MEMBRANE PROTEINS OF KNOWN STRUCTURE BY NMR

The table below provides information about integral membrane proteins whose structures have been determined by solution-state (blue background), oriented solid-state NMR (grey background) or magic-angle spinning solid-state NMR (pink background), to a resolution sufficient to have resulted in a file deposited at the RCSB Protein Data Bank.

When possible, the table below also provides chemical shift assignments deposited at the Biological Magnetic Resonance Data Bank, protein size and oligomeric state, production source, reconstitution medium and primary reference.

Last database update : 23 february 2010

Unique proteins in database : 34

Number of coordinate files in database : 46

For more membrane protein structures : Steve White's Website

For more protein structures: determined by solid state NMR


Protein	PDB Entry	BMRB Entry	Oligomer Size/State	Production Source	Reconstitution Medium	PubMed Reference
TRANSMEMBRANE PROTEINS: BETA-BARREL
OmpA	1G90		19 kDa/1	Escherichia coli	DPC	Arora et al. (2001)
OmpA with four shortened loops Also called beta-barrel platform (BBP)	2JMM	15045	16 kDa/1	Escherichia coli	DHPC	Johansson et al. (2007)
Kp OmpA	2K0L	15651	22 kDa/1	Escherichia coli	DHPC	Renault et al. (2009)
PagP	1MM4 1MM5	5557 6234	20 kDa/1	Escherichia coli	DPC and OG	Hwang et al. (2002)
OmpX Without H-bond constraints: 1Q9G	1Q9F	4936 15201	16 kDa/1	Escherichia coli	DPC	Fernández et al. (2004)
OmpG	2JQY	15426	28 kDa/1	Escherichia coli	DPC	Liang & Tamm (2007)
human VDAC-1	2K4T 2JK4		32 kDa/1	Escherichia coli	LDAO	Hiller et al. (2008) and Bayrhuber et al. (2008)

TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Gramicidin	1MAG		4 kDa/2	synthetic	lipids	Ketchem et al. (1993)
human Glycophorin A transmembrane domain	1AFO		4 kDa/2	Escherichia coli	DPC	MacKenzie et al. (1997)
AchR M2 channel	1CEK		3 kDa/1	Escherichia coli	lipids	Opella et al. (1999)
a-factor receptor M6	1PJD		2 kDa/1	synthetic	lipids	Valentine et al. (2001)
Influenza M2 channel residues 22-46	1NYJ		11 kDa/4	synthetic	lipids	Wang et al. (2001)
Influenza M2 channel residues 22-46 with amantadine	2H95		8 kDa/4	synthetic	lipids	Hu et al. (2007)
Influenza M2 proton channel residues 18-60 with rimantadine inhibitor	2RLF		20 kDa/4	Escherichia coli	DHPC	Schnell & Chou. (2008)
Influenza M2 channel residues 22-46 with amantadine	2KAD 2KQT	16020 16612	11 kDa/4	synthetic	lipids	Cady et al. (2009) and Cady et al. (2010)
fd coat protein	1MZT	5877	5 kDa/1	Enterobacteria phage fd	lipids	Marassi and Opella (2003)
HIV Vpu channel	1PJE		4 kDa/1	Escherichia coli	lipids	Park et al. (2003)
Mistic membrane-integrating protein Note: This is not a constitutive membrane protein. It is included here because of general interest	1YGM		13 kDa/1	Escherichia coli	LDAO	Roosild et al. (2005)
Mer F	1WAZ		6 kDa/1	Escherichia coli	SDS	Howell et al. (2005)
KcsA with Charybdotoxin	2A9H	6728 (methyls)	71 kDa/4	Escherichia coli	DPC	Yu et al. (2005)
human Phospholamban See also 1FJK and 1FJP.	1ZLL	4907	30 kDa/5	Escherichia coli	DPC	Oxenoid and Chou (2005)
human Phospholamban	2KB7		30 kDa/5	Escherichia coli	DPC and lipids	Traaseth et al. (2009)
Zetazeta transmembrane domain	2HAC		4 kDa/2	Escherichia coli	DPC/SDS:5/1	Call et al. (2006)
Bnip3 transmembrane domain See also 2KA1 and 2KA2	2J5D	7288 16012	10 kDa/2	Escherichia coli	bicelles	Bocharov et al. (2007)
human FXYD1 (Na,K-ATPase Regulatory Protein)	2JO1		8 kDa/1	Escherichia coli	SDS	Teriete et al. (2007)
human FXYD4 (CHIF)	2JP3		7 kDa/1	Escherichia coli	SDS	Franzin et al. (2007)
ErbB2 transmembrane segment	2JWA	15231	9 kDa/2	Escherichia coli	bicelles	Bocharov et al. (2008)
EphA1 transmembrane domain at pH 4.3 and 6.3	2K1K 2K1L	15728	8 kDa/2	Escherichia coli	bicelles	Bocharov et al. (2008)
human KCNE1	2K21		16 kDa/1	Escherichia coli	LMPG	Kang et al. (2008)
DsbB and DsbB-ubiquinone complex	2K73 2K74		18 kDa/1	Escherichia coli	DPC	Zhou et al. (2008)
Integrin alphaIIb-beta3	2K9J		9 kDa/2	Escherichia coli	bicelles	Lau et al. (2009)
i3 intracellular loop of the vasopressin V2 receptor	2JX4		6 kDa/1	synthetic	DPC	Bellot et al. (2009)
G-protein-coupled receptor double transmembrane fragment	2K9P		9 kDa/1	Escherichia coli	LPPG	Neumoin et al. (2009)
*Cytosolic domain of C. elegans* mechanosensory ion channel subunit MEC-4** The structure is not transmembrane, just membrane associated.	2K2B	15699	13 kDa/1	Escherichia coli	Zwittergent	Everett et al. (2009)
Diacylglycerol Kinase (DAGK)	2KDC	15019 7340	43 kDa/3	Escherichia coli	DPC	Van Horn et al. (2009)
Rv1761c from Mycobacterium tuberculosis	2K3M	15774	17 kDa/1	Escherichia coli	DPC	Page et al. (2009)
human alpha-defensin HNP-1	2KHT	16254	3 kDa/1	Escherichia coli	microcrystalised outside the lipid membrane	Zhang et al. (2009)

References

Arora A, Abildgaard F, Bushweller JH, & Tamm LK (2001). Structure of outer membrane protein A transmembrane domain by NMR spectroscopy. Nature Structural Biol. 8:334-338.

Bayrhuber, M., Meins, T., Habeck, M., Becker, S., Giller, K., Villinger, S., Vonrhein, C., Griesinger, C., Zweckstetter, M., Zeth, K. (2008) Structure of the Human Voltage-Dependent Anion Channel. Proc.Natl.Acad.Sci.USA 105:15370-15375

Bellot, G., Granier, S., Bourguet, W., Seyer, R., Rahmeh, R., Mouillac, B., Pascal, R., Mendre, C., Demene, H. (2009) Structure of the third intracellular loop of the vasopressin V2 receptor and conformational changes upon binding to gC1qR J. Mol. Biol. 388:491–507

Bocharov, E.V., Pustovalova, Y.E., Pavlov, K.V., Volynsky, P.E., Goncharuk, M.V., Ermolyuk, Y.S., Karpunin, D.V., Schulga, A.A., Kirpichnikov, M.P., Efremov, R.G., Maslennikov, I.V., Arseniev, A.S. (2007) Unique Dimeric Structure of Bnip3 Transmembrane Domain Suggests Membrane Permeabilization as a Cell Death Trigger. J Biol Chem. 282:16256-16266

Bocharov, E.V., Mineev, K.S., Volynsky, P.E., Ermolyuk, Y.S., Tkach, E.N., Sobol, A.G., Chupin, V.V., Kirpichnikov, M.P., Efremov, R.G., Arseniev, A.S. (2008) Spatial Structure of the Dimeric Transmembrane Domain of the Growth Factor Receptor ErbB2 Presumably Corresponding to the Receptor Active State J.Biol.Chem. 283:6950-6956

