 |
PDBsum entry 1zll
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Membrane protein/signaling protein
|
PDB id
|
|
|
|
1zll
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
|
|
|
|
|
|
| |
|
DOI no:
|
Proc Natl Acad Sci U S A
102:10870-10875
(2005)
|
|
PubMed id:
|
|
|
|
|
|
| |
|
The structure of phospholamban pentamer reveals a channel-like architecture in membranes.
|
|
K.Oxenoid,
J.J.Chou.
|
|
|
|
|
| |
ABSTRACT
|
|
|
|
| |
|
|
Contraction and relaxation of heart muscle cells is regulated by cycling of
calcium between cytoplasm and sarcoplasmic reticulum. Human phospholamban (PLN),
expressed in the sarcoplasmic reticulum membrane as a 30-kDa homopentamer,
controls cellular calcium levels by a mechanism that depends on its
phosphorylation. Since PLN was discovered approximately 30 years ago, extensive
studies have aimed to explain how it influences calcium pumps and to determine
whether it acts as an ion channel. We have determined by solution NMR methods
the atomic resolution structure of an unphosphorylated PLN pentamer in
dodecylphosphocholine micelles. The unusual bellflower-like assembly is held
together by leucine/isoleucine zipper motifs along the membrane-spanning
helices. The structure reveals a channel-forming architecture that could allow
passage of small ions. The central pore gradually widens toward the cytoplasmic
end as the transmembrane helices twist around each other and bend outward. The
dynamic N-terminal amphipathic helices point away from the membrane, perhaps
facilitating recognition and inhibition of the calcium pump.
|
|
|
|
|
|
| |
Selected figure(s)
|
|
|
|
| |
|
|
|
|
|
|
Figure 4.
Fig. 4. A model for initial recognition between the PLN
pentamer and SERCA. The backbones of PLN and SERCA are colored
in green and gray, respectively. PLN residues important for
SERCA interaction as indicated by mutagenesis studies are
colored in red, including E2, V4, L7, R9, I12, and R14 of the AP
helix (34) and L31, N34, F35, I38, L42, I48, V49, and L52 of the
TM helix (3). The model of SERCA was derived from that for the
E2 form of rabbit SERCA1a (PDB ID code 1IWO [PDB]
); residues from the proposed groove in the extramembrane domain
where PLN AP helix bind are shown in red, including K400, D557,
V607, and N645.
|
|
Figure 5.
Fig. 5. The pore surface calculated by using the program
HOLE (47) and displayed by MOLSCRIPT (48) and RASTER3D (49). The
region of the channel colored in green is only wide enough to
allow passing of one water molecule, whereas the blue portion
can accommodate two or more water molecules.
|
|
|
|
| |
Figures were
selected
by an automated process.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
 |
 |
|
Literature references that cite this PDB file's key reference
|
|
|
| |
PubMed id
|
|
Reference
|
|
|
|
|
|
H.Chen,
F.Ji,
V.Olman,
C.K.Mobley,
Y.Liu,
Y.Zhou,
J.H.Bushweller,
J.H.Prestegard,
and
Y.Xu
(2011).
Optimal Mutation Sites for PRE Data Collection and Membrane Protein Structure Prediction.
|
| |
Structure,
19,
484-495.
|
|
|
|
|
|
|
J.Zhang,
J.Sun,
and
C.Wu
(2011).
Optimal atomic-resolution structures of prion AGAAAAGA amyloid fibrils.
|
| |
J Theor Biol,
279,
17-28.
|
|
|
|
|
|
|
T.A.Cross,
M.Sharma,
M.Yi,
and
H.X.Zhou
(2011).
Influence of solubilizing environments on membrane protein structures.
|
| |
Trends Biochem Sci,
36,
117-125.
|
|
|
|
|
|
|
X.Xiao,
P.Wang,
and
K.C.Chou
(2011).
GPCR-2L: predicting G protein-coupled receptors and their types by hybridizing two different modes of pseudo amino acid compositions.
|
| |
Mol Biosyst,
7,
911-919.
|
|
|
|
|
|
|
A.Gautier,
H.R.Mott,
M.J.Bostock,
J.P.Kirkpatrick,
and
D.Nietlispach
(2010).
Structure determination of the seven-helix transmembrane receptor sensory rhodopsin II by solution NMR spectroscopy.
|
| |
Nat Struct Mol Biol,
17,
768-774.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
B.Apostolovic,
M.Danial,
and
H.A.Klok
(2010).
