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- PDB-6dd9: Structure of mouse SYCP3, P1 form -

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Basic information

Entry
Database: PDB / ID: 6dd9
TitleStructure of mouse SYCP3, P1 form
ComponentsSynaptonemal complex protein 3
KeywordsSTRUCTURAL PROTEIN / Meiosis / chromosome axis / coiled-coil
Function / homology
Function and homology information


female meiosis chromosome separation / transverse filament / lateral element assembly / meiotic DNA repair synthesis / female meiosis sister chromatid cohesion / chiasma assembly / sperm DNA condensation / synaptonemal complex assembly / homologous chromosome pairing at meiosis / synaptonemal complex ...female meiosis chromosome separation / transverse filament / lateral element assembly / meiotic DNA repair synthesis / female meiosis sister chromatid cohesion / chiasma assembly / sperm DNA condensation / synaptonemal complex assembly / homologous chromosome pairing at meiosis / synaptonemal complex / female meiosis chromosome segregation / lateral element / condensed chromosome, centromeric region / female germ cell nucleus / chromosome, centromeric region / spermatid development / condensed chromosome / meiotic cell cycle / condensed nuclear chromosome / male germ cell nucleus / cellular response to leukemia inhibitory factor / chromosome / mitotic cell cycle / spermatogenesis / cell division / DNA binding / nucleoplasm / nucleus
Similarity search - Function
XLR/SYCP3/FAM9 domain / Cor1/Xlr/Xmr conserved region
Similarity search - Domain/homology
Synaptonemal complex protein 3 / Synaptonemal complex protein 3
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsRosenberg, S.C. / Munoz, I.C. / Uson, I. / Corbett, K.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM104141 United States
CitationJournal: Elife / Year: 2019
Title: A conserved filamentous assembly underlies the structure of the meiotic chromosome axis.
Authors: West, A.M. / Rosenberg, S.C. / Ur, S.N. / Lehmer, M.K. / Ye, Q. / Hagemann, G. / Caballero, I. / Uson, I. / MacQueen, A.J. / Herzog, F. / Corbett, K.D.
History
DepositionMay 9, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 1, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Synaptonemal complex protein 3
B: Synaptonemal complex protein 3
D: Synaptonemal complex protein 3
C: Synaptonemal complex protein 3


Theoretical massNumber of molelcules
Total (without water)71,2974
Polymers71,2974
Non-polymers00
Water18010
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21860 Å2
ΔGint-203 kcal/mol
Surface area28410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.869, 52.275, 75.595
Angle α, β, γ (deg.)95.17, 103.70, 110.54
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Synaptonemal complex protein 3 / Synaptonemal complex protein 3 / isoform CRA_a


Mass: 17824.125 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Selenomethionine-derivatized / Source: (gene. exp.) Mus musculus (house mouse) / Gene: Sycp3, mCG_16771 / Production host: Escherichia coli (E. coli) / References: UniProt: A2RSE7, UniProt: P70281*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 2.32 Å3/Da / Density % sol: 46.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 100 mM Tris-HCl pH 8.5, 16% PEG 4000, 100-200 mM sodium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.3→72.11 Å / Num. obs: 51353 / % possible obs: 92 % / Redundancy: 3.7 % / CC1/2: 0.999 / Rrim(I) all: 0.088 / Net I/σ(I): 9.98
Reflection shellResolution: 2.3→2.44 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 1.45 / Num. unique obs: 8372 / CC1/2: 0.849 / Rrim(I) all: 0.967 / % possible all: 92.6

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6DD8

6dd8


Resolution: 2.3→72.103 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.94 / Phase error: 44.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.331 1307 5.01 %
Rwork0.2871 --
obs0.2894 50966 91.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→72.103 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4109 0 0 10 4119
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084155
X-RAY DIFFRACTIONf_angle_d0.9335545
X-RAY DIFFRACTIONf_dihedral_angle_d18.652611
X-RAY DIFFRACTIONf_chiral_restr0.045595
X-RAY DIFFRACTIONf_plane_restr0.005727
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.34420.40581220.38172660X-RAY DIFFRACTION92
2.3442-2.39210.40371550.36332780X-RAY DIFFRACTION94
2.3921-2.44410.36971710.33662687X-RAY DIFFRACTION92
2.4441-2.5010.39211230.32952705X-RAY DIFFRACTION93
2.501-2.56350.3781610.32232617X-RAY DIFFRACTION89
2.5635-2.63280.41221560.28722547X-RAY DIFFRACTION88
2.6328-2.71030.34861230.29782714X-RAY DIFFRACTION90
2.7103-2.79780.39271220.30492755X-RAY DIFFRACTION93
2.7978-2.89780.35291300.32082753X-RAY DIFFRACTION93
2.8978-3.01380.4081620.31642636X-RAY DIFFRACTION91
3.0138-3.1510.46371390.30912737X-RAY DIFFRACTION92
3.151-3.31710.47631380.33552695X-RAY DIFFRACTION92
3.3171-3.52490.36521400.292600X-RAY DIFFRACTION88
3.5249-3.79710.31251690.26282759X-RAY DIFFRACTION95
3.7971-4.17920.26081430.24292745X-RAY DIFFRACTION94
4.1792-4.78380.31561430.24512710X-RAY DIFFRACTION92
4.7838-6.02660.25781180.27062604X-RAY DIFFRACTION89
6.0266-72.13890.2811360.30452711X-RAY DIFFRACTION91
Refinement TLS params.Method: refined / Origin x: -29.0243 Å / Origin y: -0.6714 Å / Origin z: 83.0675 Å
111213212223313233
T0.4612 Å2-0.0151 Å2-0.0223 Å2-0.4791 Å2-0.0371 Å2--0.4579 Å2
L2.0346 °2-0.2568 °2-1.2687 °2-0.278 °20.178 °2--0.9952 °2
S0.0961 Å °0.0903 Å °0.1553 Å °0.0919 Å °-0.0339 Å °0.1087 Å °-0.0851 Å °-0.1624 Å °-0.0449 Å °
Refinement TLS groupSelection details: chain A or chain B or chain C or chain D

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