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1ctd

DETERMINATION OF THE SOLUTION STRUCTURE OF A SYNTHETIC TWO-SITE CALCIUM-BINDING HOMODIMERIC PROTEIN DOMAIN BY NMR SPECTROSCOPY

Method: SOLUTION NMR Dmax: 45.8 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

TROPONIN C SITE III - SITE III HOMODIMER

OrganismNot specified

UniProt P02588

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 93–126 Chain B； UniProt 93–126 Non-standard monomer：Yes (specific site not provided by mmCIF) CA CALCIUM ION × 2 SOLUTION NMR mmCIF provides none of the parsed experimental conditions Resolution not provided

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 1CTD Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1AVS X-RAY CRYSTALLOGRAPHIC STUDY OF CALCIUM-SATURATED N-TERMINAL DOMAIN OF TROPONIN C Deposited 1997-09-19 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–90（90 aa） Fragment：N-TERMINAL DOMAIN, RESIDUES 1 - 90
Not recorded CA CALCIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；72 % AMMONIUM SULFATE 100 MM TRIS 2 % MPD, 5 MM CALCIUM CHLORIDE PH 7.5
Resolution 1.75 Å R-free 0.250
1AVS X-RAY CRYSTALLOGRAPHIC STUDY OF CALCIUM-SATURATED N-TERMINAL DOMAIN OF TROPONIN C Deposited 1997-09-19 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–90（90 aa） Fragment：N-TERMINAL DOMAIN, RESIDUES 1 - 90
Not recorded CA CALCIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；72 % AMMONIUM SULFATE 100 MM TRIS 2 % MPD, 5 MM CALCIUM CHLORIDE PH 7.5
Resolution 1.75 Å R-free 0.250
1BLQ STRUCTURE AND INTERACTION SITE OF THE REGULATORY DOMAIN OF TROPONIN-C WHEN COMPLEXED WITH THE 96-148 REGION OF TROPONIN-I, NMR, 29 STRUCTURES Deposited 1998-07-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–90（90 aa） Fragment：REGULATORY
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.85；303 K；Ionic strength (raw mmCIF value) 100 mM KCL；Pressure 1
NMR sample composition H2O
Resolution not provided
1CTA DETERMINATION OF THE SOLUTION STRUCTURE OF A SYNTHETIC TWO-SITE CALCIUM-BINDING HOMODIMERIC PROTEIN DOMAIN BY NMR SPECTROSCOPY Deposited 1992-11-12 Parsed fields agree Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 93–126（34 aa）
Chain B 93–126（34 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) CA CALCIUM ION × 2 SOLUTION NMR mmCIF provides none of the parsed conditions Resolution not provided
1JC2 COMPLEX OF THE C-DOMAIN OF TROPONIN C WITH RESIDUES 1-40 OF TROPONIN I Deposited 2001-06-07 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 89–163（75 aa） Fragment：residues 89-163 of GB entry 212778
Not recorded CA CALCIUM ION × 2 SOLUTION NMR
NMR measurement conditions pH 6.8；303 K；Ionic strength (raw mmCIF value) 0.1；Pressure ambiant
NMR sample composition ~1.3 mM C-domain of Sqeletal Troponin C, 1.9 mM of TnI peptide (residues 1-40), 100 mM KCl, 10 mM Imidazole, 1 mM DSS | 90% H2O/10% D2O
Resolution not provided
1NCX TROPONIN C Deposited 1996-06-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–162（162 aa）
Not recorded CD CADMIUM ION × 2 SO4 SULFATE ION × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.80 Å
1NCY TROPONIN-C, COMPLEX WITH MANGANESE Deposited 1996-06-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–162（162 aa）
Not recorded MN MANGANESE (II) ION × 2 SO4 SULFATE ION × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.10 Å
1NCZ TROPONIN C Deposited 1996-06-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–162（162 aa）
Not recorded TB TERBIUM(III) ION × 2 SO4 SULFATE ION × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.80 Å
1NPQ structure of a rhodamine-labeled N-domain Troponin C mutant (Ca2+ saturated) in complex with skeletal Troponin I 115-131 Deposited 2003-01-18 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–90（90 aa） Fragment：TnC, residues 1-90
Mutation：E56C, E63C CA CALCIUM ION × 2 SOLUTION NMR
NMR measurement conditions pH 6.5；303 K；Ionic strength (raw mmCIF value) 320 mM KCl；Pressure ambiant
NMR sample composition 320 mM KCl, 10 mM imidazole, 1.3% NaN3, pH 6.5, ~1mM sNTnC.2Ca2+.TnI115-131.BR56-63 | 90% H2O/10% D2O
Resolution not provided
1PON SITE III-SITE IV TROPONIN C HETERODIMER, NMR Deposited 1996-04-02 Different construct Different ligand/ion Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 93–126（34 aa） Fragment：SITE III AND IV
Chain B 129–162（34 aa） Fragment：SITE III AND IV
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule SOLUTION NMR mmCIF provides none of the parsed conditions Resolution not provided
1SKT SOLUTION STRUCTURE OF APO N-DOMAIN OF TROPONIN C, NMR, 40 STRUCTURES Deposited 1998-04-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–90（90 aa） Fragment：N-DOMAIN, RESIDUES 1-90
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.7；277 K；Ionic strength (raw mmCIF value) 50mM KCL；Pressure 1
NMR sample composition WATER
Resolution not provided
1SMG CALCIUM-BOUND E41A MUTANT OF THE N-DOMAIN OF CHICKEN TROPONIN C, NMR, 40 STRUCTURES Deposited 1997-02-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–90（90 aa） Fragment：N-DOMAIN
Mutation：E41A CA CALCIUM ION × 1 SOLUTION NMR
NMR measurement conditions pH 6.7；303.15 K
Resolution not provided
