BMRB Entry 19961

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full
BMRB Entry DOI: doi:10.13018/BMR19961
MolProbity Validation Chart

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Title:
Solution structure of SUMO Dimer in Complex with SIM2-3 from RNF4
Deposition date:
2014-05-09
Original release date:
2014-06-30
Authors:
Xu, Yingqi; Plechanovov, Anna; Simpson, Pete; Marchant, Jan; Leidecker, Orsolya; Sebastian, Kraatz; Hay, Ronald; Matthews, Stephen
Citation:

Citation: Xu, Yingqi; Plechanovov, Anna; Simpson, Pete; Marchant, Jan; Leidecker, Orsolya; Sebastian, Kraatz; Hay, Ronald; Matthews, Stephen. "Structural insight into SUMO chain recognition and manipulation by the ubiquitin ligase RNF4"  Nat. Commun. 5, 4217-4217 (2014).
PubMed: 24969970

Assembly members:

Assembly members:
entity_1, polymer, 82 residues, 9350.515 Da.
entity_2, polymer, 90 residues, 10351.681 Da.
entity_3, polymer, 25 residues, 2713.963 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: pHIS-TEV-30a

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: GTENDHINLKVAGQDGSVVQ FKIKRHTPLSKLMKAYCERQ GLSMRQIRFRFDGQPINETD TPAQLEMEDEDTIDVFQQQT GG
entity_2: GSEEKPKEGVKTENDHINLK VAGQDGSVVQFKIKRHTPLS KLMKAYCERQGLSMRQIRFR FDGQPINETDTPAQLEMEDE DTIDVFQQQT
entity_3: TVGDEIVDLTCESLEPVVVD LTHND

Data sets:
Data typeCount
13C chemical shifts484
1H chemical shifts919
15N chemical shifts113

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

Assembly:

Entity Assembly IDEntity NameEntity ID
1entity_11
2entity_22
3entity_33

Entities:

Entity 1, entity_1 82 residues - 9350.515 Da.

1   GLYTHRGLUASNASPHISILEASNLEULYS
2   VALALAGLYGLNASPGLYSERVALVALGLN
3   PHELYSILELYSARGHISTHRPROLEUSER
4   LYSLEUMETLYSALATYRCYSGLUARGGLN
5   GLYLEUSERMETARGGLNILEARGPHEARG
6   PHEASPGLYGLNPROILEASNGLUTHRASP
7   THRPROALAGLNLEUGLUMETGLUASPGLU
8   ASPTHRILEASPVALPHEGLNGLNGLNTHR
9   GLYGLY

Entity 2, entity_2 90 residues - 10351.681 Da.

1   GLYSERGLUGLULYSPROLYSGLUGLYVAL
2   LYSTHRGLUASNASPHISILEASNLEULYS
3   VALALAGLYGLNASPGLYSERVALVALGLN
4   PHELYSILELYSARGHISTHRPROLEUSER
5   LYSLEUMETLYSALATYRCYSGLUARGGLN
6   GLYLEUSERMETARGGLNILEARGPHEARG
7   PHEASPGLYGLNPROILEASNGLUTHRASP
8   THRPROALAGLNLEUGLUMETGLUASPGLU
9   ASPTHRILEASPVALPHEGLNGLNGLNTHR

Entity 3, entity_3 25 residues - 2713.963 Da.

1   THRVALGLYASPGLUILEVALASPLEUTHR
2   CYSGLUSERLEUGLUPROVALVALVALASP
3   LEUTHRHISASNASP

Samples:

sample_1: entity_1, [U-99% 13C; U-99% 15N], 0.3 mM; entity_2 0.3 mM; entity_3 1.0 mM

sample_2: entity_1 0.3 mM; entity_2, [U-99% 13C; U-99% 15N], 0.3 mM; entity_3 1.0 mM

sample_3: entity_1, [U-99% 13C; U-99% 15N], 0.3 mM; entity_2 0.3 mM

sample_4: entity_1 0.3 mM; entity_2, [U-99% 13C; U-99% 15N], 0.3 mM

sample_conditions_1: temperature: 303 K; pH: 7.0; pressure: 1 atm; ionic strength: 0.1 M

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-15N HSQCsample_2isotropicsample_conditions_1
2D 1H-15N HSQCsample_3isotropicsample_conditions_1
2D 1H-15N HSQCsample_4isotropicsample_conditions_1
3D HNCACBsample_3isotropicsample_conditions_1
3D CBCA(CO)NHsample_3isotropicsample_conditions_1
3D HCCH-TOCSYsample_3isotropicsample_conditions_1
3D 1H-15N NOESYsample_3isotropicsample_conditions_1

Software:

CNS, Brunger, Adams, Clore, Gros, Nilges and Read - structure solution

ARIA, Linge, O'Donoghue and Nilges - structure solution

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

NMRView, Johnson, One Moon Scientific - chemical shift assignment

TOPSPIN, Bruker Biospin - collection

NMR spectrometers:

  • Bruker DRX 600 MHz

Related Database Links:

BMRB 11267
PDB
DBJ BAB28360 BAB28442 BAB28601 BAC39397 BAD96311 BAB28442 BAB28601 BAD96311 BAE28469 BAE29276 BAB31585 BAC41119 BAE26531 BAE27641 BAE30125
EMBL CAA67896 CAA67897 CAG10356 CAG32064 CAG32742 CAA67896 CAG32742 CAG46970 CAG46985 CAJ81372
GB AAB49682 AAB92355 AAC99333 AAD45399 AAH00036 AAC99333 AAH00036 AAH08420 AAH54172 AAH58303 AAC35248 AAC53539 AAF00620 AAH03282 AAH62024
REF NP_001002677 NP_001003422 NP_001004853 NP_001016406 NP_001019466 NP_001002677 NP_001004853 NP_001019466 NP_001069917 NP_001072966 NP_001291198 NP_001291199 NP_035408 NP_062055 XP_006503868
SP P55854 P61955 P61956 P61957 P61958 P55854 Q17QV3 Q5XIF4 Q5ZHQ1 Q6DI05 O88846 Q9QZS2
TPG DAA13334 DAA18189 DAA33002 DAA22297 DAA33002
AlphaFold P55854 P61955 P61956 P61957 P61958 P55854 Q17QV3 Q5XIF4 Q5ZHQ1 Q6DI05 O88846 Q9QZS2

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