Coiled coils: attractive protein folding motifs for the fabrication of self-assembled, responsive and bioactive materials.
|
| |
Chem Soc Rev,
39,
3541-3575.
|
|
|
|
|
|
|
P.Palladino,
F.Rossi,
and
R.Ragone
(2010).
Effective critical micellar concentration of a zwitterionic detergent: a fluorimetric study on n-dodecyl phosphocholine.
|
| |
J Fluoresc,
20,
191-196.
|
|
|
|
|
|
|
S.Chu,
A.T.Coey,
and
G.A.Lorigan
(2010).
Solid-state (2)H and (15)N NMR studies of side-chain and backbone dynamics of phospholamban in lipid bilayers: investigation of the N27A mutation.
|
| |
Biochim Biophys Acta,
1798,
210-215.
|
|
|
|
|
|
|
S.Chu,
S.Abu-Baker,
J.Lu,
and
G.A.Lorigan
(2010).
(15)N Solid-state NMR spectroscopic studies on phospholamban at its phosphorylated form at ser-16 in aligned phospholipid bilayers.
|
| |
Biochim Biophys Acta,
1798,
312-317.
|
|
|
|
|
|
|
T.Huang,
X.H.Shi,
P.Wang,
Z.He,
K.Y.Feng,
L.Hu,
X.Kong,
Y.X.Li,
Y.D.Cai,
and
K.C.Chou
(2010).
Analysis and prediction of the metabolic stability of proteins based on their sequential features, subcellular locations and interaction networks.
|
| |
PLoS One,
5,
e10972.
|
|
|
|
|
|
|
T.Kolev,
M.Spiteller,
and
B.Koleva
(2010).
Spectroscopic and structural elucidation of amino acid derivatives and small peptides: experimental and theoretical tools.
|
| |
Amino Acids,
38,
45-50.
|
|
|
|
|
|
|
Z.He,
J.Zhang,
X.H.Shi,
L.L.Hu,
X.Kong,
Y.D.Cai,
and
K.C.Chou
(2010).
Predicting drug-target interaction networks based on functional groups and biological features.
|
| |
PLoS One,
5,
e9603.
|
|
|
|
|
|
|
B.R.Donald,
and
J.Martin
(2009).
Automated NMR Assignment and Protein Structure Determination using Sparse Dipolar Coupling Constraints.
|
| |
Prog Nucl Magn Reson Spectrosc,
55,
101-127.
|
|
|
|
|
|
|
C.Maffeo,
and
A.Aksimentiev
(2009).
Structure, dynamics, and ion conductance of the phospholamban pentamer.
|
| |
Biophys J,
96,
4853-4865.
|
|
|
|
|
|
|
H.J.Kim,
S.C.Howell,
W.D.Van Horn,
Y.H.Jeon,
and
C.R.Sanders
(2009).
Recent Advances in the Application of Solution NMR Spectroscopy to Multi-Span Integral Membrane Proteins.
|
| |
Prog Nucl Magn Reson Spectrosc,
55,
335-360.
|
|
|
|
|
|
|
J.F.Ellena,
B.Liang,
M.Wiktor,
A.Stein,
D.S.Cafiso,
R.Jahn,
and
L.K.Tamm
(2009).
Dynamic structure of lipid-bound synaptobrevin suggests a nucleation-propagation mechanism for trans-SNARE complex formation.
|
| |
Proc Natl Acad Sci U S A,
106,
20306-20311.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
J.M.Kielec,
K.G.Valentine,
C.R.Babu,
and
A.J.Wand
(2009).
Reverse micelles in integral membrane protein structural biology by solution NMR spectroscopy.
|
| |
Structure,
17,
345-351.
|
|
|
|
|
|
|
K.Chen,
Y.Jiang,
L.Du,
and
L.Kurgan
(2009).
Prediction of integral membrane protein type by collocated hydrophobic amino acid pairs.
|
| |
J Comput Chem,
30,
163-172.
|
|
|
|
|
|
|
L.Becucci,
A.Cembran,
C.B.Karim,
D.D.Thomas,
R.Guidelli,
J.Gao,
and
G.Veglia
(2009).
On the function of pentameric phospholamban: ion channel or storage form?
|
| |
Biophys J,
96,
L60-L62.
|
|
|
|
|
|
|
M.Freigassner,
H.Pichler,
and
A.Glieder
(2009).
wTuning microbial hosts for membrane protein production.
|
| |
Microb Cell Fact,
8,
69.
|
|
|
|
|
|
|
S.Raunser,
and
T.Walz
(2009).
