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- PDB-7nyq: Crystal structure of the Mei-P26 NHL domain -

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Basic information

Entry
Database: PDB / ID: 7nyq
TitleCrystal structure of the Mei-P26 NHL domain
ComponentsMeiotic P26, isoform C
KeywordsRNA BINDING PROTEIN / Mei-P26 / NHL / RNA recognition / TRIM-NHL proteins
Function / homology
Function and homology information


regulation of macromolecule metabolic process / gamete generation / germ cell development / meiotic cell cycle / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / spermatogenesis / protein ubiquitination / zinc ion binding / cytoplasm
Similarity search - Function
: / NHL repeat profile. / NHL repeat / NHL repeat / B-box, C-terminal / B-Box C-terminal domain / B-box zinc finger / B-Box-type zinc finger / B-box-type zinc finger / Zinc finger B-box type profile. ...: / NHL repeat profile. / NHL repeat / NHL repeat / B-box, C-terminal / B-Box C-terminal domain / B-box zinc finger / B-Box-type zinc finger / B-box-type zinc finger / Zinc finger B-box type profile. / Six-bladed beta-propeller, TolB-like / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Meiotic P26, isoform C
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsSalerno-Kochan, A. / Gaik, M. / Medenbach, J. / Glatt, S.
Funding support Poland, 3items
OrganizationGrant numberCountry
Polish National Science Centre2015/19/P/NZ1/02514 Poland
Polish National Science Centre2019/32/T/NZ1/00420 Poland
Foundation for Polish ScienceTECH CORE FACILITY/2017-4/6 Poland
Citation
Journal: Life Sci Alliance / Year: 2022
Title: Molecular insights into RNA recognition and gene regulation by the TRIM-NHL protein Mei-P26.
Authors: Salerno-Kochan, A. / Horn, A. / Ghosh, P. / Nithin, C. / Koscielniak, A. / Meindl, A. / Strauss, D. / Krutyholowa, R. / Rossbach, O. / Bujnicki, J.M. / Gaik, M. / Medenbach, J. / Glatt, S.
#1: Journal: To Be Published
Title: Molecular insights into RNA recognition and gene regulation by the TRIM-NHL protein Mei-P26
Authors: Salerno-Kochan, A. / Horn, A. / Gosh, P. / Nithin, C. / Koscielniak, A. / Strauss, D. / Rossbach, O. / Bujnicki, J.M. / Gaik, M. / Medenbach, J. / Glatt, S.
History
DepositionMar 23, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 4, 2022Provider: repository / Type: Initial release
Revision 1.1May 18, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed ..._citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Meiotic P26, isoform C
B: Meiotic P26, isoform C


Theoretical massNumber of molelcules
Total (without water)66,5882
Polymers66,5882
Non-polymers00
Water5,765320
1
A: Meiotic P26, isoform C


Theoretical massNumber of molelcules
Total (without water)33,2941
Polymers33,2941
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Meiotic P26, isoform C


Theoretical massNumber of molelcules
Total (without water)33,2941
Polymers33,2941
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.710, 116.500, 64.700
Angle α, β, γ (deg.)90.000, 96.360, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Meiotic P26, isoform C / Meiotic P26 / isoform E


Mass: 33293.996 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly)
Gene: mei-P26, AF145661, BcDNA:GH10646, Dmel\CG12218, MEI-P26, Mei-P26, mei-p26, meiP26, CG12218, Dmel_CG12218
Production host: Trichoplusia ni (cabbage looper) / Variant (production host): Hi5 / References: UniProt: M9PH32
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 320 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.95 Å3/Da / Density % sol: 37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: KSCN, PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.599→50 Å / Num. obs: 66500 / % possible obs: 98.8 % / Redundancy: 3.82 % / CC1/2: 0.999 / Net I/σ(I): 10.15
Reflection shellResolution: 1.6→1.64 Å / Mean I/σ(I) obs: 0.85 / Num. unique obs: 4807 / CC1/2: 0.459

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Q7F

1q7f


Resolution: 1.6→43.17 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2146 3325 5 %
Rwork0.1955 63153 -
obs0.1964 66478 98.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 132.73 Å2 / Biso mean: 40.2099 Å2 / Biso min: 13.03 Å2
Refinement stepCycle: final / Resolution: 1.6→43.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4263 0 0 320 4583
Biso mean---38.31 -
Num. residues----549
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 24

