1S5G - JenaLib

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Title :   STRUCTURE OF SCALLOP MYOSIN S1 REVEALS A NOVEL NUCLEOTIDE CONFORMATION

Authors :   D. Risal, S. Gourinath, D. M. Himmel, A. G. Szent-Gyorgyi, C. Cohen

Date :   20 Jan 04 (Deposition) - 22 Jun 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.10

Chains :   Asym./Biol. Unit : A,Y,Z

Keywords :   Scallop Myosin S1, Near Rigor, Complex Salt Bridge, Novel Conformation Of Nucleotide, Contractile Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. Risal, S. Gourinath, D. M. Himmel, A. G. Szent-Gyorgyi, C. Cohen
Myosin Subfragment 1 Structures Reveal A Partially Bound Nucleotide And A Complex Salt Bridge That Helps Couple Nucleotide And Actin Binding.
Proc. Natl. Acad. Sci. Usa V. 101 8930 2004
PubMed-ID: 15184651 | Reference-DOI: 10.1073/PNAS.0403002101
(for further references see the PDB file header)

Molecule 1 - MYOSIN HEAVY CHAIN, STRIATED MUSCLE
	Chains	:	A
	Fragment	:	RESIDUES 1-840
	Organism Scientific	:	ARGOPECTEN IRRADIANS
	Organism Taxid	:	31199

Molecule 2 - MYOSIN REGULATORY LIGHT CHAIN, STRIATED ADDUCTOR MUSCLE
	Chains	:	Y
	Organism Scientific	:	ARGOPECTEN IRRADIANS
	Organism Taxid	:	31199
	Synonym	:	R-LC

Molecule 3 - MYOSIN ESSENTIAL LIGHT CHAIN, STRIATED ADDUCTOR MUSCLE
	Chains	:	Z
	Organism Scientific	:	ARGOPECTEN IRRADIANS
	Organism Taxid	:	31199
	Synonym	:	E-LC, SULFHYDRYL LIGHT CHAIN, SHLC

		1	2	3
Asymmetric/Biological Unit	:	A	Y	Z

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (4, 4)

No.	Name	Count	Type	Full Name
1	ADP	1	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	CA	1	Ligand/Ion	CALCIUM ION
3	MG	1	Ligand/Ion	MAGNESIUM ION
4	SO4	1	Ligand/Ion	SULFATE ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:179 , ALA A:180 , GLY A:181 , LYS A:182 , THR A:183 , ASN A:237 , HOH A:997	BINDING SITE FOR RESIDUE SO4 A 996
2	AC2	SOFTWARE	ASP Z:19 , ASP Z:22 , GLY Z:23 , ASP Z:25 , ALA Z:27	BINDING SITE FOR RESIDUE CA Z 998
3	AC3	SOFTWARE	ASP Y:30 , ASP Y:32 , ASP Y:39	BINDING SITE FOR RESIDUE MG Y 999
4	AC4	SOFTWARE	ASN A:124 , PRO A:125 , TYR A:126 , ARG A:127 , ARG A:128 , TYR A:132 , GLU A:184 , ASN A:237 , ASN A:238 , ASN A:239 , ASN A:321	BINDING SITE FOR RESIDUE ADP A 995

(no "SS Bond" information available for 1S5G)

(no "Cis Peptide Bond" information available for 1S5G)

(no "SAP(SNP)/Variant" information available for 1S5G)

Asymmetric/Biological Unit (4, 7)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	EF_HAND_2	PS50222	EF-hand calcium-binding domain profile.	MLE_ARGIR	7-44 82-117	2	Z:6-43 Z:81-116
1	EF_HAND_2	PS50222	EF-hand calcium-binding domain profile.	MLR_ARGIR	16-51 85-120	2	Y:15-50 Y:84-119
2	EF_HAND_1	PS00018	EF-hand calcium-binding domain.	MLR_ARGIR	29-41	1	Y:28-40
3	MYOSIN_MOTOR	PS51456	Myosin motor domain profile.	MYS_ARGIR	83-775	1	A:83-775
4	IQ	PS50096	IQ motif profile.	MYS_ARGIR	778-805	1	A:778-805

(no "Exon" information available for 1S5G)

Asymmetric/Biological 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
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Chain A from PDB  Type:PROTEIN  Length:802
 aligned with MYS_ARGIR | P24733 from UniProtKB/Swiss-Prot  Length:1938

