SAXSdb — 2c46

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

MRNA CAPPING ENZYME

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 homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 1–219 Chain B； UniProt 1–219 Chain C； UniProt 1–219 Chain D； UniProt 1–219	Fragment：TPASE REGION, RESIDUES 1-219	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：2 M POTASSIUM CITRATE	Resolution 1.60 Å R-free 0.234
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 1–219	Fragment：TPASE REGION, RESIDUES 1-219	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：2 M POTASSIUM CITRATE	Resolution 1.60 Å R-free 0.234
3	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 1–219	Fragment：TPASE REGION, RESIDUES 1-219	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：2 M POTASSIUM CITRATE	Resolution 1.60 Å R-free 0.234
4	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain C； UniProt 1–219	Fragment：TPASE REGION, RESIDUES 1-219	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：2 M POTASSIUM CITRATE	Resolution 1.60 Å R-free 0.234
5	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain D； UniProt 1–219	Fragment：TPASE REGION, RESIDUES 1-219	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：2 M POTASSIUM CITRATE	Resolution 1.60 Å R-free 0.234

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 2C46	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3S24 Crystal structure of human mRNA guanylyltransferase Deposited 2011-05-16	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 229–567（339 aa） Fragment：UNP Residues 229-567	Not recorded	SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；1.7 M ammonium sulfate, 10% glucose, 5 mM 2-mercaptoethanol, 5 mM MgCl2, 5% isopropanol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.01 Å R-free 0.296
3S24 Crystal structure of human mRNA guanylyltransferase Deposited 2011-05-16	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 229–567（339 aa） Fragment：UNP Residues 229-567	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；1.7 M ammonium sulfate, 10% glucose, 5 mM 2-mercaptoethanol, 5 mM MgCl2, 5% isopropanol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.01 Å R-free 0.296
3S24 Crystal structure of human mRNA guanylyltransferase Deposited 2011-05-16	Different construct Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 229–567（339 aa） Fragment：UNP Residues 229-567	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；1.7 M ammonium sulfate, 10% glucose, 5 mM 2-mercaptoethanol, 5 mM MgCl2, 5% isopropanol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.01 Å R-free 0.296
3S24 Crystal structure of human mRNA guanylyltransferase Deposited 2011-05-16	Different construct Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 229–567（339 aa） Fragment：UNP Residues 229-567	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；1.7 M ammonium sulfate, 10% glucose, 5 mM 2-mercaptoethanol, 5 mM MgCl2, 5% isopropanol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.01 Å R-free 0.296
3S24 Crystal structure of human mRNA guanylyltransferase Deposited 2011-05-16	Different construct Different experimental conditions Different structure-quality metrics	Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain E 229–567（339 aa） Fragment：UNP Residues 229-567	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；1.7 M ammonium sulfate, 10% glucose, 5 mM 2-mercaptoethanol, 5 mM MgCl2, 5% isopropanol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.01 Å R-free 0.296
3S24 Crystal structure of human mRNA guanylyltransferase Deposited 2011-05-16	Different construct Different experimental conditions Different structure-quality metrics	Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain G 229–567（339 aa） Fragment：UNP Residues 229-567	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；1.7 M ammonium sulfate, 10% glucose, 5 mM 2-mercaptoethanol, 5 mM MgCl2, 5% isopropanol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.01 Å R-free 0.296
3S24 Crystal structure of human mRNA guanylyltransferase Deposited 2011-05-16	Different construct Different experimental conditions Different structure-quality metrics	Assembly 7 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain F 229–567（339 aa） Fragment：UNP Residues 229-567	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；1.7 M ammonium sulfate, 10% glucose, 5 mM 2-mercaptoethanol, 5 mM MgCl2, 5% isopropanol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.01 Å R-free 0.296
8P4A Structural insights into human co-transcriptional capping - structure 1 Deposited 2023-05-20	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric	Chain M 1–597（597 aa）	Not recorded	MG MAGNESIUM ION × 1 ZN ZINC ION × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
8P4B Structural insights into human co-transcriptional capping - structure 2 Deposited 2023-05-20	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric	Chain M 1–597（597 aa）	Not recorded	ZN ZINC ION × 8 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
8P4C Structural insights into human co-transcriptional capping - structure 3 Deposited 2023-05-20	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 15 PDB declaration: octadecameric	Chain M 1–597（597 aa）	Not recorded	ZN ZINC ION × 3 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.80 Å
8P4D Structural insights into human co-transcriptional capping - structure 4 Deposited 2023-05-20	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 15 PDB declaration: octadecameric	Chain M 1–597（597 aa）	Not recorded	ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
8P4E Structural insights into human co-transcriptional capping - structure 5 Deposited 2023-05-20	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 15 PDB declaration: octadecameric	Chain M 1–597（597 aa）	Not recorded	MG MAGNESIUM ION × 1 ZN ZINC ION × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.90 Å
8W8E human co-transcriptional RNA capping enzyme RNGTT Deposited 2023-09-02	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 19 PDB declaration: 22-meric	Chain a 1–597（597 aa）	Not recorded	MG MAGNESIUM ION × 1 ZN ZINC ION × 8 GTP GUANOSINE-5'-TRIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.90 Å
8W8F human co-transcriptional RNA capping enzyme RNGTT-CMTR1 Deposited 2023-09-02	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 16 PDB declaration: nonadecameric	Chain a 1–597（597 aa）	Not recorded	MG MAGNESIUM ION × 1 ZN ZINC ION × 8 GTP GUANOSINE-5'-TRIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 4.00 Å

