BMRB Entry 25139

Name: The solution structure of the MANEC-type domain from Hepatocyte Growth Factor Inhibitor 1 reveals an unexpected PAN/apple domain-type fold
Published: 2015-09-02

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PDB ID: 2msx
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR25139
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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:

The solution structure of the MANEC-type domain from Hepatocyte Growth Factor Inhibitor 1 reveals an unexpected PAN/apple domain-type fold

Deposition date:

2014-08-09

Original release date:

2015-09-02

Authors:

Hong, Zebin; Nowakowski, Michal; Spronk, Chris; Petersen, Steen; Petersen, Jan; Kozminski, Wiktor; Mulder, Frans; Jensen, Jan

Citation:

Citation: Hong, Zebin; Nowakowski, Michal; Spronk, Chris; Petersen, Steen; Petersen, Jan; Kozminski, Wiktor; Mulder, Frans; Jensen, Jan. "The solution structure of the MANEC-type domain from Hepatocyte Growth Factor Activator Inhibitor 1 reveals an unexpected PAN/apple domain-type fold" Biochem. J. 466, 299-309 (2015).
PubMed: 25510835

Assembly members:

Assembly members:
entity_1, polymer, 114 residues, 12837.496 Da.

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: Pichia pastoris Vector: pPICZ A

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: GADCLNSFTAGVPGFVLDTQ ASVSNGATFLESPTVRRGWD CVRACCTTQNCNLALVELQP DRGEDAIAACFLINCLYEQN FVCKFAPREGFINYLTREVY RSYRQLVDHHHHHH

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1
- Assigned_chemical_shift_list_2

Data type	Count
13C chemical shifts	713
15N chemical shifts	205
1H chemical shifts	1215

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity_1	1

Entities:

Entity 1, entity_1 114 residues - 12837.496 Da.

1

GLY

ALA

ASP

CYS

LEU

ASN

SER

PHE

THR

ALA

2

GLY

VAL

PRO

GLY

PHE

VAL

LEU

ASP

THR

GLN

3

ALA

SER

VAL

SER

ASN

GLY

ALA

THR

PHE

LEU

4

GLU

SER

PRO

THR

VAL

ARG

GLY

TRP

ASP

5

CYS

VAL

ARG

ALA

CYS

THR

GLN

ASN

6

CYS

ASN

LEU

ALA

LEU

VAL

GLU

LEU

GLN

PRO

7

ASP

ARG

GLY

GLU

ASP

ALA

ILE

ALA

CYS

8

PHE

LEU

ILE

ASN

CYS

LEU

TYR

GLU

GLN

ASN

9

PHE

VAL

CYS

LYS

PHE

ALA

PRO

ARG

GLU

GLY

10

PHE

ILE

ASN

TYR

LEU

THR

ARG

GLU

VAL

TYR

11

ARG

SER

TYR

ARG

GLN

LEU

VAL

ASP

HIS

12

HIS

Samples:

sample_1: entity_1, [U-99% 13C; U-99% 15N], 1 mM; H2O 93%; D2O 7%; NaH2PO4 pH 6.5 20 mM; NaCl 100 mM

sample_conditions_1: ionic strength: 100 mM; pH: 6.5; pressure: 1 atm; temperature: 310 K

sample_conditions_2: ionic strength: 100 mM; pH: 6.5; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D HNCA	sample_1	isotropic	sample_conditions_1
4D HabCab(CO)NH	sample_1	isotropic	sample_conditions_2
4D HCCH-TOCSY	sample_1	isotropic	sample_conditions_2
2D (HB)CB(CGCD)HD	sample_1	isotropic	sample_conditions_2
2D (HB)CB(CGCDCE)HE	sample_1	isotropic	sample_conditions_2
3D HBCB(CGCD)HD	sample_1	isotropic	sample_conditions_2
3D HBCB(CGCDCE)HE	sample_1	isotropic	sample_conditions_2
3D 13C-edited NOESY HSQC	sample_1	isotropic	sample_conditions_2
4D 13Cali,13Caro-edited HMQC-NOESY-HSQC	sample_1	isotropic	sample_conditions_2
4D 13Cali,13Cali-edited HMQC-NOESY-HMQC	sample_1	isotropic	sample_conditions_2
4D 15N,13C edited HMQC-NOESY-HSQC	sample_1	isotropic	sample_conditions_2
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_2
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_2
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_2
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1

Software:

CYANA, Guntert, Mumenthaler and Wuthrich - structure solution

SPARKY, Goddard - chemical shift assignment

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

YASARA2, YASARA2-Krieger - refinement

SSA_software_package, Stanek, Kosinski, Kozminski - processing

NMR spectrometers:

Bruker Plus 500 MHz
Agilent DDR2 600 MHz
Agilent DDR2 800 MHz

PDB	2MSX
DBJ	BAA25014 BAG37346 BAG61968
GB	AAH04140 AAH18702 AAP36093 AAP44001 AAP88884
REF	NP_001027539 NP_003701 NP_857593 XP_003266791 XP_003314674
SP	O43278
AlphaFold	O43278