    Alignment length:834
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642       652       662       672       682       692       702       712       722       732       742       752       762       772       782       792       802       812       822       832    
            MYS_ARGIR     3 IDFSDPDFQYLAVDRKKLMKEQTAAFDGKKNCWVPDEKEGFASAEIQSSKGDEITVKIVADSSTRTVKKDDIQSMNPPKFEKLEDMANMTYLNEASVLYNLRSRYTSGLIYTYSGLFCIAVNPYRRLPIYTDSVIAKYRGKRKTEIPPHLFSVADNAYQNMVTDRENQSCLITGESGAGKTENTKKVIMYLAKVACAVKKKDEEASDKKEGSLEDQIIQANPVLEAYGNAKTTRNNNSSRFGKFIRIHFGPTGKIAGADIETYLLEKSRVTYQQSAERNYHIFYQICSNAIPELNDVMLVTPDSGLYSFINQGCLTVDNIDDVEEFKLCDEAFDILGFTKEEKQSMFKCTASILHMGEMKFKQRPREEQAESDGTAEAEKVAFLCGINAGDLLKALLKPKVKVGTEMVTKGQNMNQVVNSVGALAKSLYDRMFNWLVRRVNKTLDTKAKRNYYIGVLDIAGFEIFDFNSFEQLCINYTNERLQQFFNHHMFILEQEEYKKEGIAWEFIDFGMDLQMCIDLIEKPMGILSILEEECMFPKADDKSFQDKLYQNHMGKNRMFTKPGKPTRPNQGPAHFELHHYAGNVPYSITGWLEKNKDPINENVVALLGASKEPLVAELFKAPEEPAGGGKKKKGKSSAFQTISAVHRESLNKLMKNLYSTHPHFVRCIIPNELKQPGLVDAELVLHQLQCNGVLEGIRICRKGFPSRLIYSEFKQRYSILAPNAIPQGFVDGKTVSEKILAGLQMDPAEYRLGTTKVFFKAGVLGNLEEMRDERLSKIISMFQAHIRGYLIRKAYKKLQDQRIGLSVIQRNIRKWLVLRNWQWWKLYSKVKPL 836
               SCOP domains d1s5ga2 A:3-28,A:77-     8d1s5ga1 A:29-76                                 d1s5ga2 A:3-28,A:77-836 Myosin S1, motor domain                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....hhhhhhh.........-----.....eeeeee...eeeeeeeeee...eeeee.......eeee.hhhee..hhhhh...........hhhhhhhhhhhhhhh...eeee..eeeee.........hhhhhhhhh.........hhhhhhhhhhhhhhhhh..eeeeee.....hhhhhhhhhhhhhhh.....-----------..hhhhhhhhhhhhhhhhhee.......ee..eeeeeeee.....eeeee..ee..hhhhhh........hhhhhhhh...hhhhhhhhh...hhhhh...............hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh.ee........ee..hhhhhhhhhhhh.hhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeeeee..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhh..hhhhhhhhh......hhhhhhhhhhhhhh.....ee..............eeeee..eeeee...hhhhhhh...hhhhhhhhhh..hhhhhhhh....----------------.hhhhhhhhhhhhhhhhhh.....eeeee...........hhhhhhhhhhhhhhhhhhhhhhh....eehhhhhhhhhh..hhhhh.....hhhhhhhhhhhhh......eee....eee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE (2)
                PROSITE (3) --------------------------------------------------------------------------------MYOSIN_MOTOR  PDB: A:83-775 UniProt: 83-775                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          ------------------------------------------------------------- PROSITE (3)
                PROSITE (1) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------IQ  PDB: A:778-805          ------------------------------- PROSITE (1)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1s5g A   3 IDFSDPDFQYLAVDRKKLMK-----FDGKKNCWVPDEKEGFASAEIQSSKGDEITVKIVADSSTRTVKKDDIQSMNPPKFEKLEDMANMTYLNEASVLYNLRSRYTSGLIYTYSGLFCIAVNPYRRLPIYTDSVIAKYRGKRKTEIPPHLFSVADNAYQNMVTDRENQSCLITGESGAGKTENTKKVIMYLAKVACAV-----------EGSLEDQIIQANPVLEAYGNAKTTRNNNSSRFGKFIRIHFGPTGKIAGADIETYLLEKSRVTYQQSAERNYHIFYQICSNAIPELNDVMLVTPDSGLYSFINQGCLTVDNIDDVEEFKLCDEAFDILGFTKEEKQSMFKCTASILHMGEMKFKQRPREEQAESDGTAEAEKVAFLCGINAGDLLKALLKPKVKVGTEMVTKGQNMNQVVNSVGALAKSLYDRMFNWLVRRVNKTLDTKAKRNYYIGVLDIAGFEIFDFNSFEQLCINYTNERLQQFFNHHMFILEQEEYKKEGIAWEFIDFGMDLQMCIDLIEKPMGILSILEEECMFPKADDKSFQDKLYQNHMGKNRMFTKPGKPTRPNQGPAHFELHHYAGNVPYSITGWLEKNKDPINENVVALLGASKEPLVAELFKAPE----------------QTISAVHRESLNKLMKNLYSTHPHFVRCIIPNELKQPGLVDAELVLHQLQCNGVLEGIRICRKGFPSRLIYSEFKQRYSILAPNAIPQGFVDGKTVSEKILAGLQMDPAEYRLGTTKVFFKAGVLGNLEEMRDERLSKIISMFQAHIRGYLIRKAYKKLQDQRIGLSVIQRNIRKWLVLRNWQWWKLYSKVKPL 836
                                    12        22     |  32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       | -       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622   |     -         -|      652       662       672       682       692       702       712       722       732       742       752       762       772       782       792       802       812       822       832    
                                              22    28                                                                                                                                                                         200         212                                                                                                                                                                                                                                                                                                                                                                                                                           626              643

