BMRB Entry 25048

Name: Transient Collagen Triple Helix Binding to a Key Metalloproteinase in Invasion and Development: Spin Labels to Structure
Published: 2015-02-09

Click here to enlarge.

PDB ID: 2mqs
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR25048
MolProbity Validation Chart

NMR-STAR file interactive viewer.
NMR-STAR v3 text file.
XML gzip file.
RDF gzip file.
All files associated with the entry

Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

Select model:

I am color blind

Download raw data. Direct link to this display. Help

Title:

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

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).
PubMed: 25651059

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:

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

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Hemopexin-like_(HPX): PNICDGNFDTVAMLRGEMFV FKERWFWRVRNNQVMDGYPM PIGQFWRGLPASINTAYERK DGKFVFFKGDKHWVFDEASL EPGYPKHIKELGRGLPTDKI DAALFWMPNGKTYFFRGNKY YRFNEELRAVDSEYPKNIKV WEGIPESPRGSFMGSDEVFT YFYKGNKYWKFNNQKLKVEP GYPKSALRDWMGCPSG
THP_L_and_M_chain: GPPGPPGPPGPQGIAGQRGV VGLPGPPGPPGPPGPP
THP_T_chain: GPPGPPGPPGPQGIAGQRGV VGLPGPPGPPGPP

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
1H chemical shifts	281
13C chemical shifts	502
15N chemical shifts	167

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
Hide all

Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	Hemopexin-like_(HPX)	1
2	THP_L_and_M_chain	2
3	THP_T_chain	3
4	4-HYDROXYPROLINE	4

Entities:

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

1

PRO

ASN

ILE

CYS

ASP

GLY

ASN

PHE

ASP

THR

2

VAL

ALA

MET

LEU

ARG

GLY

GLU

MET

PHE

VAL

3

PHE

LYS

GLU

ARG

TRP

PHE

TRP

ARG

VAL

ARG

4

ASN

GLN

VAL

MET

ASP

GLY

TYR

PRO

MET

5

PRO

ILE

GLY

GLN

PHE

TRP

ARG

GLY

LEU

PRO

6

ALA

SER

ILE

ASN

THR

ALA

TYR

GLU

ARG

LYS

7

ASP

GLY

LYS

PHE

VAL

PHE

LYS

GLY

ASP

8

LYS

HIS

TRP

VAL

PHE

ASP

GLU

ALA

SER

LEU

9

GLU

PRO

GLY

TYR

PRO

LYS

HIS

ILE

LYS

GLU

10

LEU

GLY

ARG

GLY

LEU

PRO

THR

ASP

LYS

ILE

11

ASP

ALA

LEU

PHE

TRP

MET

PRO

ASN

GLY

12

LYS

THR

TYR

PHE

ARG

GLY

ASN

LYS

TYR

13

TYR

ARG

PHE

ASN

GLU

LEU

ARG

ALA

VAL

14

ASP

SER

GLU

TYR

PRO

LYS

ASN

ILE

LYS

VAL

15

TRP

GLU

GLY

ILE

PRO

GLU

SER

PRO

ARG

GLY

16

SER

PHE

MET

GLY

SER

ASP

GLU

VAL

PHE

THR

17

TYR

PHE

TYR

LYS

GLY

ASN

LYS

TYR

TRP

LYS

18

PHE

ASN

GLN

LYS

LEU

LYS

VAL

GLU

PRO

19

GLY

TYR

PRO

LYS

SER

ALA

LEU

ARG

ASP

TRP

20

MET

GLY

CYS

PRO

SER

GLY

Entity 2, THP_L_and_M_chain 36 residues - 3293.611 Da.

1

GLY

PRO

HYP

GLY

PRO

HYP

GLY

PRO

HYP

GLY

2

PRO

GLN

GLY

ILE

ALA

GLY

GLN

ARG

GLY

VAL

3

VAL

GLY

LEU

HYP

GLY

PRO

HYP

GLY

PRO

HYP

4

GLY

PRO

HYP

GLY

PRO

HYP

Entity 3, THP_T_chain 33 residues - 3026.327 Da.

1

GLY

PRO

HYP

GLY

PRO

HYP

GLY

PRO

HYP

GLY

2

PRO

GLN

GLY

ILE

ALA

GLY

GLN

ARG

GLY

VAL

3

VAL

GLY

LEU

HYP

GLY

PRO

HYP

GLY

PRO

HYP

4

GLY

PRO

HYP

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:

Name	Sample	Sample state	Sample conditions
2D 1H-13C HSQC aromatic	Hemopexin_domain_of_MT1-MMP	isotropic	free_state_HPX_domain
2D 1H-13C HSQC aliphatic	Hemopexin_domain_of_MT1-MMP	isotropic	free_state_HPX_domain
3D CBCA(CO)NH	Hemopexin_domain_of_MT1-MMP	isotropic	free_state_HPX_domain
3D HNCO	Hemopexin_domain_of_MT1-MMP	isotropic	free_state_HPX_domain
3D HNCA	Hemopexin_domain_of_MT1-MMP	isotropic	free_state_HPX_domain
3D HNCACB	Hemopexin_domain_of_MT1-MMP	isotropic	free_state_HPX_domain
3D HN(CO)CA	Hemopexin_domain_of_MT1-MMP	isotropic	free_state_HPX_domain
3D HN(COCA)CB	Hemopexin_domain_of_MT1-MMP	isotropic	free_state_HPX_domain
3D 1H-15N NOESY	Hemopexin_domain_of_MT1-MMP	isotropic	free_state_HPX_domain
3D HCCH-TOCSY	Hemopexin_domain_of_MT1-MMP	isotropic	free_state_HPX_domain

Software:

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

SPARKY, Goddard - chemical shift assignment

NMR spectrometers:

Bruker Avance 800 MHz

PDB	2MQS 3C7X
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	P50281 P53690 Q10739 Q5RES1 Q95220