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- PDB-6akj: The crystal structure of EMC complex -

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Basic information

Entry
Database: PDB / ID: 6akj
TitleThe crystal structure of EMC complex
ComponentsEnhancer of rudimentary homolog,YTH domain-containing protein mmi1 fusion protein
KeywordsRNA BINDING PROTEIN / Protein-protein interaction
Function / homology
Function and homology information


ascospore-type prospore nucleus / : / lncRNA catabolic process / regulation of termination of RNA polymerase II transcription, poly(A)-coupled / nuclear RNA surveillance / siRNA-independent facultative heterochromatin formation / regulation of siRNA-independent facultative heterochromatin formation / nuclear exosome focus / nuclear mRNA surveillance of spliceosomal pre-mRNA splicing / nuclear-transcribed mRNA catabolic process, meiosis-specific transcripts ...ascospore-type prospore nucleus / : / lncRNA catabolic process / regulation of termination of RNA polymerase II transcription, poly(A)-coupled / nuclear RNA surveillance / siRNA-independent facultative heterochromatin formation / regulation of siRNA-independent facultative heterochromatin formation / nuclear exosome focus / nuclear mRNA surveillance of spliceosomal pre-mRNA splicing / nuclear-transcribed mRNA catabolic process, meiosis-specific transcripts / Mei2 nuclear dot complex / heterochromatin island / nuclear mRNA surveillance of mRNA 3'-end processing / CCR4-NOT complex binding / protein-RNA adaptor activity / termination of RNA polymerase II transcription, poly(A)-coupled / regulatory ncRNA 3'-end processing / rDNA heterochromatin / N6-methyladenosine-containing RNA reader activity / pre-mRNA binding / lncRNA binding / molecular function inhibitor activity / mRNA destabilization / pre-mRNA intronic binding / mRNA binding / chromatin / DNA binding / RNA binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Enhancer of rudimentary / Enhancer of rudimentary superfamily / Enhancer of rudimentary / YTH domain / YT521-B-like domain / YTH domain profile.
Similarity search - Domain/homology
Enhancer of rudimentary homolog 1 / Enhancer of rudimentary homolog 1 / RNA binding exosome specificity factor Mmi1
Similarity search - Component
Biological speciesSchizosaccharomyces pombe 972h- (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsLi, F.
CitationJournal: Nat Commun / Year: 2019
Title: A conserved dimer interface connects ERH and YTH family proteins to promote gene silencing.
Authors: Xie, G. / Vo, T.V. / Thillainadesan, G. / Holla, S. / Zhang, B. / Jiang, Y. / Lv, M. / Xu, Z. / Wang, C. / Balachandran, V. / Shi, Y. / Li, F. / Grewal, S.I.S.
History
DepositionSep 1, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 13, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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

Downloads & links

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Assembly

Deposited unit
A: Enhancer of rudimentary homolog,YTH domain-containing protein mmi1 fusion protein
B: Enhancer of rudimentary homolog,YTH domain-containing protein mmi1 fusion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3307
Polymers35,8502
Non-polymers4805
Water21612
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3400 Å2
ΔGint-70 kcal/mol
Surface area11630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.689, 86.689, 105.391
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Enhancer of rudimentary homolog,YTH domain-containing protein mmi1 fusion protein / Meiotic mRNA interception protein 1


Mass: 17924.785 Da / Num. of mol.: 2 / Fragment: UNP residues 1-104, UNP residues 96-122
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe 972h- (yeast)
Strain: 972h- / Production host: Escherichia coli (E. coli)
References: UniProt: K7PD52, UniProt: O74958, UniProt: G2TRN4*PLUS
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 3.19 Å3/Da / Density % sol: 61.43 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I/F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 1.6M (NH4)2SO4, 0.1M MES pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.7→75.075 Å / Num. all: 13026 / Num. obs: 13026 / % possible obs: 100 % / Redundancy: 15.8 % / Biso Wilson estimate: 70.23 Å2 / Rpim(I) all: 0.027 / Rrim(I) all: 0.109 / Rsym value: 0.105 / Net I/av σ(I): 6.1 / Net I/σ(I): 18.6 / Num. measured all: 206285
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
2.7-2.8514.51.3360.618560.3581.3851.336100
2.85-3.0216.50.7161.117770.180.7390.716100
3.02-3.2316.40.4051.916630.1020.4180.405100
3.23-3.49150.2133.515600.0560.2210.213100
3.49-3.8216.90.1425.214390.0360.1470.142100
3.82-4.2716.80.0897.713110.0220.0920.089100
4.27-4.9315.50.06110.811590.0160.0630.061100
4.93-6.0416.80.06310.59980.0160.0650.063100
6.04-8.5414.90.0698.87960.0180.0710.069100
8.54-37.53813.90.03715.64670.010.0380.03798.8

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
SCALA3.3.22data scaling
PDB_EXTRACT3.24data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WZ7

