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- PDB-6r17: Crystal structure of the SYCE2-TEX12 delta-Ctip 2:2 complex -

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Basic information

Entry
Database: PDB / ID: 6r17
TitleCrystal structure of the SYCE2-TEX12 delta-Ctip 2:2 complex
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: 2.424 Å
AuthorsDunce, J.M. / Salmon, L.J. / Davies, O.R.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Wellcome Trust104158/Z/14/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
DepositionMar 13, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 30, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 15, 2021Group: Database references / Refinement description
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_refine_tls_group
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 / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2May 1, 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
Water18010
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS, light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12030 Å2
ΔGint-116 kcal/mol
Surface area18450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.520, 24.190, 88.480
Angle α, β, γ (deg.)90.00, 115.74, 90.00
Int Tables number4
Space group name H-MP1211

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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
#3: 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: 2.02 Å3/Da / Density % sol: 39.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 35 % MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9786 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.42→79.74 Å / Num. obs: 8501 / % possible obs: 63.2 % / Redundancy: 3.4 % / Rpim(I) all: 0.049 / Rrim(I) all: 0.074 / Net I/σ(I): 10.2
Reflection shellResolution: 2.42→2.74 Å / Mean I/σ(I) obs: 1.2 / Num. unique obs: 424 / Rpim(I) all: 0.914 / Rrim(I) all: 1.293

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Processing

Software
NameVersionClassification
PHENIX(dev_3126: ???)refinement
XDSdata reduction
XSCALEdata scaling
STARANISOdata scaling
PHASERphasing
Arcimboldophasing
SHELXEmodel building
PHENIXmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 18 amino-acid ideal helices

Resolution: 2.424→79.739 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 46.33
RfactorNum. reflection% reflection
Rfree0.3296 871 10.27 %
Rwork0.2871 --
obs0.2915 8481 62.59 %
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å
Refinement stepCycle: LAST / Resolution: 2.424→79.739 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2518 0 0 10 2528
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052550
X-RAY DIFFRACTIONf_angle_d0.7883415
X-RAY DIFFRACTIONf_dihedral_angle_d16.8491612
X-RAY DIFFRACTIONf_chiral_restr0.04393
X-RAY DIFFRACTIONf_plane_restr0.004438
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4176-2.5690.477380.46698X-RAY DIFFRACTION5
2.569-2.76740.3693410.3903351X-RAY DIFFRACTION18
2.7674-3.04590.41551300.36021045X-RAY DIFFRACTION52
3.0459-3.48670.36432250.33242003X-RAY DIFFRACTION100
3.4867-4.39280.31632230.25852036X-RAY DIFFRACTION99
4.3928-79.78190.31052440.27622077X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: 13.9354 Å / Origin y: -4.9562 Å / Origin z: 19.656 Å
111213212223313233
T0.4999 Å2-0.0061 Å20.0052 Å2-0.4059 Å2-0.0283 Å2--0.383 Å2
L8.086 °21.9102 °2-2.7492 °2-0.5588 °2-0.6825 °2--1.6669 °2
S0.1958 Å °-0.467 Å °0.1412 Å °0.1022 Å °-0.1194 Å °0.0846 Å °0.0347 Å °-0.1389 Å °-0.0309 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A58 - 150
2X-RAY DIFFRACTION1B57 - 150
3X-RAY DIFFRACTION1C49 - 111
4X-RAY DIFFRACTION1D50 - 105

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