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6-1.620.42371320.41432517264995
1.62-1.650.3571390.37842639277899
1.65-1.670.40261380.36392622276099
1.67-1.70.37231390.3332627276699
1.7-1.730.35521380.32182634277299
1.73-1.760.30741380.29862610274898
1.76-1.790.33651370.28882613275098
1.79-1.830.25661400.26052652279299
1.83-1.870.28271370.24962608274599
1.87-1.910.25181410.242666280799
1.91-1.960.25481380.22532628276699
1.96-2.010.24791380.21212633277199
2.01-2.070.24421380.21312620275899
2.07-2.140.22431370.20172603274098
2.14-2.220.20871380.18532617275598
2.22-2.310.19421400.18922652279299
2.31-2.410.22511390.1872649278899
2.41-2.540.23371390.19012628276799
2.54-2.70.19091410.19272677281899
2.7-2.910.2071390.19312640277999
2.91-3.20.19241390.18162647278699
3.2-3.660.19821390.16172634277399
3.66-4.610.15931380.14262637277598
4.61-43.170.17931430.17652700284399
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)
13.1918-0.78181.94112.125-0.17022.2275-0.0670.01940.1863-0.0255-0.0018-0.0235-0.08320.03390.0740.1377-0.0035-0.01060.1119-0.00840.127919.376341.06343.5351
25.6565-1.1169-0.56297.87741.11367.5832-0.1071-0.0741-0.29060.20090.1785-0.24180.17710.0806-0.00240.1747-0.0084-0.03640.10490.02730.149822.075130.524912.195
31.6386-0.31840.93514.89812.03352.84050.0268-0.0894-0.21990.25490.2215-0.1810.22330.1189-0.24360.21630.012-0.04630.16510.05850.220421.722824.084711.0359
42.4621-2.27632.20852.6668-1.68742.58960.65680.0954-0.848-0.60670.07680.691.0258-0.2381-0.63590.4993-0.0412-0.23710.2584-0.01290.510516.387617.0804-1.6884
56.6347-0.07431.69136.8379-0.67177.17590.15470.5842-0.3117-0.62610.14350.6110.149-0.4056-0.34050.22620.0153-0.10660.2437-0.02370.245611.000728.4789-9.3372
64.9487-0.6032.3276.21590.75765.35570.36560.13980.0595-0.7525-0.04850.50630.265-0.1344-0.25310.41540.0149-0.13880.2666-0.05630.35999.289629.4283-13.3395
73.66642.78020.25424.27390.06663.3542-0.07390.3645-0.1502-0.3950.14310.03420.1479-0.0437-0.07080.17160.023-0.02490.15970.01070.154611.364837.8283-5.7909
80.32140.14990.46920.4617-0.05396.17860.06690.0063-0.09750.01380.1069-0.11750.49330.4147-0.16190.30710.0741-0.12630.2044-0.05730.339228.40549.42928.4744
90.73920.97050.44516.68252.58833.1929-0.07780.03870.1566-0.1448-0.07780.0713-0.4454-0.17090.12110.34380.0567-0.13920.2078-0.01370.298819.492763.897422.9595
102.42820.02140.50363.817-0.35964.9283-0.01570.06740.0193-0.159-0.06350.0532-0.4653-0.0220.05040.3334-0.0147-0.09520.1753-0.04030.246126.527367.177542.8964
114.66880.9111-4.47573.5517-2.44697.9250.0702-0.2534-0.10630.0866-0.15580.0107-0.10890.49020.1090.23930.0221-0.10720.1793-0.04530.251628.506751.244443.6137
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 931 through 1001 )A931 - 1001
2X-RAY DIFFRACTION2chain 'A' and (resid 1002 through 1027 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 1028 through 1069 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 1070 through 1131 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 1132 through 1151 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 1152 through 1177 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 1178 through 1203 )A0
8X-RAY DIFFRACTION8chain 'B' and (resid 931 through 1001 )B931 - 1001
9X-RAY DIFFRACTION9chain 'B' and (resid 1002 through 1080 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 1081 through 1177 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 1178 through 1206 )B0

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