1wz7


Resolution: 2.7→37.538 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.39 / Stereochemistry target values: ML
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflection
Rfree0.2409 708 5.45 %
Rwork0.2067 12289 -
obs0.2086 12997 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 174.97 Å2 / Biso mean: 75.9801 Å2 / Biso min: 38.8 Å2
Refinement stepCycle: final / Resolution: 2.7→37.538 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1852 0 25 12 1889
Biso mean--137.98 60.99 -
Num. residues----216
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0011936
X-RAY DIFFRACTIONf_angle_d0.3842631
X-RAY DIFFRACTIONf_chiral_restr0.04260
X-RAY DIFFRACTIONf_plane_restr0.004329
X-RAY DIFFRACTIONf_dihedral_angle_d13.3631085
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.7001-2.90850.36371370.303724142551
2.9085-3.2010.27521540.252324052559
3.201-3.66390.27771210.216324522573
3.6639-4.61480.21181460.176424522598
4.6148-37.54130.22231500.198625662716
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)
18.5476-2.0031-2.76587.0846-0.77132.8603-0.166-0.75220.96190.4986-0.22240.27190.8810.60270.26760.4852-0.21070.00180.6846-0.0220.6276-18.330336.46841.8082
29.679-3.2989-6.37671.29751.89857.5838-0.41520.7229-2.04371.3493-1.01240.58511.0131-0.56680.92570.7931-0.23990.09210.44330.0480.474-16.932338.34175.0053
38.86950.59352.54412.11252.02882.6022-1.0416-0.0357-0.15510.621-0.1964-0.93780.79570.83131.11440.6539-0.0764-0.00690.5410.09770.959-11.481627.18754.1363
43.8592-1.48564.73866.9411.35897.7856-0.4649-1.0598-0.23350.64770.13030.7620.9069-1.49940.17410.9269-0.25130.19350.6994-0.00910.6829-19.356222.021210.9817
56.36222.0694-1.41573.83210.66742.6963-0.1270.5401-0.4684-0.07150.33840.07520.5259-0.6957-0.30250.4142-0.17230.07320.5198-0.00290.5412-20.832735.7893-6.6609
62.4816-4.943-0.19.2021-0.71987.24830.07440.9655-0.5106-0.804-0.75710.78980.7656-0.71790.50660.6644-0.29780.02270.56330.03560.5241-17.940321.8641-0.8591
78.18953.7256-1.42528.2854-1.65167.15560.392-0.7604-0.81970.8253-0.6173-0.39640.56610.48030.28320.7044-0.1851-0.12530.81960.1120.6635-9.984236.25177.5613
84.9920.62061.39342.32053.46065.2826-0.12360.63930.4173-0.3442-0.0403-1.1855-0.28531.90410.28690.5323-0.310.00340.72760.12330.7954-8.370546.4105-8.8222
93.5954-0.02490.38657.99581.95592.5705-0.0643-0.22280.13740.4234-0.26780.3780.0433-0.02210.3760.5113-0.22960.07710.62760.02840.5785-23.206549.70764.3693
104.8526-2.5719-4.48258.81891.02834.5401-0.0313-0.8781.32440.31920.7276-0.2406-1.22551.8662-0.65540.9618-0.1845-0.00710.7234-0.20280.8211-17.555662.54337.3944
117.36193.43792.55636.38673.92154.0971-0.01370.41190.4799-0.0526-0.16530.20580.1237-0.1390.29450.467-0.1676-0.00310.60830.03530.5921-22.199945.6375-7.5561
125.9887-6.1151-1.70825.91971.6427.04850.85791.3182-1.1082-0.9455-0.48440.2826-0.5151-0.1362-0.13810.8947-0.27940.01690.7001-0.05890.725-24.21261.512-3.151
135.61473.30542.18926.12660.21358.67430.0895-1.09560.91361.0572-1.03510.7776-0.572-1.22680.76340.8019-0.23590.16380.7083-0.09390.9881-27.611947.79189.476
148.16424.41273.32458.3397-1.86793.61780.29670.2209-0.383-0.0660.23511.63810.2626-2.5994-0.24520.7314-0.49080.01031.041-0.10490.7894-33.887135.1599-3.6609
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 19 )A6 - 19
2X-RAY DIFFRACTION2chain 'A' and (resid 20 through 30 )A20 - 30
3X-RAY DIFFRACTION3chain 'A' and (resid 31 through 42 )A31 - 42
4X-RAY DIFFRACTION4chain 'A' and (resid 43 through 65 )A43 - 65
5X-RAY DIFFRACTION5chain 'A' and (resid 66 through 85 )A66 - 85
6X-RAY DIFFRACTION6chain 'A' and (resid 86 through 98 )A86 - 98
7X-RAY DIFFRACTION7chain 'A' and (resid 121 through 133 )A121 - 133
8X-RAY DIFFRACTION8chain 'A' and (resid 134 through 144 )A134 - 144
9X-RAY DIFFRACTION9chain 'B' and (resid 7 through 44 )B7 - 44
10X-RAY DIFFRACTION10chain 'B' and (resid 45 through 65 )B45 - 65
11X-RAY DIFFRACTION11chain 'B' and (resid 66 through 85 )B66 - 85
12X-RAY DIFFRACTION12chain 'B' and (resid 86 through 101 )B86 - 101
13X-RAY DIFFRACTION13chain 'B' and (resid 121 through 133 )B121 - 133
14X-RAY DIFFRACTION14chain 'B' and (resid 134 through 144 )B134 - 144

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