BMRB Entry 19329

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR19329
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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
Deposition date:
2013-06-28
Original release date:
2013-07-19
Authors:
Ramelot, Theresa; Yang, Yunhuang; Janjua, Haleema; Kohan, Eitan; Wang, Huang; Xiao, Rong; Acton, Thomas; Everett, John; Montelione, Gaetano; Kennedy, Michael
Citation:

Citation: Ramelot, Theresa; Yang, Yunhuang; Janjua, Haleema; Kohan, Eitan; Wang, Huang; Xiao, Rong; Acton, Thomas; Everett, John; Montelione, Gaetano; Kennedy, Michael. "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"  To be published ., .-..

Assembly members:

Assembly members:
HR8700A, polymer, 61 residues, 6977.676 Da.
entity_ZN, non-polymer, 65.409 Da.

Natural source:

Natural source:   Common Name: Human   Taxonomy ID: 9606   Superkingdom: Eukaryota   Kingdom: Metazoa   Genus/species: Homo sapiens

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli   Vector: pET15Avi6HT_NESG

Entity Sequences (FASTA):

Entity Sequences (FASTA):
HR8700A: SHMPTSEEDLCPICYAHPIS AVFQPCGHKSCKACINQHLM NNKDCFFCKTTIVSVEDWEK G

Data sets:
Data typeCount
13C chemical shifts268
15N chemical shifts68
1H chemical shifts409

Time Domain Data

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
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Assembly:

Entity Assembly IDEntity NameEntity ID
1HR8700A1
2ZN ion, 12
3ZN ion, 22

Entities:

Entity 1, HR8700A 61 residues - 6977.676 Da.

First three residues, SHM, are non-native. Residues 1254-1292 of RNF123

1   SERHISMETPROTHRSERGLUGLUASPLEU
2   CYSPROILECYSTYRALAHISPROILESER
3   ALAVALPHEGLNPROCYSGLYHISLYSSER
4   CYSLYSALACYSILEASNGLNHISLEUMET
5   ASNASNLYSASPCYSPHEPHECYSLYSTHR
6   THRILEVALSERVALGLUASPTRPGLULYS
7   GLY

Entity 2, ZN ion, 1 - Zn - 65.409 Da.

1   ZN

Samples:

sample_NC_HR8700A.005: HR8700A.005, [U-15N] 5% 13C-fractional labeling, 1.0 mM; NaN3 0.02%; DTT 10 mM; CaCL2 5 mM; NaCL 100 mM; Proteinase Inhibitors 1 x; MES pH 6.5 20 mM; D2O 10%; DSS 50 uM

sample_D2O_NC_HR8700A.005: HR8700A.005, [U-100% 13C; U-100% 15N], 1.0 mM; NaN3 0.02%; DTT 10 mM; CaCL2 5 mM; NaCL 100 mM; Proteinase Inhibitors 1 x; MES pH 6.5 20 mM; D2O 100%; DSS 50 uM

sample_NC5_HR8700A.007: HR8700A.007, [U-100% 15N] 5% 13C-fractional labeling, 0.9 mM; NaN3 0.02%; DTT 10 mM; CaCL2 5 mM; NaCL 100 mM; Proteinase Inhibitors 1 x; MES pH 6.5 20 mM; D2O 10%; DSS 50 uM

sample_conditions_1: pH: 6.5; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_NC_HR8700A.005isotropicsample_conditions_1
2D 1H-13C HSQC aliphaticsample_NC_HR8700A.005isotropicsample_conditions_1
2D 1H-13C HSQC aromatic CTsample_NC_HR8700A.005isotropicsample_conditions_1
2D 1H-13C HSQC aromatic noCTsample_NC_HR8700A.005isotropicsample_conditions_1
3D 1H-15N NOESYsample_NC_HR8700A.005isotropicsample_conditions_1
3D 1H-15N NOESY NUSsample_NC_HR8700A.005isotropicsample_conditions_1
3D 1H-13C NOESY aliphaticsample_NC_HR8700A.005isotropicsample_conditions_1
3D 1H-13C NOESY aliphatic NUSsample_NC_HR8700A.005isotropicsample_conditions_1
3D 1H-13C NOESY aromaticsample_NC_HR8700A.005isotropicsample_conditions_1
2D 1H-13C HSQC aliphaticsample_D2O_NC_HR8700A.005isotropicsample_conditions_1
3D C(CO)NHsample_NC_HR8700A.005isotropicsample_conditions_1
3D H(CCO)NHsample_NC_HR8700A.005isotropicsample_conditions_1
3D HCCH-COSYsample_NC_HR8700A.005isotropicsample_conditions_1
2D 1H-15N HSQCsample_NC5_HR8700A.007isotropicsample_conditions_1
2D 1H-13C HSQC aliphaticsample_NC5_HR8700A.007isotropicsample_conditions_1
2D 1H-15N HSQC HISsample_NC5_HR8700A.007isotropicsample_conditions_1
1D T1 NSQC arraysample_NC_HR8700A.005isotropicsample_conditions_1
1D T2 NHSQC arraysample_NC_HR8700A.005isotropicsample_conditions_1
3D CBCA(CO)NHsample_NC_HR8700A.005isotropicsample_conditions_1
3D HNCACBsample_NC_HR8700A.005isotropicsample_conditions_1
3D HBHA(CO)NHsample_NC_HR8700A.005isotropicsample_conditions_1
3D HNCOsample_NC_HR8700A.005isotropicsample_conditions_1
2D 1H-15N HSQC NH2 onlysample_NC_HR8700A.005isotropicsample_conditions_1
4D HCCH NOESYsample_D2O_NC_HR8700A.005isotropicsample_conditions_1
3D CCH-TOCSYsample_D2O_NC_HR8700A.005isotropicsample_conditions_1
2D 1H-15N HSQCsample_D2O_NC_HR8700A.005isotropicsample_conditions_1
2D 1H-15N HSQCsample_NC_HR8700A.005isotropicsample_conditions_1
3D HCCH-TOCSYsample_NC_HR8700A.005isotropicsample_conditions_1

Software:

CNS v1.3, Brunger, Adams, Clore, Gros, Nilges and Read - refinemen,structure solution,geometry optimization

CYANA v3.0, Guntert, Mumenthaler and Wuthrich - refinement,geometry optimization,structure solution

AutoStruct v2.1, Huang, Tejero, Powers and Montelione - data analysis,refinement

NMRPipe vNMRPipe-2008, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

TOPSPIN v2.4, Bruker Biospin - collection

VNMRJ vvnmrj_1.1_D, Varian - collection

PINE, Bahrami, Markley, Assadi, and Eghbalnia - chemical shift assignment

SPARKY v3.113, Goddard - data analysis

TALOS+ vVersion 1.2009.0721.18, Shen, Cornilescu, Delaglio and Bax - geometry optimization

PSVS v1.4, Bhattacharya, Montelione - structure validation

FMCGUI vfmcgui2.5_linux, Alex Lemak, Cheryl Arrowmith - refinement

NMR spectrometers:

  • Bruker Avance II 850 MHz
  • Varian INOVA 600 MHz
  • Bruker Avance III 600 MHz

Related Database Links:

UNP Q5XPI4
PDB
AlphaFold Q9H9T2

Download HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated peaks
SPARKY: Backbone or all simulated peaks