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- PDB-8ou1: Crystal structure of the SPOC domain of mouse SPOCD1 -

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Basic information

Entry
Database: PDB / ID: 8ou1
TitleCrystal structure of the SPOC domain of mouse SPOCD1
ComponentsSPOC domain-containing protein 1
KeywordsGENE REGULATION / piRNA PIWI DNA methylation Germline
Function / homology
Function and homology information


gene silencing by piRNA-directed DNA methylation / transposable element silencing by piRNA-mediated heterochromatin formation / transposable element silencing by piRNA-mediated DNA methylation / chromosome / spermatogenesis / cell differentiation / DNA-templated transcription / nucleus
Similarity search - Function
Spen paralogue and orthologue SPOC, C-terminal / SPOC domain / Transcription factor S-II (TFIIS), central domain / Domain in the central regions of transcription elongation factor S-II (and elsewhere) / Transcription elongation factor S-II, central domain / Transcription elongation factor S-II, central domain superfamily / TFIIS central domain profile.
Similarity search - Domain/homology
CITRATE ANION / SPOC domain-containing protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsHeep, M. / Cook, A.G. / O'Carroll, D.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Wellcome Trust106144 United Kingdom
Wellcome Trust200898 United Kingdom
Wellcome Trust203149 United Kingdom
CitationJournal: Mol.Cell / Year: 2024
Title: C19ORF84 connects piRNA and DNA methylation machineries to defend the mammalian germ line.
Authors: Zoch, A. / Konieczny, G. / Auchynnikava, T. / Stallmeyer, B. / Rotte, N. / Heep, M. / Berrens, R.V. / Schito, M. / Kabayama, Y. / Schopp, T. / Kliesch, S. / Houston, B. / Nagirnaja, L. / ...Authors: Zoch, A. / Konieczny, G. / Auchynnikava, T. / Stallmeyer, B. / Rotte, N. / Heep, M. / Berrens, R.V. / Schito, M. / Kabayama, Y. / Schopp, T. / Kliesch, S. / Houston, B. / Nagirnaja, L. / O'Bryan, M.K. / Aston, K.I. / Conrad, D.F. / Rappsilber, J. / Allshire, R.C. / Cook, A.G. / Tuttelmann, F. / O'Carroll, D.
History
DepositionApr 21, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 21, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Apr 3, 2024Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SPOC domain-containing protein 1
B: SPOC domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9113
Polymers32,7222
Non-polymers1891
Water4,648258
1
A: SPOC domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5502
Polymers16,3611
Non-polymers1891
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: SPOC domain-containing protein 1


Theoretical massNumber of molelcules
Total (without water)16,3611
Polymers16,3611
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.520, 56.624, 97.657
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and ((resid 685 and (name N or name...
d_2ens_1(chain "B" and (resid 685 through 690 or resid 692...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ASPGLYA1 - 6
d_12ens_1LEUHISA8 - 26
d_13ens_1CYSMETA28 - 56
d_14ens_1SERILEA59 - 64
d_15ens_1VALLEUA66 - 69
d_16ens_1PROGLYA71 - 73
d_17ens_1ARGGLYA75 - 125
d_18ens_1GLUASPA127 - 142
d_21ens_1ASPGLYD2 - 7
d_22ens_1LEUHISD9 - 27
d_23ens_1CYSILED29 - 63
d_24ens_1VALLEUD65 - 68
d_25ens_1PROGLYD70 - 72
d_26ens_1ARGGLYD74 - 124
d_27ens_1GLUASPD126 - 141

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Components

#1: Protein SPOC domain-containing protein 1


Mass: 16361.143 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Spocd1 / Production host: Escherichia coli (E. coli) / References: UniProt: B1ASB6
#2: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 258 / 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: 2.36 Å3/Da / Density % sol: 47.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 1.6M Ammonium citrate tribasic, pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Feb 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.7→54.52 Å / Num. obs: 33752 / % possible obs: 99.2 % / Redundancy: 4.7 % / Biso Wilson estimate: 24.59 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.028 / Rrim(I) all: 0.062 / Rsym value: 0.055 / Net I/σ(I): 13.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allRsym value% possible all
1.7-1.793.42.147990.8020.2660.5130.43598.7
1.79-1.94.946440.910.1580.3510.31299.9
1.9-2.035.243700.9590.1070.2430.217100
2.03-2.19540710.9820.0710.160.143100
2.19-2.44.937400.9890.0550.1240.11199.8
2.4-2.695.234230.9930.040.0920.08399.9
2.69-3.1530260.9960.0290.0650.05899.9
3.1-3.84.825030.9980.0190.0430.03996.2
3.8-5.384.919710.9990.0150.0330.0396
5.38-54.524.512050.9990.0140.030.02799.6

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
autoPROC1.0.5data processing
XDSMarch 15, 2019 (built 20191211)data reduction
pointless1.11.21data scaling
Aimless0.7.4data scaling
SCALA3.3.22data scaling
PHASER2.8.3phasing
Coot0.8.9.2model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→47.6 Å / SU ML: 0.2412 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.5587
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2373 1677 4.98 %
Rwork0.2013 32000 -
obs0.2031 33677 99.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.19 Å2
Refinement stepCycle: LAST / Resolution: 1.7→47.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2173 0 13 258 2444
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00672285
X-RAY DIFFRACTIONf_angle_d1.03713131
X-RAY DIFFRACTIONf_chiral_restr0.0566362
X-RAY DIFFRACTIONf_plane_restr0.0079406
X-RAY DIFFRACTIONf_dihedral_angle_d6.6117321
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.962967238805 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.750.37041440.34722571X-RAY DIFFRACTION97.28
1.75-1.810.3271250.2992645X-RAY DIFFRACTION99.5
1.81-1.870.2891320.2522670X-RAY DIFFRACTION99.79
1.87-1.950.29951160.22972669X-RAY DIFFRACTION99.89
1.95-2.030.26741370.21782650X-RAY DIFFRACTION99.86
2.03-2.140.23751420.22552656X-RAY DIFFRACTION99.96
2.14-2.280.24131770.21962652X-RAY DIFFRACTION99.68
2.28-2.450.28541530.19872660X-RAY DIFFRACTION99.65
2.45-2.70.25751180.212698X-RAY DIFFRACTION99.89
2.7-3.090.23871600.20562670X-RAY DIFFRACTION99.75
3.09-3.880.21511150.17332660X-RAY DIFFRACTION96.56
3.91-47.60.19671580.17522799X-RAY DIFFRACTION99.6

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