BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
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BMRB Entry 16871

Title: Solution structure of the second PDZ domain from human zonula occludens-1: A dimeric form with 3D domain swapping   PubMed: 21387411

Authors: Ji, Peng; wu, Jiawen; Zhang, Jiahai; Yang, Yinshan; wu, Jihui; Shi, Yunyu

Citation: Ji, Peng; Yang, Guang; Zhang, Jiahai; Wu, Jiawen; Chen, Zhengjun; Gong, Qingguo; Wu, Jihui; Shi, Yunyu. "Solution structure of the second PDZ domain of Zonula Occludens 1."  Proteins 79, 1342-1346 (2011).

Assembly members:
ZO-1 PDZ2, polymer, 88 residues, 2507.023 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):
ZO-1 PDZ2: TKVTLVKSRKNEEYGLRLAS HIFVKEISQDSLAARDGNIQ EGDVVLKINGTVTENMSLTD AKTLIERSKGKLKMVVQRDE LEHHHHHH

Data sets:
Data typeCount
13C chemical shifts351
15N chemical shifts88
1H chemical shifts602

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1ZO-1 PDZ21

Entities:

Entity 1, ZO-1 PDZ2 88 residues - 2507.023 Da.

1   THRLYSVALTHRLEUVALLYSSERARGLYS
2   ASNGLUGLUTYRGLYLEUARGLEUALASER
3   HISILEPHEVALLYSGLUILESERGLNASP
4   SERLEUALAALAARGASPGLYASNILEGLN
5   GLUGLYASPVALVALLEULYSILEASNGLY
6   THRVALTHRGLUASNMETSERLEUTHRASP
7   ALALYSTHRLEUILEGLUARGSERLYSGLY
8   LYSLEULYSMETVALVALGLNARGASPGLU
9   LEUGLUHISHISHISHISHISHIS

Samples:

sample_1: PDZ2, [U-99% 13C; U-99% 15N], 0.8 – 1 mM; H2O 90%; D2O 10%

sample_2: PDZ2, [U-99% 13C; U-99% 15N], 0.8 – 1 mM; D2O 100%

sample_3: PDZ2, [U-99% 13C; U-99% 15N], 0.4 – 0.5 mM; PDZ20.5 – 0.8 mM; D2O 100%

sample_4: PDZ20.5 – 0.8 mM; D2O 100%

sample_conditions_1: pH: 6.5; pressure: 1 atm; temperature: 310 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D HN(CA)COsample_1isotropicsample_conditions_1
3D HBHA(CO)NHsample_1isotropicsample_conditions_1
3D H(CCO)NHsample_1isotropicsample_conditions_1
3D C(CO)NHsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D HCCH-TOCSYsample_2isotropicsample_conditions_1
3D HCCH-COSYsample_2isotropicsample_conditions_1
3D 1H-13C NOESYsample_2isotropicsample_conditions_1
2D 1H-13C HSQCsample_3isotropicsample_conditions_1
2D 1H-1H 13C-Filtered NOESYsample_3isotropicsample_conditions_1
2D 1H-13C HSQCsample_2isotropicsample_conditions_1
2D 1H-1H TOCSYsample_4isotropicsample_conditions_1
2D 1H-1H NOESYsample_4isotropicsample_conditions_1
2D 1H-13C HSQCsample_1isotropicsample_conditions_1

Software:

CNSSOLVE v1.2, Brunger, Adams, Clore, Gros, Nilges and Read - refinement, structure solution

xwinnmr v3.5, Bruker Biospin - collection

NMRPipe v2.3, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

SPARKY v3.112, Goddard - chemical shift assignment, data analysis, peak picking

TALOS v2003.027.13.05, Cornilescu, Delaglio and Bax - predicts angles from chemical shift homology

Molmol v2K.2, Koradi, Billeter and Wuthrich - data analysis

ProcheckNMR v3.5.4, Laskowski and MacArthur - data analysis

NMR spectrometers:

  • Bruker DMX 600 MHz

Related Database Links:

PDB
GB EAW51509
REF XP_004320454 XP_005193388 XP_009874121 XP_009922511 XP_010151333
TPG DAA17568