BMRB Entry 25048

Title:
Transient Collagen Triple Helix Binding to a Key Metalloproteinase in Invasion and Development: Spin Labels to Structure   PubMed: 25651059
Deposition date:
2014-06-26
Original release date:
2015-02-09
Authors:
Zhao, Yingchu; Marcink, Thomas
Citation:

Citation: Zhao, Yingchu; Marcink, Thomas; Sanganna Gari, R.; Marsh, B.; King, G.; Stawikowska, R.; Fields, Gregg; VanDoren, Steven. "Transient collagen triple helix binding to a key metalloproteinase in invasion and development"  Structure 23, 257-269 (2015).

Assembly members:

Assembly members:
Hemopexin-like_(HPX), polymer, 196 residues, 23131.535 Da.
THP_L_and_M_chain, polymer, 36 residues, 3293.611 Da.
THP_T_chain, polymer, 33 residues, 3026.327 Da.
4-HYDROXYPROLINE, non-polymer, 131.130 Da.

Natural source:

Natural source:   Common Name: human   Taxonomy ID: 9606   Superkingdom: Eukaryota   Kingdom: Metazoa   Genus/species: Homo sapiens

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli   Vector: pET-27b(+)

Experimental source:

Natural source:   Common Name: human   Taxonomy ID: 9606   Superkingdom: Eukaryota   Kingdom: Metazoa   Genus/species: Homo sapiens

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli   Vector: pET-27b(+)

Data sets:
Data typeCount
1H chemical shifts281
13C chemical shifts502
15N chemical shifts167

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

Assembly:

Entity Assembly IDEntity NameEntity ID
1Hemopexin-like_(HPX)1
2THP_L_and_M_chain2
3THP_T_chain3
44-HYDROXYPROLINE4

Entities:

Entity 1, Hemopexin-like_(HPX) 196 residues - 23131.535 Da.

1   PROASNILECYSASPGLYASNPHEASPTHR
2   VALALAMETLEUARGGLYGLUMETPHEVAL
3   PHELYSGLUARGTRPPHETRPARGVALARG
4   ASNASNGLNVALMETASPGLYTYRPROMET
5   PROILEGLYGLNPHETRPARGGLYLEUPRO
6   ALASERILEASNTHRALATYRGLUARGLYS
7   ASPGLYLYSPHEVALPHEPHELYSGLYASP
8   LYSHISTRPVALPHEASPGLUALASERLEU
9   GLUPROGLYTYRPROLYSHISILELYSGLU
10   LEUGLYARGGLYLEUPROTHRASPLYSILE
11   ASPALAALALEUPHETRPMETPROASNGLY
12   LYSTHRTYRPHEPHEARGGLYASNLYSTYR
13   TYRARGPHEASNGLUGLULEUARGALAVAL
14   ASPSERGLUTYRPROLYSASNILELYSVAL
15   TRPGLUGLYILEPROGLUSERPROARGGLY
16   SERPHEMETGLYSERASPGLUVALPHETHR
17   TYRPHETYRLYSGLYASNLYSTYRTRPLYS
18   PHEASNASNGLNLYSLEULYSVALGLUPRO
19   GLYTYRPROLYSSERALALEUARGASPTRP
20   METGLYCYSPROSERGLY

Entity 2, THP_L_and_M_chain 36 residues - 3293.611 Da.

1   GLYPROHYPGLYPROHYPGLYPROHYPGLY
2   PROGLNGLYILEALAGLYGLNARGGLYVAL
3   VALGLYLEUHYPGLYPROHYPGLYPROHYP
4   GLYPROHYPGLYPROHYP

Entity 3, THP_T_chain 33 residues - 3026.327 Da.

1   GLYPROHYPGLYPROHYPGLYPROHYPGLY
2   PROGLNGLYILEALAGLYGLNARGGLYVAL
3   VALGLYLEUHYPGLYPROHYPGLYPROHYP
4   GLYPROHYP

Entity 4, 4-HYDROXYPROLINE - C5 H9 N O3 - 131.130 Da.

1   HYP

Samples:

Hemopexin_domain_of_MT1-MMP: Hemopexin-like (HPX) of MT1-MMP, [U-13C; U-15N; U-2H], 0.2 – 0.4 mM; Sodium acetate 10 mM; EDTA 1 mM; Sodium azide 1 mM; H2O 93%; D2O 7%

THP: THP0.3 – 1.4 mM; Sodium acetate 10 mM; EDTA 1 mM; Sodium azide 1 mM; H2O 93%; D2O 7%

free_state_HPX_domain: temperature: 310 K; pH: 5; pressure: 1 atm; ionic strength: 10 mM

THP+HPX_domain_complex: temperature: 292 K; pH: 5.0; pressure: 1 atm; ionic strength: 10 mM

Experiments:

NameSampleSample stateSample conditions
2D 1H-13C HSQC aromaticHemopexin_domain_of_MT1-MMPisotropicfree_state_HPX_domain
2D 1H-13C HSQC aliphaticHemopexin_domain_of_MT1-MMPisotropicfree_state_HPX_domain
3D CBCA(CO)NHHemopexin_domain_of_MT1-MMPisotropicfree_state_HPX_domain
3D HNCOHemopexin_domain_of_MT1-MMPisotropicfree_state_HPX_domain
3D HNCAHemopexin_domain_of_MT1-MMPisotropicfree_state_HPX_domain
3D HNCACBHemopexin_domain_of_MT1-MMPisotropicfree_state_HPX_domain
3D HN(CO)CAHemopexin_domain_of_MT1-MMPisotropicfree_state_HPX_domain
3D HN(COCA)CBHemopexin_domain_of_MT1-MMPisotropicfree_state_HPX_domain
3D 1H-15N NOESYHemopexin_domain_of_MT1-MMPisotropicfree_state_HPX_domain
3D HCCH-TOCSYHemopexin_domain_of_MT1-MMPisotropicfree_state_HPX_domain

Software:

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

SPARKY, Goddard - chemical shift assignment

NMR spectrometers:

  • Bruker Avance 800 MHz

Related Database Links:

PDB
DBJ BAA05519 BAA36551 BAC40377 BAE23719 BAE29158
EMBL CAA58519 CAA58521 CAA62432 CAA62897 CAA88372
GB AAA83770 AAB41500 AAB51753 AAB86602 AAD13803
REF NP_001076262 NP_001124793 NP_001159653 NP_001233698 NP_001253739
SP P50281 P53690 Q10739 Q5RES1 Q95220
TPG DAA25704
AlphaFold Q5RES1

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