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Title :   CRYSTAL STRUCTURE OF THE AMINO-TERMINAL DOMAIN OF HUMAN CARDIAC TROPONIN C IN COMPLEX WITH CADMIUM AT 1.4 RESOLUTION.

Authors :   X. L. Zhang, M. Paetzel

Date :   08 Jun 11 (Deposition) - 13 Jun 12 (Release) - 15 May 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.37

Chains :   Asym./Biol. Unit : A

Keywords :   Helix-Loop-Helix Ef-Hand Motif, Contractile Protein, Calcium Sensor, Cadmium Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   X. L. Zhang, G. F. Tibbits, M. Paetzel
The Structure Of Cardiac Troponin C Regulatory Domain With Bound Cd(2+) Reveals A Closed Conformation And Unique Ion Coordination.
Acta Crystallogr. , Sect. D V. 69 722 2013
PubMed-ID: 23633581 | Reference-DOI: 10.1107/S0907444913001182

Molecule 1 - TROPONIN C, SLOW SKELETAL AND CARDIAC MUSCLES
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET21A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	N-TERMINAL DOMAIN, UNP RESIDUES 1-89
	Gene	:	TNNC, TNNC1
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	TN-C

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 11)

No.	Name	Count	Type	Full Name
1	ACT	2	Ligand/Ion	ACETATE ION
2	CA	2	Ligand/Ion	CALCIUM ION
3	CD	7	Ligand/Ion	CADMIUM ION

Asymmetric Unit (11, 11)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	PHE A:27 , GLU A:40 , GLU A:63 , HOH A:125 , HOH A:145	BINDING SITE FOR RESIDUE CD A 101
02	AC2	SOFTWARE	GLU A:56 , CYS A:84 , ASP A:87 , SER A:89 , CD A:103	BINDING SITE FOR RESIDUE CD A 102
03	AC3	SOFTWARE	GLN A:50 , CYS A:84 , ASP A:87 , ASP A:88 , SER A:89 , CD A:102	BINDING SITE FOR RESIDUE CD A 103
04	AC4	SOFTWARE	ASP A:33 , CYS A:35 , ACT A:90 , HOH A:97	BINDING SITE FOR RESIDUE CD A 104
05	AC5	SOFTWARE	CYS A:35 , GLU A:66 , ASP A:73 , ASP A:75	BINDING SITE FOR RESIDUE CD A 105
06	AC6	SOFTWARE	MET A:1 , GLU A:59 , HOH A:131 , HOH A:132 , HOH A:133 , HOH A:146	BINDING SITE FOR RESIDUE CD A 106
07	AC7	SOFTWARE	ASP A:65 , THR A:71 , GLU A:76 , HOH A:147 , HOH A:148 , HOH A:151	BINDING SITE FOR RESIDUE CD A 107
08	AC8	SOFTWARE	MET A:1 , ASP A:33 , CYS A:35 , THR A:71 , CD A:104 , HOH A:125 , HOH A:145 , HOH A:146	BINDING SITE FOR RESIDUE ACT A 90
09	AC9	SOFTWARE	GLU A:15 , GLU A:19 , CA A:93 , CA A:94	BINDING SITE FOR RESIDUE ACT A 91
10	BC1	SOFTWARE	GLU A:10 , GLU A:19 , ACT A:91 , HOH A:129	BINDING SITE FOR RESIDUE CA A 93
11	BC2	SOFTWARE	GLU A:15 , GLU A:19 , ACT A:91	BINDING SITE FOR RESIDUE CA A 94

(no "SS Bond" information available for 3SD6)

(no "Cis Peptide Bond" information available for 3SD6)

Asymmetric/Biological Unit (3, 3)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_063070	A	8	V	TNNC1_HUMAN	Disease (CMH13)	267607125	A	A	8	V
2	UniProt	VAR_019776	L	29	Q	TNNC1_HUMAN	Disease (CMH13)	267607123	A	L	29	Q
3	UniProt	VAR_063071	C	84	Y	TNNC1_HUMAN	Disease (CMH13)	267607126	A	C	84	Y

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric/Biological Unit (2, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	EF_HAND_2	PS50222	EF-hand calcium-binding domain profile.	TNNC1_HUMAN	33-51 52-87 92-127 128-161	2	A:33-51 A:52-87 - -
2	EF_HAND_1	PS00018	EF-hand calcium-binding domain.	TNNC1_HUMAN	65-77 105-117 141-153	1	A:65-77 - -

Asymmetric/Biological Unit (4, 4)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000232975	1	ENSE00001063786	chr3:52488086-52488008	79	TNNC1_HUMAN	1-8	8	1	A:1-8	8
1.2b	ENST00000232975	2b	ENSE00000770833	chr3:52486529-52486499	31	TNNC1_HUMAN	9-19	11	1	A:9-19	11
1.3	ENST00000232975	3	ENSE00000770832	chr3:52486268-52486122	147	TNNC1_HUMAN	19-68	50	1	A:19-66	48
1.4b	ENST00000232975	4b	ENSE00000770831	chr3:52485874-52485760	115	TNNC1_HUMAN	68-106	39	1	A:70-89	20
1.5c	ENST00000232975	5c	ENSE00000770830	chr3:52485543-52485407	137	TNNC1_HUMAN	106-152	47	0	-	-
1.6	ENST00000232975	6	ENSE00001063787	chr3:52485322-52485118	205	TNNC1_HUMAN	152-161	10	0	-	-

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
	(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:86
 aligned with TNNC1_HUMAN | P63316 from UniProtKB/Swiss-Prot  Length:161

