[English] 日本語
Yorodumi
- PDB-9bc9: Structure of KLHDC2 bound to SJ10278 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9bc9
TitleStructure of KLHDC2 bound to SJ10278
ComponentsKelch domain-containing protein 2
KeywordsLIGASE/INHIBITOR / Kelch domain / inhibitor / complex / KLHDC2 / LIGASE / LIGASE-INHIBITOR complex
Function / homology
Function and homology information


ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / Cul2-RING ubiquitin ligase complex / ubiquitin-like ligase-substrate adaptor activity / nuclear membrane / proteasome-mediated ubiquitin-dependent protein catabolic process / protein ubiquitination / nuclear body / nucleoplasm / nucleus
Similarity search - Function
KLHDC2/KLHL20/DRC7 Kelch-repeats domain / Kelch-type beta propeller
Similarity search - Domain/homology
: / COBALT HEXAMMINE(III) / Kelch domain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å
AuthorsScott, D.C. / Dharuman, S. / Griffith, E. / Chai, S.C. / Ronnebaum, J. / King, M.T. / Tangallapally, R. / Lee, C. / Gee, C.T. / Lee, H.W. ...Scott, D.C. / Dharuman, S. / Griffith, E. / Chai, S.C. / Ronnebaum, J. / King, M.T. / Tangallapally, R. / Lee, C. / Gee, C.T. / Lee, H.W. / Ochoada, J. / Miller, D.J. / Jayasinghe, T. / Paulo, J.A. / Elledge, S.J. / Harper, J.W. / Chen, T. / Lee, R.E. / Schulman, B.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01CA247365-04 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01-AI157312 United States
CitationJournal: Nat Commun / Year: 2024
Title: Principles of paralog-specific targeted protein degradation engaging the C-degron E3 KLHDC2.
Authors: Scott, D.C. / Dharuman, S. / Griffith, E. / Chai, S.C. / Ronnebaum, J. / King, M.T. / Tangallapally, R. / Lee, C. / Gee, C.T. / Yang, L. / Li, Y. / Loudon, V.C. / Lee, H.W. / Ochoada, J. / ...Authors: Scott, D.C. / Dharuman, S. / Griffith, E. / Chai, S.C. / Ronnebaum, J. / King, M.T. / Tangallapally, R. / Lee, C. / Gee, C.T. / Yang, L. / Li, Y. / Loudon, V.C. / Lee, H.W. / Ochoada, J. / Miller, D.J. / Jayasinghe, T. / Paulo, J.A. / Elledge, S.J. / Harper, J.W. / Chen, T. / Lee, R.E. / Schulman, B.A.
History
DepositionApr 8, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 5, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Kelch domain-containing protein 2
B: Kelch domain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,3175
Polymers79,4152
Non-polymers9033
Water5,513306
1
A: Kelch domain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2393
Polymers39,7071
Non-polymers5322
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Kelch domain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0782
Polymers39,7071
Non-polymers3711
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.528, 87.877, 89.896
Angle α, β, γ (deg.)90.00, 104.31, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Kelch domain-containing protein 2 / Hepatocellular carcinoma-associated antigen 33 / Host cell factor homolog LCP / Host cell factor- ...Hepatocellular carcinoma-associated antigen 33 / Host cell factor homolog LCP / Host cell factor-like protein 1 / HCLP-1


Mass: 39707.367 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KLHDC2, HCA33 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y2U9
#2: Chemical ChemComp-A1APK / N-({2-[2-chloro-4-(methoxymethoxy)phenyl]-1,3-thiazol-4-yl}acetyl)glycine / SJ10278


Mass: 370.808 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H15ClN2O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NCO / COBALT HEXAMMINE(III)


Mass: 161.116 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CoH18N6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 306 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 42.6 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 13-18% PEG3350, 0.2M NaSCN, 0.1 M Bis-Tris Propane, pH = 7.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 25, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.91→50 Å / Num. obs: 49105 / % possible obs: 96.7 % / Redundancy: 3 % / CC1/2: 0.985 / CC star: 0.996 / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.08 / Rrim(I) all: 0.14 / Χ2: 2.568 / Net I/σ(I): 8.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.95-2.022.90.64649260.4640.7960.4460.7891.17898.3
2.02-2.130.51349660.7260.9170.350.6231.2997.6
2.1-2.230.42749800.7870.9390.2910.5191.56599
2.2-2.313.10.3649980.8430.9560.2440.4371.76198.1
2.31-2.4630.28949260.9020.9740.1990.3532.13197.3
2.46-2.652.80.2248850.9270.9810.1570.2722.61795.6
2.65-2.913.30.17349280.9670.9920.1150.2092.87398.1
2.91-3.333.10.11548920.9770.9940.080.1413.58596.2
3.33-4.22.90.07547480.9870.9970.0550.0944.35492.8
4.2-502.90.05948560.990.9980.0420.0734.51993.6

