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BMRB: 25139

2MSX

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

Authors

Hong, Z., Nowakowski, M.E., Spronk, C., Petersen, S.V., Petersen, J.S., Kozminski, W., Mulder, F., Jensen, J.K.

Assembly

MANEC-type domain from Hepatocyte Growth Factor Inhibitor 1

Entity

1. MANEC-type domain from Hepatocyte Growth Factor Inhibitor 1 (polymer, Thiol state: all free), 114 monomers, 12822.28 Da Detail

GADCLNSFTA GVPGFVLDTQ ASVSNGATFL ESPTVRRGWD CVRACCTTQN CNLALVELQP DRGEDAIAAC FLINCLYEQN FVCKFAPREG FINYLTREVY RSYRQLVDHH HHHH

Formula weight

12822.28 Da

Entity Connection

disulfide 4 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS4:SG	1:CYS46:SG
2	disulfide	sing	1:CYS41:SG	1:CYS70:SG
3	disulfide	sing	1:CYS45:SG	1:CYS51:SG
4	disulfide	sing	1:CYS75:SG	1:CYS83:SG

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

DGSA-distance geometry simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete1

Sequence coverage: 95.6 %, Completeness: 75.9 %, Completeness (bb): 90.5 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	75.9 % (978 of 1288)	72.6 % (479 of 660)	78.4 % (396 of 505)	83.7 % (103 of 123)
Backbone	90.5 % (612 of 676)	86.1 % (199 of 231)	93.1 % (312 of 335)	91.8 % (101 of 110)
Sidechain	64.8 % (466 of 719)	65.3 % (280 of 429)	66.4 % (184 of 277)	15.4 % (2 of 13)
Aromatic	21.7 % (30 of 138)	37.7 % (26 of 69)	4.4 % (3 of 68)	100.0 % (1 of 1)
Methyl	81.1 % (99 of 122)	77.0 % (47 of 61)	85.2 % (52 of 61)

1. entity 1

GADCLNSFTA GVPGFVLDTQ ASVSNGATFL ESPTVRRGWD CVRACCTTQN CNLALVELQP DRGEDAIAAC FLINCLYEQN FVCKFAPREG FINYLTREVY RSYRQLVDHH HHHH

Show sample condition

Sample

Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 310 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	entity_1	[U-99% 13C; U-99% 15N]	1 mM
2	H2O	natural abundance	93 %
3	D2O	natural abundance	7 %
4	NaH2PO4 pH 6.5	natural abundance	20 mM
5	NaCl	natural abundance	100 mM

Chem. Shift Complete2

Sequence coverage: 94.7 %, Completeness: 78.6 %, Completeness (bb): 85.0 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	78.6 % (2024 of 2576)	79.3 % (1047 of 1320)	75.8 % (766 of 1010)	85.8 % (211 of 246)
Backbone	85.0 % (1149 of 1352)	87.9 % (406 of 462)	80.7 % (541 of 670)	91.8 % (202 of 220)
Sidechain	74.5 % (1071 of 1438)	74.7 % (641 of 858)	76.0 % (421 of 554)	34.6 % (9 of 26)
Aromatic	42.8 % (118 of 276)	50.7 % (70 of 138)	33.8 % (46 of 136)	100.0 % (2 of 2)
Methyl	88.1 % (215 of 244)	86.1 % (105 of 122)	90.2 % (110 of 122)

1. entity 1

GADCLNSFTA GVPGFVLDTQ ASVSNGATFL ESPTVRRGWD CVRACCTTQN CNLALVELQP DRGEDAIAAC FLINCLYEQN FVCKFAPREG FINYLTREVY RSYRQLVDHH HHHH

Show sample condition

Sample

Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	entity_1	[U-99% 13C; U-99% 15N]	1 mM
2	H2O	natural abundance	93 %
3	D2O	natural abundance	7 %
4	NaH2PO4 pH 6.5	natural abundance	20 mM
5	NaCl	natural abundance	100 mM

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: -0.37 ppm, Outliers: 1 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: -0.37 ppm, Outliers: 1 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: -0.07 ppm, Outliers: 2 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2MSX, Strand ID: A Detail

Release date

2015-09-01

Citation

The solution structure of the MANEC-type domain from hepatocyte growth factor activator inhibitor-1 reveals an unexpected PAN/apple domain-type fold
Hong, Z., Nowakowski, M.E., Spronk, C., Petersen, S.V., Petersen, J.S., Kozminski, W., Mulder, F., Jensen, J.K.
Biochem. J. (2015), 466, 299-309, PubMed 25510835 , DOI 10.1042/BJ20141236 , Abstract

Related entities 1. MANEC-type domain from Hepatocyte Growth Factor Inhibitor 1, : 1 : 3 : 11 entities Detail

Interaction partners 1. MANEC-type domain from Hepatocyte Growth Factor Inhibitor 1, : 5 interactors Detail

More details for 5 interactors identified by 5 citations

Experiments performed 20 experiments Detail

1 2D 1H-15N HSQC

Instrument

Agilent DDR2 - 800 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 310 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	entity_1	[U-99% 13C; U-99% 15N]	1 mM
2	H2O	natural abundance	93 %
3	D2O	natural abundance	7 %
4	NaH2PO4 pH 6.5	natural abundance	20 mM
5	NaCl	natural abundance	100 mM

2 2D 1H-13C HSQC

Instrument

Agilent DDR2 - 800 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 310 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	entity_1	[U-99% 13C; U-99% 15N]	1 mM
2	H2O	natural abundance	93 %
3	D2O	natural abundance	7 %
4	NaH2PO4 pH 6.5	natural abundance	20 mM
5	NaCl	natural abundance	100 mM

3 3D CBCA(CO)NH

Instrument

Bruker Plus - 500 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 310 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	entity_1	[U-99% 13C; U-99% 15N]	1 mM
2	H2O	natural abundance	93 %
3	D2O	natural abundance	7 %
4	NaH2PO4 pH 6.5	natural abundance	20 mM
5	NaCl	natural abundance	100 mM

4 3D HNCACB

Instrument

Bruker Plus - 500 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 310 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	entity_1	[U-99% 13C; U-99% 15N]	1 mM
2	H2O	natural abundance	93 %
3	D2O	natural abundance	7 %
4	NaH2PO4 pH 6.5	natural abundance	20 mM
5	NaCl	natural abundance	100 mM

5 3D HNCO

Instrument

Bruker Plus - 500 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 310 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	entity_1	[U-99% 13C; U-99% 15N]	1 mM
2	H2O	natural abundance	93 %
3	D2O	natural abundance	7 %
4	NaH2PO4 pH 6.5	natural abundance	20 mM
5	NaCl	natural abundance	100 mM

6 3D HNCA

Instrument

Bruker Plus - 500 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 310 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	entity_1	[U-99% 13C; U-99% 15N]	1 mM
2	H2O	natural abundance	93 %
3	D2O	natural abundance	7 %
4	NaH2PO4 pH 6.5	natural abundance	20 mM
5	NaCl	natural abundance	100 mM

7 4D HabCab(CO)NH