1TNP STRUCTURES OF THE APO AND CALCIUM TROPONIN-C REGULATORY DOMAINS: THE MUSCLE CONTRACTION SWITCH Deposited 1995-07-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–90（90 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR mmCIF provides none of the parsed conditions Resolution not provided
1TNQ STRUCTURES OF THE APO AND CALCIUM TROPONIN-C REGULATORY DOMAINS: THE MUSCLE CONTRACTION SWITCH Deposited 1995-07-07 Different construct Different mutation/modification Different oligomeric state Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–90（90 aa）
Not recorded CA CALCIUM ION × 2 SOLUTION NMR mmCIF provides none of the parsed conditions Resolution not provided
1TNW NMR SOLUTION STRUCTURE OF CALCIUM SATURATED SKELETAL MUSCLE TROPONIN C Deposited 1995-08-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–163（162 aa）
Mutation：T130I No recorded non-water small molecule SOLUTION NMR mmCIF provides none of the parsed conditions Resolution not provided
1TNX NMR SOLUTION STRUCTURE OF CALCIUM SATURATED SKELETAL MUSCLE TROPONIN C Deposited 1995-08-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–163（162 aa）
Mutation：T130I No recorded non-water small molecule SOLUTION NMR mmCIF provides none of the parsed conditions Resolution not provided
1TOP STRUCTURE OF CHICKEN SKELETAL MUSCLE TROPONIN-C AT 1.78 ANGSTROMS RESOLUTION Deposited 1993-08-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–162（162 aa）
Not recorded CA CALCIUM ION × 2 SO4 SULFATE ION × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.78 Å
1YTZ Crystal structure of skeletal muscle troponin in the Ca2+-activated state Deposited 2005-02-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–162（162 aa）
Not recorded DR6 ALPHA-[4-(1,1,3,3 - TETRAMETHYLBUTYL)PHENYL]-OMEGA-HYDROXY-POLY(OXY-1,2-ETHANEDIYL) × 3 CA CALCIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；0.4 M NaH2PO4/1.6 M K2HPO4, 200 mM NaCl, 0.1 M immidazole, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 3.00 Å R-free 0.338
1YTZ Crystal structure of skeletal muscle troponin in the Ca2+-activated state Deposited 2005-02-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain C 1–162（162 aa）
Not recorded DR6 ALPHA-[4-(1,1,3,3 - TETRAMETHYLBUTYL)PHENYL]-OMEGA-HYDROXY-POLY(OXY-1,2-ETHANEDIYL) × 6 CA CALCIUM ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；0.4 M NaH2PO4/1.6 M K2HPO4, 200 mM NaCl, 0.1 M immidazole, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 3.00 Å R-free 0.338
1YV0 Crystal structure of skeletal muscle troponin in the Ca2+-free state Deposited 2005-02-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–162（162 aa）
Not recorded MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；1.6 M tri-Sodium Citrate dihydrate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 7.00 Å R-free 0.359
1YV0 Crystal structure of skeletal muscle troponin in the Ca2+-free state Deposited 2005-02-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain C 1–162（162 aa）
Not recorded MG MAGNESIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；1.6 M tri-Sodium Citrate dihydrate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 7.00 Å R-free 0.359
1ZAC N-DOMAIN OF TROPONIN C FROM CHICKEN SKELETAL MUSCLE, NMR, MINIMIZED AVERAGE STRUCTURE Deposited 1998-04-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–90（90 aa） Fragment：N-DOMAIN, RESIDUES 1-90
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.7；277 K；Ionic strength (raw mmCIF value) 50mM KCL；Pressure 1
NMR sample composition WATER
Resolution not provided
2W49 ISOMETRICALLY CONTRACTING INSECT ASYNCHRONOUS FLIGHT MUSCLE Deposited 2008-11-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric
Chain 0 5–163（159 aa） Fragment：RESIDUES 5-163
Chain 3 5–163（159 aa） Fragment：RESIDUES 5-163
Chain 6 5–163（159 aa） Fragment：RESIDUES 5-163
Chain 9 5–163（159 aa） Fragment：RESIDUES 5-163
Not recorded CA CALCIUM ION × 16 ELECTRON MICROSCOPY
cryo-EM buffer 20 MM MOPS BUFFER, 5 MM NAN3, AND MGCL2, ATP, CACL2, AND EGTA IN VARYING MILLIMOLAR CONCENTRATIONS；20 MM MOPS BUFFER, 5 MM NAN3, AND MGCL2, ATP, CACL2, AND EGTA IN VARYING MILLIMOLAR CONCENTRATIONS
cryo-EM vitrification conditions Cryogen HELIUM；SMASH AGAINST A LIQUID HELIUM COOLED GOLD COATED COPPER MIRROR
Resolution 35.00 Å
2W4U Isometrically contracting insect asynchronous flight muscle quick frozen after a length step Deposited 2008-12-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric
Chain 0 5–163（159 aa） Fragment：RESIDUES 5-163
Chain 3 5–163（159 aa） Fragment：RESIDUES 5-163
Chain 6 5–163（159 aa） Fragment：RESIDUES 5-163
Chain 9 5–163（159 aa） Fragment：RESIDUES 5-163
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 20 MM MOPS BUFFER, 5 MM NAN3, AND MGCL2, ATP, CACL2, AND EGTA IN VARYING MILLIMOLAR CONCENTRATIONS；20 MM MOPS BUFFER, 5 MM NAN3, AND MGCL2, ATP, CACL2, AND EGTA IN VARYING MILLIMOLAR CONCENTRATIONS
cryo-EM vitrification conditions Cryogen HELIUM；SMASH AGAINST A LIQUID HELIUM COOLED GOLD COATED COPPER MIRROR
Resolution 35.00 Å
4TNC REFINED STRUCTURE OF CHICKEN SKELETAL MUSCLE TROPONIN C IN THE TWO-CALCIUM STATE AT 2-ANGSTROMS RESOLUTION Deposited 1987-09-28 Different construct Different mutation/modification Different oligomeric state Different experimental method Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–162（161 aa）
Not recorded CA CALCIUM ION × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.00 Å

