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- PDB-6f64: Crystal structure of the SYCP1 C-terminal back-to-back assembly -

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Basic information

Entry
Database: PDB / ID: 6f64
TitleCrystal structure of the SYCP1 C-terminal back-to-back assembly
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 / double-stranded DNA binding / spermatogenesis / protein homotetramerization / cell division / DNA binding
Similarity search - Function
Synaptonemal complex protein 1 / Synaptonemal complex protein 1 (SCP-1)
Similarity search - Domain/homology
ACETATE ION / Synaptonemal complex protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.493 Å
AuthorsDunce, J.M. / Millan, C. / Uson, I. / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Synaptonemal complex protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,4432
Polymers11,3841
Non-polymers591
Water28816
1
A: Synaptonemal complex protein 1
hetero molecules

A: Synaptonemal complex protein 1
hetero molecules

A: Synaptonemal complex protein 1
hetero molecules

A: Synaptonemal complex protein 1
hetero molecules


  • defined by author&software
  • Evidence: SAXS, The structure undergoes pH-induced assembly from a dimeric parallel coiled-coil at pH 8.0 to the tetrameric assembly observed in the crystal structure at pH 5.5. This has been validated by MALS and SAXS.
  • 45.8 kDa, 4 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)45,7738
Polymers45,5364
Non-polymers2364
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_666-y+1,-x+1,-z+11
crystal symmetry operation10_665-x+1,-y+1,z1
crystal symmetry operation15_556y,x,-z+11
Buried area18390 Å2
ΔGint-142 kcal/mol
Surface area21060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.380, 43.380, 292.180
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-902-

HOH

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Components

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


Mass: 11384.086 Da / Num. of mol.: 1
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-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 3.02 Å3/Da / Density % sol: 59.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M sodium cacodylate pH 6.5, 1.4M sodium acetate; soaked in 0.1 M sodium cacodylate pH 6.5, 1.4 M sodium acetate, 20% PEG400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.48→42.91 Å / Num. obs: 5424 / % possible obs: 99.8 % / Redundancy: 13.2 % / CC1/2: 1 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.023 / Rrim(I) all: 0.084 / Net I/σ(I): 14.8
Reflection shellResolution: 2.48→2.58 Å / Redundancy: 13.2 % / Rmerge(I) obs: 2.567 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 591 / CC1/2: 0.935 / Rpim(I) all: 0.727 / Rrim(I) all: 2.671 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX(1.12rc1_2807: ???)refinement
XDSdata reduction
XSCALEdata scaling
Arcimboldophasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.493→39.627 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 2.01 / Phase error: 20.85
Details: Refined against data corrected for anisotropy (FP_ISOB/SIGFP_ISOB) using the UCLA diffraction anisotropy server.
RfactorNum. reflection% reflection
Rfree0.2517 219 5.29 %
Rwork0.2251 --
obs0.2271 4138 77.16 %
Solvent computationShrinkage radii: 0 Å / VDW probe radii: 0.5 Å
Refinement stepCycle: LAST / Resolution: 2.493→39.627 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms774 0 4 16 794
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004795
X-RAY DIFFRACTIONf_angle_d0.5751059
X-RAY DIFFRACTIONf_dihedral_angle_d11.548520
X-RAY DIFFRACTIONf_chiral_restr0.032121
X-RAY DIFFRACTIONf_plane_restr0.003136
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4931-3.14090.3586720.26261302X-RAY DIFFRACTION53
3.1409-39.63190.22651470.2162617X-RAY DIFFRACTION100

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