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- PDB-7o6n: Crystal structure of C. elegans ERH-2 PID-3 complex -

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Basic information

Entry
Database: PDB / ID: 7o6n
TitleCrystal structure of C. elegans ERH-2 PID-3 complex
Components
  • Enhancer of rudimentary homolog 2
  • Protein pid-3
KeywordsPROTEIN BINDING / ERH-2 PID-3 complex piRNA processing PETISCO
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
FORMIC ACID / Protein pid-3 / Enhancer of rudimentary homolog 2
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.17 Å
AuthorsFalk, S. / Ketting, R.F.
CitationJournal: Genes Dev. / Year: 2021
Title: Structural basis of PETISCO complex assembly during piRNA biogenesis in C. elegans .
Authors: Perez-Borrajero, C. / Podvalnaya, N. / Holleis, K. / Lichtenberger, R. / Karaulanov, E. / Simon, B. / Basquin, J. / Hennig, J. / Ketting, R.F. / Falk, S.
History
DepositionApr 11, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 25, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 6, 2021Group: Data collection / Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / pdbx_contact_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 31, 2024Group: 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

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Assembly

Deposited unit
A: Enhancer of rudimentary homolog 2
B: Enhancer of rudimentary homolog 2
C: Protein pid-3
D: Protein pid-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7075
Polymers32,6604
Non-polymers461
Water48627
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, SEC MALS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.987, 52.945, 125.608
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 3 through 96 or (resid 97...
d_2ens_1(chain "B" and (resid 3 through 42 or (resid 43...
d_1ens_2(chain "C" and (resid 179 through 180 or (resid 181...
d_2ens_2chain "D"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1THRARGA1 - 95
d_21ens_1THRARGB1 - 95
d_11ens_2SERGLUD3 - 17
d_21ens_2SERGLUE1 - 15

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(-0.765359633472, -0.472881827197, 0.436586084247), (-0.455791051855, -0.0806871204236, -0.886422080979), (0.454399767276, -0.877423709564, -0.153780640508)-5.40713474349, 10.2311124826, 13.5743628654
2given(-0.769311880506, -0.461789261486, 0.441486022982), (-0.484980253694, -0.0277089363109, -0.874086018865), (0.41587664522, -0.886556762325, -0.202641859288)-5.45318176564, 10.4338068279, 13.7135241015

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Components

#1: Protein Enhancer of rudimentary homolog 2


Mass: 11843.388 Da / Num. of mol.: 2
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
#2: Protein/peptide Protein pid-3 / piRNA biogenesis and chromosome segregation protein 1 / piRNA-induced silencing defective protein 3


Mass: 4486.856 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: pid-3, pics-1, Y23H5A.3 / Production host: Escherichia coli (E. coli) / References: UniProt: O76616
#3: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.29 Å3/Da / Density % sol: 46.29 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Magnesium formate dihydrate 20 % w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 6, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.17→48.79 Å / Num. obs: 16511 / % possible obs: 98.93 % / Redundancy: 12.8 % / Biso Wilson estimate: 59.32 Å2 / CC1/2: 0.998 / CC star: 1 / Net I/σ(I): 13.3
Reflection shellResolution: 2.17→2.248 Å / Mean I/σ(I) obs: 1.3 / Num. unique obs: 1463 / CC1/2: 0.646 / CC star: 0.886 / % possible all: 90.04

