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- PDB-5wc2: Crystal Structure of ADP-bound human TRIP13 -

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Basic information

Entry
Database: PDB / ID: 5wc2
TitleCrystal Structure of ADP-bound human TRIP13
ComponentsPachytene checkpoint protein 2 homolog
KeywordsCELL CYCLE / TRIP13 / ATPase / Spindle Assembly Checkpoint / Mad2 / p31comet
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
ADENOSINE-5'-DIPHOSPHATE / Pachytene checkpoint protein 2 homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsJeong, B.-C. / Luo, X.
Funding support United States, 2items
OrganizationGrant numberCountry
Cancer Prevention and Research Institute of Texas (CPRIT)RP160255 United States
Welch FoundationI-1932 United States
CitationJournal: Nat Commun / Year: 2017
Title: Mechanistic insight into TRIP13-catalyzed Mad2 structural transition and spindle checkpoint silencing.
Authors: Brulotte, M.L. / Jeong, B.C. / Li, F. / Li, B. / Yu, E.B. / Wu, Q. / Brautigam, C.A. / Yu, H. / Luo, X.
History
DepositionJun 29, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 25, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 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

Downloads & links

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Assembly

Deposited unit
A: Pachytene checkpoint protein 2 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,9772
Polymers48,5501
Non-polymers4271
Water2,486138
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area750 Å2
ΔGint-5 kcal/mol
Surface area19570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.369, 98.369, 122.109
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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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: 48549.613 Da / Num. of mol.: 1 / Mutation: E253A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRIP13, PCH2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): T1 / References: UniProt: Q15645
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 138 / 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: 3.52 Å3/Da / Density % sol: 65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: HEPES, sodium chloride, isopropanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 14, 2016
RadiationMonochromator: Rosenbaum-Rock high-resolution double-crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.5→32.199 Å / Num. obs: 23254 / % possible obs: 100 % / Redundancy: 15.2 % / Biso Wilson estimate: 32.77 Å2 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.021 / Χ2: 0.947 / Net I/σ(I): 40.6
Reflection shellResolution: 2.5→2.61 Å / Redundancy: 10.9 % / Rmerge(I) obs: 1.49 / Mean I/σ(I) obs: 2 / Num. unique obs: 1349 / CC1/2: 0.772 / Rpim(I) all: 0.461 / Χ2: 0.907 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4xgu

4xgu


Resolution: 2.5→32.199 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.49 / Phase error: 22.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.226 1081 5.04 %
Rwork0.1877 --
obs0.1896 21458 92.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→32.199 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2895 0 27 138 3060
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032971
X-RAY DIFFRACTIONf_angle_d0.6154031
X-RAY DIFFRACTIONf_dihedral_angle_d12.6211796
X-RAY DIFFRACTIONf_chiral_restr0.043488
X-RAY DIFFRACTIONf_plane_restr0.002497
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4999-2.61360.294730.23661349X-RAY DIFFRACTION49
2.6136-2.75130.26111350.22962505X-RAY DIFFRACTION91
2.7513-2.92360.24611470.20592732X-RAY DIFFRACTION100
2.9236-3.14910.23971440.20532747X-RAY DIFFRACTION100
3.1491-3.46570.22131480.18692753X-RAY DIFFRACTION100
3.4657-3.96640.20631410.17632756X-RAY DIFFRACTION100
3.9664-4.99430.19391510.1562755X-RAY DIFFRACTION100
4.9943-32.20150.24271420.19442780X-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)
11.8270.43870.33273.0969-0.63283.8961-0.09910.09330.4518-0.53860.10720.5465-1.0167-0.2424-0.06040.64940.04240.06230.3257-0.09080.483632.3163136.9048-1.2953
23.10811.06171.51951.44210.45621.99370.0431-0.04150.09150.12990.0186-0.04990.0854-0.052-0.05290.21240.0052-0.01240.123-0.00810.130435.338115.4155-10.1904
34.8531-0.8936-0.17797.37930.12684.088-0.0254-0.7114-0.81990.83520.14920.37610.394-0.4426-0.05710.3578-0.1007-0.04160.35380.05360.218531.7253105.9536-0.1525
44.912-1.4288-0.37565.6710.77393.41520.14190.2216-0.75620.0944-0.03520.04640.7549-0.2155-0.04810.3766-0.0455-0.10770.3018-0.03290.287635.4867100.6455-9.7716
51.9870.6362-0.42392.0515-0.61351.1957-0.02050.37360.2985-0.1170.1267-0.054-0.17530.06980.01170.21930.04630.03590.21030.04650.203253.5774128.0707-15.1397
63.03472.3771-0.09542.2604-0.61691.9772-0.31030.86240.3491-0.67570.2043-0.3635-0.05980.36180.00970.3097-0.00130.05480.39670.08520.294562.7249127.0485-19.3829
73.8828-0.05890.29583.20090.17094.27130.1059-0.0372-0.3397-0.2588-0.1507-0.59520.14480.5939-0.03990.15990.03120.03910.27770.04780.263466.943120.8117-9.5927
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 19 through 100 )
2X-RAY DIFFRACTION2chain 'A' and (resid 101 through 199 )
3X-RAY DIFFRACTION3chain 'A' and (resid 200 through 241 )
4X-RAY DIFFRACTION4chain 'A' and (resid 242 through 307 )
5X-RAY DIFFRACTION5chain 'A' and (resid 308 through 367 )
6X-RAY DIFFRACTION6chain 'A' and (resid 368 through 384 )
7X-RAY DIFFRACTION7chain 'A' and (resid 385 through 429 )

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