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- PDB-4tzo: Structure of C. elegans HTP-1 bound to HIM-3 closure motif -

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Basic information

Entry
Database: PDB / ID: 4tzo
TitleStructure of C. elegans HTP-1 bound to HIM-3 closure motif
Components
  • C. elegans HIM-3 closure motif
  • Protein HTP-1
KeywordsPEPTIDE BINDING PROTEIN / HORMA domain / Meiosis / Chromosome axis
Function / homology
Function and homology information


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 nuclear chromosome ...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 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 / MOLECULAR REPLACEMENT / Resolution: 2.4 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-1
B: C. elegans HIM-3 closure motif
C: Protein HTP-1
D: C. elegans HIM-3 closure motif
E: Protein HTP-1
F: C. elegans HIM-3 closure motif
G: Protein HTP-1
H: C. elegans HIM-3 closure motif


Theoretical massNumber of molelcules
Total (without water)123,7038
Polymers123,7038
Non-polymers00
Water5,098283
1
A: Protein HTP-1
B: C. elegans HIM-3 closure motif


Theoretical massNumber of molelcules
Total (without water)30,9262
Polymers30,9262
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2080 Å2
ΔGint-5 kcal/mol
Surface area11720 Å2
MethodPISA
2
C: Protein HTP-1
D: C. elegans HIM-3 closure motif


Theoretical massNumber of molelcules
Total (without water)30,9262
Polymers30,9262
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2030 Å2
ΔGint-6 kcal/mol
Surface area11720 Å2
MethodPISA
3
E: Protein HTP-1
F: C. elegans HIM-3 closure motif


Theoretical massNumber of molelcules
Total (without water)30,9262
Polymers30,9262
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2070 Å2
ΔGint-5 kcal/mol
Surface area11570 Å2
MethodPISA
4
G: Protein HTP-1
H: C. elegans HIM-3 closure motif


Theoretical massNumber of molelcules
Total (without water)30,9262
Polymers30,9262
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2120 Å2
ΔGint-6 kcal/mol
Surface area11710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.897, 107.873, 82.968
Angle α, β, γ (deg.)90.00, 90.10, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Protein HTP-1


Mass: 28742.455 Da / Num. of mol.: 4 / Fragment: UNP residues 1-253 / Mutation: P84L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: htp-1, CELE_F41H10.10, F41H10.10 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 pLysS / References: UniProt: Q20305
#2: Protein/peptide
C. elegans HIM-3 closure motif / Protein HIM-3 / isoform a


Mass: 2183.381 Da / Num. of mol.: 4 / Fragment: UNP residues 275-291
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: him-3, CELE_ZK381.1, ZK381.1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 pLysS / References: UniProt: G5EBG0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 283 / 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: 2.42 Å3/Da / Density % sol: 49.17 %
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: Dec 5, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 43476 / % possible obs: 94.1 % / Redundancy: 2 % / Rsym value: 0.132 / Net I/σ(I): 6.3

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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: 2.4→45.221 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 31.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2822 2203 5.08 %
Rwork0.2457 --
obs0.2475 43408 93.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→45.221 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7952 0 0 283 8235
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0048104
X-RAY DIFFRACTIONf_angle_d0.7710940
X-RAY DIFFRACTIONf_dihedral_angle_d15.1453012
X-RAY DIFFRACTIONf_chiral_restr0.0331204
X-RAY DIFFRACTIONf_plane_restr0.0031432
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.45050.34771400.32722533X-RAY DIFFRACTION92
2.4505-2.50750.35191330.31542521X-RAY DIFFRACTION93
2.5075-2.57020.35171430.30762557X-RAY DIFFRACTION93
2.5702-2.63970.33571550.30482514X-RAY DIFFRACTION94
2.6397-2.71740.29521590.29182558X-RAY DIFFRACTION94
2.7174-2.80510.31881370.28682575X-RAY DIFFRACTION94
2.8051-2.90530.31881320.28522569X-RAY DIFFRACTION95
2.9053-3.02160.34621210.27412603X-RAY DIFFRACTION94
3.0216-3.15910.25921420.25742589X-RAY DIFFRACTION95
3.1591-3.32560.26521290.24332623X-RAY DIFFRACTION95
3.3256-3.53390.2541330.23632629X-RAY DIFFRACTION96
3.5339-3.80660.27281220.21862613X-RAY DIFFRACTION95
3.8066-4.18950.28931210.20982627X-RAY DIFFRACTION95
4.1895-4.79510.22321550.18572569X-RAY DIFFRACTION94
4.7951-6.03910.25771400.21672593X-RAY DIFFRACTION94
6.0391-45.2210.24891410.22212532X-RAY DIFFRACTION90
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)
11.49730.16330.29111.79370.21352.2335-0.02190.03280.1899-0.0295-0.0607-0.1107-0.12290.10780.07660.16910.1249-0.00110.50140.24340.271373.0325121.4177-125.0954
21.79410.262-0.54221.76930.52721.7674-0.1754-0.03150.02410.0563-0.02070.08970.15740.02160.02260.15490.127-0.0120.00920.25980.163106.1021121.2189-150.9105
30.99010.14550.371.7240.47811.8168-0.0547-0.0305-0.030.0673-0.0041-0.00610.18430.01330.07040.23350.05850.03780.28950.17740.2251106.5867106.9741-109.4741
41.4259-0.13830.08961.47690.53911.6107-0.03250.0257-0.06680.0031-0.05350.1429-0.051-0.06370.0570.1430.08910.01310.2990.13450.197572.7298106.8486-166.5186
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' or chain 'B'
2X-RAY DIFFRACTION2chain 'C' or chain 'D'
3X-RAY DIFFRACTION3chain 'E' or chain 'F'
4X-RAY DIFFRACTION4chain 'G' or chain 'H'

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