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 25340

Title: Backbone assignments for human Cyclophilin D with saturating concentrations of the model peptide GSFGPDLRAGD   PubMed: 25923019

Deposition date: 2014-11-13 Original release date: 2014-12-16

Authors: Holliday, Michael; Camilloni, Carlo; Armstrong, Geoffrey; Isern, Nancy; Zhang, Fengli; Vendruscolo, Michele; Eisenmesser, Elan

Citation: Holliday, Michael; Camilloni, Carlo; Armstrong, Geoffrey; Isern, Nancy; Zhang, Fengli; Vendruscolo, Michele; Eisenmesser, Elan. "Structure and Dynamics of GeoCyp: A Thermophilic Cyclophilin with a Novel Substrate Binding Mechanism That Functions Efficiently at Low Temperatures"  Biochemistry 54, 3207-3217 (2015).

Assembly members:
CypD, polymer, 166 residues, 17787.2 Da.
GSFGPDLRAGD, polymer, 11 residues, Formula weight is not available

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):
CypD: GSGNPLVYLDVDANGKPLGR VVLELKADVVPKTAENFRAL CTGEKGFGYKGSTFHRVIPS FMCQAGDFTNHNGTGGKSIY GSRFPDENFTLKHVGPGVLS MANAGPNTNGSQFFICTIKT DWLDGKHVVFGHVKEGMDVV KKIESFGSKSGRTSKKIVIT DCGQLS
GSFGPDLRAGD: GSFGPDLRAGD

Data sets:
Data typeCount
13C chemical shifts291
15N chemical shifts150
1H chemical shifts150

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1CypD1
2GSFGPDLRAGD2

Entities:

Entity 1, CypD 166 residues - 17787.2 Da.

Residues 43-207 of human Cyclophilin D with one additional N-terminal residue, Gly-, remaining after removal of affinity tag

1   GLYSERGLYASNPROLEUVALTYRLEUASP
2   VALASPALAASNGLYLYSPROLEUGLYARG
3   VALVALLEUGLULEULYSALAASPVALVAL
4   PROLYSTHRALAGLUASNPHEARGALALEU
5   CYSTHRGLYGLULYSGLYPHEGLYTYRLYS
6   GLYSERTHRPHEHISARGVALILEPROSER
7   PHEMETCYSGLNALAGLYASPPHETHRASN
8   HISASNGLYTHRGLYGLYLYSSERILETYR
9   GLYSERARGPHEPROASPGLUASNPHETHR
10   LEULYSHISVALGLYPROGLYVALLEUSER
11   METALAASNALAGLYPROASNTHRASNGLY
12   SERGLNPHEPHEILECYSTHRILELYSTHR
13   ASPTRPLEUASPGLYLYSHISVALVALPHE
14   GLYHISVALLYSGLUGLYMETASPVALVAL
15   LYSLYSILEGLUSERPHEGLYSERLYSSER
16   GLYARGTHRSERLYSLYSILEVALILETHR
17   ASPCYSGLYGLNLEUSER

Entity 2, GSFGPDLRAGD 11 residues - Formula weight is not available

1   GLYSERPHEGLYPROASPLEUARGALAGLY
2   ASP

Samples:

CypD-GSFGPDLRAGD: CypD, [U-100% 13C; U-100% 15N], 1 mM; GSFGPDLRAGD 4 mM; sodium phosphate 50 mM; EDTA 1 mM; DTT 1 mM; H2O 93%; D2O 7%

sample_conditions: ionic strength: 0.05 M; pH: 6.5; pressure: 1 atm; temperature: 283 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQC/HMQCCypD-GSFGPDLRAGDisotropicsample_conditions
3D HNCACBCypD-GSFGPDLRAGDisotropicsample_conditions
3D CBCA(CO)NHCypD-GSFGPDLRAGDisotropicsample_conditions

Software:

CcpNmr_Analysis v2.1, CCPN - chemical shift assignment, peak picking

nmrPipe vany, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax, Varian - Spectrum processing, collection

NMR spectrometers:

  • Varian Varian 800 MHz

Related Database Links:

PDB
DBJ BAG35623 BAG59266 BAI47316
GB AAA58434 AAH05020 AAI10300 ACE87134 ADQ32373
REF NP_001253053 NP_005720 XP_001929518 XP_002820831 XP_002922456
SP P30405

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