    Alignment length:89
                                    10        20        30        40        50        60        70        80         
           TNNC1_HUMAN    1 MDDIYKAAVEQLTEEQKNEFKAAFDIFVLGAEDGCISTKELGKVMRMLGQNPTPEELQEMIDEVDEDGSGTVDFDEFLVMMVRCMKDDS 89
               SCOP domains d3sd6a_ A: Troponin C                                                                     SCOP domains
               CATH domains ----------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhh..hhhhhhhhhhhhhh........eeehhhhhhhhhhh....hhhhhhhhhhhhh.---.eeehhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------V--------------------Q------------------------------------------------------Y----- SAPs(SNPs)
                PROSITE (1) --------------------------------EF_HAND_2          EF_HAND_2  PDB: A:52-87             -- PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------EF_HAND_1    ------------ PROSITE (2)
           Transcript 1 (1) Exon 1.1Exon 1.2b  ------------------------------------------------Exon 1.4b  PDB: A:70-8 Transcript 1 (1)
           Transcript 1 (2) ------------------Exon 1.3  PDB: A:19-66 UniProt: 19-68 [INCOMPLETE]--------------------- Transcript 1 (2)
                  3sd6 A  1 MDDIYKAAVEQLTEEQKNEFKAAFDIFVLGAEDGCISTKELGKVMRMLGQNPTPEELQEMIDEVDE---GTVDFDEFLVMMVRCMKDDS 89
                                    10        20        30        40        50        60     |  70        80         
                                                                                            66  70

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(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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Class: All alpha proteins (14657)

Fold: EF Hand-like (739)

Superfamily: EF-hand (657)

Family: Calmodulin-like (356)

Protein domain: Troponin C (53)

Human (Homo sapiens), cardiac isoform [TaxId: 9606] (16)

d3sd6a_

(no "CATH Domain" information available for 3SD6)

(no "Pfam Domain" information available for 3SD6)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (TNNC1_HUMAN | P63316)

molecular function
	GO:0051015	actin filament binding	Interacting selectively and non-covalently with an actin filament, also known as F-actin, a helical filamentous polymer of globular G-actin subunits.
	GO:0005509	calcium ion binding	Interacting selectively and non-covalently with calcium ions (Ca2+).
	GO:0048306	calcium-dependent 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), in the presence of calcium.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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).
	GO:0042803	protein homodimerization activity	Interacting selectively and non-covalently with an identical protein to form a homodimer.
	GO:0031013	troponin I binding	Interacting selectively and non-covalently with troponin I, the inhibitory subunit of the troponin complex.
	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:0002086	diaphragm contraction	A process in which force is generated within involuntary skeletal muscle tissue, resulting in a change in muscle geometry. This process occurs in the diaphragm. 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. The diaphragm is a striated muscle that is necessary for the process of respiratory gaseous exchange.
	GO:0030049	muscle filament sliding	The sliding of actin thin filaments and myosin thick filaments past each other in muscle contraction. This involves a process of interaction of myosin located on a thick filament with actin located on a thin filament. During this process ATP is split and forces are generated.
	GO:0043462	regulation of ATPase activity	Any process that modulates the rate of ATP hydrolysis by an ATPase.
	GO:0006937	regulation of muscle contraction	Any process that modulates the frequency, rate or extent of muscle contraction.
	GO:0032972	regulation of muscle filament sliding speed	Any process that modulates the velocity of muscle filament sliding.
	GO:0010038	response to metal ion	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a metal ion stimulus.
	GO:0014883	transition between fast and slow fiber	The process of conversion of fast-contracting muscle fibers to a slower character. This may involve slowing of contractile rate, slow myosin gene induction, increase in oxidative metabolic properties, altered electrophysiology and altered innervation. This process also regulates skeletal muscle adapatation.
	GO:0055010	ventricular cardiac muscle tissue morphogenesis	The process in which the anatomical structures of cardiac ventricle muscle is generated and organized.
cellular component
	GO:0015629	actin cytoskeleton	The part of the cytoskeleton (the internal framework of a cell) composed of actin and associated proteins. Includes actin cytoskeleton-associated complexes.
	GO:0043292	contractile fiber	Fibers, composed of actin, myosin, and associated proteins, found in cells of smooth or striated muscle.
	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:0005739	mitochondrion	A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
	GO:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.
	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/Biological Unit
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1ap4	CALCIUM BOUND HUMAN N-CTNC
1j1d	FULL LENGTH & CALCUIM SATURATED HUMAN CTNC IN COMPLEX WITH CTNI AND CTNT
1mxl	CALCIUM BOUND HUMAN N-CTNC IN COMPLEX WITH CTNI (147-163)
1spy	CALCIUM FREE HUMAN N-CTNC
1wrk	CALCIUM BOUND HUMAN N-CTNC IN COMPLEX WITH TRIFLUOROPERAZINE
3rv5	N-TERMINAL DOMAIN HUMAN CTNC IN COMPLEX WITH CADMIUM AND DEOXYCHOLIC ACID
3swb	CRYSTAL STRUCTURE OF THE AMINO-TERMINAL DOMAIN OF HUMAN CARDIAC TROPONIN C IN COMPLEX WITH CADMIUM AT 1.7 RESOLUTION.
4gje
4gjf
4gjg

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 11)

Sites (11, 11)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (3, 3)

PROSITE Motifs (2, 3)

Exons (4, 4)

Sequences/Alignments

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SCOP Domains (1, 1)

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Gene Ontology (23, 23)

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