BMRB Entry 25340

Name: Backbone assignments for human Cyclophilin D with saturating concentrations of the model peptide GSFGPDLRAGD
Published: 2014-12-16

Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR25340

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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Backbone assignments for human Cyclophilin D with saturating concentrations of the model peptide GSFGPDLRAGD

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:

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).
PubMed: 25923019

Assembly members:

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

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: pET-28

Entity Sequences (FASTA):

Entity Sequences (FASTA):
CypD: GSGNPLVYLDVDANGKPLGR VVLELKADVVPKTAENFRAL CTGEKGFGYKGSTFHRVIPS FMCQAGDFTNHNGTGGKSIY GSRFPDENFTLKHVGPGVLS MANAGPNTNGSQFFICTIKT DWLDGKHVVFGHVKEGMDVV KKIESFGSKSGRTSKKIVIT DCGQLS
GSFGPDLRAGD: GSFGPDLRAGD

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list
spectral_peak_list

Data type	Count
13C chemical shifts	291
15N chemical shifts	150
1H chemical shifts	150

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
Hide all

Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	CypD	1
2	GSFGPDLRAGD	2

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

GLY

SER

GLY

ASN

PRO

LEU

VAL

TYR

LEU

ASP

2

VAL

ASP

ALA

ASN

GLY

LYS

PRO

LEU

GLY

ARG

3

VAL

LEU

GLU

LEU

LYS

ALA

ASP

VAL

4

PRO

LYS

THR

ALA

GLU

ASN

PHE

ARG

ALA

LEU

5

CYS

THR

GLY

GLU

LYS

GLY

PHE

GLY

TYR

LYS

6

GLY

SER

THR

PHE

HIS

ARG

VAL

ILE

PRO

SER

7

PHE

MET

CYS

GLN

ALA

GLY

ASP

PHE

THR

ASN

8

HIS

ASN

GLY

THR

GLY

LYS

SER

ILE

TYR

9

GLY

SER

ARG

PHE

PRO

ASP

GLU

ASN

PHE

THR

10

LEU

LYS

HIS

VAL

GLY

PRO

GLY

VAL

LEU

SER

11

MET

ALA

ASN

ALA

GLY

PRO

ASN

THR

ASN

GLY

12

SER

GLN

PHE

ILE

CYS

THR

ILE

LYS

THR

13

ASP

TRP

LEU

ASP

GLY

LYS

HIS

VAL

PHE

14

GLY

HIS

VAL

LYS

GLU

GLY

MET

ASP

VAL

15

LYS

ILE

GLU

SER

PHE

GLY

SER

LYS

SER

16

GLY

ARG

THR

SER

LYS

ILE

VAL

ILE

THR

17

ASP

CYS

GLY

GLN

LEU

SER

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

1

GLY

SER

PHE

GLY

PRO

ASP

LEU

ARG

ALA

GLY

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:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC/HMQC	CypD-GSFGPDLRAGD	isotropic	sample_conditions
3D HNCACB	CypD-GSFGPDLRAGD	isotropic	sample_conditions
3D CBCA(CO)NH	CypD-GSFGPDLRAGD	isotropic	sample_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

PDB	2BIT 2BIU 2Z6W 3QYU 3R49 3R4G 3R54 3R56 3R57 3R59 3RCF 3RCG 3RCI 3RCK 3RCL 3RD9 3RDA 3RDB 3RDC 4J58 4J59 4J5A 4J5B 4J5C 4J5D 4J5E 4O8H 4O8I 4XNC 4ZSC 4ZSD
DBJ	BAG35623 BAG59266 BAI47316
GB	AAA58434 AAH05020 AAI10300 ACE87134 ADQ32373
REF	NP_001253053 NP_005720 XP_001929518 XP_002820831 XP_002922456
SP	P30405
AlphaFold	P30405