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- PDB-3rv5: Crystal structure of human cardiac troponin C regulatory domain i... -

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Basic information

Entry
Database: PDB / ID: 3rv5
TitleCrystal structure of human cardiac troponin C regulatory domain in complex with cadmium and deoxycholic acid
ComponentsTroponin C, slow skeletal and cardiac muscles
KeywordsCONTRACTILE PROTEIN / helix-loop-helix EF-hand motif / Metal ion coordination / calcium sensor
Function / homology
Function and homology information


diaphragm contraction / regulation of ATP-dependent activity / regulation of muscle filament sliding speed / troponin T binding / cardiac Troponin complex / troponin complex / regulation of muscle contraction / transition between fast and slow fiber / Striated Muscle Contraction / muscle filament sliding ...diaphragm contraction / regulation of ATP-dependent activity / regulation of muscle filament sliding speed / troponin T binding / cardiac Troponin complex / troponin complex / regulation of muscle contraction / transition between fast and slow fiber / Striated Muscle Contraction / muscle filament sliding / response to metal ion / ventricular cardiac muscle tissue morphogenesis / troponin I binding / skeletal muscle contraction / cardiac muscle contraction / sarcomere / calcium-dependent protein binding / actin filament binding / calcium ion binding / protein homodimerization activity / cytosol
Similarity search - Function
EF-hand domain pair / : / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair
Similarity search - Domain/homology
: / Troponin C, slow skeletal and cardiac muscles
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsLi, A.Y. / Lee, J. / Borek, D. / Otwinowski, Z. / Tibbits, G. / Paetzel, M.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Crystal structure of cardiac troponin C regulatory domain in complex with cadmium and deoxycholic Acid reveals novel conformation.
Authors: Li, A.Y. / Lee, J. / Borek, D. / Otwinowski, Z. / Tibbits, G.F. / Paetzel, M.
History
DepositionMay 6, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2011Group: Database references
Revision 1.2Nov 16, 2011Group: Database references
Revision 1.3Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Troponin C, slow skeletal and cardiac muscles
B: Troponin C, slow skeletal and cardiac muscles
C: Troponin C, slow skeletal and cardiac muscles
D: Troponin C, slow skeletal and cardiac muscles
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,03833
Polymers41,5944
Non-polymers4,44429
Water2,396133
1
A: Troponin C, slow skeletal and cardiac muscles
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,7468
Polymers10,3991
Non-polymers1,3477
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Troponin C, slow skeletal and cardiac muscles
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,65811
Polymers10,3991
Non-polymers1,26010
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Troponin C, slow skeletal and cardiac muscles
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,3938
Polymers10,3991
Non-polymers9957
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Troponin C, slow skeletal and cardiac muscles
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2416
Polymers10,3991
Non-polymers8425
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: Troponin C, slow skeletal and cardiac muscles
B: Troponin C, slow skeletal and cardiac muscles
hetero molecules

A: Troponin C, slow skeletal and cardiac muscles
B: Troponin C, slow skeletal and cardiac muscles
hetero molecules

C: Troponin C, slow skeletal and cardiac muscles
D: Troponin C, slow skeletal and cardiac muscles
hetero molecules

C: Troponin C, slow skeletal and cardiac muscles
D: Troponin C, slow skeletal and cardiac muscles
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,07666
Polymers83,1898
Non-polymers8,88758
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation1_655x+1,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area24710 Å2
ΔGint-445 kcal/mol
Surface area34350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.844, 81.783, 100.469
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
Troponin C, slow skeletal and cardiac muscles / TN-C


Mass: 10398.569 Da / Num. of mol.: 4 / Fragment: N-terminal domain (N-cTnC), UNP residues 1-89
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNNC, TNNC1, TNNC1 (Amino acids 1-89) / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P63316
#2: Chemical...
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: Cd
#3: Chemical
ChemComp-DXC / (3ALPHA,5BETA,12ALPHA)-3,12-DIHYDROXYCHOLAN-24-OIC ACID / DEOXYCHOLIC ACID