Bocharov, E.V., Mayzel, M.L., Volynsky, P.E., Goncharuk, M.V., Ermolyuk, Y.S., Schulga, A.A., Artemenko, E.O., Efremov, R.G., Arseniev, A.S. (2008) Spatial structure and pH-dependent conformational diversity of dimeric transmembrane domain of the receptor tyrosine kinase EphA1. J.Biol.Chem. 283:29385-29395

Cady, S.D., Mishanina, T.V., Hong, M. (2009) Structure of amantadine-bound M2 transmembrane peptide of influenza A in lipid bilayers from magic-angle-spinning solid-state NMR: the role of Ser31 in amantadine binding J. Mol. Biol. 385:1127-1141

Cady, S.D., Schmidt-Rohr K., Wang J., Soto C.S., Degrado W.F., Hong, M. (2010) Structure of the amantadine binding site of influenza M2 proton channels in lipid bilayers Nature 463:689-692

Call, M.E., Schnell, J.R., Xu, C., Lutz, R.A., Chou, J.J., Wucherpfennig, K.W. (2006) The structure of the zetazeta transmembrane dimer reveals features essential for its assembly with the T cell receptor. Cell 127:355-368

Fernández C, Hilty C, Wider G, Guntert P, & Wuthrich K (2004). NMR structure of the integral membrane protein OmpX. J Mol Biol. 336:1211-1221.

Franzin, C.M., Teriete, P., Marassi, F.M. (2007) Structural similarity of a membrane protein in micelles and membranes J.Am.Chem.Soc. 129:8078-8079

Hiller, S., Garces, R.G., Malia, T.J., Orekhov, V.Y., Colombini, M., Wagner, G. (2008) Solution structure of the integral human membrane protein VDAC-1 in detergent micelles. Science 321:1206-1210

Howell, S.C., Mesleh, M.F., Opella, S.J. (2005) NMR Structure Determination of a Membrane Protein with Two Transmembrane Helices in Micelles: Merf of the Bacterial Mercury Detoxification System Biochemistry 44:5196-5206

Hu, J., Asbury, T., Achuthan, S., Li, C., Bertram, R., Quine, J.R., Fu, R., Cross, T.A. (2007) Backbone structure of the amantadine-blocked trans-membrane domain m2 proton channel from influenza a virus Biophys. J. 92:4335-4343

Hwang PM, Choy WY, Lo EI, Chen L, Forman-Kay JD, Raetz CR, Privé GG, Bishop RE & Kay LE (2002). Solution structure and dynamics of the outer membrane enzyme PagP by NMR. Proc Natl Acad Sci USA 99:13560-13565.

Johansson MU, Alioth S, Hu K, Walser R, Koebnik R, & Pervushin K (2007). A minimal transmembrane β-barrel platform protein studied by nuclear magnetic resonance. Biochemistry 46:1128-1140.

Ketchem, R.R., W. Hu, and T.A. Cross (1993) High-resolution conformation of gramicidin A in a lipid bilayer by solid-state NMR. Science 261:1457-1460

Lau, T.L., Kim, C., Ginsberg, M.H., Ulmer, T.S. (2009) The structure of the integrin alphaIIbbeta3 transmembrane complex explains integrin transmembrane signalling. EMBO J. 28:1351-1361

Liang B & Tamm LK (2007). Structure of outer membrane protein G by solution NMR Spectroscopy Proc Natl Acad Sci USA 104:16140-16145

MacKenzie, K.R., Prestegard, J.H., Engelman, D.M. (1997) A transmembrane helix dimer: structure and implications. Science 276:131-133

Marassi, FM, & Opella, SJ (2003) Simultaneous assignment and structure determination of a membrane protein from NMR orientational restraints. Protein Sci. 12:403-411

Neumoin, A., Cohen, L.S., Arshava, B., Tantry, S., Becker, J.M., Zerbe, O., Naider, F. (2009) Structure of a double transmembrane fragment of a G-protein-coupled receptor in micelles Biophys. J. 96:3187-3196

