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- PDB-6f62: Crystal structure of the SYCP1 N-terminal head-to-head assembly i... -

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Basic information

Entry
Database: PDB / ID: 6f62
TitleCrystal structure of the SYCP1 N-terminal head-to-head assembly in open conformation
ComponentsSynaptonemal complex protein 1
KeywordsSTRUCTURAL PROTEIN / Meiosis / Chromosome structure / Coiled-coil / Self-assembly
Function / homology
Function and homology information


transverse filament / lateral element assembly / meiotic DNA repair synthesis / chiasma assembly / autosome / central element / sperm DNA condensation / synaptonemal complex assembly / homologous chromosome pairing at meiosis / synaptonemal complex ...transverse filament / lateral element assembly / meiotic DNA repair synthesis / chiasma assembly / autosome / central element / sperm DNA condensation / synaptonemal complex assembly / homologous chromosome pairing at meiosis / synaptonemal complex / reciprocal meiotic recombination / chromosome, centromeric region / Meiotic synapsis / male germ cell nucleus / regulation of protein localization / chromosome / spermatogenesis / double-stranded DNA binding / protein homotetramerization / cell division / DNA binding
Similarity search - Function
Synaptonemal complex protein 1 / Synaptonemal complex protein 1 (SCP-1)
Similarity search - Domain/homology
Synaptonemal complex protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.066 Å
AuthorsDunce, J.M. / Davies, O.R.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust and Royal Society104158/Z/14/Z United Kingdom
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2018
Title: Structural basis of meiotic chromosome synapsis through SYCP1 self-assembly.
Authors: Dunce, J.M. / Dunne, O.M. / Ratcliff, M. / Millan, C. / Madgwick, S. / Uson, I. / Davies, O.R.
History
DepositionDec 4, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 6, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 4, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Aug 1, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Apr 22, 2020Group: Database references / Category: pdbx_related_exp_data_set
Revision 1.4May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Synaptonemal complex protein 1
B: Synaptonemal complex protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0836
Polymers25,7752
Non-polymers3074
Water1,874104
1
A: Synaptonemal complex protein 1
B: Synaptonemal complex protein 1
hetero molecules

A: Synaptonemal complex protein 1
B: Synaptonemal complex protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,16512
Polymers51,5514
Non-polymers6158
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_357-x-2,y,-z+21
Buried area13310 Å2
ΔGint-189 kcal/mol
Surface area30880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.670, 37.310, 108.520
Angle α, β, γ (deg.)90.00, 106.66, 90.00
Int Tables number5
Space group name H-MI121

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Components

#1: Protein Synaptonemal complex protein 1 / SCP-1 / Cancer/testis antigen 8 / CT8


Mass: 12887.740 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SYCP1, SCP1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15431
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 2.47 Å3/Da / Density % sol: 50.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 100 mM MES pH 6.0, 40% (v/v) MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9282 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9282 Å / Relative weight: 1
ReflectionResolution: 2.06→34.87 Å / Num. obs: 15862 / % possible obs: 99.9 % / Redundancy: 11 % / Biso Wilson estimate: 30.44 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.023 / Rrim(I) all: 0.075 / Net I/σ(I): 15
Reflection shellResolution: 2.06→2.12 Å / Redundancy: 11.4 % / Rmerge(I) obs: 0.919 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 1217 / CC1/2: 0.969 / Rpim(I) all: 0.286 / Rrim(I) all: 0.963 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.12rc1_2807: ???)refinement
XDSdata reduction
XSCALEdata scaling
AMPLEphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.066→27.234 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 30.03
Details: Refined against data corrected for anisotropy (FP_ISOB/SIGFP_ISOB) using the UCLA diffraction anisotropy server.
RfactorNum. reflection% reflection
Rfree0.2441 664 5.33 %
Rwork0.2264 --
obs0.2274 12467 79.18 %
Solvent computationShrinkage radii: 0.7 Å / VDW probe radii: 1 Å
Refinement stepCycle: LAST / Resolution: 2.066→27.234 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1739 0 18 104 1861
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021773
X-RAY DIFFRACTIONf_angle_d0.3342356
X-RAY DIFFRACTIONf_dihedral_angle_d21.524732
X-RAY DIFFRACTIONf_chiral_restr0.024255
X-RAY DIFFRACTIONf_plane_restr0.001297
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0655-2.22490.3275560.2878844X-RAY DIFFRACTION29
2.2249-2.44870.30111150.26142043X-RAY DIFFRACTION69
2.4487-2.80270.25571700.25862876X-RAY DIFFRACTION97
2.8027-3.52990.26931620.2362978X-RAY DIFFRACTION100
3.5299-27.2360.20821610.23062X-RAY DIFFRACTION99

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