Mass: 392.572 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C24H40O4 / Comment: detergent*YM
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.56 Å3/Da / Density % sol: 51.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 100 mM Tris-HCl (pH 8), 50 mM cadmium sulfate, 900 mM sodium acetate (reservoir) and 50 mM deoxycholic acid (additive), VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.98066 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jul 30, 2008 / Details: vertical collimating mirror
RadiationMonochromator: double crystal monochromator (DCM) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98066 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 22061 / Num. obs: 21706 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 28.4
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.176 / Mean I/σ(I) obs: 5.7 / % possible all: 99.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHELXSphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.2→33.01 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.879 / SU B: 7.948 / SU ML: 0.15 / Cross valid method: THROUGHOUT / ESU R: 0.274 / ESU R Free: 0.232 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28148 1128 5.1 %RANDOM
Rwork0.22541 ---
obs0.22826 20909 98.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.299 Å2
Baniso -1Baniso -2Baniso -3
1--0.69 Å20 Å20 Å2
2--1.52 Å20 Å2
3----0.84 Å2
Refinement stepCycle: LAST / Resolution: 2.2→33.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2518 0 164 133 2815
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0320.0232815
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8872.053661
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9765318
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.99227.273132
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.30115488
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.612156
X-RAY DIFFRACTIONr_chiral_restr0.1230.2430
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021934
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3381.51638
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.50922554
X-RAY DIFFRACTIONr_scbond_it4.0331173
X-RAY DIFFRACTIONr_scangle_it4.3254.51107
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 84 -
Rwork0.236 1541 -
obs--98.84 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.03410.3324-0.10291.65490.39673.33160.01150.40640.1484-0.4134-0.00360.2872-0.0986-0.1668-0.0080.2294-0.00290.00990.2204-0.0060.249338.143713.2906-16.7578
23.7571-1.33020.4863.27050.23823.3306-0.09160.1619-0.4296-0.15050.0238-0.09450.2650.05450.06770.1499-0.0011-0.00470.1291-0.00140.130432.458712.6204-5.8927
33.66710.8747-0.21870.49120.16450.224-0.005-0.037-0.11040.0196-0.019-0.04970.06250.02420.0240.10430.0035-0.00180.09490.00230.083723.397720.441-1.5538
47.1442-1.97210.9190.6144-0.20480.15820.060.39460.2741-0.143-0.0931-0.0642-0.08550.07190.0330.2375-0.0107-0.00010.18290.00070.176523.606531.1948-7.3507
51.47580.53450.58022.65141.49513.22550.04560.02110.2948-0.138-0.0259-0.0213-0.3822-0.0492-0.01960.1156-0.00060.00140.12310.0090.123310.869624.7572-7.3017
611.15013.6866-0.89724.8615-5.33879.2685-0.08710.5307-0.101-0.5952-0.105-0.74240.26050.57250.19210.3895-0.02150.17960.2557-0.03140.499316.4623.6766-17.4914
72.13320.774-1.76991.57280.56643.39230.01790.05250.0455-0.10790.07-0.37380.11560.3153-0.08790.30980.01080.02950.29190.04710.330111.942219.879-32.6952
