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- PDB-7ejo: Structure of ERH-2 bound to TOST-1 -

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Basic information

Entry
Database: PDB / ID: 7ejo
TitleStructure of ERH-2 bound to TOST-1
Components
  • Enhancer of rudimentary homolog 2
  • Enhancer of rudimentary homolog 2,Protein tost-1
KeywordsPEPTIDE BINDING PROTEIN / 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
ERH-like fold / Enhancer of rudimentary / Enhancer of rudimentary / Enhancer of rudimentary superfamily / Enhancer of rudimentary / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Protein tost-1 / Enhancer of rudimentary homolog 2
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.191 Å
AuthorsWang, X. / Xu, C.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
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 tost-1
B: Enhancer of rudimentary homolog 2


Theoretical massNumber of molelcules
Total (without water)28,0192
Polymers28,0192
Non-polymers00
Water1,33374
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2060 Å2
ΔGint-10 kcal/mol
Surface area11220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.117, 51.882, 57.038
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Enhancer of rudimentary homolog 2,Protein tost-1 / Twenty one u antagonist 1


Mass: 16008.853 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: erh-2, F35G12.11, tost-1, C35D10.13 / Production host: Escherichia coli (E. coli) / References: UniProt: Q20057, UniProt: Q18490
#2: Protein Enhancer of rudimentary homolog 2


Mass: 12010.642 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: erh-2, F35G12.11 / Production host: Escherichia coli (E. coli) / References: UniProt: Q20057
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 2.72 Å3/Da / Density % sol: 54.82 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1M Bis-tris pH 6.2, tascimate pH 6.0 20%

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 23, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.19→50 Å / Num. obs: 22224 / % possible obs: 100 % / Redundancy: 11.4 % / CC1/2: 1 / Net I/σ(I): 34
Reflection shellResolution: 2.19→2.28 Å / Num. unique obs: 1744 / CC1/2: 0.924

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WZ7

1wz7


Resolution: 2.191→25.941 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 24.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2235 2200 9.9 %
Rwork0.1777 20024 -
obs0.1823 22224 73.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 89.3 Å2 / Biso mean: 36.2696 Å2 / Biso min: 12.87 Å2
Refinement stepCycle: final / Resolution: 2.191→25.941 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1628 0 0 74 1702
Biso mean---40.23 -
Num. residues----203
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2-2.23830.309630.233657134
2.2383-2.29030.2708750.225267239
2.2903-2.34750.2438790.200672442
2.3475-2.4110.2384900.22482348
2.411-2.48190.2781040.214193754
2.4819-2.56190.24981100.203102661
2.5619-2.65340.2411210.209112967
2.6534-2.75950.22531330.196123371
2.7595-2.88490.23021510.1896133879
2.8849-3.03680.26951720.1892147686
3.0368-3.22680.231690.1984157992
3.2268-3.47540.23721820.1772167798
3.4754-3.82410.21471930.15081695100
3.8241-4.37520.18161880.14151723100
4.3752-5.50360.18321860.1521701100
5.5036-25.940.25731840.20721720100
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)
10.57490.0296-0.34540.23210.11010.2673-0.02130.12350.0184-0.06590.20970.1908-0.06290.10960.00310.1251-0.01690.00560.1553-0.0240.21854.22511.113312.7945
20.9201-0.5616-0.64991.3715-0.27910.85530.17340.16210.13130.20950.0746-0.016-0.30470.02020.04730.234-0.05660.0520.20.02510.156615.964917.140810.4262
30.8271-0.1848-0.80040.5791-0.15591.27060.17090.31340.1166-0.16-0.1582-0.0428-0.1480.03230.02020.2319-0.06960.0350.28390.04210.195420.251416.77041.3446
40.93321.0685-0.71551.9113-1.03042.51990.2282-0.1974-0.20740.3888-0.3242-0.1549-0.5390.54-0.15210.2412-0.0229-0.01610.19910.00060.221119.25286.074424.6132
50.48010.07830.17961.338-0.29230.7689-0.1126-0.0372-0.27390.19210.0242-0.29240.1812-0.0748-0.02450.20390.0626-0.00410.16170.04460.217315.7884-3.210324.3868
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 123 through 142)A123 - 142
2X-RAY DIFFRACTION2(chain 'A' and resid 4 through 43)A4 - 43
3X-RAY DIFFRACTION3(chain 'A' and resid 51 through 103)A51 - 103
4X-RAY DIFFRACTION4(chain 'B' and resid 4 through 44)B4 - 44
5X-RAY DIFFRACTION5(chain 'B' and resid 51 through 97)B51 - 97

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