[English] 日本語
Yorodumi
- PDB-2ma6: Solution NMR Structure of the RING finger domain from the Kip1 ub... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2ma6
TitleSolution NMR Structure of the RING finger domain from the Kip1 ubiquitination-promoting E3 complex protein 1 (KPC1/RNF123) from Homo sapiens, Northeast Structural Genomics Consortium (NESG) Target HR8700A
ComponentsE3 ubiquitin-protein ligase RNF123
KeywordsLIGASE / Structural Genomics / NORTHEAST STRUCTURAL GENOMICS CONSORTIUM / NESG / PSI-Biology / Protein Structure Initiative / Ring fing domain / Zinc binding protein
Function / homology
Function and homology information


protein deubiquitination / proteolysis involved in protein catabolic process / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / Antigen processing: Ubiquitination & Proteasome degradation / nuclear membrane / Ub-specific processing proteases / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Ring finger protein 123, SPRY domain / Zinc finger, C3HC4 type (RING finger) / SPRY domain / B30.2/SPRY domain / B30.2/SPRY domain profile. / SPRY domain / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 ...Ring finger protein 123, SPRY domain / Zinc finger, C3HC4 type (RING finger) / SPRY domain / B30.2/SPRY domain / B30.2/SPRY domain profile. / SPRY domain / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Concanavalin A-like lectin/glucanase domain superfamily / Zinc finger, RING/FYVE/PHD-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
E3 ubiquitin-protein ligase RNF123
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing, null
Model detailslowest energy, model1
AuthorsRamelot, T.A. / Yang, Y. / Janjua, H. / Kohan, E. / Wang, H. / Xiao, R. / Acton, T.B. / Everett, J.K. / Montelione, G.T. / Kennedy, M.A. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution NMR Structure of the RING finger domain from the Kip1 ubiquitination-promoting E3 complex protein 1 (KPC1/RNF123) from Homo sapiens, Northeast Structural Genomics Consortium (NESG) Target HR8700A
Authors: Ramelot, T.A. / Yang, Y. / Janjua, H. / Kohan, E. / Wang, H. / Xiao, R. / Acton, T.B. / Everett, J.K. / Montelione, G.T. / Kennedy, M.A.
History
DepositionJun 28, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 31, 2013Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: E3 ubiquitin-protein ligase RNF123
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,0143
Polymers6,8831
Non-polymers1312
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein E3 ubiquitin-protein ligase RNF123 / Kip1 ubiquitination-promoting complex protein 1 / RING finger protein 123


Mass: 6882.918 Da / Num. of mol.: 1 / Fragment: UNP residues 1247-1304
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: plasmid / Gene: FP1477, KPC1, RNF123 / Plasmid details: pET15Avi6HT_NESG / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pMgK
References: UniProt: Q5XPI4, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC aliphatic
1312D 1H-13C HSQC aromatic CT
1412D 1H-13C HSQC aromatic noCT
1513D 1H-15N NOESY
1613D 1H-15N NOESY NUS
1713D 1H-13C NOESY aliphatic
1813D 1H-13C NOESY aliphatic NUS
1913D 1H-13C NOESY aromatic
11022D 1H-13C HSQC aliphatic
11113D C(CO)NH
11213D H(CCO)NH
11313D (H)CCH-COSY
11432D 1H-15N HSQC
11532D 1H-13C HSQC aliphatic
11632D 1H-15N HSQC HIS
11711D T1 NSQC array
11811D T2 NHSQC array
11913D CBCA(CO)NH
12013D HN(CA)CB
12113D HBHA(CO)NH
12213D HNCO
12312D 1H-15N HSQC NH2 only
12424D (H)CCH NOESY
12523D CCH-TOCSY
12622D 1H-15N HSQC
12712D 1H-15N HSQC
12813D (H)CCH-TOCSY

-
Sample preparation

Details
Solution-IDContentsSolvent system
11.0 mM [U-15N] 5% 13C-fractional labeling HR8700A.005, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 100 mM NaCL, 1 x Proteinase Inhibitors, 20 mM MES pH 6.5, 10 % D2O, 50 uM DSS, 90% H2O/10% D2O90% H2O/10% D2O
21.0 mM [U-100% 13C; U-100% 15N] HR8700A.005, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 100 mM NaCL, 1 x Proteinase Inhibitors, 20 mM MES pH 6.5, 100 % D2O, 50 uM DSS, 90% H2O/10% D2O90% H2O/10% D2O
30.9 mM [U-100% 15N] 5% 13C-fractional labeling HR8700A.007, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 100 mM NaCL, 1 x Proteinase Inhibitors, 20 mM MES pH 6.5, 10 % D2O, 50 uM DSS, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMHR8700A.005-1[U-15N] 5% 13C-fractional labeling1
0.02 %NaN3-21
10 mMDTT-31
5 mMCaCL2-41
100 mMNaCL-51
1 %Proteinase Inhibitors-61
20 mMMES pH 6.5-71
10 %D2O-81
50 uMDSS-91
1.0 mMHR8700A.005-10[U-100% 13C; U-100% 15N]2
0.02 %NaN3-112
10 mMDTT-122
5 mMCaCL2-132
100 mMNaCL-142
1 %Proteinase Inhibitors-152
20 mMMES pH 6.5-162
100 %D2O-172
50 uMDSS-182
0.9 mMHR8700A.007-19[U-100% 15N] 5% 13C-fractional labeling3
0.02 %NaN3-203
10 mMDTT-213
5 mMCaCL2-223
100 mMNaCL-233
1 %Proteinase Inhibitors-243
20 mMMES pH 6.5-253
10 %D2O-263
50 uMDSS-273
Sample conditionspH: 6.5 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker Avance IIBrukerAVANCE II8501
Varian INOVAVarianINOVA6002
Bruker Avance IIIBrukerAVANCE III6003

-
Processing

NMR software
NameVersionDeveloperClassification
CNS1.3Brunger, Adams, Clore, Gros, Nilges and Readrefinemen,structure solution,geometry optimization
CYANA3Guntert, Mumenthaler and Wuthrichrefinement,geometry optimization,structure solution
AutoStructure2.1Huang, Tejero, Powers and Montelionedata analysis,refinement
NMRPipeNMRPipe-2008Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TopSpin2.4Bruker Biospincollection
VnmrJvnmrj_1.1_DVariancollection
PINEBahrami, Markley, Assadi, and Eghbalniachemical shift assignment
Sparky3.113Goddarddata analysis
TALOS+Version 1.2009.0721.18Shen, Cornilescu, Delaglio and Baxgeometry optimization
PSVS1.4Bhattacharya, Montelionestructure validation
FMCGUIfmcgui2.5_linuxAlex Lemak, Cheryl Arrowmithrefinement
CNSrefinement
RefinementMethod: simulated annealing, null / Software ordinal: 1
Details: CNS water refinement of Cyana structures via fmcGui, null
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

+
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