8 other PDB entries and 14 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	MCE1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 23–241； UniProt 1–219 Author chain B； PDBConstruct 23–241； UniProt 1–219 Author chain C； PDBConstruct 23–241； UniProt 1–219 Author chain D； PDBConstruct 23–241； UniProt 1–219

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	2c46
Deposition date deposition_date	2005-10-15
Structure title title	CRYSTAL STRUCTURE OF THE HUMAN RNA guanylyltransferase and 5'- phosphatase
Keywords keywords	PHOSPHATASE, TRANSFERASE, HYDROLASE, MRNA PROCESSING, MULTIFUNCTIONAL ENZYME, NUCLEOTIDYLTRANSFERASE; TRANSFERASE
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	36.34 Å
Radius of gyration Rg (electron density) rg_electron	36.52 Å
Forward intensity I(0) i0	120407000.00
Molecular weight molecular_weight	88224.0 kDa
Excluded volume excluded_volume	110240 Å³
Envelope volume envelope_volume	145660 Å³
Hydration-shell volume shell_volume	36631 Å³
Envelope diameter envelope_diameter	129.9 Å
Shell Rg shell_rg	38.50 Å
Envelope Rg envelope_rg	35.93 Å
Shape Rg shape_rg	36.51 Å
Total Rg total_rg	36.70 Å
Total atoms total_atoms	6215
Residues n_residues	787
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	123.5 Å
Rg (real space) rg_real	36.75 Å
Rg uncertainty (real space) rg_real_error	1.23 Å
I(0) (real space) i0_real	1.2040e+08
I(0) uncertainty (real space) i0_real_error	1.9820e+06
Rg (reciprocal space) rg_reciprocal	36.50 Å
I(0) (reciprocal space) i0_reciprocal	120400000.0000
Solution quality estimate total_estimate	0.8126
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	39.3 Å
Skewness Skewness skewness	0.593
Kurtosis Kurtosis kurtosis	-0.180
Angular range angular_range	— – 0.2200 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	19610000.0000
Real-space data points n_real_points	45
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.780; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.744; Smooth: 0.477

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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) 11 domains

SCOP 2.08 (7 domains)

Domain ID domain_id	d2c46a1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.45 — (Phosphotyrosine protein) phosphatases II
Superfamily Superfamily superfamily	c.45.1 — (Phosphotyrosine protein) phosphatases II
Family Family family	c.45.1.1 — Dual specificity phosphatase-like

Domain ID domain_id	d2c46a2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d2c46b1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.45 — (Phosphotyrosine protein) phosphatases II
Superfamily Superfamily superfamily	c.45.1 — (Phosphotyrosine protein) phosphatases II
Family Family family	c.45.1.1 — Dual specificity phosphatase-like

Domain ID domain_id	d2c46b2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d2c46c1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.45 — (Phosphotyrosine protein) phosphatases II
Superfamily Superfamily superfamily	c.45.1 — (Phosphotyrosine protein) phosphatases II
Family Family family	c.45.1.1 — Dual specificity phosphatase-like

Domain ID domain_id	d2c46c2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d2c46d_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.45 — (Phosphotyrosine protein) phosphatases II
Superfamily Superfamily superfamily	c.45.1 — (Phosphotyrosine protein) phosphatases II
Family Family family	c.45.1.1 — Dual specificity phosphatase-like

CATH v4.4 (4 domains)

Domain ID domain_id	2c46A00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	190 — Protein-Tyrosine Phosphatase; Chain A
Homologous superfamily homologous superfamily	10 — Protein tyrosine phosphatase superfamily

Domain ID domain_id	2c46B00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	190 — Protein-Tyrosine Phosphatase; Chain A
Homologous superfamily homologous superfamily	10 — Protein tyrosine phosphatase superfamily

Domain ID domain_id	2c46C00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	190 — Protein-Tyrosine Phosphatase; Chain A
Homologous superfamily homologous superfamily	10 — Protein tyrosine phosphatase superfamily

Domain ID domain_id	2c46D00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	190 — Protein-Tyrosine Phosphatase; Chain A
Homologous superfamily homologous superfamily	10 — Protein tyrosine phosphatase superfamily

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8. Citations (1)

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Unit-cell length a length_a	60.400 Å
Unit-cell length b length_b	161.600 Å
Unit-cell length c length_c	60.700 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	104.70 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.600 Å
Low-resolution limit resolution_low	80.850 Å
R factor r_factor	0.2060
R_work r_work	0.2040
R_free r_free	0.2340

Description description	MRNA CAPPING ENZYME
Molecular weight formula_weight	27688.2 kDa
EC 编号 ec_number	2.7.7.50
Source method src_method	man
Copy count entity_count	4

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	6719

CRYSTAL STRUCTURE OF THE HUMAN RNA guanylyltransferase and 5'- phosphatase

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

MRNA CAPPING ENZYME

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) 11 domains

SCOP 2.08 (7 domains)

CATH v4.4 (4 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	460

fit	/app/data/saxs_computation/c4/2c46/2c46.fit
pddf	/app/data/pr_computation/c4/2c46/2c46.pr.out
profile	/app/data/saxs_computation/c4/2c46/2c46.dat