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- PDB-5vq9: Structure of human TRIP13, Apo form -

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Basic information

Entry
Database: PDB / ID: 5vq9
TitleStructure of human TRIP13, Apo 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 / oocyte maturation / female meiosis I / 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 / oocyte maturation / female meiosis I / 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
Pachytene checkpoint protein 2 homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.02 Å
AuthorsYe, Q. / Corbett, K.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM104141 United States
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 1.3Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 1, 2020Group: Author supporting evidence
Category: pdbx_audit_support / pdbx_struct_assembly_auth_evidence
Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 4, 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

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Assembly

Deposited unit
D: Pachytene checkpoint protein 2 homolog


Theoretical massNumber of molelcules
Total (without water)48,6071
Polymers48,6071
Non-polymers00
Water55831
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)96.964, 96.964, 122.646
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65
DetailsThe crystal packing cannot be used to generate the relevant homohexamer assembly, as the protein forms a helical filament in the crystal but a closed hexameric ring in solution.

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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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 3.42 Å3/Da / Density % sol: 64.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Tris-HCl pH 8.5, 0.8 M LiCl, 4% PEG 3350, cryoprotected with 20% glycerol

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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: Dec 5, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 3.02→122.65 Å / Num. obs: 12908 / % possible obs: 100 % / Redundancy: 5.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.04 / Net I/σ(I): 19
Reflection shellResolution: 3.02→3.2 Å / Redundancy: 5.7 % / Rmerge(I) obs: 1.116 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2069 / CC1/2: 0.619 / Rpim(I) all: 0.514 / % possible all: 100

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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: 3.02→83.973 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.03
RfactorNum. reflection% reflection
Rfree0.2383 649 5.05 %
Rwork0.199 --
obs0.2009 12857 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.02→83.973 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2907 0 0 31 2938
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092952
X-RAY DIFFRACTIONf_angle_d1.0523997
X-RAY DIFFRACTIONf_dihedral_angle_d12.3641800
X-RAY DIFFRACTIONf_chiral_restr0.056484
X-RAY DIFFRACTIONf_plane_restr0.005499
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0205-3.25370.36711350.31062427X-RAY DIFFRACTION100
3.2537-3.58110.28651320.23322419X-RAY DIFFRACTION100
3.5811-4.09930.2171340.18912440X-RAY DIFFRACTION100
4.0993-5.16460.19771240.16462438X-RAY DIFFRACTION100
5.1646-84.00570.23371240.19642484X-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)
110.0894-1.99583.22449.2438-0.31949.6886-0.2459-0.56890.834-0.0870.34740.5678-1.0243-1.370.01980.78160.1327-0.02050.93190.13590.721-83.1021123.05510.5616
24.84293.24051.27476.3835-0.12914.92890.10250.2497-0.6724-0.10520.2547-0.92270.38351.1055-0.32540.46150.1151-0.02450.9423-0.14210.6546-60.9301107.62869.7648
38.34213.9034-0.3839.4977-0.44787.64810.0391-0.2225-0.27640.2344-0.0280.24220.2362-0.3699-0.07420.48050.00950.06810.49420.05040.4796-91.353393.352513.2727
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain D and resi 19:107
2X-RAY DIFFRACTION2chain D and resi 119:322
3X-RAY DIFFRACTION3chain D and resi 323:430

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