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Title :   HIGH RESOLUTION CRYSTAL STRUCTURE OF TRANSMEMBRANE DOMAIN OF M2 PROTEIN

Authors :   A. L. Stouffer, R. Acharya, D. Salom

Date :   06 Dec 07 (Deposition) - 29 Jan 08 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.05

Chains :   Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: E,F,G,H  (1x)
Biol. Unit 2: A,B,C,D  (1x)

Keywords :   Proton Channel, M2Tm, Influenza A Virus M2 Protein, Viral Protein, Membrane Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. L. Stouffer, R. Acharya, D. Salom, A. S. Levine, L. Di Costanzo, C. S. Soto, V. Tereshko, V. Nanda, S. Stayrook, W. F. Degrado
Structural Basis For The Function And Inhibition Of An Influenza Virus Proton Channel
Nature V. 451 596 2008
PubMed-ID: 18235504 | Reference-DOI: 10.1038/NATURE06528

Molecule 1 - TRANSMEMBRANE DOMAIN OF MATRIX PROTEIN M2
	Chains	:	A, B, C, D, E, F, G, H
	Engineered	:	YES
	Fragment	:	RESIDUES 22-46
	Other Details	:	CHEMICALLY SYNTHESIZED; TRANSMEMBRANE DOMAIN OF M2 PROTEIN FROM INFLUENZA A VIRUS
	Synthetic	:	YES

		1	2	3	4	5	6	7	8
Asymmetric Unit	:	A	B	C	D	E	F	G	H
Biological Unit 1 (1x)	:					E	F	G	H
Biological Unit 2 (1x)	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (5, 30)

No.	Name	Count	Type	Full Name
1	BOG	6	Ligand/Ion	B-OCTYLGLUCOSIDE
2	CL	2	Ligand/Ion	CHLORIDE ION
3	MSE	8	Mod. Amino Acid	SELENOMETHIONINE
4	NH2	8	Mod. Amino Acid	AMINO GROUP
5	PEG	6	Ligand/Ion	DI(HYDROXYETHYL)ETHER

Biological Unit 1 (4, 13)

No.	Name	Count	Type	Full Name
1	BOG	3	Ligand/Ion	B-OCTYLGLUCOSIDE
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	MSE	4	Mod. Amino Acid	SELENOMETHIONINE
4	NH2	4	Mod. Amino Acid	AMINO GROUP
5	PEG	2	Ligand/Ion	DI(HYDROXYETHYL)ETHER

Biological Unit 2 (4, 15)

No.	Name	Count	Type	Full Name
1	BOG	3	Ligand/Ion	B-OCTYLGLUCOSIDE
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	MSE	4	Mod. Amino Acid	SELENOMETHIONINE
4	NH2	4	Mod. Amino Acid	AMINO GROUP
5	PEG	4	Ligand/Ion	DI(HYDROXYETHYL)ETHER

Asymmetric Unit (11, 11)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ALA A:30 , HIS A:37 , TRP A:41 , ALA D:30 , MSE D:33 , HIS D:37 , LEU D:40	BINDING SITE FOR RESIDUE BOG A 302
02	AC2	SOFTWARE	MSE B:33 , LEU B:36 , HIS B:37 , HIS C:37 , TRP C:41 , TRP D:41	BINDING SITE FOR RESIDUE BOG B 301
03	AC3	SOFTWARE	ARG A:45 , SER C:23 , PRO C:25 , VAL C:28	BINDING SITE FOR RESIDUE BOG C 303
04	AC4	SOFTWARE	GLY E:34 , HIS E:37 , TRP E:41 , PEG E:802 , HOH E:807 , ALA H:30 , GLY H:34 , HIS H:37	BINDING SITE FOR RESIDUE BOG E 702
05	AC5	SOFTWARE	HIS F:37 , HIS G:37 , TRP G:41	BINDING SITE FOR RESIDUE BOG G 701
06	AC6	SOFTWARE	SER G:22 , SER G:23 , PRO G:25 , VAL G:28	BINDING SITE FOR RESIDUE BOG G 703
07	AC7	SOFTWARE	SER A:23 , SER B:23 , SER C:23 , SER D:23	BINDING SITE FOR RESIDUE CL A 101
08	AC8	SOFTWARE	SER E:23 , SER F:23 , SER G:23 , SER H:23	BINDING SITE FOR RESIDUE CL E 501
09	AC9	SOFTWARE	MSE A:33	BINDING SITE FOR RESIDUE PEG A 401
10	BC1	SOFTWARE	LEU A:43 , NH2 A:47	BINDING SITE FOR RESIDUE PEG A 803
11	BC2	SOFTWARE	HIS E:37 , BOG E:702 , HIS F:37 , TRP F:41	BINDING SITE FOR RESIDUE PEG E 802

