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- PDB-7ejs: Structure of ERH-2 bound to PICS-1 -

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Basic information

Entry
Database: PDB / ID: 7ejs
TitleStructure of ERH-2 bound to PICS-1
ComponentsEnhancer of rudimentary homolog 2,Protein pid-3
KeywordsPEPTIDE BINDING PROTEIN / PICS complex
Function / homology
Function and homology information


21U-RNA metabolic process / positive regulation of chromosome segregation / RNA cap binding complex / piRNA processing / embryo development ending in birth or egg hatching / positive regulation of cell division / chromosome segregation / cell division / perinuclear region of cytoplasm / nucleus / cytoplasm
Similarity search - Function
Enhancer of rudimentary / Enhancer of rudimentary superfamily / Enhancer of rudimentary
Similarity search - Domain/homology
Protein pid-3 / Enhancer of rudimentary homolog 2
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.387 Å
AuthorsWang, X. / Xu, C.
CitationJournal: Nat Commun / Year: 2021
Title: Molecular basis for PICS-mediated piRNA biogenesis and cell division.
Authors: Wang, X. / Zeng, C. / Liao, S. / Zhu, Z. / Zhang, J. / Tu, X. / Yao, X. / Feng, X. / Guang, S. / Xu, C.
History
DepositionApr 2, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 25, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 6, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Enhancer of rudimentary homolog 2,Protein pid-3
B: Enhancer of rudimentary homolog 2,Protein pid-3


Theoretical massNumber of molelcules
Total (without water)31,8852
Polymers31,8852
Non-polymers00
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1830 Å2
ΔGint-10 kcal/mol
Surface area11010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.825, 52.528, 125.119
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Enhancer of rudimentary homolog 2,Protein pid-3 / piRNA biogenesis and chromosome segregation protein 1 / piRNA-induced silencing defective protein 3


Mass: 15942.616 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: erh-2, F35G12.11, pid-3, pics-1, Y23H5A.3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q20057, UniProt: O76616
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 2.31 Å3/Da / Density % sol: 46.75 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 15% v/v 2-propanol, 0.1M sodium citrate tribasic dihydrate pH 5.0, 10% PEG 10000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 26, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.38→50 Å / Num. obs: 11991 / % possible obs: 100 % / Redundancy: 11.6 % / CC1/2: 0.996 / Net I/σ(I): 24
Reflection shellResolution: 2.4→2.44 Å / Num. unique obs: 1679 / CC1/2: 0.83

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WZ7

1wz7


Resolution: 2.387→26.264 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 23.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2381 1203 10.03 %
Rwork0.2008 10788 -
obs0.2046 11991 97.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 149.76 Å2 / Biso mean: 71.0806 Å2 / Biso min: 40.62 Å2
Refinement stepCycle: final / Resolution: 2.387→26.264 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1671 0 0 8 1679
Biso mean---55.8 -
Num. residues----217
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3872-2.48270.29871230.2436111793
2.4827-2.59560.25081280.2298115096
2.5956-2.73230.29831280.2329115396
2.7323-2.90330.30611320.2295117797
2.9033-3.12710.26561340.221119899
3.1271-3.44120.26231370.2068122099
3.4412-3.93770.21691360.18371226100
3.9377-4.95570.2091400.181264100
4.9557-26.260.23271450.2049128397
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)
12.53911.2502-0.39433.6532-1.79274.5217-0.07430.30890.1985-0.10650.34540.1835-1.076-0.3088-0.26010.71970.05090.10160.55710.06330.513518.94577.4354-22.0038
21.28380.03121.32892.3613-0.2755.42180.0662-0.0426-0.3054-0.04390.1135-0.11070.010.1631-0.19460.38310.02110.07410.47250.04920.464924.603-11.673-5.5021
35.5804-0.76035.28158.4121.93556.1993-1.054-1.03340.1078-0.0290.1912-0.1175-1.9762-0.12310.62981.58350.16850.08040.98890.05840.80921.593413.0399-11.8148
49.5197-2.3438-0.9622.09433.10256.9696-0.8408-1.11460.52250.261-0.3087-0.3591-1.48950.66440.98510.79490.0259-0.09820.75480.1390.79629.1849-1.0693-0.1097
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 5 through 97)A5 - 97
2X-RAY DIFFRACTION2(chain 'B' and resid 4 through 98)B4 - 98
3X-RAY DIFFRACTION3(chain 'A' and resid 124 through 137)A124 - 137
4X-RAY DIFFRACTION4(chain 'B' and resid 123 through 137)B123 - 137

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