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- PDB-4tzn: Structure of HTP-2 bound to HTP-3 motif-6 -

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Basic information

Entry
Database: PDB / ID: 4tzn
TitleStructure of HTP-2 bound to HTP-3 motif-6
Components
  • Protein HTP-2
  • Protein 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 pairing at meiosis / synaptonemal complex / lateral element / reciprocal meiotic recombination / condensed chromosome / chromosome / chromatin
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: 3.115 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 / 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 1.4Sep 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein HTP-2
B: Protein HTP-2
C: Protein HTP-3
D: Protein HTP-3


Theoretical massNumber of molelcules
Total (without water)61,1394
Polymers61,1394
Non-polymers00
Water00
1
A: Protein HTP-2
C: Protein HTP-3


Theoretical massNumber of molelcules
Total (without water)30,5692
Polymers30,5692
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1600 Å2
ΔGint-3 kcal/mol
Surface area11410 Å2
MethodPISA
2
B: Protein HTP-2
D: Protein HTP-3


Theoretical massNumber of molelcules
Total (without water)30,5692
Polymers30,5692
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1560 Å2
ΔGint-1 kcal/mol
Surface area11670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)165.820, 38.310, 103.820
Angle α, β, γ (deg.)90.00, 126.24, 90.00
Int Tables number5
Space group name H-MC121

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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 Protein HTP-3


Mass: 1825.063 Da / Num. of mol.: 2 / Fragment: UNP residues 724-739
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: htp-3, CELE_F57C9.5, F57C9.5 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 pLysS / References: 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: 2.18 Å3/Da / Density % sol: 43.45 %
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: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 9, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.1→80 Å / Num. obs: 8218 / % possible obs: 83.4 % / Redundancy: 3.6 % / Net I/σ(I): 8.7

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Processing

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

4tzl


Resolution: 3.115→80 Å / SU ML: 0.51 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 36.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3198 377 4.59 %
Rwork0.2801 --
obs0.282 8216 83.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.115→80 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3815 0 0 0 3815
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033897
X-RAY DIFFRACTIONf_angle_d0.6045263
X-RAY DIFFRACTIONf_dihedral_angle_d12.7611429
X-RAY DIFFRACTIONf_chiral_restr0.023578
X-RAY DIFFRACTIONf_plane_restr0.004682
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.115-3.5660.3559790.35731595X-RAY DIFFRACTION52
3.566-4.49280.31981570.29623051X-RAY DIFFRACTION100
4.4928-83.76390.31231410.25533193X-RAY DIFFRACTION99
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)
110.34220.81232.90236.5367-0.56486.2358-0.618-0.2998-0.6820.00060.45441.1537-0.2382-0.9160.17980.60140.13990.19290.58440.06330.6979259.8423-86.4779-46.2096
28.29860.09851.26333.84240.46323.97310.5615-0.26350.36830.2382-0.2639-0.34170.06240.3479-0.25620.5662-0.03360.06810.32280.04130.5132247.4385-67.0485-83.337
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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