(no "SS Bond" information available for 3BKD)

(no "Cis Peptide Bond" information available for 3BKD)

(no "SAP(SNP)/Variant" information available for 3BKD)

(no "PROSITE Motif" information available for 3BKD)

(no "Exon" information available for 3BKD)

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:26
 aligned with Q9Q0P0_9INFA | Q9Q0P0 from UniProtKB/TrEMBL  Length:97

    Alignment length:26
                                    31        41      
          Q9Q0P0_9INFA   22 SSDPLVVAASIXGILHLILWILDRLF 47
               SCOP domains d3bkda1 A:22-46          - SCOP domains
               CATH domains -------------------------- CATH domains
               Pfam domains -------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------- SAPs(SNPs)
                    PROSITE -------------------------- PROSITE
                 Transcript -------------------------- Transcript
                  3bkd A 22 SSDPLVVAASImGILHLILWILDRLx 47
                                    31 |      41     |
                                      33-MSE        47-NH2

Chain B from PDB  Type:PROTEIN  Length:26
 aligned with Q9Q0P0_9INFA | Q9Q0P0 from UniProtKB/TrEMBL  Length:97

    Alignment length:26
                                    31        41      
          Q9Q0P0_9INFA   22 SSDPLVVAASIXGILHLILWILDRLF 47
               SCOP domains d3bkdb1 B:22-46          - SCOP domains
               CATH domains -------------------------- CATH domains
               Pfam domains -------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------- SAPs(SNPs)
                    PROSITE -------------------------- PROSITE
                 Transcript -------------------------- Transcript
                  3bkd B 22 SSDPLVVAASImGILHLILWILDRLx 47
                                    31 |      41     |
                                      33-MSE        47-NH2

Chain C from PDB  Type:PROTEIN  Length:26
 aligned with Q9Q0P0_9INFA | Q9Q0P0 from UniProtKB/TrEMBL  Length:97

    Alignment length:26
                                    31        41      
          Q9Q0P0_9INFA   22 SSDPLVVAASIXGILHLILWILDRLF 47
               SCOP domains d3bkdc1 C:22-46          - SCOP domains
               CATH domains -------------------------- CATH domains
               Pfam domains -------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------- SAPs(SNPs)
                    PROSITE -------------------------- PROSITE
                 Transcript -------------------------- Transcript
                  3bkd C 22 SSDPLVVAASImGILHLILWILDRLx 47
                                    31 |      41     |
                                      33-MSE        47-NH2

Chain D from PDB  Type:PROTEIN  Length:26
 aligned with Q9Q0P0_9INFA | Q9Q0P0 from UniProtKB/TrEMBL  Length:97

    Alignment length:26
                                    31        41      
          Q9Q0P0_9INFA   22 SSDPLVVAASIXGILHLILWILDRLF 47
               SCOP domains d3bkdd1 D:22-46          - SCOP domains
               CATH domains -------------------------- CATH domains
               Pfam domains -------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------- SAPs(SNPs)
                    PROSITE -------------------------- PROSITE
                 Transcript -------------------------- Transcript
                  3bkd D 22 SSDPLVVAASImGILHLILWILDRLx 47
                                    31 |      41     |
                                      33-MSE        47-NH2

Chain E from PDB  Type:PROTEIN  Length:26
 aligned with Q9Q0P0_9INFA | Q9Q0P0 from UniProtKB/TrEMBL  Length:97

    Alignment length:26
                                    31        41      
          Q9Q0P0_9INFA   22 SSDPLVVAASIXGILHLILWILDRLF 47
               SCOP domains d3bkde1 E:22-46          - SCOP domains
               CATH domains -------------------------- CATH domains
               Pfam domains -------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------- SAPs(SNPs)
                    PROSITE -------------------------- PROSITE
                 Transcript -------------------------- Transcript
                  3bkd E 22 SSDPLVVAASImGILHLILWILDRLx 47
                                    31 |      41     |
                                      33-MSE        47-NH2