Electron crystallography as a technique to study the structure on membrane proteins in a lipidic environment.
|
| |
Annu Rev Biophys,
38,
89.
|
|
|
|
|
|
|
T.Kim,
J.Lee,
and
W.Im
(2009).
Molecular dynamics studies on structure and dynamics of phospholamban monomer and pentamer in membranes.
|
| |
Proteins,
76,
86-98.
|
|
|
|
|
|
|
W.D.Van Horn,
H.J.Kim,
C.D.Ellis,
A.Hadziselimovic,
E.S.Sulistijo,
M.D.Karra,
C.Tian,
F.D.Sönnichsen,
and
C.R.Sanders
(2009).
Solution nuclear magnetic resonance structure of membrane-integral diacylglycerol kinase.
|
| |
Science,
324,
1726-1729.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
W.Z.Lin,
X.Xiao,
and
K.C.Chou
(2009).
GPCR-GIA: a web-server for identifying G-protein coupled receptors and their families with grey incidence analysis.
|
| |
Protein Eng Des Sel,
22,
699-705.
|
|
|
|
|
|
|
A.Rath,
and
C.M.Deber
(2008).
Surface recognition elements of membrane protein oligomerization.
|
| |
Proteins,
70,
786-793.
|
|
|
|
|
|
|
D.T.Moore,
B.W.Berger,
and
W.F.DeGrado
(2008).
Protein-protein interactions in the membrane: sequence, structural, and biological motifs.
|
| |
Structure,
16,
991.
|
|
|
|
|
|
|
E.M.Kelly,
Z.Hou,
J.Bossuyt,
D.M.Bers,
and
S.L.Robia
(2008).
Phospholamban oligomerization, quaternary structure, and sarco(endo)plasmic reticulum calcium ATPase binding measured by fluorescence resonance energy transfer in living cells.
|
| |
J Biol Chem,
283,
12202-12211.
|
|
|
|
|
|
|
J.R.Schnell,
and
J.J.Chou
(2008).
Structure and mechanism of the M2 proton channel of influenza A virus.
|
| |
Nature,
451,
591-595.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
N.J.Traaseth,
K.N.Ha,
R.Verardi,
L.Shi,
J.J.Buffy,
L.R.Masterson,
and
G.Veglia
(2008).
Structural and dynamic basis of phospholamban and sarcolipin inhibition of Ca(2+)-ATPase.
|
| |
Biochemistry,
47,
3.
|
|
|
|
|
|
|
N.J.Traaseth,
R.Verardi,
and
G.Veglia
(2008).
Asymmetric methyl group labeling as a probe of membrane protein homo-oligomers by NMR spectroscopy.
|
| |
J Am Chem Soc,
130,
2400-2401.
|
|
|
|
|
|
|
S.C.Shih,
I.Stoica,
and
N.K.Goto
(2008).
Investigation of the utility of selective methyl protonation for determination of membrane protein structures.
|
| |
J Biomol NMR,
42,
49-58.
|
|
|
|
|
|
|
S.J.Opella,
A.C.Zeri,
and
S.H.Park
(2008).
Structure, dynamics, and assembly of filamentous bacteriophages by nuclear magnetic resonance spectroscopy.
|
| |
Annu Rev Phys Chem,
59,
635-657.
|
|
|
|
|
|
|
S.W.Zhang,
W.Chen,
F.Yang,
and
Q.Pan
(2008).
Using Chou's pseudo amino acid composition to predict protein quaternary structure: a sequence-segmented PseAAC approach.
|
| |
Amino Acids,
35,
591-598.
|
|
|
|
|
|
|
T.Kikuchi
(2008).
Analysis of 3D structural differences in the IgG-binding domains based on the interresidue average-distance statistics.
|
| |
Amino Acids,
35,
541-549.
|
|
|
|
|
|
|
Z.Hou,
E.M.Kelly,
and
S.L.Robia
(2008).
Phosphomimetic mutations increase phospholamban oligomerization and alter the structure of its regulatory complex.
|
| |
J Biol Chem,
283,
28996-29003.
|
|
|
|
|
|
|
B.Liang,
and
L.K.Tamm
(2007).
Structure of outer membrane protein G by solution NMR spectroscopy.
|
| |
Proc Natl Acad Sci U S A,
104,
16140-16145.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
C.M.Franzin,
X.M.Gong,
K.Thai,
J.Yu,
and
F.M.Marassi
(2007).
