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Biological Unit 2 (Jmol Viewer)

Title :   STRUCTURE OF NBD1 FROM MURINE CFTR- F508R MUTANT

Authors :   P. H. Thibodeau, C. A. Brautigam, M. Machius, P. J. Thomas

Date :   14 Sep 04 (Deposition) - 28 Dec 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.10

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)

Keywords :   Cystic Fibrosis, Abc Transporters, Atp, Nucleotide-Binding Domain, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. H. Thibodeau, C. A. Brautigam, M. Machius, P. J. Thomas
Side Chain And Backbone Contributions Of Phe508 To Cftr Folding.
Nat. Struct. Mol. Biol. V. 12 10 2005
PubMed-ID: 15619636 | Reference-DOI: 10.1038/NSMB881
(for further references see the PDB file header)

Molecule 1 - CYSTIC FIBROSIS TRANSMEMBRANE CONDUCTANCE REGULATOR
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PSMT3-NBD1-F508R
	Expression System Strain	:	BL21(DE3) CODON PLUS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	NBD1
	Gene	:	CFTR, ABCC7
	Mutation	:	YES
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Synonym	:	CFTR, CAMP-DEPENDENT CHLORIDE CHANNEL

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 10)

No.	Name	Count	Type	Full Name
1	ACY	4	Ligand/Ion	ACETIC ACID
2	ATP	2	Ligand/Ion	ADENOSINE-5'-TRIPHOSPHATE
3	CL	2	Ligand/Ion	CHLORIDE ION
4	MG	2	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (2, 3)

No.	Name	Count	Type	Full Name
1	ACY	2	Ligand/Ion	ACETIC ACID
2	ATP	1	Ligand/Ion	ADENOSINE-5'-TRIPHOSPHATE
3	CL	-1	Ligand/Ion	CHLORIDE ION
4	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 2 (2, 3)

No.	Name	Count	Type	Full Name
1	ACY	2	Ligand/Ion	ACETIC ACID
2	ATP	1	Ligand/Ion	ADENOSINE-5'-TRIPHOSPHATE
3	CL	-1	Ligand/Ion	CHLORIDE ION
4	MG	-1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ATP A:1 , THR A:465 , GLN A:493	BINDING SITE FOR RESIDUE MG A 3
02	AC2	SOFTWARE	ATP B:2 , THR B:465 , GLN B:493 , ASP B:572	BINDING SITE FOR RESIDUE MG B 4
03	AC3	SOFTWARE	LEU A:548 , SER A:549 , GLY A:550 , ARG A:553 , VAL B:546 , THR B:547 , LEU B:548	BINDING SITE FOR RESIDUE CL A 5
04	AC4	SOFTWARE	VAL A:546 , THR A:547 , LEU A:548 , LEU B:548 , GLY B:550 , ARG B:553	BINDING SITE FOR RESIDUE CL A 6
05	AC5	SOFTWARE	MG A:3 , TRP A:401 , LEU A:433 , ASN A:438 , PRO A:439 , GLY A:461 , SER A:462 , GLY A:463 , LYS A:464 , THR A:465 , SER A:466 , GLN A:493 , MET B:498 , ARG B:508	BINDING SITE FOR RESIDUE ATP A 1
06	AC6	SOFTWARE	MG B:4 , TRP B:401 , GLY B:461 , SER B:462 , GLY B:463 , LYS B:464 , THR B:465 , SER B:466 , GLN B:493	BINDING SITE FOR RESIDUE ATP B 2
07	AC7	SOFTWARE	LEU A:541 , GLY A:542 , GLY A:545 , VAL A:546 , THR A:547	BINDING SITE FOR RESIDUE ACY A 7
08	AC8	SOFTWARE	LEU B:541 , GLY B:542 , GLY B:545 , VAL B:546 , THR B:547	BINDING SITE FOR RESIDUE ACY B 8
09	AC9	SOFTWARE	LYS A:532 , SER A:549 , LYS B:532 , GLN B:552	BINDING SITE FOR RESIDUE ACY A 9
10	BC1	SOFTWARE	GLY B:451 , ALA B:596	BINDING SITE FOR RESIDUE ACY B 10

