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- PDB-4tzj: Structure of C. elegans HIM-3 bound to HTP-3 closure motif-4 -

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Basic information

Entry
Database: PDB / ID: 4tzj
TitleStructure of C. elegans HIM-3 bound to HTP-3 closure motif-4
ComponentsC. elegans HIM-3 and HTP-3
KeywordsPEPTIDE BINDING PROTEIN / HORMA domain meiosis chromosome axis
Function / homology
Function and homology information


meiotic DNA double-strand break formation / regulation of centriole-centriole cohesion / meiotic chromosome segregation / homologous chromosome segregation / synaptonemal complex assembly / homologous chromosome pairing at meiosis / synaptonemal complex / lateral element / reciprocal meiotic recombination / sister chromatid cohesion ...meiotic DNA double-strand break formation / regulation of centriole-centriole cohesion / meiotic chromosome segregation / homologous chromosome segregation / synaptonemal complex assembly / homologous chromosome pairing at meiosis / synaptonemal complex / lateral element / reciprocal meiotic recombination / sister chromatid cohesion / condensed chromosome / condensed nuclear chromosome / chromosome / chromatin / DNA binding
Similarity search - Function
: / Cell Cycle, Spindle Assembly Checkpoint Protein; Chain A / HORMA domain / HORMA domain / HORMA domain / HORMA domain profile. / HORMA domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
HORMA domain-containing protein / HORMA domain-containing protein
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.851 Å
AuthorsRosenberg, S.C. / Corbett, K.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM104141 United States
CitationJournal: Dev.Cell / Year: 2014
Title: The Chromosome Axis Controls Meiotic Events through a Hierarchical Assembly of HORMA Domain Proteins.
Authors: Kim, Y. / Rosenberg, S.C. / Kugel, C.L. / Kostow, N. / Rog, O. / Davydov, V. / Su, T.Y. / Dernburg, A.F. / Corbett, K.D.
History
DepositionJul 10, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 19, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 17, 2014Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Derived calculations ...Author supporting evidence / Derived calculations / Other / Source and taxonomy / Structure summary
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_oper_list / struct_keywords
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.pdbx_keywords
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 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 / refine_hist
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: C. elegans HIM-3 and HTP-3


Theoretical massNumber of molelcules
Total (without water)33,3921
Polymers33,3921
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)161.791, 161.791, 110.545
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein C. elegans HIM-3 and HTP-3


Mass: 33392.059 Da / Num. of mol.: 1
Fragment: UNP G5EBG0 residues 1-276,UNP O01820 residues 649-663
Source method: isolated from a genetically manipulated source
Details: Chimera / Source: (gene. exp.) Caenorhabditis elegans (invertebrata)
Gene: him-3, CELE_ZK381.1, ZK381.1, htp-3, CELE_F57C9.5, F57C9.5
Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 pLysS, Rosetta2 pLysS / References: UniProt: G5EBG0, UniProt: O01820

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.17 Å3/Da / Density % sol: 70.5 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop / pH: 4.75 / Details: 15-22% PEG 3350 / PH range: 4.75

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 1, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.85→50 Å / Num. all: 12444 / Num. obs: 12444 / % possible obs: 95.7 % / Redundancy: 7.5 % / Rsym value: 0.057 / Net I/σ(I): 20.1

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.9_1692) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4TRK

4trk


Resolution: 2.851→38.239 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2299 580 4.69 %
Rwork0.1779 --
obs0.1802 12376 94.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.851→38.239 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1923 0 0 0 1923
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041961
X-RAY DIFFRACTIONf_angle_d0.8392640
X-RAY DIFFRACTIONf_dihedral_angle_d14.955730
X-RAY DIFFRACTIONf_chiral_restr0.032289
X-RAY DIFFRACTIONf_plane_restr0.004340
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.851-3.13770.31881380.29682917X-RAY DIFFRACTION94
3.1377-3.59140.26731540.20682959X-RAY DIFFRACTION96
3.5914-4.52360.22091420.17012951X-RAY DIFFRACTION95
4.5236-38.24260.2141460.1612969X-RAY DIFFRACTION93
Refinement TLS params.Method: refined / Origin x: 188.226 Å / Origin y: -8.254 Å / Origin z: 40.796 Å
111213212223313233
T0.5599 Å2-0.0026 Å20.1284 Å2-0.5229 Å20.0704 Å2--0.5693 Å2
L5.025 °2-0.1084 °2-1.0495 °2-3.5908 °20.6593 °2--3.2757 °2
S0.3445 Å °0.3038 Å °0.6064 Å °-0.1876 Å °0.0278 Å °-0.008 Å °-0.3465 Å °-0.2946 Å °-0.3429 Å °
Refinement TLS groupSelection details: (CHAIN A AND RESID 19:246)

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