BMRB Entry 25337

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

Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR25337

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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 A 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:
CypA, polymer, 165 residues, 18017.4843 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-3a

Entity Sequences (FASTA):

Entity Sequences (FASTA):
CypA: MVNPTVFFDIAVDGEPLGRV SFELFADKVPKTAENFRALS TGEKGFGYKGSCFHRIIPGF MCQGGDFTRHNGTGGKSIYG EKFEDENFILKHTGPGILSM ANAGPNTNGSQFFICTAKTE WLDGKHVVFGKVKEGMNIVE AMERFGSRNGKTSKKITIAD CGQLE
GSFGPDLRAGD: GSFGPDLRAGD

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list
spectral_peak_list

Data type	Count
13C chemical shifts	298
15N chemical shifts	157
1H chemical shifts	157

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	CypA	1
2	GSFGPDLRAGD	2

Entities:

Entity 1, CypA 165 residues - 18017.4843 Da.

Full length human Cyclophilin A

1

MET

VAL

ASN

PRO

THR

VAL

PHE

ASP

ILE

2

ALA

VAL

ASP

GLY

GLU

PRO

LEU

GLY

ARG

VAL

3

SER

PHE

GLU

LEU

PHE

ALA

ASP

LYS

VAL

PRO

4

LYS

THR

ALA

GLU

ASN

PHE

ARG

ALA

LEU

SER

5

THR

GLY

GLU

LYS

GLY

PHE

GLY

TYR

LYS

GLY

6

SER

CYS

PHE

HIS

ARG

ILE

PRO

GLY

PHE

7

MET

CYS

GLN

GLY

ASP

PHE

THR

ARG

HIS

8

ASN

GLY

THR

GLY

LYS

SER

ILE

TYR

GLY

9

GLU

LYS

PHE

GLU

ASP

GLU

ASN

PHE

ILE

LEU

10

LYS

HIS

THR

GLY

PRO

GLY

ILE

LEU

SER

MET

11

ALA

ASN

ALA

GLY

PRO

ASN

THR

ASN

GLY

SER

12

GLN

PHE

ILE

CYS

THR

ALA

LYS

THR

GLU

13

TRP

LEU

ASP

GLY

LYS

HIS

VAL

PHE

GLY

14

LYS

VAL

LYS

GLU

GLY

MET

ASN

ILE

VAL

GLU

15

ALA

MET

GLU

ARG

PHE

GLY

SER

ARG

ASN

GLY

16

LYS

THR

SER

LYS

ILE

THR

ILE

ALA

ASP

17

CYS

GLY

GLN

LEU

GLU

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

1

GLY

SER

PHE

GLY

PRO

ASP

LEU

ARG

ALA

GLY

2

ASP

Samples:

CypA-GSFGPDLRAGD: CypA, [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
3D HNCACB	CypA-GSFGPDLRAGD	isotropic	sample_conditions
3D CBCA(CO)NH	CypA-GSFGPDLRAGD	isotropic	sample_conditions
2D 1H-15N HSQC/HMQC	CypA-GSFGPDLRAGD	isotropic	sample_conditions
3D HNCA	CypA-GSFGPDLRAGD	isotropic	sample_conditions

Software:

CcpNmr_Analysis v2.4, CCPN - chemical shift assignment, peak picking

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

NMR spectrometers:

Varian UnityInova 800 MHz
Varian UnityInova 600 MHz

Related Database Links:

BMRB	17218 2208 25104 25502
PDB	1AK4 1AWQ 1AWR 1AWS 1AWT 1AWU 1AWV 1BCK 1CWA 1CWB 1CWC 1CWF 1CWH 1CWI 1CWJ 1CWK 1CWL 1CWM 1CWO 1FGL 1M63 1M9C 1M9D 1M9E 1M9F 1M9X 1M9Y 1MF8 1MIK 1NMK 1OCA 1RMH 1VBS 1VBT 1W8L 1W8M 1W8V 1YND 1ZKF 2ALF 2CPL 2CYH 2MS4 2MZU 2N0T 2RMA 2RMB 2WLW 2X25 2X2A 2X2C 2X2D 2X83 2XGY 3CYH 3CYS 3K0M 3K0N 3K0O 3K0P 3K0Q 3K0R 3ODI 3ODL 3RDD 4CYH 4DGA 4DGB 4DGC 4DGD 4DGE 4IPZ 4N1M 4N1N 4N1O 4N1P 4N1Q 4N1R 4N1S 4YUG 4YUH 4YUI 4YUJ 4YUK 4YUL 4YUM 4YUN 4YUO 4YUP 5CYH
DBJ	BAE01146 BAE30323 BAE87660 BAF82774 BAF83540
EMBL	CAA34961 CAA37039 CAA68264 CAG32988 CAH91833
GB	AAB81959 AAB81960 AAB81961 AAF69142 AAF78600
PIR	CSHYAC
PRF	1503232A
REF	NP_001009370 NP_001027981 NP_001126060 NP_001270275 NP_001271703
SP	P14851 P62935 P62936 P62937 P62938
TPG	DAA25853 DAA25854
AlphaFold	P14851 P62935 P62936 P62937 P62938

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