Chain Y from PDB  Type:PROTEIN  Length:142
 aligned with MLR_ARGIR | P13543 from UniProtKB/Swiss-Prot  Length:157

    Alignment length:142
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153  
            MLR_ARGIR    14 PQKQIQEMKEAFSMIDVDRDGFVSKEDIKAISEQLGRAPDDKELTAMLKEAPGPLNFTMFLSIFSDKLSGTDSEETIRNAFAMFDEQETKKLNIEYIKDLLENMGDNFNKDEMRMTFKEAPVEGGKFDYVKFTAMIKGSGEE 155
               SCOP domains d1s5gy_ Y: Myosin Essential Chain                                                                                                              SCOP domains
               CATH domains 1s5gY01 Y:13-81 EF-hand                                              1s5gY02 Y:82-149 EF-hand                                            ----- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh..hhhhh............hhhhhhhhh......hhhhhh..........................hhhhhhhhhhhhh......eehhhhhhhhhhh....hhhhhhhhh....ee..eehhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) --EF_HAND_2  PDB: Y:15-50             ---------------------------------EF_HAND_2  PDB: Y:84-119            ----------------------------------- PROSITE (2)
                PROSITE (3) ---------------EF_HAND_1    ------------------------------------------------------------------------------------------------------------------ PROSITE (3)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1s5g Y  13 PQKQIQEMKEAFSMIDVDRDGFVSKEDIKAISEQLGRAPDDKELTAMLKEAPGPLNFTMFLSIFSDKLSGTDSEETIRNAFAMFDEQETKKLNIEYIKDLLENMGDNFNKDEMRMTFKEAPVEGGKFDYVKFTAMIKGSGEE 154
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152

Chain Z from PDB  Type:PROTEIN  Length:155
 aligned with MLE_ARGIR | P07291 from UniProtKB/Swiss-Prot  Length:157

