1KK8 - JenaLib

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Title :   SCALLOP MYOSIN (S1-ADP-BEFX) IN THE ACTIN-DETACHED CONFORMATION

Authors :   M. Himmel, S. Gourinath, L. Reshetnikova, Y. Shen, G. Szent-Gyorgyi, C

Date :   06 Dec 01 (Deposition) - 09 Oct 02 (Release) - 01 Jun 16 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

Chains :   Asym./Biol. Unit : A,B,C

Keywords :   Actin-Detached, Myosin, Mechanics Of Motor, Contractile Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. M. Himmel, S. Gourinath, L. Reshetnikova, Y. Shen, A. G. Szent-Gyorgyi, C. Cohen
Crystallographic Findings On The Internally Uncoupled And Near-Rigor States Of Myosin: Further Insights Into The Mechanics Of The Motor.
Proc. Natl. Acad. Sci. Usa V. 99 12645 2002
PubMed-ID: 12297624 | Reference-DOI: 10.1073/PNAS.202476799
(for further references see the PDB file header)

Molecule 1 - MYOSIN HEAVY CHAIN, STRIATED MUSCLE
	Chains	:	A
	Fragment	:	MYOSIN HEAVY CHAIN
	Mutation	:	YES
	Organism Scientific	:	ARGOPECTEN IRRADIANS
	Organism Taxid	:	31199
	Other Details	:	PAPAIN DIGESTION OF MYOSIN
	Strain	:	BAY SCALLOP

Molecule 2 - MYOSIN REGULATORY LIGHT CHAIN, STRIATED ADDUCTOR MUSCLE
	Chains	:	B
	Fragment	:	MYOSIN REGULATORY LIGHT CHAIN
	Organism Scientific	:	ARGOPECTEN IRRADIANS
	Organism Taxid	:	31199
	Other Details	:	PAPAIN DIGESTION OF MYOSIN
	Strain	:	BAY SCALLOP
	Synonym	:	R-LC

Molecule 3 - MYOSIN ESSENTIAL LIGHT CHAIN,STRIATED ADDUCTOR MUSCLE
	Chains	:	C
	Fragment	:	MYOSIN ESSENTIAL LIGHT CHAIN
	Organism Scientific	:	ARGOPECTEN IRRADIANS
	Organism Taxid	:	31199
	Other Details	:	PAPAIN DIGESTION OF MYOSIN
	Strain	:	BAY SCALLOP
	Synonym	:	E-LC

		1	2	3
Asymmetric/Biological Unit	:	A	B	C

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (5, 6)

No.	Name	Count	Type	Full Name
1	ADP	1	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	BEF	1	Ligand/Ion	BERYLLIUM TRIFLUORIDE ION
3	CA	1	Ligand/Ion	CALCIUM ION
4	GOL	1	Ligand/Ion	GLYCEROL
5	MG	2	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	THR A:183 , SER A:241 , BEF A:995 , ADP A:996 , HOH A:1041 , HOH A:1042	BINDING SITE FOR RESIDUE MG A 997
2	AC2	SOFTWARE	ASP B:28 , ASP B:30 , ASP B:32 , PHE B:34 , ASP B:39	BINDING SITE FOR RESIDUE MG B 998
3	AC3	SOFTWARE	ASP C:19 , ASP C:22 , GLY C:23 , ASP C:25 , ALA C:27 , HOH C:1001	BINDING SITE FOR RESIDUE CA C 999
4	AC4	SOFTWARE	SER A:178 , GLY A:179 , LYS A:182 , ASN A:237 , SER A:240 , SER A:241 , ADP A:996 , MG A:997 , HOH A:1042	BINDING SITE FOR RESIDUE BEF A 995
5	AC5	SOFTWARE	ASN A:124 , ARG A:127 , TYR A:132 , GLU A:177 , SER A:178 , GLY A:179 , ALA A:180 , GLY A:181 , LYS A:182 , THR A:183 , GLU A:184 , ASN A:237 , BEF A:995 , MG A:997 , HOH A:1035 , HOH A:1041 , HOH A:1042 , HOH A:1102	BINDING SITE FOR RESIDUE ADP A 996
6	AC6	SOFTWARE	SER A:178 , THR A:234 , THR A:235 , ARG A:236 , SER A:240 , ARG A:242 , HOH A:1019	BINDING SITE FOR RESIDUE GOL A 998

(no "SS Bond" information available for 1KK8)

(no "Cis Peptide Bond" information available for 1KK8)

(no "SAP(SNP)/Variant" information available for 1KK8)

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	C:6-43 C:81-116
1	EF_HAND_2	PS50222	EF-hand calcium-binding domain profile.	MLR_ARGIR	16-51 85-120	2	B:15-50 B:84-119
2	EF_HAND_1	PS00018	EF-hand calcium-binding domain.	MLR_ARGIR	29-41	1	B: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 1KK8)

