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- PDB-7cnc: cystal structure of human ERH in complex with DGCR8 -

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Basic information

Entry
Database: PDB / ID: 7cnc
Titlecystal structure of human ERH in complex with DGCR8
Components
  • Enhancer of rudimentary homolog
  • Microprocessor complex subunit DGCR8
KeywordsPROTEIN BINDING / Protein-protein interaction
Function / homology
Function and homology information


positive regulation of pre-miRNA processing / pyrimidine nucleoside metabolic process / protein-RNA adaptor activity / primary miRNA binding / Transcriptional Regulation by MECP2 / primary miRNA processing / regulation of stem cell proliferation / microprocessor complex / methylosome / methyl-CpG binding ...positive regulation of pre-miRNA processing / pyrimidine nucleoside metabolic process / protein-RNA adaptor activity / primary miRNA binding / Transcriptional Regulation by MECP2 / primary miRNA processing / regulation of stem cell proliferation / microprocessor complex / methylosome / methyl-CpG binding / nucleobase-containing compound metabolic process / MicroRNA (miRNA) biogenesis / double-stranded RNA binding / midbody / postsynaptic density / nuclear body / cell cycle / glutamatergic synapse / heme binding / nucleolus / protein homodimerization activity / RNA binding / nucleoplasm / identical protein binding / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Enhancer of rudimentary signature. / Enhancer of rudimentary / Enhancer of rudimentary superfamily / Enhancer of rudimentary / Microprocessor complex subunit DGCR8 / Double-stranded RNA binding motif / Double-stranded RNA binding motif / Double stranded RNA-binding domain (dsRBD) profile. / Double-stranded RNA-binding domain / WW domain superfamily ...Enhancer of rudimentary signature. / Enhancer of rudimentary / Enhancer of rudimentary superfamily / Enhancer of rudimentary / Microprocessor complex subunit DGCR8 / Double-stranded RNA binding motif / Double-stranded RNA binding motif / 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
Enhancer of rudimentary homolog / Microprocessor complex subunit DGCR8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsLi, F. / Shen, S.
CitationJournal: Nucleic Acids Res. / Year: 2020
Title: ERH facilitates microRNA maturation through the interaction with the N-terminus of DGCR8.
Authors: Kwon, S.C. / Jang, H. / Shen, S. / Baek, S.C. / Kim, K. / Yang, J. / Kim, J. / Kim, J.S. / Wang, S. / Shi, Y. / Li, F. / Kim, V.N.
History
DepositionJul 30, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 28, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 18, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 29, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Enhancer of rudimentary homolog
B: Microprocessor complex subunit DGCR8


Theoretical massNumber of molelcules
Total (without water)16,8072
Polymers16,8072
Non-polymers00
Water3,513195
1
A: Enhancer of rudimentary homolog
B: Microprocessor complex subunit DGCR8

A: Enhancer of rudimentary homolog
B: Microprocessor complex subunit DGCR8


Theoretical massNumber of molelcules
Total (without water)33,6144
Polymers33,6144
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area3660 Å2
ΔGint-29 kcal/mol
Surface area17490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.848, 45.072, 43.479
Angle α, β, γ (deg.)90.000, 107.440, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Enhancer of rudimentary homolog


Mass: 13291.054 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ERH / Production host: Escherichia coli (E. coli) / References: UniProt: P84090
#2: Protein/peptide Microprocessor complex subunit DGCR8 / / DiGeorge syndrome critical region 8


Mass: 3516.142 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DGCR8, C22orf12, DGCRK6, LP4941 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8WYQ5
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 195 / 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: 2.42 Å3/Da / Density % sol: 49.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2 M Imidazole malate pH 6, 8% w/v PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 23, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.6→40 Å / Num. obs: 20184 / % possible obs: 94.8 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.036 / Rrim(I) all: 0.093 / Χ2: 0.994 / Net I/σ(I): 5.5 / Num. measured all: 127866
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.6-1.634.50.4067510.8270.1970.4540.90971.8
1.63-1.664.70.4217670.830.1990.4680.96573
1.66-1.695.30.3938810.8910.1770.4330.96482.8
1.69-1.725.60.3819620.9110.1710.4190.93592.6
1.72-1.765.90.3510190.9220.1520.3830.95696.5
1.76-1.86.20.31310770.9490.1330.3410.98398.4
1.8-1.856.40.30810130.9510.1310.3351.00899
1.85-1.96.40.26910520.9650.1140.2930.99999
1.9-1.956.40.22910450.9740.0960.2481.07397.1
1.95-2.026.40.1989940.980.0830.2151.08395.4
2.02-2.096.90.17910660.9850.0730.1941.14799.5
2.09-2.176.80.15310710.9880.0630.1661.16499.9
2.17-2.276.80.13710340.9890.0560.1481.18899.9
2.27-2.396.80.1210690.9910.0490.131.15499.3
2.39-2.546.30.10310090.9920.0440.1131.04696.2
2.54-2.7470.09310840.9950.0370.11.03899.4
2.74-3.017.10.0810510.9940.0320.0860.97299.4
3.01-3.456.70.06310760.9960.0260.0680.84499.4
3.45-4.346.60.05210630.9980.0210.0560.798.2
4.34-406.60.05211000.9970.0210.0560.66399

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.16_3549refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1W9G

1w9g


Resolution: 1.6→39.593 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.4 / Phase error: 20.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1859 920 4.83 %
Rwork0.168 18120 -
obs0.169 19040 89.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 48.3 Å2 / Biso mean: 18.5273 Å2 / Biso min: 6.89 Å2
Refinement stepCycle: final / Resolution: 1.6→39.593 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1041 0 0 195 1236
Biso mean---26.81 -
Num. residues----130
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.6-1.68390.2268540.2065167457
1.6839-1.78940.19591100.1918228679
1.7894-1.92760.19321390.1867270694
1.9276-2.12160.22711290.1625282597
2.1216-2.42850.17041530.16222884100
2.4285-3.05950.17821620.1694283098
3.0595-39.5930.1811730.1599291599

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