(no "SS Bond" information available for 1XFA)

(no "Cis Peptide Bond" information available for 1XFA)

(no "SAP(SNP)/Variant" information available for 1XFA)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ABC_TRANSPORTER_1	PS00211	ABC transporters family signature.	CFTR_MOUSE	548-562	2	A:548-562 B:548-562

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ABC_TRANSPORTER_1	PS00211	ABC transporters family signature.	CFTR_MOUSE	548-562	1	A:548-562 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ABC_TRANSPORTER_1	PS00211	ABC transporters family signature.	CFTR_MOUSE	548-562	1	- B:548-562

(no "Exon" information available for 1XFA)

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:264
 aligned with CFTR_MOUSE | P26361 from UniProtKB/Swiss-Prot  Length:1476

    Alignment length:281
                                   399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609       619       629       639       649       659       669 
           CFTR_MOUSE   390 TGIIMENVTAFWEEGFGELLEKVQQSNGDRKHSSDENNVSFSHLCLVGNPVLKNINLNIEKGEMLAITGSTGSGKTSLLMLILGELEASEGIIKHSGRVSFCSQFSWIMPGTIKENIIFGVSYDEYRYKSVVKACQLQQDITKFAEQDNTVLGEGGVTLSGGQRARISLARAVYKDADLYLLDSPFGYLDVFTEEQVFESCVCKLMANKTRILVTSKMEHLRKADKILILHQGSSYFYGTFSELQSLRPDFSSKLMGYDTFDQFTEERRSSILTETLRRFS 670
               SCOP domains d1xfaa_ A: Cystic fibr                 osis transmembrane conductance regulator, CFTR, nucleotide-binding domain                                                                                                                                                                          SCOP domains
               CATH domains 1xfaA00 A:390-670 P-lo                 op containing nucleotide triphosphate hydrolases                                                                                                                                                                                                   CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeee...hhhhhhh.-----------------hhhhhhhhh.eeeeeeeeee....eeeeee....hhhhhhhhhh......eeeeee...eeee........eehhhhhhh....hhhhhhhhhhhh.hhhhhh...hhhh.ee.......hhhhhhhhhhhhhhhh...eeeee......hhhhhhhhhhhhhh......eeeee..hhhhhhh..eeeeee..eeeeeehhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------ABC_TRANSPORTER------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xfa A 390 TGIIMENVTAFWEEGFGELLEK-----------------SFSHLCLVGNPVLKNINLNIEKGEMLAITGSTGSGKTSLLMLILGELEASEGIIKHSGRVSFCSQFSWIMPGTIKENIIRGVSYDEYRYKSVVKACQLQQDITKFAEQDNTVLGEGGVTLSGGQRARISLARAVYKDADLYLLDSPFGYLDVFTEEQVFESCVCKLMANKTRILVTSKMEHLRKADKILILHQGSSYFYGTFSELQSLRPDFSSKLMGYDTFDQFTEERRSSILTETLRRFS 670
                                   399       409 |       -       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609       619       629       639       649       659       669 
                                               411               429

Chain B from PDB  Type:PROTEIN  Length:264
 aligned with CFTR_MOUSE | P26361 from UniProtKB/Swiss-Prot  Length:1476

