BMRB Entry 17407

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR17407
MolProbity Validation Chart

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Title:
The complex structure of homeodomain in solution
Deposition date:
2011-01-12
Original release date:
2012-06-04
Authors:
LIU, Changdong; ZHOU, Bo; ZHU, Guang
Citation:

Citation: Zhou, Bo; Liu, Changdong; Xu, Zhiwen; Zhu, Guang. "Structural basis for homeodomain recognition by the cell-cycle regulator Geminin."  Proc. Natl. Acad. Sci. U.S.A. 109, 8931-8936 (2012).
PubMed: 22615398

Assembly members:

Assembly members:
entity_1, polymer, 60 residues, 7739.270 Da.
entity_2, polymer, 20 residues, 2330.259 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: pet32

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: TRKKRCPYTKYQTLELEKEF LFNMYLTRDRRYEVARVLNL TERQVKIWFQNRRMKMKKMN
entity_2: NQEFDSEEETVEDSLVEDSE

Data sets:
Data typeCount
13C chemical shifts300
15N chemical shifts88
1H chemical shifts550

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1entity_11
2entity_22

Entities:

Entity 1, entity_1 60 residues - 7739.270 Da.

1   THRARGLYSLYSARGCYSPROTYRTHRLYS
2   TYRGLNTHRLEUGLULEUGLULYSGLUPHE
3   LEUPHEASNMETTYRLEUTHRARGASPARG
4   ARGTYRGLUVALALAARGVALLEUASNLEU
5   THRGLUARGGLNVALLYSILETRPPHEGLN
6   ASNARGARGMETLYSMETLYSLYSMETASN

Entity 2, entity_2 20 residues - 2330.259 Da.

1   ASNGLNGLUPHEASPSERGLUGLUGLUTHR
2   VALGLUASPSERLEUVALGLUASPSERGLU

Samples:

sample_1: entity_1, [U-100% 13C; U-100% 15N], 0.8 mM; entity_2 1.0 mM; potassium phosphate 25 mM; sodium chloride 100 mM; DTT 5 mM; H2O 90%; D2O 10%

sample_2: entity_1, [U-99% 13C; U-99% 15N], 0.80 mM; entity_2 1.0 mM; potassium phosphate 25 mM; sodium chloride 100 mM; DTT 5 mM; D2O 100%

sample_3: entity_2, [U-100% 13C; U-100% 15N], 0.8 mM; entity_1 1.0 mM; potassium phosphate 25 mM; sodium chloride 100 mM; DTT 5 mM; H2O 90%; D2O 10%

sample_conditions_1: ionic strength: 0.125 M; pH: 6.5; pressure: 1 atm; temperature: 296 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-13C HSQCsample_2isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D H(CCO)NHsample_1isotropicsample_conditions_1
3D C(CO)NHsample_1isotropicsample_conditions_1
3D HCCH-COSYsample_2isotropicsample_conditions_1
3D HCCH-TOCSYsample_2isotropicsample_conditions_1
3D 1H-15N TOCSYsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-13C NOESY aliphaticsample_2isotropicsample_conditions_1
3D 13C-filtered 13C-edited NOESYsample_2isotropicsample_conditions_1
2D 1H-15N HSQCsample_3isotropicsample_conditions_1
2D 1H-13C HSQCsample_3isotropicsample_conditions_1
3D HNCOsample_3isotropicsample_conditions_1
3D CBCA(CO)NHsample_3isotropicsample_conditions_1
3D HNCACBsample_3isotropicsample_conditions_1
3D 1H-15N NOESYsample_3isotropicsample_conditions_1
3D 1H-13C NOESY aliphaticsample_3isotropicsample_conditions_1

Software:

VNMRJ v2.3, Varian - collection

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

SPARKY, Goddard - chemical shift assignment, data analysis, peak picking

CYANA, Guntert, Mumenthaler and Wuthrich - structure solution

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

HADDOCK v1.3, Alexandre Bonvin, Utrecht University - refinement

ProcheckNMR, Laskowski and MacArthur - geometry optimization

NMR spectrometers:

  • Varian INOVA 750 MHz
  • Varian INOVA 500 MHz

Related Database Links:

BMRB 25142
PDB
DBJ BAA86253 BAB28077 BAC37378 BAE44282 BAE53490 BAD96712 BAG51040 BAI46867
EMBL CAA30487 CAA39026 CAJ82440 CBL59361 CDQ56636
GB AAA37856 AAB04756 AAB68680 AAD15960 AAF44633 AAC39787 AAH05185 AAH05389 ADQ32794 AIC51377
PIR C45187 D45187
REF NP_001017256 NP_001094377 NP_001133005 NP_001133012 NP_001133018 NP_001238918 NP_001238919 NP_001238920 NP_056979 XP_001171903
SP O42502 P09633 P31274 Q28601 Q9IA13 O75496
TPG DAA30041
AlphaFold O42502 P09633 P31274 Q28601 Q9IA13 O75496

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