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1pd6

The NMR structure of domain C2 of human cardiac Myosin Binding Protein C

Method: SOLUTION NMR Dmax: 38.0 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Myosin-binding protein C, cardiac-type, Domain C2

Homo sapiens

UniProt Q14896

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 358–451 Fragment：Domain C2 No other associated polymer SOLUTION NMR NMR measurement conditions：pH 7；298 K；Ionic strength (raw mmCIF value) 0.1；Pressure ambient NMR measurement conditions：pH 7；298 K；Ionic strength (raw mmCIF value) 0.1；Pressure ambient NMR measurement conditions：pH 7；298 K；Ionic strength (raw mmCIF value) 7.0；Pressure ambient NMR sample composition：0.75mM C2; 15N; 20mM phosphate buffer; 90% H2O, 10% D2O | 90% H2O/10% D2O NMR sample composition：0.75mM C2; 15N, 13C; 20mM phosphate buffer; 90% H2O, 10% D2O | 90% H2O/10% D2O NMR sample composition：0.75mM C2; 15N, 13C; 20mM phosphate buffer; 100% D2O | 100% D2O 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 1PD6 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1GXE Central domain of cardiac myosin binding protein C Deposited 2002-04-03 Different construct Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 641–770（130 aa） Fragment：DOMAIN C5, RESIDUES 641-770
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；293 K；Ionic strength (raw mmCIF value) 100 MM NACL；Pressure 1
Resolution not provided
2AVG NMR structure of cC1 domain from Human Cardiac Myosin Binding Protein C Deposited 2005-08-30 Different construct Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 151–260（110 aa） Fragment：cC1 domain
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 0.1M；Pressure ambient
NMR sample composition 0.8mM cC1 U-15N; 20mM phosphate buffer; 90% H2O, 10% D2O | 90% H2O/10% D2O
NMR sample composition 0.8mM cC1 U-15N, 13C; 20mM phosphate buffer; 90% H2O, 10% D2O | 90% H2O/10% D2O
NMR sample composition 0.8mM cC1 U-15N, 13C; 20mM phosphate buffer; 100% D2O | 100% D2O
Resolution not provided
2K1M 3D NMR structure of domain cC0 of cardiac myosin binding protein C (MyBPC) Deposited 2008-03-10 Different construct Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–96（95 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；303 K；Ionic strength (raw mmCIF value) 185；Pressure ambient
NMR sample composition 1-1.5 mM [U-95% 13C; U-95% 15N] cC0_MyBPC, 55.5 M [U-2H] D2O, 40 mM sodium phosphate, 50 mM sodium chloride, 2 mM DTT, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 1-1.5 mM [U-95% 15N] cC0_MyBPC, 55.5 M H2O, 40 mM sodium phosphate, 50 mM sodium chloride, 2 mM DTT, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 1-1.5 mM cC0_MyBPC, 55.5 M H2O, 40 mM sodium phosphate, 50 mM sodium chloride, 2 mM DTT, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
2MQ0 NMR structure of the c3 domain of human cardiac myosin binding protein-c Deposited 2014-06-10 Different construct Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 453–543（91 aa） Fragment：unp residues 453-543
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 0.4；Pressure ambient
NMR sample composition 50 mM sodium phosphate, 100 mM sodium chloride, 0.8 mM [U-100% 13C; U-100% 15N] protein, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
2MQ3 NMR structure of the c3 domain of human cardiac myosin binding protein-c with a hypertrophic cardiomyopathy-related mutation R502W. Deposited 2014-06-12 Different construct Different mutation/modification Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 453–543（91 aa） Fragment：unp residues 453-543
Mutation：R502W No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 0.4；Pressure ambient
NMR sample composition 50 mM sodium phosphate, 100 mM sodium chloride, 0.8 mM [U-100% 13C; U-100% 15N] protein, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
2V6H Crystal structure of the C1 domain of cardiac myosin binding protein-C Deposited 2007-07-18 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 151–258（108 aa） Fragment：C1 DOMAIN, RESIDUES 151-258
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.3；293 K；HANGING DROP; 20 C; 18%PEG, 0.1M BUFFER, PH 7.3
Resolution 1.55 Å R-free 0.241
3CX2 Crystal structure of the C1 domain of cardiac isoform of myosin binding protein-C at 1.3A Deposited 2008-04-23 Different construct Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 151–258（108 aa） Fragment：Ig-like C2-type 1 domain
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.9；293 K；Crystals were grown at 20 C using the hanging drop method with a 2 microlitre drop containing a 1:1 mixture of protein solution and crystallising solution consisting of 8.5% PEG 3350 and 0.05M Hepes pH 6.8 over 500 microlitres of crystallising solution in the reservoir, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.30 Å R-free 0.209
5K6P The NMR structure of the m domain tri-helix bundle and C2 of human cardiac Myosin Binding Protein C Deposited 2016-05-25 Different construct Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 319–451（133 aa） Fragment：residues 319-451
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 50；Pressure 1
