.9737.6
4.024.1510.1090.9137.6
3.914.0210.1340.9327.6
3.813.9110.1650.9587.6
3.713.8110.1980.9387.6
3.633.7110.21917.6
3.553.6310.3280.9697.6
3.483.5510.3570.9877.6
3.423.4810.4360.9787.6
3.363.4210.5611.0317.6
3.33.3610.650.977.6
ReflectionResolution: 3.2→20 Å / Num. obs: 26854 / % possible obs: 99.9 % / Redundancy: 7.3 % / Biso Wilson estimate: 49.52 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 10.7
Reflection shellResolution: 3.2→3.25 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.577 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
SCALEPACKdata scaling
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→19.93 Å / Cross valid method: FREE R-VALUE / Details: ANOMALOUS DATA WAS USED FOR REFINEMENT.
RfactorNum. reflection% reflection
Rfree0.3 3143 8.86 %
Rwork0.267 --
obs-22695 67.3 %
Displacement parametersBiso mean: 61.56 Å2
Refinement stepCycle: LAST / Resolution: 3.2→19.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6157 0 2 0 6159
LS refinement shellResolution: 3.2→3.25 Å
RfactorNum. reflection% reflection
Rfree0.5292 49 -
Rwork0.3999 504 -
obs--24 %
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)
10.14240.1956-0.16970.46130.03530.49320.0845-0.3172-0.00740.1706-0.05850.411-0.1365-0.4497-0.14040.10130.14090.31040.71740.22280.0968116.7057-7.295165.7279
20.17770.06050.01290.61840.0780.37030.03150.0704-0.1519-0.6980.26010.09350.072-0.29180.36760.6151-0.4712-0.4146-0.14610.1460.4659114.1126-22.8182118.5785
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and ((resseq 411:711) or (resseq 735:756) or (resseq 850:863) or (resseq 904:929) or (resseq 1401;1402)))
2X-RAY DIFFRACTION2(chain 'A' and ((resseq 864:903) or (resseq 958:1333))) or (chain 'B') or (chain 'C')

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