2MLS | pdb_00002mls

Membrane Bilayer complex with Matrix Metalloproteinase-12 at its Beta-face

Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 14 
  • Conformers Submitted: 14 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history. 

Literature

Ambidextrous binding of cell and membrane bilayers by soluble matrix metalloproteinase-12.

Koppisetti, R.K., Fulcher, Y.G., Jurkevich, A., Prior, S.H., Xu, J., Lenoir, M., Overduin, M., Van Doren, S.R.

(2014) Nat Commun 5: 5552-5552

  • DOI: https://doi.org/10.1038/ncomms6552
  • Primary Citation Related Structures: 
    2MLR, 2MLS

  • PubMed Abstract: 

    Matrix metalloproteinases (MMPs) regulate tissue remodelling, inflammation and disease progression. Some soluble MMPs are inexplicably active near cell surfaces. Here we demonstrate the binding of MMP-12 directly to bilayers and cellular membranes using paramagnetic NMR and fluorescence. Opposing sides of the catalytic domain engage spin-labelled membrane mimics. Loops project from the β-sheet interface to contact the phospholipid bilayer with basic and hydrophobic residues. The distal membrane interface comprises loops on the other side of the catalytic cleft. Both interfaces mediate MMP-12 association with vesicles and cell membranes. MMP-12 binds plasma membranes and is internalized to hydrophobic perinuclear features, the nuclear membrane and inside the nucleus within minutes. While binding of TIMP-2 to MMP-12 hinders membrane interactions beside the active site, TIMP-2-inhibited MMP-12 binds vesicles and cells, suggesting compensatory rotation of its membrane approaches. MMP-12 association with diverse cell membranes may target its activities to modulate innate immune responses and inflammation.

    • Organizational Affiliation: 
    • Department of Biochemistry, University of Missouri, 117 Schweitzer Hall, Columbia, Missouri 65211, USA.

Macromolecule Content 

  • Total Structure Weight: 103.3 kDa 
  • Atom Count: 7,042 
  • Modeled Residue Count: 164 
  • Deposited Residue Count: 164 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Macrophage metalloelastase164Homo sapiensMutation(s): 1 
Gene Names: MMP12, HME
EC: 3.4.24.65
UniProt & NIH Common Fund Data Resources
Find proteins for P39900 (Homo sapiens)
Explore P39900 
Go to UniProtKB:  P39900
PHAROS:  P39900
GTEx:  ENSG00000262406 
Entity Groups
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UniProt GroupP39900
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PX4

Query on PX4


Download:Ideal Coordinates CCD File
AA [auth A]
AB [auth A]
AC [auth A]
AD [auth A]
AE [auth A]
AA [auth A],
AB [auth A],
AC [auth A],
AD [auth A],
AE [auth A],
BA [auth A],
BB [auth A],
BC [auth A],
BD [auth A],
CA [auth A],
CB [auth A],
CC [auth A],
CD [auth A],
DA [auth A],
DB [auth A],
DC [auth A],
DD [auth A],
EA [auth A],
EB [auth A],
EC [auth A],
ED [auth A],
FA [auth A],
FB [auth A],
FC [auth A],
FD [auth A],
G [auth A],
GA [auth A],
GB [auth A],
GC [auth A],
GD [auth A],
H [auth A],
HA [auth A],
HB [auth A],
HC [auth A],
HD [auth A],
I [auth A],
IA [auth A],
IB [auth A],
IC [auth A],
ID [auth A],
J [auth A],
JA [auth A],
JB [auth A],
JC [auth A],
JD [auth A],
K [auth A],
KA [auth A],
KB [auth A],
KC [auth A],
KD [auth A],
L [auth A],
LA [auth A],
LB [auth A],
LC [auth A],
LD [auth A],
M [auth A],
MA [auth A],
MB [auth A],
MC [auth A],
MD [auth A],
N [auth A],
NA [auth A],
NB [auth A],
NC [auth A],
ND [auth A],
O [auth A],
OA [auth A],
OB [auth A],
OC [auth A],
OD [auth A],
P [auth A],
PA [auth A],
PB [auth A],
PC [auth A],
PD [auth A],
Q [auth A],
QA [auth A],
QB [auth A],
QC [auth A],
QD [auth A],
R [auth A],
RA [auth A],
RB [auth A],
RC [auth A],
RD [auth A],
S [auth A],
SA [auth A],
SB [auth A],
SC [auth A],
SD [auth A],
T [auth A],
TA [auth A],
TB [auth A],
TC [auth A],
TD [auth A],
U [auth A],
UA [auth A],
UB [auth A],
UC [auth A],
UD [auth A],
V [auth A],
VA [auth A],
VB [auth A],
VC [auth A],
VD [auth A],
W [auth A],
WA [auth A],
WB [auth A],
WC [auth A],
WD [auth A],
X [auth A],
XA [auth A],
XB [auth A],
XC [auth A],
XD [auth A],
Y [auth A],
YA [auth A],
YB [auth A],
YC [auth A],
YD [auth A],
Z [auth A],
ZA [auth A],
ZB [auth A],
ZC [auth A],
ZD [auth A]
1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C36 H73 N O8 P
CITHEXJVPOWHKC-UUWRZZSWSA-O
ZN

Query on ZN


Download:Ideal Coordinates CCD File
B [auth A],
C [auth A]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA

Query on CA


Download:Ideal Coordinates CCD File
D [auth A],
E [auth A],
F [auth A]		CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 14 
  • Conformers Submitted: 14 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

View Full Validation Report



View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-12-03
    Type: Initial release
  • Version 1.1: 2014-12-10
    Changes: Database references
  • Version 1.2: 2024-05-01
    Changes: Data collection, Database references, Derived calculations