NMR sample composition 412 uM [U-99% 13C; U-99% 15N] human cMyBP-C (319-451), 10 mM MES, 1 mM CaCl2, 50 mM NaCl, 2 mM TCEP, 1 mM Na azide, 10 mM DSS, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 920 uM [U-99% 13C; U-99% 15N] human cMyBP-C (319-451), 10 mM MES, 1 mM CaCl2, 50 mM NaCl, 2 mM TCEP, 1 mM Na azide, 10 mM DSS, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 550 uM [U-99% 13C; U-99% 15N] human cMyBP-C (319-451), 10 mM MES, 1 mM CaCl2, 50 mM NaCl, 1 mM Na azide, 2 mM TCEP, 10 mM DSS, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 500 uM [U-99% 13C; U-99% 15N] human cMyBP-C (319-451), 10 mM MES, 1 mM CaCl2, 50 mM NaCl, 2 mM TCEP, 1 mM Na azide, 10 mM DSS, 99% D2O | 99% D2O
NMR sample composition 800 uM [U-99% 13C; U-99% 15N] human cMyBP-C (319-451), 10 mM MES, 1 mM CaCl2, 50 mM NaCl, 2 mM TCEP, 1 mM Na azide, 10 mM DSS, 99% D2O | 99% D2O
Resolution not provided
6CXI Cardiac thin filament decorated with C0C1 fragment of cardiac myosin binding protein C mode 1 Deposited 2018-04-03 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 20 PDB declaration: eicosameric
Chain G 151–258（108 aa） Fragment：C1 Ig-domain (UNP residues 151-258)
Chain H 151–258（108 aa） Fragment：C1 Ig-domain (UNP residues 151-258)
Chain I 151–258（108 aa） Fragment：C1 Ig-domain (UNP residues 151-258)
Chain J 151–258（108 aa） Fragment：C1 Ig-domain (UNP residues 151-258)
Chain K 151–258（108 aa） Fragment：C1 Ig-domain (UNP residues 151-258)
Chain L 151–258（108 aa） Fragment：C1 Ig-domain (UNP residues 151-258)
Chain M 1–101（101 aa） Fragment：C0 Ig-domain (UNP residues 1-101)
Chain N 1–101（101 aa） Fragment：C0 Ig-domain (UNP residues 1-101)
Chain O 1–101（101 aa） Fragment：C0 Ig-domain (UNP residues 1-101)
Chain P 1–101（101 aa） Fragment：C0 Ig-domain (UNP residues 1-101)
Chain Q 1–101（101 aa） Fragment：C0 Ig-domain (UNP residues 1-101)
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 11.00 Å
6CXJ Cardiac thin filament decorated with C0C1 fragment of cardiac myosin binding protein C mode 2 Deposited 2018-04-03 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 20 PDB declaration: eicosameric
Chain G 151–258（108 aa） Fragment：C1 Ig-domain (UNP residues 151-258)
Chain H 151–258（108 aa） Fragment：C1 Ig-domain (UNP residues 151-258)
Chain I 151–258（108 aa） Fragment：C1 Ig-domain (UNP residues 151-258)
Chain J 151–258（108 aa） Fragment：C1 Ig-domain (UNP residues 151-258)
Chain K 151–258（108 aa） Fragment：C1 Ig-domain (UNP residues 151-258)
Chain L 151–258（108 aa） Fragment：C1 Ig-domain (UNP residues 151-258)
Chain M 1–101（101 aa） Fragment：C0 Ig-domain (UNP residues 1-101)
Chain N 1–101（101 aa） Fragment：C0 Ig-domain (UNP residues 1-101)
Chain O 1–101（101 aa） Fragment：C0 Ig-domain (UNP residues 1-101)
Chain P 1–101（101 aa） Fragment：C0 Ig-domain (UNP residues 1-101)
Chain Q 1–101（101 aa） Fragment：C0 Ig-domain (UNP residues 1-101)
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 11.00 Å
6G2T human cardiac myosin binding protein C C1 Ig-domain bound to native cardiac thin filament Deposited 2018-03-23 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric
Chain G 151–258（108 aa）
Chain H 151–258（108 aa）
Chain I 151–258（108 aa）
Chain J 151–258（108 aa）
Chain K 151–258（108 aa）
Chain L 151–258（108 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 9.00 Å
7LRG Filamentous actin decorated with human cardiac myosin binding protein C C2 domain Deposited 2021-02-16 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain G 358–451（94 aa）
Chain H 358–451（94 aa）
Chain I 358–451（94 aa）
Chain J 358–451（94 aa）
Chain K 358–451（94 aa）
Chain L 358–451（94 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.10 Å
7TIJ Cardiac F-actin decorated with regulatory M-domain of cardiac myosin binding protein C Deposited 2022-01-13 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain G 151–370（220 aa）
Chain H 151–370（220 aa）
Chain I 151–370（220 aa）
Chain J 151–370（220 aa）
Chain K 151–370（220 aa）
Chain L 151–370（220 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.00 Å
7TIT Cardiac thin filament decorated with regulatory M-domain of cardiac myosin binding protein C Deposited 2022-01-14 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric
Chain G 151–370（220 aa）
Chain H 151–370（220 aa）
Chain I 151–370（220 aa）
Chain J 151–370（220 aa）
Chain K 151–370（220 aa）
Chain L 151–370（220 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.00 Å
7TJ7 Cardiac thin filament decorated with C1 Ig-domain and regulatory M-domain of cardiac myosin binding protein C (cMyBP-C) Deposited 2022-01-14 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 22 PDB declaration: 22-meric
Chain G 151–370（220 aa）
Chain H 151–370（220 aa）
Chain I 151–370（220 aa）
Chain J 151–370（220 aa）
Chain K 151–370（220 aa）
Chain L 151–370（220 aa）
Chain M 151–370（220 aa）
Chain N 151–370（220 aa）
Chain O 151–370（220 aa）
Chain P 151–370（220 aa）
Chain Q 151–370（220 aa）
Chain R 151–370（220 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.00 Å
8G4L Cryo-EM structure of the human cardiac myosin filament Deposited 2023-02-10 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 123 PDB declaration: 123-meric
Chain ao 1–1274（1274 aa）
Chain bo 1–1274（1274 aa）
Chain o 1–1274（1274 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 6.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.40 Å

