1YTZ - JenaLib

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Title :   CRYSTAL STRUCTURE OF SKELETAL MUSCLE TROPONIN IN THE CA2+-ACTIVATED STATE

Authors :   M. V. Vinogradova, D. B. Stone, G. G. Malanina, C. Karatzaferi, R. Cooke, R. A. Mendelson, R. J. Fletterick

Date :   11 Feb 05 (Deposition) - 12 Apr 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.00

Chains :   Asym. Unit : C,I,T
Biol. Unit 1: C,I,T  (1x)
Biol. Unit 2: C,I,T  (2x)

Keywords :   Troponin, Muscle, Thin Filament, Actin Binding, Calcium, Contractile Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. V. Vinogradova, D. B. Stone, G. G. Malanina, C. Karatzaferi, R. Cooke, R. A. Mendelson, R. J. Fletterick
Ca2+-Regulated Structural Changes In Troponin
Proc. Natl. Acad. Sci. Usa V. 102 5038 2005
PubMed-ID: 15784741 | Reference-DOI: 10.1073/PNAS.0408882102
(for further references see the PDB file header)

Molecule 1 - TROPONIN T
	Chains	:	T
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET3A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Organism Common	:	CHICKEN
	Organism Scientific	:	GALLUS GALLUS
	Organism Taxid	:	9031

Molecule 2 - TROPONIN I
	Chains	:	I
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET3A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Organism Common	:	CHICKEN
	Organism Scientific	:	GALLUS GALLUS
	Organism Taxid	:	9031
	Synonym	:	TROPONIN I, FAST-TWITCH ISOFORM

Molecule 3 - TROPONIN C
	Chains	:	C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET3A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	TNNC2
	Organism Common	:	CHICKEN
	Organism Scientific	:	GALLUS GALLUS
	Organism Taxid	:	9031

		1	2	3
Asymmetric Unit	:	C	I	T
Biological Unit 1 (1x)	:	C	I	T
Biological Unit 2 (2x)	:	C	I	T

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 7)

No.	Name	Count	Type	Full Name
1	CA	4	Ligand/Ion	CALCIUM ION
2	DR6	3	Ligand/Ion	ALPHA-[4-(1,1,3,3 - TETRAMETHYLBUTYL)PHENYL]-OMEGA-HYDROXY-POLY(OXY-1,2-ETHANEDIYL)

Biological Unit 1 (1, 3)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	DR6	3	Ligand/Ion	ALPHA-[4-(1,1,3,3 - TETRAMETHYLBUTYL)PHENYL]-OMEGA-HYDROXY-POLY(OXY-1,2-ETHANEDIYL)

Biological Unit 2 (1, 6)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	DR6	6	Ligand/Ion	ALPHA-[4-(1,1,3,3 - TETRAMETHYLBUTYL)PHENYL]-OMEGA-HYDROXY-POLY(OXY-1,2-ETHANEDIYL)

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP C:105 , ASN C:107 , ASP C:109 , PHE C:111 , GLU C:116	BINDING SITE FOR RESIDUE CA C 201
2	AC2	SOFTWARE	ASP C:141 , ASN C:143 , ASP C:145 , ARG C:147 , GLU C:152	BINDING SITE FOR RESIDUE CA C 202
3	AC3	SOFTWARE	ASP C:29 , ASP C:31 , ASP C:35 , GLU C:40	BINDING SITE FOR RESIDUE CA C 203
4	AC4	SOFTWARE	ASP C:65 , ASP C:67 , SER C:69 , THR C:71 , ASP C:73 , GLU C:76	BINDING SITE FOR RESIDUE CA C 204
5	AC5	SOFTWARE	MET C:45 , LEU C:48 , GLY C:49 , GLN C:50 , MET C:81 , GLN C:84 , ARG I:115 , MET I:116 , MET I:121	BINDING SITE FOR RESIDUE DR6 C 205
6	AC6	SOFTWARE	TYR I:43 , HIS I:47 , LYS I:66 , LYS T:220	BINDING SITE FOR RESIDUE DR6 I 183
7	AC7	SOFTWARE	LYS T:183 , LYS T:190 , ASN T:193 , ILE T:194 , GLU T:208	BINDING SITE FOR RESIDUE DR6 T 103

