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- PDB-4tzl: Structure of C. elegans HTP-2 bound to HIM-3 closure motif, P21 form -

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Basic information

Entry
Database: PDB / ID: 4tzl
TitleStructure of C. elegans HTP-2 bound to HIM-3 closure motif, P21 form
Components
  • C. elegans HIM-3 closure motif
  • Protein HTP-2
KeywordsPEPTIDE BINDING PROTEIN / HORMA domain / Meiosis / Chromosome axis
Function / homology
Function and homology information


regulation of centriole-centriole cohesion / meiotic chromosome segregation / synaptonemal complex assembly / homologous chromosome segregation / homologous chromosome pairing at meiosis / synaptonemal complex / lateral element / reciprocal meiotic recombination / sister chromatid cohesion / condensed nuclear chromosome ...regulation of centriole-centriole cohesion / meiotic chromosome segregation / synaptonemal complex assembly / homologous chromosome segregation / homologous chromosome pairing at meiosis / synaptonemal complex / lateral element / reciprocal meiotic recombination / sister chromatid cohesion / condensed nuclear chromosome / chromosome / 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 / Resolution: 2.537 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 / Structure summary
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Derived calculations ...Author supporting evidence / Derived calculations / Source and taxonomy / Structure summary
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / 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_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 1.4Dec 27, 2023Group: 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: Protein HTP-2
B: Protein HTP-2
C: C. elegans HIM-3 closure motif
D: C. elegans HIM-3 closure motif


Theoretical massNumber of molelcules
Total (without water)61,8554
Polymers61,8554
Non-polymers00
Water73941
1
A: Protein HTP-2
C: C. elegans HIM-3 closure motif


Theoretical massNumber of molelcules
Total (without water)30,9282
Polymers30,9282
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2260 Å2
ΔGint-4 kcal/mol
Surface area11530 Å2
MethodPISA
2
B: Protein HTP-2
D: C. elegans HIM-3 closure motif


Theoretical massNumber of molelcules
Total (without water)30,9282
Polymers30,9282
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2280 Å2
ΔGint-4 kcal/mol
Surface area11640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.745, 65.685, 93.685
Angle α, β, γ (deg.)90.00, 90.70, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Protein HTP-2


Mass: 28744.303 Da / Num. of mol.: 2 / Fragment: UNP residues 1-253
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: htp-2, CELE_Y73B6BL.2, Y73B6BL.2 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 pLysS / References: UniProt: Q95XC8
#2: Protein/peptide C. elegans HIM-3 closure motif


Mass: 2183.381 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: HIM-3 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 pLysS / References: UniProt: G5EBG0*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.33 Å3/Da / Density % sol: 47.1 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 15-22% PEG 3350 / PH range: 7.5 - 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 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: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.537→40 Å / Num. obs: 21690 / % possible obs: 99 % / Redundancy: 6.6 % / Rsym value: 0.057 / Net I/σ(I): 15.8

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.9_1692) / Classification: refinement
RefinementResolution: 2.537→38.136 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.23 977 5.18 %
Rwork0.1961 --
obs0.198 18858 99.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.537→38.136 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3855 0 0 41 3896
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023937
X-RAY DIFFRACTIONf_angle_d0.575318
X-RAY DIFFRACTIONf_dihedral_angle_d12.5381439
X-RAY DIFFRACTIONf_chiral_restr0.022588
X-RAY DIFFRACTIONf_plane_restr0.003687
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.537-2.67060.34011530.27242435X-RAY DIFFRACTION97
2.6706-2.83790.28491360.25012532X-RAY DIFFRACTION100
2.8379-3.05690.3171230.23222562X-RAY DIFFRACTION100
3.0569-3.36440.28011440.22222585X-RAY DIFFRACTION100
3.3644-3.85080.22981260.18712574X-RAY DIFFRACTION100
3.8508-4.85010.19441340.15852567X-RAY DIFFRACTION100
4.8501-38.14040.20451610.19392626X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.4119-0.28310.15425.52180.1136.54480.039-0.0711-0.01320.2877-0.1352-0.4056-0.20220.26550.05080.3564-0.0338-0.02630.36330.02120.3945-136.733273.83133.0036
24.9241-1.0248-0.06056.59960.45135.01110.1052-0.2342-0.31130.0336-0.16950.07860.0548-0.22830.05630.3577-0.01020.05520.37590.0060.4035-125.129749.594898.6064
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' or chain 'C'
2X-RAY DIFFRACTION2chain 'B' or chain 'D'

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