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7O6L

7o6l


Resolution: 2.17→48.79 Å / SU ML: 0.3055 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.9821
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2447 1634 10 %
Rwork0.2068 14704 -
obs0.2107 16338 98.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 76.44 Å2
Refinement stepCycle: LAST / Resolution: 2.17→48.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1735 0 3 27 1765
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00271768
X-RAY DIFFRACTIONf_angle_d0.65162391
X-RAY DIFFRACTIONf_chiral_restr0.0393274
X-RAY DIFFRACTIONf_plane_restr0.0052302
X-RAY DIFFRACTIONf_dihedral_angle_d4.299240
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS1.39017007063
ens_2d_2DX-RAY DIFFRACTIONTorsion NCS0.819217476452
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.17-2.230.37991170.33411054X-RAY DIFFRACTION86.42
2.23-2.310.32251360.31411216X-RAY DIFFRACTION99.78
2.31-2.390.31731340.28681213X-RAY DIFFRACTION99.93
2.39-2.480.39061340.30761211X-RAY DIFFRACTION100
2.48-2.60.34221340.27041203X-RAY DIFFRACTION100
2.6-2.730.29631360.23541227X-RAY DIFFRACTION100
2.73-2.90.26051380.24181237X-RAY DIFFRACTION99.78
2.91-3.130.2891370.26661236X-RAY DIFFRACTION99.85
3.13-3.440.27581370.21711237X-RAY DIFFRACTION99.93
3.44-3.940.2191380.18381236X-RAY DIFFRACTION99.78
3.94-4.960.20881440.15311291X-RAY DIFFRACTION100
4.97-48.790.21651490.20321343X-RAY DIFFRACTION100
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)
18.97610603686-4.379194036021.941830505343.11198536672-2.156220652575.32295886198-0.8949484169350.5574942462160.4058877143110.5362105617880.136984188622-0.12568378972-1.322068011940.3303753042530.5218233815210.591903864332-0.05447531806570.04329291208710.532835879336-0.1365788437560.6452013918581.632362306322.5194955236316.8408549472
24.621395493671.34608400111-0.2902558699748.877347528940.9006357686529.564944349340.120045024958-0.238578152341-0.212069275268-0.2087573178460.311964550916-0.742875056384-1.216009901030.689959309811-0.2099157221250.542625822866-0.04064876564040.1007504696160.453012753851-0.07814563065690.3260756677482.65582351552.3448316425413.0854271552
33.35840517199-4.739642996690.1664242233082.05748486167-2.517493172017.741851060160.225529808783-0.0166978410691.6512832977-0.07919645484790.199645614066-0.773784408529-2.204126456560.564532317579-0.4056496241031.26191576896-0.2964981799080.1564016354560.719703867139-0.1387473417670.8520089979916.7852181116313.838303131720.1497953926
45.39228643737-2.05952381495-1.558421226350.8047740424960.2365994174898.565181692283.74977490877-0.02781343069730.554381908844-2.01347369856-0.0361281265911.296712723870.9184035902060.640105160914-2.159300223082.17889839654-0.1751314729710.2788294994070.8011087943290.07168598582631.036873248332.6989358732227.175881371723.8189311224
52.96067851798-3.5302725822-2.908223138186.009418110956.20592225517.04518631174-0.250384133309-0.1241756161830.0258561495592-0.395468803308-0.7684510184931.66396558767-2.18904454926-1.220109237610.9697342776881.525553318890.171707336086-0.1046842314470.763905760021-0.0911141663140.629213832952-1.8040562733214.129174424327.1688077784
64.52515405954-4.17257310132-0.6434239107583.830875969921.796168066284.08323468770.363172380694-0.5565722496380.312040512201-0.6713030626050.196368898123-0.437970289609-0.6616037181350.144750561981-0.5968845185850.71822747943-0.06347143163790.07153556696780.602122892872-0.10587540970.4993197587222.82288844869-0.59683062359721.5427750377
77.393339007950.890361294525-0.4591477556162.206323666070.3660629263639.723092063040.398093456933-0.9562999582790.4575123286821.235410828090.07126582966050.08209647417050.2482182289130.150709303485-0.1315139251570.589462738312-0.014784481134-0.02762202924570.620519066767-0.07843470033880.4559296602687.18008207939-8.1430963112824.2915892586
82.804074898281.319060594851.184889595628.690946274084.897670257713.03118338791-0.379211287705-1.807710216210.5283228184430.5383528987040.594810078663-1.18778654029-1.063903890960.0124923041942-0.5323325252190.831232750312-0.06572881266960.110970393950.686058542437-0.1600416567320.7349513198375.591649596268.2527652115230.4997758182
91.87265881884-1.054818233311.011903545372.74540146509-0.995223220188.91585777265-0.0095422848566-0.0594898860323-0.110451566099-0.03730148530540.1270627145650.209708447401-0.127862184696-0.520910769913-0.1129628145820.384142618164-0.003398351937680.08549231296330.489966518213-0.08221596172010.541394325498-4.3863952885-7.141975470676.27062420702
107.809494045870.2773290652164.653861525650.0163418801120.8737739214168.517265431120.09464505195850.585256452494-0.308650596995-0.462287556859-0.00932916226475-0.2307386254730.4044146655950.533858198544-0.2375304518650.5215208661560.00780223565580.02234263562450.721277051585-0.1674458153650.561606365158-3.92019035746-14.2754063766-7.69759303524
114.28098364421-1.307709071862.750329893348.18394591946-2.149526381923.173066014410.165287577040.0294172521909-0.4553616300760.8527448909940.0985037815541-0.0418578129198-0.3654488119350.447737137847-0.2809842751540.5272854061850.0122586796143-0.01607497904230.478342145124-0.08181172695880.5186838428342.58593102119-12.570088714116.6244366718
122.95444897470.3148076557214.438524256269.34749378312.554503624577.12559157290.2240282414290.475898748621-0.9105014496140.4505699427130.407385917666-0.1086502561281.206544600980.0260926481064-0.5210539907430.497198543631-0.06833963239150.008439969042630.586180726017-0.09164726525110.723120032231-1.05473935245-20.41688605464.09240600055
133.943504293690.762629793289-3.230117011952.131615676210.2865743655463.392435377940.1072796292141.622464317730.773416646156-0.4122305742450.136119473790.700936864162-1.12473552574-1.69620989-0.081382980440.6447492947930.0622745312842-0.07710903325480.7617653241310.05818481000650.592406627814-7.4242651153-0.9940723078140.233390216847
143.0045550688-2.760225815480.2888950083913.206478187610.5043447348278.268650868560.0832960459710.06063468983190.1303538183690.1967125202810.261712282921-0.74333717141-3.022385685180.154532976021-0.3430793232961.45816421075-0.2104185076880.1306454430850.704525925292-0.0476338664890.6230681915281.4681858247912.712896516711.2660234004
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 3 through 16 )AA3 - 161 - 14
22chain 'A' and (resid 17 through 27 )AA17 - 2715 - 25
33chain 'A' and (resid 28 through 45 )AA28 - 4526 - 43
44chain 'A' and (resid 46 through 54 )AA46 - 5444 - 52
55chain 'A' and (resid 55 through 64 )AA55 - 6453 - 62
66chain 'A' and (resid 65 through 74 )AA65 - 7463 - 72
77chain 'A' and (resid 75 through 84 )AA75 - 8473 - 82
88chain 'A' and (resid 85 through 97 )AA85 - 9783 - 95
99chain 'B' and (resid 3 through 45 )BB3 - 451 - 43
1010chain 'B' and (resid 46 through 64 )BB46 - 6444 - 62
1111chain 'B' and (resid 65 through 84 )BB65 - 8463 - 82
1212chain 'B' and (resid 85 through 99 )BB85 - 9983 - 97
1313chain 'C' and (resid 177 through 193 )CD177 - 1931 - 17
1414chain 'D' and (resid 179 through 193 )DE179 - 1931 - 15

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