22 other PDB entries and 25 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TPCS_CHICK
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 2–35； UniProt 93–126 Author chain B； PDBConstruct 2–35； UniProt 93–126

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 1ctd

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1ctd
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1ctd
Deposition date deposition_date1992-11-12
Structure title titleDETERMINATION OF THE SOLUTION STRUCTURE OF A SYNTHETIC TWO-SITE CALCIUM-BINDING HOMODIMERIC PROTEIN DOMAIN BY NMR SPECTROSCOPY
Keywords keywordsMUSCLE PROTEIN; MUSCLE PROTEIN
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier12.42 Å
Radius of gyration Rg (electron density) rg_electron11.74 Å
Forward intensity I(0) i046488900.00
Molecular weight molecular_weight54674.0 kDa
Excluded volume excluded_volume67855 ų
Envelope volume envelope_volume19412 ų
Hydration-shell volume shell_volume12011 ų
Envelope diameter envelope_diameter51.0 Å
Shell Rg shell_rg19.60 Å
Envelope Rg envelope_rg14.24 Å
Shape Rg shape_rg11.71 Å
Total Rg total_rg12.35 Å
Total atoms total_atoms4662
Residues n_residues476
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax45.8 Å
Rg (real space) rg_real12.38 Å
Rg uncertainty (real space) rg_real_error0.42 Å
I(0) (real space) i0_real4.6490e+07
I(0) uncertainty (real space) i0_real_error5.3600e+05
Rg (reciprocal space) rg_reciprocal12.38 Å
I(0) (reciprocal space) i0_reciprocal46490000.0000
Solution quality estimate total_estimate0.7445
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary16.2 Å
Skewness Skewness skewness0.235
Kurtosis Kurtosis kurtosis-0.017
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha89440.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.577; Stabil: 0.996; Sysdev: 1.000; Positv: 1.000; Valcen: 0.954; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1ctda_
Class classa — All alpha proteins
Fold Fold folda.39 — EF Hand-like
Superfamily Superfamily superfamilya.39.1 — EF-hand
Family Family familya.39.1.5 — Calmodulin-like
Domain ID domain_idd1ctdb_
Class classa — All alpha proteins
Fold Fold folda.39 — EF Hand-like
Superfamily Superfamily superfamilya.39.1 — EF-hand
Family Family familya.39.1.5 — Calmodulin-like
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8. Citations (1)

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9. Files and Curves (10)