Opella, S.J., F.M. Marassi, J.J. Gesell, A.P. Valente, Y. Kim, M. Oblatt-Montal, and M. Montal (1999) Structures of the M2 channel-lining segments from nicotinic acetylcholine and NMDA receptors by NMR spectroscopy. Nat. Struct. Biol. 6:374-379

Oxenoid K & Chou JJ (2005). The structure of phospholamban pentamer reveals a channel-like architecture in membranes Proc Natl Acad Sci USA 102:10870-10875

Page, R.C., Lee, S., Moore, J.D., Opella, S.J., Cross, T.A. (2009) Backbone structure of a small helical integral membrane protein: A unique structural characterization Protein Sci 18:134-146

Park, S.H., A.A. Mrse, A.A. Nevzorov, M.F. Mesleh, M. Oblatt-Montal, M. Montal, and S.J. Opella (2003) Three-dimensional structure of the channel-forming trans-membrane domain of virus protein "u" (Vpu) from HIV-1. J. Mol. Biol. 333:409-424

Renault, M., Saurel, O., Czaplicki, J., Demange, P., Gervais, V., Lohr, F., Reat, V., Piotto, M., Milon, A. (2009) Solution state NMR structure and dynamics of KpOmpA, a 210 residue transmembrane domain possessing a high potential for immunological applications. J. Mol. Biol. 385:117-130

Roosild TP, Greenwald J, Vega M, Castronovo S, Riek R, & Choe S (2005). NMR structure of Mistic, a membrane-integrating protein for membrane protein expression. Science 307:1317-1321

Schnell JR & Chou JJ (2008). Structure and mechanism of the M2 proton channel of influenza A virus. Nature 451:591-595

Teriete P, Franzin CM, Choi J, & Marassi FM (2007). Structure of the Na,K-ATPase regulatory protein FXYD1 in micelles. Biochemistry 46:6774-6783

Traaseth, N.J., Shi, L., Verardi, R., Mullen, D.G., Barany, G., Veglia, G. (2009) Structure and topology of monomeric phospholamban in lipid membranes determined by a hybrid solution and solid-state NMR approach. Proc. Natl. Acad. Sci.USA 106:10165-10170

Valentine, K.G., S.F. Liu, F.M. Marassi, G. Veglia, S.J. Opella, F.X. Ding, S.H. Wang, B. Arshava, J.M. Becker, and F. Naider (2001) Structure and topology of a peptide segment of the 6th transmembrane domain of the Saccharomyces cerevisae alpha-factor receptor in phospholipid bilayers. Biopolymers 59:243-256

Van Horn, W.D., Kim, H.J., Ellis, C.D., Hadziselimovic, A., Sulistijo, E.S., Karra, M.D., Tian, C., Sonnichsen, F.D., Sanders, C.R. (2009) Solution nuclear magnetic resonance structure of membrane-integral diacylglycerol kinase. Science 324:1726-1729

Wang, J., S. Kim, F. Kovacs, and T.A. Cross (2001) Structure of the transmembrane region of the M2 protein H(+) channel. Protein Sci 10:2241-2250

Yu, L., Sun, C., Song, D., Shen, J., Xu, N., Gunasekera, A., Hajduk, P.J., Olejniczak, E.T. (2005) Nuclear magnetic resonance structural studies of a potassium channel-charybdotoxin complex. Biochemistry 44:15834-15841

Zhang Y., Doherty T., Li J., Lu W., Barinka C., Lubkowski J., Hong M. (2010) Resonance Assignment and Three-Dimensional Structure Determination of a Human a-Defensin, HNP-1, by solid-state NMR J. Mol. Biol.

Zhou, Y., Cierpicki, T., Flores Jimenez, R.H., Lukasik, S.M., Ellena, J.F., Cafiso, D.S., Kadokura, H., Beckwith, J., Bushweller, J.H. (2008) NMR Solution Structure of the Integral Membrane Enzyme DsbB: Functional Insights into DsbB-Catalyzed Disulfide Bond Formation. Mol.Cell 31:896-908

MEMBRANE PROTEINS OF KNOWN 3D STRUCTURE

DETERMINED BY NMR

References