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:793
 aligned with MYS_ARGIR | P24733 from UniProtKB/Swiss-Prot  Length:1938

    Alignment length:837
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730       740       750       760       770       780       790       800       810       820       830       
            MYS_ARGIR     1 MNIDFSDPDFQYLAVDRKKLMKEQTAAFDGKKNCWVPDEKEGFASAEIQSSKGDEITVKIVADSSTRTVKKDDIQSMNPPKFEKLEDMANMTYLNEASVLYNLRSRYTSGLIYTYSGLFCIAVNPYRRLPIYTDSVIAKYRGKRKTEIPPHLFSVADNAYQNMVTDRENQSCLITGESGAGKTENTKKVIMYLAKVACAVKKKDEEASDKKEGSLEDQIIQANPVLEAYGNAKTTRNNNSSRFGKFIRIHFGPTGKIAGADIETYLLEKSRVTYQQSAERNYHIFYQICSNAIPELNDVMLVTPDSGLYSFINQGCLTVDNIDDVEEFKLCDEAFDILGFTKEEKQSMFKCTASILHMGEMKFKQRPREEQAESDGTAEAEKVAFLCGINAGDLLKALLKPKVKVGTEMVTKGQNMNQVVNSVGALAKSLYDRMFNWLVRRVNKTLDTKAKRNYYIGVLDIAGFEIFDFNSFEQLCINYTNERLQQFFNHHMFILEQEEYKKEGIAWEFIDFGMDLQMCIDLIEKPMGILSILEEECMFPKADDKSFQDKLYQNHMGKNRMFTKPGKPTRPNQGPAHFELHHYAGNVPYSITGWLEKNKDPINENVVALLGASKEPLVAELFKAPEEPAGGGKKKKGKSSAFQTISAVHRESLNKLMKNLYSTHPHFVRCIIPNELKQPGLVDAELVLHQLQCNGVLEGIRICRKGFPSRLIYSEFKQRYSILAPNAIPQGFVDGKTVSEKILAGLQMDPAEYRLGTTKVFFKAGVLGNLEEMRDERLSKIISMFQAHIRGYLIRKAYKKLQDQRIGLSVIQRNIRKWLVLRNWQWWKLYSKVKPLL 837
               SCOP domains d1kk8a2 A:1-28,A:77-83  7   d1kk8a1 A:29-76                                 d1kk8a2 A:1-28,A:77-837 Myosin S1, motor domain                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhh...........--........eeeeee...eeeeeeeeeee..eeeeee.....eeeee.hhhee..hhhhh...hhhhh...hhhhhhhhhhhhhhh...eeee..eeeee.........hhhhhhhhh..hhhhh..hhhhhhhhhhhhhhhhh.eeeeeee.....hhhhhhhhhhhhhhhhh....--------....hhhhhhhhhhhhhhhhhee.......ee..eeeeeeee.....eeeeeeeee..hhhhhh........hhhhhhhh...hhhhhhhhh...hhhhh.............hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh...ee.----...ee..hhhhhhhhhhhh.hhhhhhhhhhh.ee.----.ee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeeeee..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhh..hhhhhhhhhh.....hhhhhhhhhhhhhh.....ee..............eeeee..eeeee...hhhhhhh...hhhhhhhhhh..hhhhhhhh..------------------.hhhhhhhhhhhhhhhhhh.eeeeeeeee...........hhhhhhhhhh......-----.....eeeehhhhhhhhhhhhhhhh..---hhhhhhhhhhhhhh.hhh.eee...eeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh 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
                 1kk8 A   1 MNIDFSDPDFQYLAVDRKKLMK--TAAFDGKKNCWVPDEKEGFASAEIQSSKGDEITVKIVADSSTRTVKKDDIQSMNPPKFEKLEDMANMTYLNEASVLYNLRSRYTSGLIYTYSGLFCIAVNPYRRLPIYTDSVIAKYRGKRKTEIPPHLFSVADNAYQNMVTDRENQSCLITGESGAGKTENTKKVIMYLAKVACAVK--------KKEGSLEDQIIQANPVLEAYGNAKTTRNNNSSRFGKFIRIHFGPTGKIAGADIETYLLEKSRVTYQQSAERNYHIFYQICSNAIPELNDVMLVTPDSGLYSFINQGCLTVDNIDDVEEFKLCDEAFDILGFTKEEKQSMFKCTASILHMGEMKFKQ----EQAESDGTAEAEKVAFLCGINAGDLLKALLKPKVK----MVTKGQNMNQVVNSVGALAKSLYDRMFNWLVRRVNKTLDTKAKRNYYIGVLDIAGFEIFDFNSFEQLCINYTNERLQQFFNHHMFILEQEEYKKEGIAWEFIDFGMDLQMCIDLIEKPMGILSILEEECMFPKADDKSFQDKLYQNHMGKNRMFTKPGKPTRPNQGPAHFELHHYAGNVPYSITGWLEKNKDPINENVVALLGASKEPLVAELFKA------------------QTISAVHRESLNKLMKNLYSTHPHFVRCIIPNELKQPGLVDAELVLHQLQCNGVLE-----RKGFPSRLIYSEFKQRYSILAPNAIPQ---DGKTVSEKILAGLQMDPAEYRLGTTKVFFKAGVLGNLEEMRDERLSKIISMFQAHIRGYLIRKAYKKLQDQRIGLSVIQRNIRKWLVLRNWQWWKLYSKVKPLL 837
                                    10        20 |  |   30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200|      210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360    |  370       380       390       400   |   410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620   |     -         -  |    650       660       670       680       690       | -   |   710       720       730   |   740       750       760       770       780       790       800       810       820       830       
                                                22 25                                                                                                                                                                             201      210                                                                                                                                                        365  370                               404  409                                                                                                                                                                                                                    624                643                                                    698   704                       730 734