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

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

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

Asymmetric Unit (2, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	EF_HAND_2	PS50222	EF-hand calcium-binding domain profile.	TNNC2_CHICK	18-53 54-89 94-129 130-163	4	C:16-51 C:52-87 C:92-127 C:128-161
2	EF_HAND_1	PS00018	EF-hand calcium-binding domain.	TNNC2_CHICK	31-43 67-79 107-119 143-155	4	C:29-41 C:65-77 C:105-117 C:141-153

Biological Unit 1 (2, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	EF_HAND_2	PS50222	EF-hand calcium-binding domain profile.	TNNC2_CHICK	18-53 54-89 94-129 130-163	4	C:16-51 C:52-87 C:92-127 C:128-161
2	EF_HAND_1	PS00018	EF-hand calcium-binding domain.	TNNC2_CHICK	31-43 67-79 107-119 143-155	4	C:29-41 C:65-77 C:105-117 C:141-153

Biological Unit 2 (2, 16)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	EF_HAND_2	PS50222	EF-hand calcium-binding domain profile.	TNNC2_CHICK	18-53 54-89 94-129 130-163	8	C:16-51 C:52-87 C:92-127 C:128-161
2	EF_HAND_1	PS00018	EF-hand calcium-binding domain.	TNNC2_CHICK	31-43 67-79 107-119 143-155	8	C:29-41 C:65-77 C:105-117 C:141-153

Asymmetric Unit (4, 4)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENSGALT00000011060	1	ENSGALE00000073521	Un_random:20732110-20732258	149	TNNC2_CHICK	1-50	50	1	C:3-48	46
1.2	ENSGALT00000011060	2	ENSGALE00000073519	Un_random:20732332-20732446	115	TNNC2_CHICK	50-88	39	1	C:48-86	39
1.3	ENSGALT00000011060	3	ENSGALE00000073522	Un_random:20732522-20732658	137	TNNC2_CHICK	88-134	47	1	C:86-132	47
1.4	ENSGALT00000011060	4	ENSGALE00000073520	Un_random:20732749-20732979	231	TNNC2_CHICK	134-143	10	1	C:132-141	10

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 C from PDB  Type:PROTEIN  Length:159
 aligned with TNNC2_CHICK | P02588 from UniProtKB/Swiss-Prot  Length:163

    Alignment length:159
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154         
          TNNC2_CHICK     5 TDQQAEARAFLSEEMIAEFKAAFDMFDADGGGDISTKELGTVMRMLGQNPTKEELDAIIEEVDEDGSGTIDFEEFLVMMVRQMKEDAKGKSEEELANCFRIFDKNADGFIDIEELGEILRATGEHVTEEDIEDLMKDSDKNNDGRIDFDEFLKMMEGVQ 163
               SCOP domains d1ytzc_ C: Troponin C                                                                                                                                           SCOP domains
               CATH domains 1ytzC01 C:3-89 EF-hand                                                                 1ytzC02 C:90-161 EF-hand                                                 CATH domains
           Pfam domains (1) ----------EF_hand_5-1ytzC01 C:13-81                                            --------------------------------------------------efhand-1ytzC03 C:132-160     - Pfam domains (1)
           Pfam domains (2) -----------------------------EF_hand_6-1ytzC02 C:32-84                            -----------------------------------------------efhand-1ytzC04 C:132-160     - Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhh.....eehhhhhhhhhhhh....hhhhhhhhhh.........eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhh....hhhhhhhhhhhhh.......hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------------EF_HAND_2  PDB: C:16-51             EF_HAND_2  PDB: C:52-87             ----EF_HAND_2  PDB: C:92-127            EF_HAND_2  PDB: C:128-161          PROSITE (1)
                PROSITE (2) --------------------------EF_HAND_1    -----------------------EF_HAND_1    ---------------------------EF_HAND_1    -----------------------EF_HAND_1    -------- PROSITE (2)
           Transcript 1 (1) Exon 1.1  PDB: C:3-48 UniProt: 1-50           -------------------------------------Exon 1.3  PDB: C:86-132 UniProt: 88-134        ----------------------------- Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------Exon 1.2  PDB: C:48-86 UniProt: 50-88  ---------------------------------------------Exon 1.4  -------------------- Transcript 1 (2)
                 1ytz C   3 TDQQAEARAFLSEEMIAEFKAAFDMFDADGGGDISTKELGTVMRMLGQNPTKEELDAIIEEVDEDGSGTIDFEEFLVMMVRQMKEDAKGKSEEELANCFRIFDKNADGFIDIEELGEILRATGEHVTEEDIEDLMKDSDKNNDGRIDFDEFLKMMEGVQ 161
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152

