BMRB Entry 30426

Name: MT1-MMP HPX Domain with Blade 2 Loop Bound to Nanodiscs
Published: 2018-12-04

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PDB ID: 6cm1
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR30426
MolProbity Validation Chart

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NMR-STAR v3 text file.
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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:

MT1-MMP HPX Domain with Blade 2 Loop Bound to Nanodiscs

Deposition date:

2018-03-02

Original release date:

2018-12-04

Authors:

Marcink, T.; Van Doren, S.

Citation:

Citation: Marcink, Tara; Simoncic, Jayce; An, Bo; Knapinska, Anna; Fulcher, Yan; Akkaladevi, Narahari; Fields, Gregg; Van Doren, Steven. "MT1-MMP Binds Membranes by Opposite Tips of Its beta Propeller to Position It for Pericellular Proteolysis" Structure 27, 281-292 (2019).
PubMed: 30471921

Assembly members:

Assembly members:
entity_1, polymer, 196 residues, 23131.346 Da.
entity_2, polymer, 211 residues, 24912.156 Da.
entity_PX4, non-polymer, 678.940 Da.
entity_NA, non-polymer, 22.990 Da.
entity_CL, non-polymer, 35.453 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

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: PNICDGNFDTVAMLRGEMFV FKERWFWRVRNNQVMDGYPM PIGQFWRGLPASINTAYERK DGKFVFFKGDKHWVFDEASL EPGYPKHIKELGRGLPTDKI DAALFWMPNGKTYFFRGNKY YRFNEELRAVDSEYPKNIKV WEGIPESPRGSFMGSDEVFT YFYKGNKYWKFNNQKLKVEP GYPKSALRDWMGCPSG
entity_2: STFSKLREQLGPVTQEFWDN LEKETEGLRQEMSKDLEEVK AKVQPYLDDFQKKWQEEMEL YRQKVEPYLDDFQKKWQEEM ELYRQKVEPLRAELQEGARQ KLHELQEKLSPLGEEMRDRA RAHVDALRTHLAPYSDELRQ RLAARLEALKENGGARLAEY HAKATEHLSTLSEKAKPALE DLRQGLLPVLESFKVSFLSA LEEYTKKLNTQ

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	35
15N chemical shifts	92
1H chemical shifts	197