    Alignment length:281
                                   399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609       619       629       639       649       659       669 
           CFTR_MOUSE   390 TGIIMENVTAFWEEGFGELLEKVQQSNGDRKHSSDENNVSFSHLCLVGNPVLKNINLNIEKGEMLAITGSTGSGKTSLLMLILGELEASEGIIKHSGRVSFCSQFSWIMPGTIKENIIFGVSYDEYRYKSVVKACQLQQDITKFAEQDNTVLGEGGVTLSGGQRARISLARAVYKDADLYLLDSPFGYLDVFTEEQVFESCVCKLMANKTRILVTSKMEHLRKADKILILHQGSSYFYGTFSELQSLRPDFSSKLMGYDTFDQFTEERRSSILTETLRRFS 670
               SCOP domains d1xfab_ B: Cystic fibr                 osis transmembrane conductance regulator, CFTR, nucleotide-binding domain                                                                                                                                                                          SCOP domains
               CATH domains 1xfaB00 B:390-670 P-lo                 op containing nucleotide triphosphate hydrolases                                                                                                                                                                                                   CATH domains
           Pfam domains (1) ---------------------------------------------------------------------------ABC_tran-1xfaB01 B:465-576                                                                                      --------------------------------------------------------------CFTR_R-1xfaB03 B:639-670         Pfam domains (1)
           Pfam domains (2) ---------------------------------------------------------------------------ABC_tran-1xfaB02 B:465-576                                                                                      --------------------------------------------------------------CFTR_R-1xfaB04 B:639-670         Pfam domains (2)
         Sec.struct. author ..eeeeeeeee...hhhhhh..-----------------hhhhhhhhh.eeeeeeeeee....eeeeee....hhhhhhhhhh......eeeeee...eeee........eehhhhhhh....hhhhhhhhhhhh.hhhhhh...hhhh.eehhhhh..hhhhhhhhhhhhhhhh...eeee.......hhhhhhhhhhhhhh......eeeee..hhhhhhh..eeeeee..eeeeeehhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------ABC_TRANSPORTER------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xfa B 390 TGIIMENVTAFWEEGFGELLEK-----------------SFSHLCLVGNPVLKNINLNIEKGEMLAITGSTGSGKTSLLMLILGELEASEGIIKHSGRVSFCSQFSWIMPGTIKENIIRGVSYDEYRYKSVVKACQLQQDITKFAEQDNTVLGEGGVTLSGGQRARISLARAVYKDADLYLLDSPFGYLDVFTEEQVFESCVCKLMANKTRILVTSKMEHLRKADKILILHQGSSYFYGTFSELQSLRPDFSSKLMGYDTFDQFTEERRSSILTETLRRFS 670
                                   399       409 |       -       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609       619       629       639       649       659       669 
                                               411               429

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(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: P-loop containing nucleotide triphosphate hydrolases (1378)

House mouse (Mus musculus) (47)

1a	1xfaA00	A:390-670
1b	1xfaB00	B:390-670

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: P-loop_NTPase (1112)

Family: ABC_tran (53)

Mus musculus (Mouse) (8)

1a	ABC_tran-1xfaB01	B:465-576
1b	ABC_tran-1xfaB02	B:465-576

Clan: no clan defined [family: CFTR_R] (12)

Family: CFTR_R (12)

Mus musculus (Mouse) (8)

2a	CFTR_R-1xfaB03	B:639-670
2b	CFTR_R-1xfaB04	B:639-670

Asymmetric Unit(hide GO term definitions)

