SAXSdb — 3cx2

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Myosin-binding protein C, cardiac-type

Homo sapiens

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 151–258	Fragment：Ig-like C2-type 1 domain	No other associated polymer	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

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 3CX2	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 method Different experimental conditions Different structure-quality metrics	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
1PD6 The NMR structure of domain C2 of human cardiac Myosin Binding Protein C Deposited 2003-05-19	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 358–451（94 aa） Fragment：Domain C2	Not recorded	No recorded non-water small molecule	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
2AVG NMR structure of cC1 domain from Human Cardiac Myosin Binding Protein C Deposited 2005-08-30	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 151–260（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 method Different experimental conditions Different structure-quality metrics	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 method Different experimental conditions Different structure-quality metrics	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 method Different experimental conditions Different structure-quality metrics	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 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
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 method Different experimental conditions Different structure-quality metrics	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 1–108； UniProt 151–258

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	3cx2
Deposition date deposition_date	2008-04-23
Structure title title	Crystal structure of the C1 domain of cardiac isoform of myosin binding protein-C at 1.3A
Keywords keywords	;myosin-binding protein; protonation states, Actin-binding, Cardiomyopathy, Cell adhesion, Disease mutation, Immunoglobulin domain, Muscle protein, Phosphoprotein, Polymorphism, Thick filament, CONTRACTILE PROTEIN ;; CONTRACTILE PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	15.53 Å
Radius of gyration Rg (electron density) rg_electron	14.46 Å
Forward intensity I(0) i0	2870030.00
Molecular weight molecular_weight	11929.0 kDa
Excluded volume excluded_volume	14987 Å³
Envelope volume envelope_volume	17721 Å³
Hydration-shell volume shell_volume	10898 Å³
Envelope diameter envelope_diameter	53.9 Å
Shell Rg shell_rg	19.61 Å
Envelope Rg envelope_rg	14.99 Å
Shape Rg shape_rg	14.42 Å
Total Rg total_rg	15.70 Å
Total atoms total_atoms	843
Residues n_residues	107
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	56.5 Å
Rg (real space) rg_real	15.52 Å
Rg uncertainty (real space) rg_real_error	0.39 Å
I(0) (real space) i0_real	2.8700e+06
I(0) uncertainty (real space) i0_real_error	3.6580e+04
Rg (reciprocal space) rg_reciprocal	15.52 Å
I(0) (reciprocal space) i0_reciprocal	2870000.0000
Solution quality estimate total_estimate	0.8344
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	17.9 Å
Skewness Skewness skewness	0.342
Kurtosis Kurtosis kurtosis	-0.214
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	573500.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.647; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.903; Smooth: 1.000

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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 (1 domains)

Domain ID domain_id	d3cx2a_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.4 — I set domains

CATH v4.4 (1 domains)

Domain ID domain_id	3cx2A00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

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8. Citations (1)

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Unit-cell length a length_a	48.848 Å
Unit-cell length b length_b	48.848 Å
Unit-cell length c length_c	95.132 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	I 41
Space-group number int_tables_number	80
Crystal system crystal_system	—

Resolution resolution	1.300 Å
Low-resolution limit resolution_low	10.000 Å
R factor r_factor	0.1640
R_work r_work	—
R_free r_free	0.2090

Description description	Myosin-binding protein C, cardiac-type
Molecular weight formula_weight	12049.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1044

Crystal structure of the C1 domain of cardiac isoform of myosin binding protein-C at 1.3A

1. Protein Identity and Related Structures Protein Identity & Related Structures

Myosin-binding protein C, cardiac-type

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	176

fit	/app/data/saxs_computation/cx/3cx2/3cx2.fit
pddf	/app/data/pr_computation/cx/3cx2/3cx2.pr.out
profile	/app/data/saxs_computation/cx/3cx2/3cx2.dat