Chain F from PDB  Type:PROTEIN  Length:26
 aligned with Q9Q0P0_9INFA | Q9Q0P0 from UniProtKB/TrEMBL  Length:97

    Alignment length:26
                                    31        41      
          Q9Q0P0_9INFA   22 SSDPLVVAASIXGILHLILWILDRLF 47
               SCOP domains d3bkdf1 F:22-46          - SCOP domains
               CATH domains -------------------------- CATH domains
               Pfam domains -------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------- SAPs(SNPs)
                    PROSITE -------------------------- PROSITE
                 Transcript -------------------------- Transcript
                  3bkd F 22 SSDPLVVAASImGILHLILWILDRLx 47
                                    31 |      41     |
                                      33-MSE        47-NH2

Chain G from PDB  Type:PROTEIN  Length:26
 aligned with Q9Q0P0_9INFA | Q9Q0P0 from UniProtKB/TrEMBL  Length:97

    Alignment length:26
                                    31        41      
          Q9Q0P0_9INFA   22 SSDPLVVAASIXGILHLILWILDRLF 47
               SCOP domains d3bkdg1 G:22-46          - SCOP domains
               CATH domains -------------------------- CATH domains
               Pfam domains -------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------- SAPs(SNPs)
                    PROSITE -------------------------- PROSITE
                 Transcript -------------------------- Transcript
                  3bkd G 22 SSDPLVVAASImGILHLILWILDRLx 47
                                    31 |      41     |
                                      33-MSE        47-NH2

Chain H from PDB  Type:PROTEIN  Length:26
 aligned with Q9Q0P0_9INFA | Q9Q0P0 from UniProtKB/TrEMBL  Length:97

    Alignment length:26
                                    31        41      
          Q9Q0P0_9INFA   22 SSDPLVVAASIXGILHLILWILDRLF 47
               SCOP domains d3bkdh1 H:22-46          - SCOP domains
               CATH domains -------------------------- CATH domains
               Pfam domains -------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------- SAPs(SNPs)
                    PROSITE -------------------------- PROSITE
                 Transcript -------------------------- Transcript
                  3bkd H 22 SSDPLVVAASImGILHLILWILDRLx 47
                                    31 |      41     |
                                      33-MSE        47-NH2

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric Unit

Classes(

)

Folds(

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Superfamilies( (-)

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Families(

)

Protein Domains( (-)

)

Organisms( (-)

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Class: Peptides (792)

Fold: Transmembrane helical fragments (68)

Superfamily: Transmembrane helical fragments (68)

Family: Transmembrane helical fragments (68)

Protein domain: Matrix protein M2 transmembrane peptide (4)

Synthetic, Inluenza A virus-based (3)

1a	d3bkda1	A:22-46
1b	d3bkdb1	B:22-46
1c	d3bkdc1	C:22-46
1d	d3bkdd1	D:22-46
1e	d3bkde1	E:22-46
1f	d3bkdf1	F:22-46
1g	d3bkdg1	G:22-46
1h	d3bkdh1	H:22-46

(no "CATH Domain" information available for 3BKD)

(no "Pfam Domain" information available for 3BKD)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D,E,F,G,H (Q9Q0P0_9INFA | Q9Q0P0)

molecular function
	GO:0015078	hydrogen ion transmembrane transporter activity	Enables the transfer of hydrogen ions from one side of a membrane to the other.
biological process
	GO:1902600	hydrogen ion transmembrane transport	The directed movement of hydrogen ion (proton) across a membrane.
	GO:0006811	ion transport	The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0015992	proton transport	The directed movement of protons (hydrogen ions) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0039521	suppression by virus of host autophagy	Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of autophagy in the host.
	GO:0006810	transport	The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
	GO:0016032	viral process	A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
cellular component
	GO:0033644	host cell membrane	Double layer of lipid molecules as it encloses host cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins. The host is defined as the larger of the organisms involved in a symbiotic interaction.
	GO:0020002	host cell plasma membrane	The plasma membrane surrounding a host cell.
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0019012	virion	The complete fully infectious extracellular virus particle.
	GO:0055036	virion membrane	The lipid bilayer surrounding a virion.

Asymmetric Unit
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Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (5, 30)

Sites (11, 11)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

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