16 other PDB entries and 16 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name MYPC3_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 11–104； UniProt 358–451

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 1pd6

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1pd6
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1pd6
Deposition date deposition_date2003-05-19
Structure title titleThe NMR structure of domain C2 of human cardiac Myosin Binding Protein C
Keywords keywordsIg domain, STRUCTURAL PROTEIN; STRUCTURAL 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_guinier12.30 Å
Radius of gyration Rg (electron density) rg_electron12.04 Å
Forward intensity I(0) i01198600000.00
Molecular weight molecular_weight293550.0 kDa
Excluded volume excluded_volume367230 ų
Envelope volume envelope_volume19271 ų
Hydration-shell volume shell_volume12135 ų
Envelope diameter envelope_diameter43.0 Å
Shell Rg shell_rg19.33 Å
Envelope Rg envelope_rg13.62 Å
Shape Rg shape_rg12.02 Å
Total Rg total_rg12.22 Å
Total atoms total_atoms41300
Residues n_residues2632
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 dmax38.0 Å
Rg (real space) rg_real12.22 Å
Rg uncertainty (real space) rg_real_error0.26 Å
I(0) (real space) i0_real1.1990e+09
I(0) uncertainty (real space) i0_real_error1.3510e+07
Rg (reciprocal space) rg_reciprocal12.23 Å
I(0) (reciprocal space) i0_reciprocal1199000000.0000
Solution quality estimate total_estimate0.8247
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary15.9 Å
Skewness Skewness skewness0.097
Kurtosis Kurtosis kurtosis-0.413
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha184100.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.913; Stabil: 0.996; Sysdev: 1.000; Positv: 1.000; Valcen: 0.992; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1pd6a_
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.4 — I set domains

CATH v4.4 (1 domains)

Domain ID domain_id1pd6A00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
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8. Citations (1)

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9. Files and Curves (10)