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Biological Magnetic Resonance Data Bank


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BMRB Entry 19394

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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/BMR19394
MolProbity Validation Chart

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Title: Solution Structure of the human Polymerase iota UBM1-Ubiquitin Complex   PubMed: 24789524

Deposition date: 2013-07-29 Original release date: 2014-06-02

Authors: Wang, Su; Zhou, Pei

Citation: Wang, Su; Zhou, Pei. "Sparsely-sampled, high-resolution 4-D omit spectra for detection and assignment of intermolecular NOEs of protein complexes"  J. Biomol. NMR 59, 51-56 (2014).

Assembly members:
GB1-UBM1, polymer, 106 residues, 4290.950 Da.
ubiquitin, polymer, 79 residues, 8576.914 Da.

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

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

Entity Sequences (FASTA):
GB1-UBM1: MQYKLILNGKTLKGETTTEA VDAATAEKVFKQYANDNGVD GEWTYDDATKTFTVTEGSNE FPLCSLPEGVDQEVFKQLPV DIQEEILSGKSREKFQGKLE HHHHHH
ubiquitin: GSHMQIFVKTLTGKTITLEV EPSDTIENVKAKIQDKEGIP PDQQRLIFAGKQLEDGRTLS DYNIQKESTLHLVLRLRGG

Data sets:
Data typeCount
13C chemical shifts582
15N chemical shifts184
1H chemical shifts1251

Additional metadata:

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

Entity Assembly IDEntity NameEntity ID
1GB1-UBM11
2ubiquitin2

Entities:

Entity 1, GB1-UBM1 106 residues - 4290.950 Da.

1   METGLNTYRLYSLEUILELEUASNGLYLYS
2   THRLEULYSGLYGLUTHRTHRTHRGLUALA
3   VALASPALAALATHRALAGLULYSVALPHE
4   LYSGLNTYRALAASNASPASNGLYVALASP
5   GLYGLUTRPTHRTYRASPASPALATHRLYS
6   THRPHETHRVALTHRGLUGLYSERASNGLU
7   PHEPROLEUCYSSERLEUPROGLUGLYVAL
8   ASPGLNGLUVALPHELYSGLNLEUPROVAL
9   ASPILEGLNGLUGLUILELEUSERGLYLYS
10   SERARGGLULYSPHEGLNGLYLYSLEUGLU
11   HISHISHISHISHISHIS

Entity 2, ubiquitin 79 residues - 8576.914 Da.

1   GLYSERHISMETGLNILEPHEVALLYSTHR
2   LEUTHRGLYLYSTHRILETHRLEUGLUVAL
3   GLUPROSERASPTHRILEGLUASNVALLYS
4   ALALYSILEGLNASPLYSGLUGLYILEPRO
5   PROASPGLNGLNARGLEUILEPHEALAGLY
6   LYSGLNLEUGLUASPGLYARGTHRLEUSER
7   ASPTYRASNILEGLNLYSGLUSERTHRLEU
8   HISLEUVALLEUARGLEUARGGLYGLY

Samples:

15N_labeled: GB1-UBM1, [U-100% 15N], 3 mM; ubiquitin, [U-100% 15N], 3 mM; potassium chloride 100 mM; sodium phosphate 25 mM; H2O 90%; D2O 10%

13C15N_labeled: GB1-UBM1, [U-100% 13C; U-100% 15N], 3 mM; ubiquitin, [U-100% 13C; U-100% 15N], 3 mM; potassium chloride 100 mM; sodium phosphate 25 mM; H2O 90%; D2O 10%

13C15N_labeled_D2O: GB1-UBM1, [U-100% 13C; U-100% 15N], 3 mM; ubiquitin, [U-100% 13C; U-100% 15N], 3 mM; potassium chloride 100 mM; sodium phosphate 25 mM; D2O 100%

DLUBM1_ULUbi: GB1-UBM1, [U-100% 13C; U-100% 15N], 3 mM; ubiquitin 3 mM; potassium chloride 100 mM; sodium phosphate 25 mM; D2O 100%

ULUBM1_DLUbi: GB1-UBM1 3 mM; ubiquitin, [U-100% 13C; U-100% 15N], 3 mM; potassium chloride 100 mM; sodium phosphate 25 mM; D2O 100%

sample_conditions_1: ionic strength: 100 mM; pH: 7; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQC15N_labeledisotropicsample_conditions_1
2D 1H-13C HSQC13C15N_labeled_D2Oisotropicsample_conditions_1
3D sparse-sampled HNCO13C15N_labeledisotropicsample_conditions_1
3D sparse-sampled HNCA13C15N_labeledisotropicsample_conditions_1
3D sparse-sampled HNCACB13C15N_labeledisotropicsample_conditions_1
3D sparse-sampled HN(CO)CA13C15N_labeledisotropicsample_conditions_1
3D 1H-15N NOESY15N_labeledisotropicsample_conditions_1
3D sparse-sampled HN(COCA)CB13C15N_labeledisotropicsample_conditions_1
3D (HACA)CO(CA)NH13C15N_labeledisotropicsample_conditions_1
3D sparse-sampled HA(CACO)NH13C15N_labeledisotropicsample_conditions_1
3D sparse-sampled HA(CA)NH13C15N_labeledisotropicsample_conditions_1
4D sparse-sampled HC(CO)NH-TOCSY13C15N_labeledisotropicsample_conditions_1
4D sparse-sampled CHNH NOESY13C15N_labeledisotropicsample_conditions_1
4D sparse-sampled CHCH NOESY13C15N_labeled_D2Oisotropicsample_conditions_1
4D sparse-sampled CHCH NOESYDLUBM1_ULUbiisotropicsample_conditions_1
4D sparse-sampled CHCH NOESYULUBM1_DLUbiisotropicsample_conditions_1

Software:

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

SPARKY, Goddard - data analysis

TALOS, Cornilescu, Delaglio and Bax - data analysis

Scrub, Coggins and Zhou - processing

CYANA, Guntert, Mumenthaler and Wuthrich - structure solution

NMR spectrometers:

  • Varian INOVA 800 MHz
  • Varian INOVA 600 MHz

Related Database Links:

BMRB 15156 15380 16444 16627 16873 17810 18397 26630 11505 11547 15047 15410 15689 15866 15907 16228 16582 16626 16763 16880 16885 16895 17059 17181 17239 17333 17439 17769 17919 18582 18583 18584 18610 18611 18737 19399 19406 19412 19447 25070 25230 4245 4375 4983 5101 5387 6457 6466 6470 6488 68 7111
PDB
GB AAY41168 AAA02769 AAA28154 AAA28997 AAA28998 AAA28999
DBJ BAA03983 BAA09860 BAA11842 BAA11843 BAA23486
EMBL CAA26488 CAA28495 CAA30183 CAA30815 CAA33466
PIR I50437 I51568 I65237 JN0790 S13928
PRF 0412265A 1212243A 1212243B 1212243C 1212243D
REF NP_001005123 NP_001006688 NP_001009117 NP_001009202 NP_001009286
SP P0C273 P0C275 P0C276 P0CG47 P0CG48
TPD FAA00319
TPG DAA18802 DAA20663 DAA20672 DAA24675 DAA28295

Download simulated HSQC data in one of the following formats:
CSV: Backbone or all simulated shifts
SPARKY: Backbone or all simulated shifts