Chain B from PDB  Type:PROTEIN  Length:139
 aligned with MLR_ARGIR | P13543 from UniProtKB/Swiss-Prot  Length:157

    Alignment length:139
                                    23        33        43        53        63        73        83        93       103       113       123       133       143         
            MLR_ARGIR    14 PQKQIQEMKEAFSMIDVDRDGFVSKEDIKAISEQLGRAPDDKELTAMLKEAPGPLNFTMFLSIFSDKLSGTDSEETIRNAFAMFDEQETKKLNIEYIKDLLENMGDNFNKDEMRMTFKEAPVEGGKFDYVKFTAMIKGS 152
               SCOP domains d1kk8b_ B: Myosin Essential Chain                                                                                                           SCOP domains
               CATH domains 1kk8B01 B:13-81 EF-hand                                              1kk8B02 B:82-149 EF-hand                                            -- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhh.......hhhhhhhhhhhhh...hhhhhhhhhhh.....hhhhhhhhhhh......hhhhhhhhhhh........eehhhhhhhhhhh....hhhhhhhhhh...ee..eehhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) --EF_HAND_2  PDB: B:15-50             ---------------------------------EF_HAND_2  PDB: B:84-119            -------------------------------- PROSITE (2)
                PROSITE (3) ---------------EF_HAND_1    --------------------------------------------------------------------------------------------------------------- PROSITE (3)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1kk8 B  13 PQKQIQEMKEAFSMIDVDRDGFVSKEDIKAISEQLGRAPDDKELTAMLKEAPGPLNFTMFLSIFSDKLSGTDSEETIRNAFAMFDEQETKKLNIEYIKDLLENMGDNFNKDEMRMTFKEAPVEGGKFDYVKFTAMIKGS 151
                                    22        32        42        52        62        72        82        92       102       112       122       132       142

Chain C from PDB  Type:PROTEIN  Length:154
 aligned with MLE_ARGIR | P07291 from UniProtKB/Swiss-Prot  Length:157

    Alignment length:154
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151    
            MLE_ARGIR     2 PKLSQDEIDDLKDVFELFDFWDGRDGAVDAFKLGDVCRCLGINPRNEDVFAVGGTHKMGEKSLPFEEFLPAYEGLMDCEQGTFADYMEAFKTFDREGQGFISGAELRHVLTALGERLSDEDVDEIIKLTDLQEDLEGNVKYEDFVKKVMAGPYP 155
               SCOP domains d1kk8c_ C: Myosin Regulatory Chain                                                                                                                         SCOP domains
               CATH domains --1kk8C01 C:3-80 EF-hand                                                        1kk8C02 C:81-152 EF-hand                                                -- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhh.....ee..hhhhhhhhh....hhhhhhhh.........eehhhhhhhhhhhhh.....hhhhhhhhhhh.......eeehhhhhhhhhhh....hhhhhhhhhhhhh.......eeehhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----EF_HAND_2  PDB: C:6-43 UniProt: 7-44  -------------------------------------EF_HAND_2  PDB: C:81-116            -------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1kk8 C   1 PKLSQDEIDDLKDVFELFDFWDGRDGAVDAFKLGDVCRCLGINPRNEDVFAVGGTHKMGEKSLPFEEFLPAYEGLMDCEQGTFADYMEAFKTFDREGQGFISGAELRHVLTALGERLSDEDVDEIIKLTDLQEDLEGNVKYEDFVKKVMAGPYP 154
                                    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. Strain: bay scallop. (2)

1a	1kk8C02	C:81-152
1b	1kk8C01	C:3-80
1c	1kk8B01	B:13-81
1d	1kk8B02	B:82-149

(no "Pfam Domain" information available for 1KK8)

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 B (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 C (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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	Cis Peptide Bonds
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	1kk8
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1b7t	1B7T CONTAINS THE SAME PROTEIN COMPLEXED WITH MGADP

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 6)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (4, 7)

Exons (0, 0)

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SCOP Domains (4, 4)

CATH Domains (1, 4)

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Gene Ontology (11, 14)

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