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity_1	1
2	entity_2, 1	2
3	entity_2, 2	2
4	entity_3, 1	3
5	entity_3, 2	3
6	entity_3, 3	3
7	entity_3, 4	3
8	entity_3, 5	3
9	entity_3, 6	3
10	entity_3, 7	3
11	entity_3, 8	3
12	entity_3, 9	3
13	entity_3, 10	3
14	entity_3, 11	3
15	entity_3, 12	3
16	entity_3, 13	3
17	entity_3, 14	3
18	entity_3, 15	3
19	entity_3, 16	3
20	entity_3, 17	3
21	entity_3, 18	3
22	entity_3, 19	3
23	entity_3, 20	3
24	entity_3, 21	3
25	entity_3, 22	3
26	entity_3, 23	3
27	entity_3, 24	3
28	entity_3, 25	3
29	entity_3, 26	3
30	entity_3, 27	3
31	entity_3, 28	3
32	entity_3, 29	3
33	entity_3, 30	3
34	entity_3, 31	3
35	entity_3, 32	3
36	entity_3, 33	3
37	entity_3, 34	3
38	entity_3, 35	3
39	entity_3, 36	3
40	entity_3, 37	3
41	entity_3, 38	3
42	entity_3, 39	3
43	entity_3, 40	3
44	entity_3, 41	3
45	entity_3, 42	3
46	entity_3, 43	3
47	entity_3, 44	3
48	entity_3, 45	3
49	entity_3, 46	3
50	entity_3, 47	3
51	entity_3, 48	3
52	entity_3, 49	3
53	entity_3, 50	3
54	entity_3, 51	3
55	entity_3, 52	3
56	entity_3, 53	3
57	entity_3, 54	3
58	entity_3, 55	3
59	entity_3, 56	3
60	entity_3, 57	3
61	entity_3, 58	3
62	entity_3, 59	3
63	entity_3, 60	3
64	entity_3, 61	3
65	entity_3, 62	3
66	entity_3, 63	3
67	entity_3, 64	3
68	entity_3, 65	3
69	entity_3, 66	3
70	entity_3, 67	3
71	entity_3, 68	3
72	entity_3, 69	3
73	entity_3, 70	3
74	entity_3, 71	3
75	entity_3, 72	3
76	entity_3, 73	3
77	entity_3, 74	3
78	entity_3, 75	3
79	entity_3, 76	3
80	entity_3, 77	3
81	entity_3, 78	3
82	entity_3, 79	3
83	entity_3, 80	3
84	entity_3, 81	3
85	entity_3, 82	3
86	entity_3, 83	3
87	entity_3, 84	3
88	entity_3, 85	3
89	entity_3, 86	3
90	entity_3, 87	3
91	entity_3, 88	3
92	entity_3, 89	3
93	entity_3, 90	3
94	entity_3, 91	3
95	entity_3, 92	3
96	entity_3, 93	3
97	entity_3, 94	3
98	entity_3, 95	3
99	entity_3, 96	3
100	entity_3, 97	3
101	entity_3, 98	3
102	entity_3, 99	3
103	entity_3, 100	3
104	entity_3, 101	3
105	entity_3, 102	3
106	entity_3, 103	3
107	entity_3, 104	3
108	entity_3, 105	3
109	entity_3, 106	3
110	entity_3, 107	3
111	entity_3, 108	3
112	entity_3, 109	3
113	entity_3, 110	3
114	entity_3, 111	3
115	entity_3, 112	3
116	entity_3, 113	3
117	entity_3, 114	3
118	entity_3, 115	3
119	entity_3, 116	3
120	entity_3, 117	3
121	entity_3, 118	3
122	entity_3, 119	3
123	entity_3, 120	3
124	entity_3, 121	3
125	entity_3, 122	3
126	entity_3, 123	3
127	entity_3, 124	3
128	entity_3, 125	3
129	entity_3, 126	3
130	entity_3, 127	3
131	entity_3, 128	3
132	entity_3, 129	3
133	entity_3, 130	3
134	entity_3, 131	3
135	entity_3, 132	3
136	entity_3, 133	3
137	entity_3, 134	3
138	entity_3, 135	3
139	entity_3, 136	3
140	entity_3, 137	3
141	entity_3, 138	3
142	entity_3, 139	3
143	entity_3, 140	3
144	entity_3, 141	3
145	entity_3, 142	3
146	entity_3, 143	3
147	entity_3, 144	3
148	entity_3, 145	3
149	entity_3, 146	3
150	entity_3, 147	3
151	entity_3, 148	3
152	entity_3, 149	3
153	entity_3, 150	3
154	entity_3, 151	3
155	entity_3, 152	3
156	entity_3, 153	3
157	entity_3, 154	3
158	entity_3, 155	3
159	entity_3, 156	3
160	entity_3, 157	3
161	entity_3, 158	3
162	entity_3, 159	3
163	entity_3, 160	3
164	entity_3, 161	3
165	entity_3, 162	3
166	entity_3, 163	3
167	entity_3, 164	3
168	entity_3, 165	3
169	entity_3, 166	3
170	entity_3, 167	3
171	entity_3, 168	3
172	entity_3, 169	3
173	entity_3, 170	3
174	entity_3, 171	3
175	entity_3, 172	3
176	entity_3, 173	3
177	entity_3, 174	3
178	entity_3, 175	3
179	entity_3, 176	3
180	entity_3, 177	3
181	entity_3, 178	3
182	entity_3, 179	3
183	entity_3, 180	3
184	entity_3, 181	3
185	entity_3, 182	3
186	entity_3, 183	3
187	entity_3, 184	3
188	entity_3, 185	3
189	entity_3, 186	3
190	entity_3, 187	3
191	entity_3, 188	3
192	entity_3, 189	3
193	entity_3, 190	3
194	entity_3, 191	3
195	entity_3, 192	3
196	entity_3, 193	3
197	entity_3, 194	3
198	entity_3, 195	3
199	entity_3, 196	3
200	entity_3, 197	3
201	entity_3, 198	3
202	entity_3, 199	3
203	entity_3, 200	3
204	entity_3, 201	3
205	entity_3, 202	3
206	entity_3, 203	3
207	entity_3, 204	3
208	entity_3, 205	3
209	entity_3, 206	3
210	entity_3, 207	3
211	entity_3, 208	3
212	entity_3, 209	3
213	entity_3, 210	3
214	entity_3, 211	3
215	entity_3, 212	3
216	entity_3, 213	3
217	entity_3, 214	3
218	entity_3, 215	3
219	entity_3, 216	3
220	entity_3, 217	3
221	entity_3, 218	3
222	entity_4	4
223	entity_5	5

