BMRB Entry 11073

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PDB ID: 2rqf
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR11073
MolProbity Validation Chart

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Nicholas Rego and David Koes
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Solution structure of juvenile hormone binding protein from silkworm in complex with JH III

Deposition date:

2009-04-27

Original release date:

2009-10-14

Authors:

Suzuki, Rintaro; Fujimoto, Zui; Shiotsuki, Takahiro; Momma, Mitsuru; Tase, Akira; Yamazaki, Toshimasa

Citation:

Citation: Suzuki, Rintaro; Fujimoto, Zui; Shiotsuki, Takahiro; Momma, Mitsuru; Tase, Akira; Miyazawa, Mitsuhiro; Yamazaki, Toshimasa. "Structural basis for juvenile hormone perception by JHBP in haemolymph" .

Assembly members:

Assembly members:
hJHBP, polymer, 227 residues, 24781.268 Da.
JH3, non-polymer, 266.376 Da.

Natural source:

Natural source: Common Name: Silkworm Taxonomy ID: 7091 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Bombyx mori

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pGEX-2T

Entity Sequences (FASTA):

Entity Sequences (FASTA):
hJHBP: GSDGDALLKPCKLGDMQCLS SATEQFLEKTSKGIPQYDIW PIDPLVVTSLDVIAPSDAGI VIRFKNLNITGLKNQQISDF QMDTKAKTVLLKTKADLHIV GDIVIELTEQSKSFTGLYTA DTNVIGAVRYGYNLKNDDNG VQHFEVQPETFTCESIGEPK ITLSSDLSSALEKDSGNNSL EPDMEPLKTLRQAAICKIAE ACYISVVHNIRASAKILPAS SFFENLN

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list

Data type	Count
13C chemical shifts	1049
15N chemical shifts	242
1H chemical shifts	1635

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	hJHBP	1
2	JH III	2

Entities:

Entity 1, hJHBP 227 residues - 24781.268 Da.

Residues (-2)-(-1) represent a non-native sequence from affinity tag.

1

GLY

SER

ASP

GLY

ASP

ALA

LEU

LYS

PRO

2

CYS

LYS

LEU

GLY

ASP

MET

GLN

CYS

LEU

SER

3

SER

ALA

THR

GLU

GLN

PHE

LEU

GLU

LYS

THR

4

SER

LYS

GLY

ILE

PRO

GLN

TYR

ASP

ILE

TRP

5

PRO

ILE

ASP

PRO

LEU

VAL

THR

SER

LEU

6

ASP

VAL

ILE

ALA

PRO

SER

ASP

ALA

GLY

ILE

7

VAL

ILE

ARG

PHE

LYS

ASN

LEU

ASN

ILE

THR

8

GLY

LEU

LYS

ASN

GLN

ILE

SER

ASP

PHE

9

GLN

MET

ASP

THR

LYS

ALA

LYS

THR

VAL

LEU

10

LEU

LYS

THR

LYS

ALA

ASP

LEU

HIS

ILE

VAL

11

GLY

ASP

ILE

VAL

ILE

GLU

LEU

THR

GLU

GLN

12

SER

LYS

SER

PHE

THR

GLY

LEU

TYR

THR

ALA

13

ASP

THR

ASN

VAL

ILE

GLY

ALA

VAL

ARG

TYR

14

GLY

TYR

ASN

LEU

LYS

ASN

ASP

ASN

GLY

15

VAL

GLN

HIS

PHE

GLU

VAL

GLN

PRO

GLU

THR

16

PHE

THR

CYS

GLU

SER

ILE

GLY

GLU

PRO

LYS

17

ILE

THR

LEU

SER

ASP

LEU

SER

ALA

18

LEU

GLU

LYS

ASP

SER

GLY

ASN

SER

LEU

19

GLU

PRO

ASP

MET

GLU

PRO

LEU

LYS

THR

LEU

20

ARG

GLN

ALA

ILE

CYS

LYS

ILE

ALA

GLU

21

ALA

CYS

TYR

ILE

SER

VAL

HIS

ASN

ILE

22

ARG

ALA

SER

ALA

LYS

ILE

LEU

PRO

ALA

SER

23

SER

PHE

GLU

ASN

LEU

ASN

Entity 2, JH III - C16 H26 O3 - 266.376 Da.

1

JH3

Samples:

15N: hJHBP, [U-15N], 0.6 – 1.0 mM; JH III0.6 – 1.0 mM; sodium phosphate 45 mM; H2O 90%; D2O 10%

13C_15N: hJHBP, [U-13C; U-15N], 0.6 – 1.0 mM; JH III0.6 – 1.0 mM; sodium phosphate 45 mM; H2O 90%; D2O 10%

13C_15N_in_100%_D2O: hJHBP, [U-13C; U-15N], 0.6 – 1.0 mM; JH III0.6 – 1.0 mM; sodium phosphate 45 mM; D2O 100%

pH_6.0_35C: pH: 6.0; pressure: 1 atm; temperature: 308 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	15N	isotropic	pH_6.0_35C
2D 1H-15N HSQC	13C_15N_in_100%_D2O	isotropic	pH_6.0_35C
2D 1H-13C HSQC	13C_15N_in_100%_D2O	isotropic	pH_6.0_35C
3D HNCO	13C_15N	isotropic	pH_6.0_35C
3D CBCA(CO)NH	13C_15N	isotropic	pH_6.0_35C
3D HNCA	13C_15N	isotropic	pH_6.0_35C
3D HCABGCO	13C_15N_in_100%_D2O	isotropic	pH_6.0_35C
3D HCCH-TOCSY	13C_15N_in_100%_D2O	isotropic	pH_6.0_35C
3D 15N-separated HOHAHA-HSQC	15N	isotropic	pH_6.0_35C
3D 15N-separated NOESY-HSQC	15N	isotropic	pH_6.0_35C
3D 13C/15N-separated NOESY-HSQC	13C_15N_in_100%_D2O	isotropic	pH_6.0_35C
3D 13C-separated NOESY-HSQC	13C_15N_in_100%_D2O	isotropic	pH_6.0_35C
3D 13C/13C-separated NOESY-HSQC	13C_15N_in_100%_D2O	isotropic	pH_6.0_35C
2D 13C-filtered COSY	13C_15N_in_100%_D2O	isotropic	pH_6.0_35C
2D 13C-filtered NOESY	13C_15N_in_100%_D2O	isotropic	pH_6.0_35C
3D 13C-filtered/13C-selected NOESY-HSQC	13C_15N_in_100%_D2O	isotropic	pH_6.0_35C

Software:

xwinnmr v3.1, Bruker Biospin - collection

NMRPipe vreleased at Feb 10, 2006, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

SPARKY v3.113, Goddard - chemical shift assignment, peak picking

TALOS v2003.027.13.05, Cornilescu, Delaglio and Bax - data analysis

CYANA v2.1, Guntert, Mumenthaler and Wuthrich - refinement, structure solution

AQUA v3.2, Rullmann, Doreleijers and Kaptein - data analysis

ProcheckNMR v3.5.4, Laskowski and MacArthur - data analysis

NMR spectrometers:

Bruker DMX 750 MHz

GB	AF098304 AAF19267 AAF19268 AAP41112
SWS	Q9U556_BOMMO
BMRB	16021
PDB	2RQF 3A1Z 3AOS 3AOT
REF	NP_001037074