Chain I from PDB  Type:PROTEIN  Length:141
 aligned with TNNI2_CHICK | P68246 from UniProtKB/Swiss-Prot  Length:183

    Alignment length:141
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143 
          TNNI2_CHICK     4 EEKKRRAATARRQHLKSAMLQLAVTEIEKEAAAKEVEKQNYLAEHCPPLSLPGSMQELQELCKKLHAKIDSVDEERYDTEVKLQKTNKELEDLSQKLFDLRGKFKRPPLRRVRMSADAMLRALLGSKHKVNMDLRANLKQV 144
               SCOP domains d1ytzi1 I:3-143 Troponin I                                                                                                                    SCOP domains
               CATH domains 1ytzI01 I:3-127  [code=1.20.5.350, no name defined]                                                                          ---------------- CATH domains
               Pfam domains -----------Troponin-1ytzI01 I:14-143                                                                                                          Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....................hhhhhhhhhhh................ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ytz I   3 EEKKRRAATARRQHLKSAMLQLAVTEIEKEAAAKEVEKQNYLAEHSPPLSLPGSMQELQELSKKLHAKIDSVDEERYDTEVKLQKTNKELEDLSQKLFDLRGKFKRPPLRRVRMSADAMLRALLGSKHKVNMDLRANLKQV 143
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142

Chain T from PDB  Type:PROTEIN  Length:90
 aligned with TNNT3_CHICK | P12620 from UniProtKB/Swiss-Prot  Length:263

    Alignment length:90
                                   169       179       189       199       209       219       229       239       249
          TNNT3_CHICK   160 SYSSYLAKADQKRGKKQTARETKKKVLAERRKPLNIDHLNEDKLRDKAKELWDWLYQLQTEKYDFAEQIKRKKYEIVTLRNRIDQAQKHS 249
               SCOP domains d1ytzt1 T:159-248 Troponin T                                                               SCOP domains
               CATH domains 1ytzT00 T:159-248  [code=1.20.5.350, no name defined]                                      CATH domains
               Pfam domains Troponin-1ytzT01 T:159-210                          -------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------ Transcript
                 1ytz T 159 SYSSYLAKADQKRGKKQTARETKKKVLAERRKPLNIDHLNEDKLRDKAKELWDWLYQLQTEKYDFAEQIKRKKYEIVTLRNRIDQAQKHS 248
                                   168       178       188       198       208       218       228       238       248

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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	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(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: EF Hand-like (739)

Superfamily: EF-hand (657)

Family: Calmodulin-like (356)

Protein domain: Troponin C (53)

Chicken (Gallus gallus) [TaxId: 9031] (28)

d1ytzc_

Class: Coiled coil proteins (689)

Fold: Parallel coiled-coil (407)

Superfamily: Troponin coil-coiled subunits (8)

Family: Troponin I (4)

Protein domain: Troponin I (4)

Chicken (Gallus gallus) [TaxId: 9031] (2)

d1ytzi1

I:3-143

Family: Troponin T (4)

