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- PDB-6yqf: Crystal structure of the SYCE2-TEX12 delta-Ctip complex in a 4:4 ... -

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Basic information

Entry
Database: PDB / ID: 6yqf
TitleCrystal structure of the SYCE2-TEX12 delta-Ctip complex in a 4:4 assembly
Components
  • Synaptonemal complex central element protein 2
  • Testis-expressed protein 12
KeywordsSTRUCTURAL PROTEIN / Synaptonemal complex meiosis recombination coiled-coil self-assembly SYCE2 TEX12 STRUCTURAL PROTEIN
Function / homology
Function and homology information


meiotic DNA repair synthesis / central element / synaptonemal complex assembly / Meiotic synapsis / chromosome / cell division / nucleoplasm
Similarity search - Function
Synaptonemal complex central element protein 2 / Testis-expressed sequence 12 protein / Testis-expressed 12
Similarity search - Domain/homology
Synaptonemal complex central element protein 2 / Testis-expressed protein 12
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.33 Å
AuthorsDunce, J.M. / Davies, O.R.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Wellcome Trust104158/Z/14/Z United Kingdom
Wellcome Trust219413/Z/19/Z United Kingdom
Royal SocietyRG170118 United Kingdom
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2021
Title: Structural basis of meiotic chromosome synaptic elongation through hierarchical fibrous assembly of SYCE2-TEX12.
Authors: Dunce, J.M. / Salmon, L.J. / Davies, O.R.
History
DepositionApr 16, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 28, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 15, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Synaptonemal complex central element protein 2
B: Synaptonemal complex central element protein 2
C: Testis-expressed protein 12
D: Testis-expressed protein 12


Theoretical massNumber of molelcules
Total (without water)42,2564
Polymers42,2564
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering, SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Synaptonemal complex central element protein 2
B: Synaptonemal complex central element protein 2
C: Testis-expressed protein 12
D: Testis-expressed protein 12

A: Synaptonemal complex central element protein 2
B: Synaptonemal complex central element protein 2
C: Testis-expressed protein 12
D: Testis-expressed protein 12


Theoretical massNumber of molelcules
Total (without water)84,5128
Polymers84,5128
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation1
Unit cell
Length a, b, c (Å)42.670, 59.680, 156.490
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

#1: Protein Synaptonemal complex central element protein 2 / Central element synaptonemal complex protein 1


Mass: 13180.025 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SYCE2, CESC1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6PIF2
#2: Protein Testis-expressed protein 12


Mass: 7947.959 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TEX12 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9BXU0

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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: 47.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M sodium acetate, 65% MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9688 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 4, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9688 Å / Relative weight: 1
ReflectionResolution: 3.327→47.452 Å / Num. obs: 4098 / % possible obs: 64.8 % / Redundancy: 6.5 % / Biso Wilson estimate: 56.56 Å2 / CC1/2: 0.995 / Rpim(I) all: 0.098 / Rrim(I) all: 0.246 / Net I/σ(I): 4.7
Reflection shellResolution: 3.327→3.594 Å / Redundancy: 7.2 % / Mean I/σ(I) obs: 1 / Num. unique obs: 342 / CC1/2: 0.516 / Rpim(I) all: 0.906 / Rrim(I) all: 2.445 / % possible all: 27.1

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
STARANISOdata scaling
PHASERphasing
Cootmodel building
PHENIX1.17.1_3660refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6R17

6r17


Resolution: 3.33→47.45 Å / SU ML: 0.3987 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 35.2763
RfactorNum. reflection% reflection
Rfree0.3672 202 4.98 %
Rwork0.3266 --
obs0.3286 4053 64.1 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso mean: 56.52 Å2
Refinement stepCycle: LAST / Resolution: 3.33→47.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2426 0 0 0 2426
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00132447
X-RAY DIFFRACTIONf_angle_d0.27153274
X-RAY DIFFRACTIONf_chiral_restr0.0311378
X-RAY DIFFRACTIONf_plane_restr0.0008419
X-RAY DIFFRACTIONf_dihedral_angle_d8.3534962
LS refinement shellResolution: 3.33→47.45 Å
RfactorNum. reflection% reflection
Rfree0.3672 202 -
Rwork0.3266 3851 -
obs--64.1 %

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