[English] 日本語
Yorodumi
- PDB-6lk0: Crystal structure of human wild type TRIP13 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6lk0
TitleCrystal structure of human wild type TRIP13
ComponentsPachytene checkpoint protein 2 homolog
KeywordsONCOPROTEIN / AAA+ ATPase / hexamer helical filament / ATP-bound / conformation dynamic
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 / SAD / Resolution: 2.6 Å
AuthorsWang, Y. / Huang, J. / Li, B. / Xue, H. / Tricot, G. / Hu, L. / Xu, Z. / Sun, X. / Chang, S. / Gao, L. ...Wang, Y. / Huang, J. / Li, B. / Xue, H. / Tricot, G. / Hu, L. / Xu, Z. / Sun, X. / Chang, S. / Gao, L. / Tao, Y. / Xu, H. / Xie, Y. / Xiao, W. / Yu, D. / Kong, Y. / Chen, G. / Sun, X. / Lian, F. / Zhang, N. / Wu, X. / Mao, Z. / Zhan, F. / Zhu, W. / Shi, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81870158 China
CitationJournal: Cancer Res. / Year: 2020
Title: A Small-Molecule Inhibitor Targeting TRIP13 Suppresses Multiple Myeloma Progression.
Authors: Wang, Y. / Huang, J. / Li, B. / Xue, H. / Tricot, G. / Hu, L. / Xu, Z. / Sun, X. / Chang, S. / Gao, L. / Tao, Y. / Xu, H. / Xie, Y. / Xiao, W. / Yu, D. / Kong, Y. / Chen, G. / Sun, X. / ...Authors: Wang, Y. / Huang, J. / Li, B. / Xue, H. / Tricot, G. / Hu, L. / Xu, Z. / Sun, X. / Chang, S. / Gao, L. / Tao, Y. / Xu, H. / Xie, Y. / Xiao, W. / Yu, D. / Kong, Y. / Chen, G. / Sun, X. / Lian, F. / Zhang, N. / Wu, X. / Mao, Z. / Zhan, F. / Zhu, W. / Shi, J.
History
DepositionDec 17, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 22, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2020Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed
Revision 1.2Feb 12, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.3Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Pachytene checkpoint protein 2 homolog


Theoretical massNumber of molelcules
Total (without water)48,6951
Polymers48,6951
Non-polymers00
Water18010
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area18480 Å2
Unit cell
Length a, b, c (Å)90.762, 90.762, 114.360
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

-
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: 48694.723 Da / Num. of mol.: 1
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) / References: UniProt: Q15645
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.79 Å3/Da / Density % sol: 56.03 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 100mM Bicine/Sodium hydroxide pH 9.0; 10%(v/v) MPD_(+/-)-2-Methyl-2,4-pentanediol

-
Data collection

DiffractionMean temperature: 277.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97778 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97778 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 16552 / % possible obs: 100 % / Redundancy: 10.1 % / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.027 / Rrim(I) all: 0.086 / Χ2: 0.883 / Net I/σ(I): 8.2 / Num. measured all: 167512
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.6-2.6410.40.8838190.8840.2870.9290.737100
2.64-2.6910.40.7888120.920.2560.8290.782100
2.69-2.7410.30.6148330.9470.2010.6460.76100
2.74-2.810.30.5488230.950.1790.5770.782100
2.8-2.8610.30.4128520.9670.1350.4340.772100
2.86-2.9310.30.3488090.9710.1140.3670.801100
2.93-310.20.2698030.9810.0880.2830.828100
3-3.089.90.2278340.990.0750.2390.889100
3.08-3.179.20.1738220.990.060.1830.946100
3.17-3.289.50.1468230.9930.050.1540.982100
3.28-3.3910.30.128210.9960.0390.1261.024100
3.39-3.5310.70.0978240.9960.0310.1021.087100
3.53-3.6910.60.0788340.9980.0250.0821.04100
3.69-3.8810.50.078190.9970.0230.0741.065100
3.88-4.1310.30.0648370.9980.0210.0670.982100
4.13-4.459.90.0588230.9980.0190.0610.982100
4.45-4.899.10.0548350.9980.0190.0570.894100
4.89-5.610.50.0578290.9980.0190.060.786100
5.6-7.0510.30.0568400.9980.0180.0590.74599.9
7.05-509.50.0548600.9980.0180.0570.778100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0232refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
Cootmodel building
SHELXCDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.6→46.28 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.894 / SU B: 9.535 / SU ML: 0.204 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.389 / ESU R Free: 0.291 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2649 822 5 %RANDOM
Rwork0.197 ---
obs0.2003 15694 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 164.52 Å2 / Biso mean: 63.899 Å2 / Biso min: 34.37 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20.01 Å20 Å2
2--0.02 Å2-0 Å2
3----0.06 Å2
Refinement stepCycle: final / Resolution: 2.6→46.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2700 0 0 10 2710
Biso mean---59.52 -
Num. residues----336
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0132743
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172672
X-RAY DIFFRACTIONr_angle_refined_deg1.561.6263711
X-RAY DIFFRACTIONr_angle_other_deg1.2441.5736177
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6015329
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.95822.446139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.30615508
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.4621517
X-RAY DIFFRACTIONr_chiral_restr0.0820.2371
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022955
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02552
LS refinement shellResolution: 2.6→2.665 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.319 72 -
Rwork0.258 1152 -
obs--100 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more