-
Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.91→39.23 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 30.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2613 2357 4.81 %
Rwork0.2144 --
obs0.2166 49023 94.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.91→39.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5025 0 55 306 5386
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055253
X-RAY DIFFRACTIONf_angle_d0.7237173
X-RAY DIFFRACTIONf_dihedral_angle_d16.9531776
X-RAY DIFFRACTIONf_chiral_restr0.051735
X-RAY DIFFRACTIONf_plane_restr0.006916
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.91-1.950.4034690.35781668X-RAY DIFFRACTION57
1.95-1.990.36731520.32412833X-RAY DIFFRACTION98
1.99-2.040.35981570.31332821X-RAY DIFFRACTION97
2.04-2.090.27551470.29452818X-RAY DIFFRACTION98
2.09-2.150.29431340.27782905X-RAY DIFFRACTION99
2.15-2.210.33531620.26622843X-RAY DIFFRACTION99
2.21-2.280.30181490.26682829X-RAY DIFFRACTION98
2.28-2.360.35121360.25542847X-RAY DIFFRACTION98
2.36-2.460.3231590.25922782X-RAY DIFFRACTION96
2.46-2.570.30711390.2422760X-RAY DIFFRACTION95
2.57-2.70.32261290.24032852X-RAY DIFFRACTION98
2.7-2.870.23631390.23212856X-RAY DIFFRACTION98
2.87-3.090.28641400.20752824X-RAY DIFFRACTION97
3.09-3.410.23731520.19512762X-RAY DIFFRACTION95
3.41-3.90.21091290.17672731X-RAY DIFFRACTION93
3.9-4.910.17241250.15392612X-RAY DIFFRACTION89
4.91-39.230.24721390.18552923X-RAY DIFFRACTION98
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)
10.7315-0.3149-0.25650.38830.18530.67360.00970.1253-0.0131-0.071-0.02620.0727-0.07490.190300.2407-0.0469-0.02410.3178-0.02080.209413.091318.227313.8403
20.24150.12240.34380.17020.12140.83250.12450.0976-0.8448-0.30520.14750.60010.0802-0.12270.04110.3276-0.0055-0.01880.28510.02730.57192.8116-4.256615.6946
30.01650.0374-0.06350.1161-0.00670.1888-0.22830.0999-0.2222-0.17860.1887-0.07350.08410.3053-0.00050.252-0.01720.01370.41510.02250.357114.81352.841516.5572
41.08050.1037-0.6460.750.06430.7912-0.0761-0.4256-0.04430.04230.07250.023-0.0607-0.02610.00240.20420.002-0.01140.2401-0.00530.2115.332214.602931.3077
50.4337-0.27920.45480.98790.3560.5371-0.0454-0.47210.04940.09930.05-0.04580.22220.08280.00020.25890.04690.01520.32170.01970.192710.87525.7441-13.3166
61.01080.29940.31890.4464-0.19390.7877-0.0393-0.34880.42130.173-0.01880.0394-0.04370.3096-0.11780.22240.0048-0.00740.2952-0.09560.235416.647719.0708-16.4433
70.30430.1160.01170.2739-0.00730.1161-0.0338-0.1370.42990.24470.17890.2068-0.1577-0.02090.00090.30220.0480.0480.3103-0.14970.49450.595929.3995-17.8676
81.34530.03690.29110.6563-0.00881.0662-0.0550.18260.0414-0.08520.04350.03150.04550.041200.19480.0161-0.00740.2836-0.04170.20086.775313.0432-30.6986
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 27 through 164 )
2X-RAY DIFFRACTION2chain 'A' and (resid 165 through 184 )
3X-RAY DIFFRACTION3chain 'A' and (resid 185 through 206 )
4X-RAY DIFFRACTION4chain 'A' and (resid 207 through 359 )
5X-RAY DIFFRACTION5chain 'B' and (resid 28 through 122 )
6X-RAY DIFFRACTION6chain 'B' and (resid 123 through 174 )
7X-RAY DIFFRACTION7chain 'B' and (resid 175 through 194 )
8X-RAY DIFFRACTION8chain 'B' and (resid 195 through 359 )

+
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