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- PDB-5vqa: Structure of human TRIP13, ATP-bound form -

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Basic information

Entry
Database: PDB / ID: 5vqa
TitleStructure of human TRIP13, ATP-bound form
ComponentsPachytene checkpoint protein 2 homolog
KeywordsPROTEIN BINDING / AAA+ ATPase / meiosis / spindle assembly checkpoint
Function / homology
Function and homology information


meiotic recombination checkpoint signaling / synaptonemal complex assembly / reciprocal meiotic recombination / female meiosis I / oocyte maturation / oogenesis / mitotic spindle assembly checkpoint signaling / male meiosis I / spermatid development / male germ cell nucleus ...meiotic recombination checkpoint signaling / synaptonemal complex assembly / reciprocal meiotic recombination / female meiosis I / oocyte maturation / oogenesis / mitotic spindle assembly checkpoint signaling / male meiosis I / spermatid development / male germ cell nucleus / transcription coregulator activity / double-strand break repair / chromosome / spermatogenesis / transcription by RNA polymerase II / ATP hydrolysis activity / ATP binding / identical protein binding / nucleus
Similarity search - Function
Pachytene checkpoint protein 2-like / ClpA/B family / ATPase, AAA-type, conserved site / AAA-protein family signature. / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Pachytene checkpoint protein 2 homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.54 Å
AuthorsYe, Q. / Corbett, K.D.
CitationJournal: EMBO J. / Year: 2017
Title: The AAA+ ATPase TRIP13 remodels HORMA domains through N-terminal engagement and unfolding.
Authors: Ye, Q. / Kim, D.H. / Dereli, I. / Rosenberg, S.C. / Hagemann, G. / Herzog, F. / Toth, A. / Cleveland, D.W. / Corbett, K.D.
History
DepositionMay 8, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 14, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 12, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Aug 30, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 4, 2023Group: Author supporting evidence / Data collection ...Author supporting evidence / 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 / pdbx_struct_assembly_auth_evidence
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: Pachytene checkpoint protein 2 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,1142
Polymers48,6071
Non-polymers5071
Water2,000111
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)98.479, 98.479, 120.979
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65
DetailsThe homohexamer can't be assembled from crystal packing, as the crystals form a helical filament and the homohexamer forms a closed hexameric ring.

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Components

#1: Protein Pachytene checkpoint protein 2 homolog / Human papillomavirus type 16 E1 protein-binding protein / HPV16 E1 protein-binding protein / ...Human papillomavirus type 16 E1 protein-binding protein / HPV16 E1 protein-binding protein / Thyroid hormone receptor interactor 13 / Thyroid receptor-interacting protein 13 / TRIP-13


Mass: 48606.664 Da / Num. of mol.: 1 / Mutation: E253Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRIP13, PCH2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15645
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.48 Å3/Da / Density % sol: 64.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Tris-HCl pH 8.5, 0.2 M KCl, 10% pentaerythritol propoxylate, 5 mM MgCl2, 1 mM ATP, cryoprotected with 10% glycerol and 12% additional pentaerythritol propoxylate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.54→121.03 Å / Num. obs: 22993 / % possible obs: 97.9 % / Redundancy: 5.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.043 / Net I/σ(I): 16.4
Reflection shellResolution: 2.54→2.66 Å / Redundancy: 5.3 % / Rmerge(I) obs: 1.767 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 2231 / CC1/2: 0.516 / Rpim(I) all: 0.821 / % possible all: 83.1

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XGU

4xgu


Resolution: 2.54→49.339 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.93
RfactorNum. reflection% reflection
Rfree0.2408 1156 5.19 %
Rwork0.1971 --
obs0.1993 22993 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.54→49.339 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2914 0 31 111 3056
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072992
X-RAY DIFFRACTIONf_angle_d0.9864058
X-RAY DIFFRACTIONf_dihedral_angle_d13.6881816
X-RAY DIFFRACTIONf_chiral_restr0.052489
X-RAY DIFFRACTIONf_plane_restr0.005501
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.54-2.60180.36591240.34092442X-RAY DIFFRACTION100
2.6018-2.72020.39061410.30742388X-RAY DIFFRACTION100
2.7202-2.86360.31151280.2682420X-RAY DIFFRACTION100
2.8636-3.0430.29311340.23892408X-RAY DIFFRACTION100
3.043-3.27790.27551580.21592390X-RAY DIFFRACTION100
3.2779-3.60770.26351280.19462431X-RAY DIFFRACTION100
3.6077-4.12950.23891410.17422427X-RAY DIFFRACTION100
4.1295-5.20180.17581200.15812430X-RAY DIFFRACTION100
5.2018-49.34890.21231190.18912464X-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)
14.25720.8139-1.27245.6172-0.41637.48990.4278-0.5991-0.02570.1001-0.0867-0.7977-0.51451.3369-0.31840.5719-0.12640.06260.907-0.08230.594651.539810.92420.5303
21.9242-0.7544-0.18315.5408-0.56163.63760.05060.0375-0.3154-0.11930.01880.68010.5275-0.5728-0.02020.4431-0.1185-0.04120.49640.05340.441627.0532-0.67029.5109
33.86351.2002-0.39796.73221.15086.8584-0.0151-0.09730.38180.25280.03070.113-0.2607-0.1407-0.03910.39840.0867-0.00480.3976-0.05170.436530.174232.787812.947
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1Chain A and resi 1:107
2X-RAY DIFFRACTION2chain A and resi 108:322
3X-RAY DIFFRACTION3chain A and resi 323:431

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