Entities:

Entity 1, entity_1 196 residues - 23131.346 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, entity_2, 1 211 residues - 24912.156 Da.

1

SER

THR

PHE

SER

LYS

LEU

ARG

GLU

GLN

LEU

2

GLY

PRO

VAL

THR

GLN

GLU

PHE

TRP

ASP

ASN

3

LEU

GLU

LYS

GLU

THR

GLU

GLY

LEU

ARG

GLN

4

GLU

MET

SER

LYS

ASP

LEU

GLU

VAL

LYS

5

ALA

LYS

VAL

GLN

PRO

TYR

LEU

ASP

PHE

6

GLN

LYS

TRP

GLN

GLU

MET

GLU

LEU

7

TYR

ARG

GLN

LYS

VAL

GLU

PRO

TYR

LEU

ASP

8

ASP

PHE

GLN

LYS

TRP

GLN

GLU

MET

9

GLU

LEU

TYR

ARG

GLN

LYS

VAL

GLU

PRO

LEU

10

ARG

ALA

GLU

LEU

GLN

GLU

GLY

ALA

ARG

GLN

11

LYS

LEU

HIS

GLU

LEU

GLN

GLU

LYS

LEU

SER

12

PRO

LEU

GLY

GLU

MET

ARG

ASP

ARG

ALA

13

ARG

ALA

HIS

VAL

ASP

ALA

LEU

ARG

THR

HIS

14

LEU

ALA

PRO

TYR

SER

ASP

GLU

LEU

ARG

GLN

15

ARG

LEU

ALA

ARG

LEU

GLU

ALA

LEU

LYS

16

GLU

ASN

GLY

ALA

ARG

LEU

ALA

GLU

TYR

17

HIS

ALA

LYS

ALA

THR

GLU

HIS

LEU

SER

THR

18

LEU

SER

GLU

LYS

ALA

LYS

PRO

ALA

LEU

GLU

19

ASP

LEU

ARG

GLN

GLY

LEU

PRO

VAL

LEU

20

GLU

SER

PHE

LYS

VAL

SER

PHE

LEU

SER

ALA

21

LEU

GLU

TYR

THR

LYS

LEU

ASN

THR

22

GLN

Entity 3, entity_3, 1 - C36 H73 N O8 P - 678.940 Da.

1

PX4

Entity 4, entity_4 - Na - 22.990 Da.

1

NA

Entity 5, entity_5 - Cl - 35.453 Da.

1

CL

Samples:

sample_1: Tri-HCl 20 mM; NaCl 300 mM; sodium azide 0.02%; H2O 93%; D2O, [U-100% 2H], 7%; MT1-MMP hemopexin-like domain, [U-2H; U-13C; U-15N], 90 ± 10 uM; MSP1D1 180 ± 10 uM; PX4 14.4 ± 10 mM

sample_conditions_1: ionic strength: 300 mM; pH: 7.2; pressure: 1 atm; temperature: 303 K

Experiments:

Name	Sample	Sample state	Sample conditions
HMQC	sample_1	isotropic	sample_conditions_1
TROSY	sample_1	isotropic	sample_conditions_1
CPMG-HMQC	sample_1	isotropic	sample_conditions_1

Software:

TOPSPIN v3.2, Bruker Biospin - processing

Analysis v2.4, CCPN - data analysis

HADDOCK vHADDOCK2.1, Bonvin - structure calculation

NAMD v2.1, Theoretical and Computational Biophysics Group in UIUC - refinement, structure calculation

NMR spectrometers:

Bruker AvanceIII 800 MHz

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