NMR of membrane proteins in micelles and bilayers: the FXYD family proteins.
|
| |
Methods,
41,
398-408.
|
|
|
|
|
|
|
J.Hu,
H.Qin,
C.Li,
M.Sharma,
T.A.Cross,
and
F.P.Gao
(2007).
Structural biology of transmembrane domains: efficient production and characterization of transmembrane peptides by NMR.
|
| |
Protein Sci,
16,
2153-2165.
|
|
|
|
|
|
|
K.Oxenoid,
A.J.Rice,
and
J.J.Chou
(2007).
Comparing the structure and dynamics of phospholamban pentamer in its unphosphorylated and pseudo-phosphorylated states.
|
| |
Protein Sci,
16,
1977-1983.
|
|
|
|
|
|
|
L.Bu,
W.Im,
and
C.L.Brooks
(2007).
Membrane assembly of simple helix homo-oligomers studied via molecular dynamics simulations.
|
| |
Biophys J,
92,
854-863.
|
|
|
|
|
|
|
N.J.Traaseth,
R.Verardi,
K.D.Torgersen,
C.B.Karim,
D.D.Thomas,
and
G.Veglia
(2007).
Spectroscopic validation of the pentameric structure of phospholamban.
|
| |
Proc Natl Acad Sci U S A,
104,
14676-14681.
|
|
|
|
|
|
|
P.Teriete,
C.M.Franzin,
J.Choi,
and
F.M.Marassi
(2007).
Structure of the Na,K-ATPase regulatory protein FXYD1 in micelles.
|
| |
Biochemistry,
46,
6774-6783.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
S.Abu-Baker,
J.X.Lu,
S.Chu,
C.C.Brinn,
C.A.Makaroff,
and
G.A.Lorigan
(2007).
Side chain and backbone dynamics of phospholamban in phospholipid bilayers utilizing 2H and 15N solid-state NMR spectroscopy.
|
| |
Biochemistry,
46,
11695-11706.
|
|
|
|
|
|
|
S.Abu-Baker,
J.X.Lu,
S.Chu,
K.K.Shetty,
P.L.Gor'kov,
and
G.A.Lorigan
(2007).
The structural topology of wild-type phospholamban in oriented lipid bilayers using 15N solid-state NMR spectroscopy.
|
| |
Protein Sci,
16,
2345-2349.
|
|
|
|
|
|
|
S.F.Poget,
and
M.E.Girvin
(2007).
Solution NMR of membrane proteins in bilayer mimics: small is beautiful, but sometimes bigger is better.
|
| |
Biochim Biophys Acta,
1768,
3098-3106.
|
|
|
|
|
|
|
S.Lee,
S.B.Howell,
and
S.J.Opella
(2007).
NMR and mutagenesis of human copper transporter 1 (hCtr1) show that Cys-189 is required for correct folding and dimerization.
|
| |
Biochim Biophys Acta,
1768,
3127-3134.
|
|
|
|
|
|
|
S.M.Douglas,
J.J.Chou,
and
W.M.Shih
(2007).
DNA-nanotube-induced alignment of membrane proteins for NMR structure determination.
|
| |
Proc Natl Acad Sci U S A,
104,
6644-6648.
|
|
|
|
|
|
|
S.Pantano,
and
E.Carafoli
(2007).
The role of phosphorylation on the structure and dynamics of phospholamban: a model from molecular simulations.
|
| |
Proteins,
66,
930-940.
|
|
|
|
|
|
|
S.Potluri,
A.K.Yan,
B.R.Donald,
and
C.Bailey-Kellogg
(2007).
A complete algorithm to resolve ambiguity for intersubunit NOE assignment in structure determination of symmetric homo-oligomers.
|
| |
Protein Sci,
16,
69-81.
|
|
|
|
|
|
|
W.Liu,
J.Z.Fei,
T.Kawakami,
and
S.O.Smith
(2007).
Structural constraints on the transmembrane and juxtamembrane regions of the phospholamban pentamer in membrane bilayers: Gln29 and Leu52.
|
| |
Biochim Biophys Acta,
1768,
2971-2978.
|
|
|
|
|
|
|
C.R.Sanders,
and
F.Sönnichsen
(2006).
Solution NMR of membrane proteins: practice and challenges.
|
| |
Magn Reson Chem,
44,
S24-S40.
|
|
|
|
|
|
|
D.L.Stokes,
A.J.Pomfret,
W.J.Rice,
J.P.Glaves,
and
H.S.Young
(2006).