Chain A,B (CFTR_MOUSE | P26361)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0016887	ATPase activity	Catalysis of the reaction: ATP + H2O = ADP + phosphate + 2 H+. May or may not be coupled to another reaction.
	GO:0042626	ATPase activity, coupled to transmembrane movement of substances	Catalysis of the reaction: ATP + H2O = ADP + phosphate, to directly drive the active transport of a substance across a membrane.
	GO:0030165	PDZ domain binding	Interacting selectively and non-covalently with a PDZ domain of a protein, a domain found in diverse signaling proteins.
	GO:0015106	bicarbonate transmembrane transporter activity	Enables the transfer of bicarbonate from one side of a membrane to the other. Bicarbonate is the hydrogencarbonate ion, HCO3-.
	GO:0005254	chloride channel activity	Enables the facilitated diffusion of a chloride (by an energy-independent process) involving passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism.
	GO:0019869	chloride channel inhibitor activity	Stops, prevents, or reduces the activity of a chloride channel.
	GO:0015108	chloride transmembrane transporter activity	Enables the transfer of chloride ions from one side of a membrane to the other.
	GO:0019899	enzyme binding	Interacting selectively and non-covalently with any enzyme.
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0005260	intracellular ATPase-gated chloride channel activity	Enables passage of a chloride ion through a transmembrane channel that opens when intracellular ATP is bound and hydrolysed. Passage is via passive diffusion once the channel is open.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
	GO:0015701	bicarbonate transport	The directed movement of bicarbonate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0071320	cellular response to cAMP	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a cAMP (cyclic AMP, adenosine 3',5'-cyclophosphate) stimulus.
	GO:1902476	chloride transmembrane transport	The directed movement of chloride across a membrane.
	GO:0006821	chloride transport	The directed movement of chloride into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0006695	cholesterol biosynthetic process	The chemical reactions and pathways resulting in the formation of cholesterol, cholest-5-en-3 beta-ol, the principal sterol of vertebrates and the precursor of many steroids, including bile acids and steroid hormones.
	GO:0030301	cholesterol transport	The directed movement of cholesterol, cholest-5-en-3-beta-ol, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0051454	intracellular pH elevation	Any process that increases the internal pH of a cell, measured by the concentration of the hydrogen ion.
	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:0060081	membrane hyperpolarization	The process in which membrane potential increases with respect to its steady-state potential, usually from negative potential to a more negative potential. For example, during the repolarization phase of an action potential the membrane potential often becomes more negative or hyperpolarized before returning to the steady-state resting potential.
	GO:1902161	positive regulation of cyclic nucleotide-gated ion channel activity	Any process that activates or increases the frequency, rate or extent of cyclic nucleotide-gated ion channel activity.
	GO:0045921	positive regulation of exocytosis	Any process that activates or increases the frequency, rate or extent of exocytosis.
	GO:0035774	positive regulation of insulin secretion involved in cellular response to glucose stimulus	Any process that increases the frequency, rate or extent of the regulated release of insulin that contributes to the response of a cell to glucose.
	GO:1902943	positive regulation of voltage-gated chloride channel activity	Any process that activates or increases the frequency, rate or extent of voltage-gated chloride channel activity.
	GO:0003254	regulation of membrane depolarization	Any process that modulates the rate, frequency or extent of membrane depolarization. Membrane depolarization is the process in which membrane potential changes in the depolarizing direction from the resting potential, usually from negative to positive.
	GO:0048240	sperm capacitation	A process required for sperm to reach fertilization competence. Sperm undergo an incompletely understood series of morphological and molecular maturational processes, termed capacitation, involving, among other processes, protein tyrosine phosphorylation and increased intracellular calcium.
	GO:0055085	transmembrane transport	The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other
	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:0006904	vesicle docking involved in exocytosis	The initial attachment of a vesicle membrane to a target membrane, mediated by proteins protruding from the membrane of the vesicle and the target membrane, that contributes to exocytosis.
cellular component
	GO:0016324	apical plasma membrane	The region of the plasma membrane located at the apical end of the cell.
	GO:0009986	cell surface	The external part of the cell wall and/or plasma membrane.
	GO:0034707	chloride channel complex	An ion channel complex through which chloride ions pass.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0005769	early endosome	A membrane-bounded organelle that receives incoming material from primary endocytic vesicles that have been generated by clathrin-dependent and clathrin-independent endocytosis; vesicles fuse with the early endosome to deliver cargo for sorting into recycling or degradation pathways.
	GO:0031901	early endosome membrane	The lipid bilayer surrounding an early endosome.
	GO:0031205	endoplasmic reticulum Sec complex	An endoplasmic reticulum membrane-associated complex involved in the translocation of proteins that are targeted to the ER. In yeast, this complex consists of two subcomplexes, namely, the Sec61 complex and the Sec62/Sec63 complex.
	GO:0005768	endosome	A vacuole to which materials ingested by endocytosis are delivered.
	GO:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	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:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
	GO:0043234	protein complex	A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.
	GO:0055037	recycling endosome	An organelle consisting of a network of tubules that functions in targeting molecules, such as receptors transporters and lipids, to the plasma membrane.

Asymmetric Unit
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	1xfa
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	CFTR_MOUSE \| P26361	:	1q3h 1r0w 1r0x 1r0y 1r0z 1r10 1xf9 3si7

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Ligands, Modified Residues, Ions (4, 10)

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SS Bonds (0, 0)

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