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- PDB-4tzm: C. elegans HTP-2 bound to HTP-3 closure motif 1 -

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Basic information

Entry
Database: PDB / ID: 4tzm
TitleC. elegans HTP-2 bound to HTP-3 closure motif 1
Components
  • C. elegans HTP-3 closure motif1
  • Protein HTP-2
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: 2.3 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: C. elegans HTP-3 closure motif1
D: C. elegans HTP-3 closure motif1


Theoretical massNumber of molelcules
Total (without water)61,0814
Polymers61,0814
Non-polymers00
Water1,00956
1
A: Protein HTP-2
C: C. elegans HTP-3 closure motif1


Theoretical massNumber of molelcules
Total (without water)30,5402
Polymers30,5402
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2100 Å2
ΔGint-2 kcal/mol
Surface area12810 Å2
MethodPISA
2
B: Protein HTP-2
D: C. elegans HTP-3 closure motif1


Theoretical massNumber of molelcules
Total (without water)30,5402
Polymers30,5402
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2140 Å2
ΔGint-3 kcal/mol
Surface area11670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.676, 66.005, 94.649
Angle α, β, γ (deg.)90.00, 90.27, 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 HTP-3 closure motif1


Mass: 1796.038 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: HTP-3 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 pLysS / References: UniProt: O01820*PLUS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 2.44 Å3/Da / Density % sol: 49.55 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop / 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: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 14, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 24989 / % possible obs: 93.8 % / Redundancy: 3.3 % / Rsym value: 0.087 / Net I/σ(I): 14.5

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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: 2.3→28.465 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 31.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2164 1269 5.14 %
Rwork0.2029 --
obs0.2036 24692 92.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→28.465 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3944 0 0 56 4000
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034025
X-RAY DIFFRACTIONf_angle_d0.6475431
X-RAY DIFFRACTIONf_dihedral_angle_d12.951478
X-RAY DIFFRACTIONf_chiral_restr0.027600
X-RAY DIFFRACTIONf_plane_restr0.003700
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.38090.33921000.27251967X-RAY DIFFRACTION70
2.3809-2.48920.30991300.27012226X-RAY DIFFRACTION81
2.4892-2.62040.35281230.25852485X-RAY DIFFRACTION88
2.6204-2.78440.29351730.24462688X-RAY DIFFRACTION97
2.7844-2.99920.28141290.24312798X-RAY DIFFRACTION99
2.9992-3.30060.30421610.23962781X-RAY DIFFRACTION100
3.3006-3.77730.22241360.20262812X-RAY DIFFRACTION100
3.7773-4.75540.17981490.16592824X-RAY DIFFRACTION99
4.7554-28.4670.16181680.18342842X-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)
11.918-0.1875-0.13034.3245-0.28674.27080.05180.0059-0.07230.7894-0.136-0.0669-0.31520.11670.06070.3356-0.022-0.05030.2661-0.00950.2611-139.775474.1011133.7168
22.8455-1.2863-0.46875.46171.68413.66910.14930.0273-0.2011-0.6832-0.336-0.22230.0104-0.24930.12850.3241-0.03450.06830.3026-0.00940.3592-126.400850.059899.9496
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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