Interactions between Ca2+-ATPase and the pentameric form of phospholamban in two-dimensional co-crystals.
|
| |
Biophys J,
90,
4213-4223.
|
|
|
|
|
|
|
J.H.Chill,
J.M.Louis,
C.Miller,
and
A.Bax
(2006).
NMR study of the tetrameric KcsA potassium channel in detergent micelles.
|
| |
Protein Sci,
15,
684-698.
|
|
|
|
|
|
|
J.K.Rainey,
L.Fliegel,
and
B.D.Sykes
(2006).
Strategies for dealing with conformational sampling in structural calculations of flexible or kinked transmembrane peptides.
|
| |
Biochem Cell Biol,
84,
918-929.
|
|
|
|
|
|
|
L.Columbus,
J.Lipfert,
H.Klock,
I.Millett,
S.Doniach,
and
S.A.Lesley
(2006).
Expression, purification, and characterization of Thermotoga maritima membrane proteins for structure determination.
|
| |
Protein Sci,
15,
961-975.
|
|
|
|
|
|
|
M.E.Call,
J.R.Schnell,
C.Xu,
R.A.Lutz,
J.J.Chou,
and
K.W.Wucherpfennig
(2006).
The structure of the zetazeta transmembrane dimer reveals features essential for its assembly with the T cell receptor.
|
| |
Cell,
127,
355-368.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
Q.S.Du,
D.P.Li,
W.Z.He,
and
K.C.Chou
(2006).
Heuristic molecular lipophilicity potential (HMLP): lipophilicity and hydrophilicity of amino acid side chains.
|
| |
J Comput Chem,
27,
685-692.
|
|
|
|
|
|
|
R.C.Page,
J.D.Moore,
H.B.Nguyen,
M.Sharma,
R.Chase,
F.P.Gao,
C.K.Mobley,
C.R.Sanders,
L.Ma,
F.D.Sönnichsen,
S.Lee,
S.C.Howell,
S.J.Opella,
and
T.A.Cross
(2006).
Comprehensive evaluation of solution nuclear magnetic resonance spectroscopy sample preparation for helical integral membrane proteins.
|
| |
J Struct Funct Genomics,
7,
51-64.
|
|
|
|
|
|
|
R.M.Johnson,
A.Rath,
and
C.M.Deber
(2006).
The position of the Gly-xxx-Gly motif in transmembrane segments modulates dimer affinity.
|
| |
Biochem Cell Biol,
84,
1006-1012.
|
|
|
|
|
|
|
R.R.Wei,
J.R.Schnell,
N.A.Larsen,
P.K.Sorger,
J.J.Chou,
and
S.C.Harrison
(2006).
Structure of a central component of the yeast kinetochore: the Spc24p/Spc25p globular domain.
|
| |
Structure,
14,
1003-1009.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
S.Abu-Baker,
and
G.A.Lorigan
(2006).
Phospholamban and its phosphorylated form interact differently with lipid bilayers: a 31P, 2H, and 13C solid-state NMR spectroscopic study.
|
| |
Biochemistry,
45,
13312-13322.
|
|
|
|
|
|
|
S.Potluri,
A.K.Yan,
J.J.Chou,
B.R.Donald,
and
C.Bailey-Kellogg
(2006).
Structure determination of symmetric homo-oligomers by a complete search of symmetry configuration space, using NMR restraints and van der Waals packing.
|
| |
Proteins,
65,
203-219.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
S.W.Zhang,
Q.Pan,
H.C.Zhang,
Z.C.Shao,
and
J.Y.Shi
(2006).
Prediction of protein homo-oligomer types by pseudo amino acid composition: Approached with an improved feature extraction and Naive Bayes Feature Fusion.
|
| |
Amino Acids,
30,
461-468.
|
|
|
|
|
|
|
T.Cierpicki,
B.Liang,
L.K.Tamm,
and
J.H.Bushweller
(2006).
Increasing the accuracy of solution NMR structures of membrane proteins by application of residual dipolar couplings. High-resolution structure of outer membrane protein A.
|
| |
J Am Chem Soc,
128,
6947-6951.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
F.P.Gao,
and
T.A.Cross
(2005).
Recent developments in membrane-protein structural genomics.
|
| |
Genome Biol,
6,
244.
|
|
|
|
|
|
The most recent references are shown first.
Citation data come partly from CiteXplore and partly
from an automated harvesting procedure. Note that this is likely to be
only a partial list as not all journals are covered by
either method. However, we are continually building up the citation data
so more and more references will be included with time.
Where a reference describes a PDB structure, the PDB
code is
shown on the right.
|
|
Links