81.0288-0.10560.7591.96030.43231.8174-0.00540.175-0.0422-0.2069-0.0067-0.08340.07410.05880.01220.11110.00150.00470.1324-0.00060.13583.929713.6954-15.8513
90.20981.0053-1.19998.7481-10.005111.69370.04280.10110.0976-0.0423-0.039-0.1144-0.17030.1227-0.00380.26820.00490.02830.2566-0.00230.27044.33561.701-21.3899
103.85341.66723.80562.13192.27944.18280.04630.0854-0.17080.00590.0139-0.10430.14670.1022-0.06030.18510.00260.00990.18010.00660.18479.60690.0544-11.6031
110.88931.1658-0.94566.8597-2.84723.32310.0021-0.2268-0.36320.2233-0.0907-0.29780.3980.14760.08860.1428-0.0159-0.04010.16660.04340.225710.55727.4583-2.7898
125.4176-2.86691.67685.3341.26482.35820.10570.5174-0.138-0.4333-0.0073-0.47130.17640.4455-0.09840.2850.03310.14820.11260.03020.232916.727310.4754-8.4178
134.8341-0.9204-1.11880.50030.02022.147-0.00250.02320.07840.03590.0190.2540.0381-0.3006-0.01650.20740.00230.00430.1683-0.00120.243-12.009320.4839-16.5263
142.0187-0.0080.83182.06021.95529.15530.0013-0.11720.12390.09270.00230.0532-0.1877-0.0288-0.00360.15980.0015-0.00030.15530.00950.1952-6.00118.5386-34.8117
151.9599-0.4011.66581.620.53476.0381-0.0092-0.3199-0.08710.29410.0116-0.07610.10930.078-0.00240.2186-0.00610.00560.21760.00190.2441-3.90199.4839-31.1489
160.3438-0.24850.99930.2269-0.68392.93760.0224-0.1048-0.0626-0.03870.06380.1640.0356-0.3406-0.08620.3069-0.0002-0.0010.3019-0.00350.3233-10.75471.6027-38.3804
173.0815-0.03171.37821.9721-1.03432.6978-0.03010.139-0.3973-0.0174-0.05260.11140.28790.03680.08260.1888-0.01180.0010.18450.00280.1846-14.135610.3035-44.3062
1811.54592.6787-0.63164.0671-4.63066.95280.0615-0.52340.05930.50550.04260.4016-0.107-0.4299-0.10410.4718-0.04350.10290.3403-0.03430.4131-20.96519.1824-35.8811
190.98110.3195-1.52240.857-0.65943.9503-0.0183-0.3421-0.13410.3766-0.0070.01020.18170.09560.02530.231-0.0002-0.00450.27210.02580.232-38.163912.6177-36.982
204.95052.5291-3.98651.5885-2.38273.6536-0.06560.1105-0.0935-0.0750.02780.04410.0936-0.06670.03780.15810.0064-0.00770.151-0.00370.1592-22.968615.0556-48.403
215.267-0.108-0.13750.5348-0.53380.78150.0296-0.00710.15150.09080.03350.1909-0.1351-0.2182-0.06310.2126-0.0005-0.00550.2123-0.03050.2164-28.21423.8753-47.8129
220.6637-0.06660.11530.0799-0.03910.0723-0.0487-0.33430.20670.13220.02430.0392-0.101-0.09680.02440.30190.00480.00680.2913-0.00740.285-21.031732.8202-44.0039
232.926-1.98780.92362.5089-2.96445.24940.0268-0.05730.36520.1894-0.1032-0.2969-0.45470.3880.07640.161-0.00140.00750.1687-0.01860.1671-11.48325.378-45.7351
242.60850.25020.47635.20746.03667.9707-0.0456-0.6030.40050.3388-0.16360.4256-0.1382-0.53830.20920.39870.10190.10510.28350.0640.2851-15.672522.9815-37.1273
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 15
2X-RAY DIFFRACTION2A16 - 25
3X-RAY DIFFRACTION3A26 - 48
4X-RAY DIFFRACTION4A49 - 63
5X-RAY DIFFRACTION5A64 - 80
6X-RAY DIFFRACTION6A81 - 85
7X-RAY DIFFRACTION7B5 - 19
8X-RAY DIFFRACTION8B20 - 48
9X-RAY DIFFRACTION9B49 - 54
10X-RAY DIFFRACTION10B55 - 64
11X-RAY DIFFRACTION11B65 - 74
12X-RAY DIFFRACTION12B75 - 82
13X-RAY DIFFRACTION13C3 - 19
14X-RAY DIFFRACTION14C20 - 35
15X-RAY DIFFRACTION15C36 - 51
16X-RAY DIFFRACTION16C52 - 67
17X-RAY DIFFRACTION17C68 - 79
18X-RAY DIFFRACTION18C80 - 85
19X-RAY DIFFRACTION19D5 - 23
20X-RAY DIFFRACTION20D24 - 33
21X-RAY DIFFRACTION21D34 - 51
22X-RAY DIFFRACTION22D52 - 65
23X-RAY DIFFRACTION23D66 - 76
24X-RAY DIFFRACTION24D77 - 82

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