Protein domain: Troponin T (4)

Chicken (Gallus gallus) [TaxId: 9031] (2)

d1ytzt1

T:159-248

Asymmetric 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)

Chicken (Gallus gallus) (34)

1a	1ytzC01	C:3-89
1b	1ytzC02	C:90-161

Architecture: Up-down Bundle (3216)

Topology: Single alpha-helices involved in coiled-coils or other helix-helix interfaces (552)

Homologous Superfamily: [code=1.20.5.350, no name defined] (3)

Chicken (Gallus gallus) (1)

2a	1ytzI01	I:3-127
2b	1ytzT00	T:159-248

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: EF_hand (270)

Family: EF_hand_5 (126)

Gallus gallus (Chicken) (32)

EF_hand_5-1ytzC01

C:13-81

Family: EF_hand_6 (75)

Gallus gallus (Chicken) (14)

EF_hand_6-1ytzC02

C:32-84

Family: efhand (70)

Gallus gallus (Chicken) (11)

3a	efhand-1ytzC03	C:132-160
3b	efhand-1ytzC04	C:132-160

Clan: no clan defined [family: Troponin] (10)

Family: Troponin (10)

Gallus gallus (Chicken) (4)

4a	Troponin-1ytzI01	I:14-143
4b	Troponin-1ytzT01	T:159-210

Asymmetric Unit(hide GO term definitions)

Chain C (TNNC2_CHICK | P02588)

molecular function
	GO:0003779	actin binding	Interacting selectively and non-covalently with monomeric or multimeric forms of actin, including actin filaments.
	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.
biological process
	GO:0003009	skeletal muscle contraction	A process in which force is generated within skeletal muscle tissue, resulting in a change in muscle geometry. Force generation involves a chemo-mechanical energy conversion step that is carried out by the actin/myosin complex activity, which generates force through ATP hydrolysis. In the skeletal muscle, the muscle contraction takes advantage of an ordered sarcomeric structure and in most cases it is under voluntary control.
cellular component
	GO:0005861	troponin complex	A complex of accessory proteins (typically troponin T, troponin I and troponin C) found associated with actin in muscle thin filaments; involved in calcium regulation of muscle contraction.

Chain I (TNNI2_CHICK | P68246)

molecular function
	GO:0003779	actin binding	Interacting selectively and non-covalently with monomeric or multimeric forms of actin, including actin filaments.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0031014	troponin T binding	Interacting selectively and non-covalently with troponin T, the tropomyosin-binding subunit of the troponin complex.
biological process
	GO:0060048	cardiac muscle contraction	Muscle contraction of cardiac muscle tissue.
	GO:0045893	positive regulation of transcription, DNA-templated	Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0003009	skeletal muscle contraction	A process in which force is generated within skeletal muscle tissue, resulting in a change in muscle geometry. Force generation involves a chemo-mechanical energy conversion step that is carried out by the actin/myosin complex activity, which generates force through ATP hydrolysis. In the skeletal muscle, the muscle contraction takes advantage of an ordered sarcomeric structure and in most cases it is under voluntary control.
cellular component
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
	GO:0005861	troponin complex	A complex of accessory proteins (typically troponin T, troponin I and troponin C) found associated with actin in muscle thin filaments; involved in calcium regulation of muscle contraction.

Chain T (TNNT3_CHICK | P12620)

biological process
	GO:0006937	regulation of muscle contraction	Any process that modulates the frequency, rate or extent of muscle contraction.
	GO:0006942	regulation of striated muscle contraction	Any process that modulates the frequency, rate or extent of striated muscle contraction.
cellular component
	GO:0005861	troponin complex	A complex of accessory proteins (typically troponin T, troponin I and troponin C) found associated with actin in muscle thin filaments; involved in calcium regulation of muscle contraction.

Asymmetric Unit
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Description

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Chains, Units

Ligands, Modified Residues, Ions (2, 7)

Sites (7, 7)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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PROSITE Motifs (2, 8)

Exons (4, 4)

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