BMRB: 25048

Transient Collagen Triple Helix Binding to a Key Metalloproteinase in Invasion and Development: Spin Labels to Structure

Authors

Zhao, Y., Marcink, T.

Assembly

Transient Collagen Triple Helix Binding to a Key Metalloproteinase

Entity

1. Hemopexin-like (HPX) (polymer), 196 monomers, 23099.06 Da Detail

PNICDGNFDT VAMLRGEMFV FKERWFWRVR NNQVMDGYPM PIGQFWRGLP ASINTAYERK DGKFVFFKGD KHWVFDEASL EPGYPKHIKE LGRGLPTDKI DAALFWMPNG KTYFFRGNKY YRFNEELRAV DSEYPKNIKV WEGIPESPRG SFMGSDEVFT YFYKGNKYWK FNNQKLKVEP GYPKSALRDW MGCPSG

2. THP L and M chain (polymer, Thiol state: not present), 36 monomers, 3292.569 Da Detail

GPXGPXGPXG PQGIAGQRGV VGLXGPXGPX GPXGPX

3. THP T chain (polymer, Thiol state: not present), 33 monomers, 3025.288 Da Detail

GPXGPXGPXG PQGIAGQRGV VGLXGPXGPX GPX

4. 4-HYDROXYPROLINE (non-polymer), 131.130 Da

Total weight

29548.049 Da

Max. entity weight

23099.06 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 64.9 %, Completeness: 35.3 %, Completeness (bb): 58.4 % Detail

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• NMR-STAR v3.1 (partial)
• BMRB/XML (partial)
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Polymer type: polypeptide(L)

	Total	1H	13C	15N
All	35.3 % (1045 of 2963)	21.1 % (331 of 1567)	47.5 % (545 of 1148)	68.1 % (169 of 248)
Backbone	58.4 % (842 of 1442)	38.2 % (196 of 513)	67.5 % (478 of 708)	76.0 % (168 of 221)
Sidechain	20.4 % (352 of 1729)	12.8 % (135 of 1054)	33.3 % (216 of 648)	3.7 % (1 of 27)
Aromatic	0.8 % (3 of 362)	1.7 % (3 of 181)	0.0 % (0 of 173)	0.0 % (0 of 8)
Methyl	57.8 % (96 of 166)	53.0 % (44 of 83)	62.7 % (52 of 83)

1. Hemopexin-like (HPX)

PNICDGNFDT VAMLRGEMFV FKERWFWRVR NNQVMDGYPM PIGQFWRGLP ASINTAYERK DGKFVFFKGD KHWVFDEASL EPGYPKHIKE LGRGLPTDKI DAALFWMPNG KTYFFRGNKY YRFNEELRAV DSEYPKNIKV WEGIPESPRG SFMGSDEVFT YFYKGNKYWK FNNQKLKVEP GYPKSALRDW MGCPSG

2. THP L and M chain

GPXGPXGPXG PQGIAGQRGV VGLXGPXGPX GPXGPX

3. THP T chain

GPXGPXGPXG PQGIAGQRGV VGLXGPXGPX GPX

Show sample condition

Sample #1

Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 310 K, pH 5

#	Name	Isotope labeling	Type	Concentration
1	Hemopexin-like (HPX) of MT1-MMP	[U-13C; U-15N; U-2H]		0.2 ~ 0.4 mM
2	Sodium acetate	natural abundance		10 mM
3	EDTA	natural abundance		1 mM
4	Sodium azide	natural abundance		1 mM
5	H2O	natural abundance		93 %
6	D2O	natural abundance		7 %

Sample #2

Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 310 K, pH 5

#	Name	Isotope labeling	Type	Concentration
7	THP	natural abundance		0.3 ~ 1.4 mM
8	Sodium acetate	natural abundance		10 mM
9	EDTA	natural abundance		1 mM
10	Sodium azide	natural abundance		1 mM
11	H2O	natural abundance		93 %
12	D2O	natural abundance		7 %

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LACS Plot; CA

Referencing offset: 1.4 ppm, Outliers: 6 Detail

Show chemical shift referencing parameters

Chemical shift reference

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
1H	DSS	methyl protons	0.0 ppm	internal	direct	1.0
13C	DSS	methyl protons	0.0 ppm	na	indirect	0.2514495
15N	DSS	methyl protons	0.0 ppm	na	indirect	0.1013291
31P	DSS	methyl protons	0.0 ppm	na	indirect	0.4048086

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LACS Plot; CB

Referencing offset: 1.4 ppm, Outliers: 6 Detail

Show chemical shift referencing parameters

Chemical shift reference

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
1H	DSS	methyl protons	0.0 ppm	internal	direct	1.0
13C	DSS	methyl protons	0.0 ppm	na	indirect	0.2514495
15N	DSS	methyl protons	0.0 ppm	na	indirect	0.1013291
31P	DSS	methyl protons	0.0 ppm	na	indirect	0.4048086

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LACS Plot; CO

Referencing offset: 3.72 ppm, Outliers: 1 Detail

Show chemical shift referencing parameters

Chemical shift reference

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
1H	DSS	methyl protons	0.0 ppm	internal	direct	1.0
13C	DSS	methyl protons	0.0 ppm	na	indirect	0.2514495
15N	DSS	methyl protons	0.0 ppm	na	indirect	0.1013291
31P	DSS	methyl protons	0.0 ppm	na	indirect	0.4048086

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Protein Blocks Logo

Calculated from 15 models in PDB: 2MQS, Strand ID: A, B, C, D Detail

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Release date

2015-02-08

Citation

Transient collagen triple helix binding to a key metalloproteinase in invasion and development
Zhao, Y., Marcink, T.C., Sanganna Gari, R.R., Marsh, B.P., King, G.M., Stawikowska, R., Fields, G.B., VanDoren, S.R.
Structure (2015), 23, 257-269, PubMed 25651059 , DOI 10.1016/j.str.2014.11.021 , Abstract

Related entities 1. Hemopexin-like (HPX), : 1 : 2 : 84 entities Detail

Related entities 2. THP L and M chain, : 144 entities Detail

Related entities 3. THP T chain, : 106 entities Detail

Experiments performed 10 experiments Detail