    Alignment length:155
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151     
            MLE_ARGIR     2 PKLSQDEIDDLKDVFELFDFWDGRDGAVDAFKLGDVCRCLGINPRNEDVFAVGGTHKMGEKSLPFEEFLPAYEGLMDCEQGTFADYMEAFKTFDREGQGFISGAELRHVLTALGERLSDEDVDEIIKLTDLQEDLEGNVKYEDFVKKVMAGPYPD 156
               SCOP domains d1s5gz_ Z: Myosin Regulatory Chain                                                                                                                          SCOP domains
               CATH domains --1s5gZ01 Z:3-80 EF-hand                                                        1s5gZ02 Z:81-152 EF-hand                                                --- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhh.......hhhhhhhhhhh.....hhhhhhh............hhhhhhhhhhhhhh....hhhhhhhhhhh.......eeehhhhhhhhhhh....hhhhhhhhhhhhh.......eeehhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----EF_HAND_2  PDB: Z:6-43 UniProt: 7-44  -------------------------------------EF_HAND_2  PDB: Z:81-116            --------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1s5g Z   1 PKLSQDEIDDLKDVFELFDFWDGRDGAVDAFKLGDVCRCLGINPRNEDVFAVGGTHKMGEKSLPFEEFLPAYEGLMDCEQGTFADYMEAFKTFDREGQGFISGAELRHVLTALGERLSDEDVDEIIKLTDLQEDLEGNVKYEDFVKKVMAGPYPD 155
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150

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/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Recoverin; domain 1 (474)

Homologous Superfamily: EF-hand (412)

Argopecten irradians. Organism_taxid: 31199. Argopecten irradians. Organism_taxid: 31199. (4)

1a	1s5gZ02	Z:81-152
1b	1s5gY01	Y:13-81
1c	1s5gY02	Y:82-149
1d	1s5gZ01	Z:3-80

(no "Pfam Domain" information available for 1S5G)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (MYS_ARGIR | P24733)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0003779	actin binding	Interacting selectively and non-covalently with monomeric or multimeric forms of actin, including actin filaments.
	GO:0005516	calmodulin binding	Interacting selectively and non-covalently with calmodulin, a calcium-binding protein with many roles, both in the calcium-bound and calcium-free states.
	GO:0003774	motor activity	Catalysis of the generation of force resulting either in movement along a microfilament or microtubule, or in torque resulting in membrane scission, coupled to the hydrolysis of a nucleoside triphosphate.
	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.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0030016	myofibril	The contractile element of skeletal and cardiac muscle; a long, highly organized bundle of actin, myosin, and other proteins that contracts by a sliding filament mechanism.
	GO:0016459	myosin complex	A protein complex, formed of one or more myosin heavy chains plus associated light chains and other proteins, that functions as a molecular motor; uses the energy of ATP hydrolysis to move actin filaments or to move vesicles or other cargo on fixed actin filaments; has magnesium-ATPase activity and binds actin. Myosin classes are distinguished based on sequence features of the motor, or head, domain, but also have distinct tail regions that are believed to bind specific cargoes.
	GO:0032982	myosin filament	A protein complex containing myosin heavy chains, plus associated light chains and other proteins, in which the myosin heavy chains are arranged into a filament.

Chain Y (MLR_ARGIR | P13543)

molecular function
	GO:0005509	calcium ion binding	Interacting selectively and non-covalently with calcium ions (Ca2+).
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
cellular component
	GO:0016459	myosin complex	A protein complex, formed of one or more myosin heavy chains plus associated light chains and other proteins, that functions as a molecular motor; uses the energy of ATP hydrolysis to move actin filaments or to move vesicles or other cargo on fixed actin filaments; has magnesium-ATPase activity and binds actin. Myosin classes are distinguished based on sequence features of the motor, or head, domain, but also have distinct tail regions that are believed to bind specific cargoes.

Chain Z (MLE_ARGIR | P07291)

molecular function
	GO:0005509	calcium ion binding	Interacting selectively and non-covalently with calcium ions (Ca2+).
cellular component
	GO:0016459	myosin complex	A protein complex, formed of one or more myosin heavy chains plus associated light chains and other proteins, that functions as a molecular motor; uses the energy of ATP hydrolysis to move actin filaments or to move vesicles or other cargo on fixed actin filaments; has magnesium-ATPase activity and binds actin. Myosin classes are distinguished based on sequence features of the motor, or head, domain, but also have distinct tail regions that are believed to bind specific cargoes.

Asymmetric/Biological Unit
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1kk7	SCALLOP MYOSIN IN THE NEAR RIGOR CONFORMATION
1kk8	SCALLOP MYOSIN (S1-ADP-BEFX) IN THE ACTIN-DETACHED CONFORMATION
1qvi	CRYSTAL STRUCTURE OF SCALLOP MYOSIN S1 IN THE PRE-POWER STROKE STATE TO 2.6 ANGSTROM RESOLUTION

Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (4, 4)

Sites (4, 4)

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PROSITE Motifs (4, 7)

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